bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aspiring to Unintended Consequences of Natural Language Processing: A Review of Recent Developments in Clinical and Consumer-Generated Text Processing
Authors: Elhadad N. , Demner-Fushman D. 
Published: November 2016

Summary
Objectives: This paper reviews work over the past two years in Natural Language Processing (NLP) applied to clinical and consumer-generated texts.
Methods: We included any application or methodological publication that leverages text to facilitate healthcare and address the health-related needs of consumers and populations.
Results: Many important developments in clinical text processing, both foundational and task-oriented, were addressed in community-wide evaluations and discussed in corresponding special issues that are referenced in this review. These focused issues and in-depth reviews of several other active research areas, such as pharmacovigilance and summarization, allowed us to discuss in greater depth disease modeling and predictive analytics using clinical texts, and text analysis in social media for healthcare quality assessment, trends towards online interventions based on rapid analysis of health-related posts, and consumer health question answering, among other issues.
Conclusions: Our analysis shows that although clinical NLP continues to advance towards practical applications and more NLP methods are used in large-scale live health information applications, more needs to be done to make NLP use in clinical applications a routine widespread reality. Progress in clinical NLP is mirrored by developments in social media text analysis: the research is moving from capturing trends to addressing individual health-related posts, thus showing potential to become a tool for precision medicine and a valuable addition to the standard healthcare quality evaluation tools.
A New Informatics Geography
Authors: Coiera E. 
Published: November 2016

Summary
Introduction: Anyone with knowledge of information systems has experienced frustration when it comes to system implementation or use. Unanticipated challenges arise frequently and unanticipated consequences may follow.
Objective: Working from first principles, to understand why information technology (IT) is often challenging, identify which IT endeavors are more likely to succeed, and predict the best role that technology can play in different tasks and settings.
Results: The fundamental purpose of IT is to enhance our ability to undertake tasks, supplying new information that changes what we decide and ultimately what occurs in the world. The value of this information (VOI) can be calculated at different stages of the decision-making process and will vary depending on how technology is used. We can imagine a task space that describes the relative benefits of task completion by humans or computers and that contains specific areas where humans or computers are superior. There is a third area where neither is strong and a final joint workspace where humans and computers working in partnership produce the best results.
Conclusion: By understanding that information has value and that VOI can be quantified, we can make decisions about how best to support the work we do. Evaluation of the expected utility of task completion by humans or computers should allow us to decide whether solutions should depend on technology, humans, or a partnership between the two.
Recent Worldwide Developments in eHealth and mHealth to more Effectively Manage Cancer and other Chronic Diseases – A Systematic Review
Authors: Ray P. , Liaw S.-T. , Lewis J. 
Published: November 2016

Summary
Objectives: This paper is a systematic literature review intended to gain an understanding of the most original, excellent, state-of-the-art research in the application of eHealth (including mHealth) in the management of chronic diseases with a focus on cancer over the past two years.
Method: This review looks at peer-reviewed papers published between 2013 and 2015 and examines the background and trends in this area. It systematically searched peer-reviewed journals in databases PubMed, Proquest, Cochrane Library, Elsevier, Sage and the Institute of Electrical and Electronic Engineers (IEEE Digital Library) using a set of pre-defined keywords. It then employed an iterative process to filter out less relevant publications.
Results: From an initial search return of 1,519,682 results returned, twenty nine of the most relevant peer reviewed articles were identified as most relevant.
Conclusions: Based on the results we conclude that innovative eHealth and its subset mHealth initiatives are rapidly emerging as an important means of managing cancer and other chronic diseases. The adoption is following different paths in the developed and developing worlds. Besides governance and regulatory issues, barriers still exist around information management, interoperability and integration. These include medical records available online information for clinicians and consumers on cancer and other chronic diseases, mobile app bundles that can help manage co-morbidities and the capacity of supporting communication technologies.
New Unintended Adverse Consequences of Electronic Health Records
Authors: Wright A. , Ash J. , Singh H. , Sittig D. F. 
Published: November 2016

SummaryAlthough the health information technology industry has made considerable progress in the design, development, implementation, and use of electronic health records (EHRs), the lofty expectations of the early pioneers have not been met. In 2006, the Provider Order Entry Team at Oregon Health & Science University described a set of unintended adverse consequences (UACs), or unpredictable, emergent problems associated with computer-based provider order entry implementation, use, and maintenance. Many of these originally identified UACs have not been completely addressed or alleviated, some have evolved over time, and some new ones have emerged as EHRs became more widely available. The rapid increase in the adoption of EHRs, coupled with the changes in the types and attitudes of clinical users, has led to several new UACs, specifically: complete clinical information unavailable at the point of care; lack of innovations to improve system usability leading to frustrating user experiences; inadvertent disclosure of large amounts of patient-specific information; increased focus on computer-based quality measurement negatively affecting clinical workflows and patient-provider interactions; information overload from marginally useful computer-generated data; and a decline in the development and use of internally-developed EHRs. While each of these new UACs poses significant challenges to EHR developers and users alike, they also offer many opportunities. The challenge for clinical informatics researchers is to continue to refine our current systems while exploring new methods of overcoming these challenges and developing innovations to improve EHR interoperability, usability, security, functionality, clinical quality measurement, and information summarization and display.
Clinical Research Informatics Contributions from 2015
Authors: Choquet R. , Daniel C. ,   Section Editors for the IMIA Yearbook Section on Clinical Research Informatics
Published: November 2016

Summary
Objectives: To summarize key contributions to current research in the field of Clinical Research Informatics (CRI) and to select best papers published in 2015.
Method: A bibliographic search using a combination of MeSH and free terms search over PubMed on Clinical Research Informatics (CRI) was performed followed by a double-blind review in order to select a list of candidate best papers to be then peer-reviewed by external reviewers. A consensus meeting between the two section editors and the editorial team was finally organized to conclude on the selection of best papers.
Results: Among the 579 returned papers published in the past year in the various areas of Clinical Research Informatics (CRI) - i) methods supporting clinical research, ii) data sharing and interoperability, iii) re-use of healthcare data for research, iv) patient recruitment and engagement, v) data privacy, security and regulatory issues and vi) policy and perspectives - the full review process selected four best papers. The first selected paper evaluates the capability of the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM) to support the representation of case report forms (in both the design stage and with patient level data) during a complete clinical study lifecycle. The second selected paper describes a prototype for secondary use of electronic health records data captured in non-standardized text. The third selected paper presents a privacy preserving electronic health record linkage tool and the last selected paper describes how big data use in US relies on access to health information governed by varying and often misunderstood legal requirements and ethical considerations.
Conclusions: A major trend in the 2015 publications is the analysis of observational, “nonexperimental” information and the potential biases and confounding factors hidden in the data that will have to be carefully taken into account to validate new predictive models. In addiction, researchers have to understand complicated and sometimes contradictory legal requirements and to consider ethical obligations in order to balance privacy and promoting discovery.
Unintended Consequences: New Problems, New Solutions
Authors: Chen Y. , Koppel R. ,   Section Editors for the IMIA Yearbook Special Section on Unintended Consequences
Published: November 2016

Summary
Objective: To select the best of the 2015 published papers on unintended consequences of healthcare information technology (HIT).
Method: Literature searches in several areas of scholarship, including IT, human factors, evaluation studies, medical errors, medical informatics, and implementation science. Also, because the specific terms “unintended consequences” were not often included in abstracts and titles, a more nuanced search algorithm was developed.
Results: We identified 754 papers that had some empirical research on unintended consequences of HIT. An initial screen of titles and abstracts reduced this to 171 papers of potential interest. We then further filtered out papers that did not meet the following criteria: 1) the paper had to report an original empirical investigation, and 2) the impact reported had to be not negligible, i.e., in quantitative studies, the results related to unintended consequences were statistically significant; and in qualitative studies the relevant themes emerged were prominent. This resulted in 33 papers of which 15 were selected as best paper candidates. Each of these 15 papers was then separately evaluated by four reviewers. The final selection of four papers was made jointly by the external reviewers and the two section editors. Conclusions: There is a growing awareness of the importance of HIT’s unintended consequences—be they generated by the HIT vendors, the implementation process, the consultants, the users, or most probably, some combination of the above. There has also been greater creativity in use of data sources, including secondary data (e.g., medical malpractice cases and surveys) and a wider acceptance of mixed methods to identify unintended consequences. Unfortunately, the complexity of causes mitigates the value of recommendations to avoid unwanted outcomes. Suggestions are often contentious rather than obvious, setting-specific, and not universally applicable. “Lessons learned” often take on generalized—and perhaps platitudinous—forms, such as: “plan extra time,” “involve all of the stakeholders,” “recognize the different needs of different units or disciplines.” The greater awareness of these problems, and the increased desire to identify and eliminate them is clearly reflected in the area’s growing literature. We are hopeful the topic will receive additional attention and the discipline will improve its ability to identify and address these unexpected and usually adverse outcomes.
Clinical Natural Language Processing in 2015: Leveraging the Variety of Texts of Clinical Interest
Authors: Zweigenbaum P. , Névéol A. ,   Section Editors for the IMIA Yearbook Section on Natural Language Processing
Published: November 2016

Summary
Objective: To summarize recent research and present a selection of the best papers published in 2015 in the field of clinical Natural Language Processing (NLP).
Method: A systematic review of the literature was performed by the two section editors of the IMIA Yearbook NLP section by searching bibliographic databases with a focus on NLP efforts applied to clinical texts or aimed at a clinical outcome. Section editors first selected a shortlist of candidate best papers that were then peer-reviewed by independent external reviewers.
Results: The clinical NLP best paper selection shows that clinical NLP is making use of a variety of texts of clinical interest to contribute to the analysis of clinical information and the building of a body of clinical knowledge. The full review process highlighted five papers analyzing patient-authored texts or seeking to connect and aggregate multiple sources of information. They provide a contribution to the development of methods, resources, applications, and sometimes a combination of these aspects.
Conclusions: The field of clinical NLP continues to thrive through the contributions of both NLP researchers and healthcare professionals interested in applying NLP techniques to impact clinical practice. Foundational progress in the field makes it possible to leverage a larger variety of texts of clinical interest for healthcare purposes.
The clinical utility of circulating neuroendocrine gene transcript analysis in well-differentiated paragangliomas and pheochromocytomas
Authors: Pęczkowska M , Cwikla J , Kidd M , Lewczuk A , Kolasinska-Ćwikła A , Niec D , Michałowska I , Prejbisz A , Januszewicz A , Chiarelli J , Bodei L , Modlin I 
Published: November 2016

Context
Paragangliomas and pheochromocytomas (PPGLs) exhibit variable malignancy, which is difficult to determine by histopathology, amine measurements or tissue genetic analyses.

Objective
To evaluate whether a 51-neuroendocrine gene blood analysis has clinical utility as a diagnostic and prognostic marker.

Design
Prospective cohort study. Well-differentiated PPGLs (n = 32), metastatic (n = 4); SDHx mutation (n = 25); 12 biochemically active, Lanreotide treated (n = 4). Nine patients had multiple sampling. Age- and gender-matched controls and GEP-NETs (comparators).

Methods
Circulating neuroendocrine tumor mRNA measured (qPCR) with multianalyte algorithmic analysis. Metabolic, epigenomic and proliferative genes as well as somatostatin receptor expression were assessed (averaged, normalized gene expression: mean ± s.e.m.). Amines were measured by HPLC and chromogranin A by ELISA. Analyses (2-tailed): Fisher’s test, non-parametric (Mann–Whitney), receiver-operator curve (ROC) and multivariate analysis (MVA). All data are presented as mean ± s.e.m.

Results
PPGL were NETest positive (100%). All exhibited higher scores than controls (55 ± 5% vs 8 ± 1%, P = 0.0001), similar to GEP-NETs (47 ± 5%). ROC analysis area under curve was 0.98 for differentiating PPGLs/controls (cut-off for normal: 26.7%). Mutation status was not directly linked to NETest. Genetic and molecular clustering was associated (P < 0.04) with NETest scores. Metastatic (80 ± 9%) and multicentric (64 ± 9%) disease had significantly (P < 0.04) higher scores than localized disease (43 ± 7%). Progressive disease (PD) had the highest scores (86 ± 2%) vs stable (SD, 41 ± 2%) (P < 0.0001). The area under the curve for PD from SD was 0.93 (cut-off for PD: 53%). Proliferation, epigenetic and somatostatin receptor gene expression was elevated (P < 0.03) in PD. Metabolic gene expression was decreased in SDHx mutations. Repeat NETest measurements defined clinical status in the 9 patients (6 SD and 3 PD). Amine measurement was non-informative. Multivariate analysis identified NETest >53% as an independent prognostic factor.

Conclusion
Circulating NET transcript analysis is positive (100% diagnostic) in well-differentiated PCC/PGL, scores were elevated in progressive disease irrespective of mutation or biochemical activity and elevated levels were prognostic.
Autoimmune comorbidities in Hashimoto’s thyroiditis: different patterns of association in adulthood and childhood/adolescence
Authors: Ruggeri R M , Trimarchi F , Giuffrida G , Certo R , Cama E , Campennì A , Alibrandi A , De Luca F , Wasniewska M 
Published: November 2016

Objective
Hashimoto’s thyroiditis (HT), the most common autoimmune thyroid disease at any age, is often associated with other autoimmune diseases. The present study was aimed to describe the type and frequency of non-thyroidal autoimmune diseases (NTADs) in HT patients and to delineate the clinical pattern of diseases clustering in pediatric/adolescent and adult age.

Design
Cross-sectional study.

Methods
1053 newly diagnosed HT patients (500 adults (467 F, mean age 40.2 ± 13.7 years) and 553 children/adolescents (449 F, mean age 11.1 ± 3.0 years)) were evaluated for common NTADs by means of careful recording of medical history, physical examination and assessment of selected autoantibody profiles.

Results
The prevalence of associated NTADs was significantly higher in adults than that in pediatric/adolescent HT patients (P < .0001). In addition, the number of adult patients suffering from two or more associated NTADs was significantly higher than that of children/adolescent (P < 0.0001). A female prevalence was evident in both cohorts, but was significant in the adults (P < 0.0001). The epidemiological distribution of NTADs was strongly different in the two cohorts, the most frequent associated diseases being arthropathies and connective tissue diseases in adults and type 1 diabetes and coeliac disease in children/adolescents. Skin diseases were represented with similar prevalence in both cohorts, vitiligo being the most common.

Conclusions
Age at HT presentation may influence autoimmune diseases clustering, favoring the association of specific NTADs in different ages of life. Moreover, the association between HT and NTADs increases with age and occurs most frequently in adults.
CRISPR Technology Reveals RAD(51)-ical Mechanisms of Repair in Roundworms: An Educational Primer for Use with “Promotion of Homologous Recombination by SWS-1 in Complex with RAD-51 Paralogs in Caenorhabditis elegans”
Authors: Turcotte Carolyn A , Andrews Nicolas P , Sloat Solomon A , Checchi Paula M 
Published: November 2016

Abstract
The mechanisms cells use to maintain genetic fidelity via DNA repair and the accuracy of these processes have garnered interest from scientists engaged in basic research to clinicians seeking improved treatment for cancer patients. Despite the continued advances, many details of DNA repair are still incompletely understood. In addition, the inherent complexity of DNA repair processes, even at the most fundamental level, makes it a challenging topic. This primer is meant to assist both educators and students in using a recent paper, “Promotion of homologous recombination by SWS-1 in complex with RAD-51 paralogs in Caenorhabditis elegans,” to understand mechanisms of DNA repair. The goals of this primer are to highlight and clarify several key techniques utilized, with special emphasis on the clustered, regularly interspaced, short palindromic repeats technique and the ways in which it has revolutionized genetics research, as well as to provide questions for deeper in-class discussion.
Co-occurring substance-related and behavioral addiction problems: A person-centered, lay epidemiology approach
Authors: Konkolÿ Thege Barna , Hodgins David C. , Wild T. Cameron 
Published: November 2016

Background and aims
The aims of this study were (a) to describe the prevalence of single versus multiple addiction problems in a large representative sample and (b) to identify distinct subgroups of people experiencing substance-related and behavioral addiction problems.

Methods
A random sample of 6,000 respondents from Alberta, Canada, completed survey items assessing self-attributed problems experienced in the past year with four substances (alcohol, tobacco, marijuana, and cocaine) and six behaviors (gambling, eating, shopping, sex, video gaming, and work). Hierarchical cluster analyses were used to classify patterns of co-occurring addiction problems on an analytic subsample of 2,728 respondents (1,696 women and 1032 men; Mage = 45.1 years, SDage = 13.5 years) who reported problems with one or more of the addictive behaviors in the previous year.

Results
In the total sample, 49.2% of the respondents reported zero, 29.8% reported one, 13.1% reported two, and 7.9% reported three or more addiction problems in the previous year. Cluster-analytic results suggested a 7-group solution. Members of most clusters were characterized by multiple addiction problems; the average number of past year addictive behaviors in cluster members ranged between 1 (Cluster II: excessive eating only) and 2.5 (Cluster VII: excessive video game playing with the frequent co-occurrence of smoking, excessive eating and work).

Discussion and conclusions
Our findings replicate previous results indicating that about half of the adult population struggles with at least one excessive behavior in a given year; however, our analyses revealed a higher number of co-occurring addiction clusters than typically found in previous studies.
Automated problem generation in Learning Management Systems: a tutorial
Authors: Romero Jaime , Rozano Mercedes 
Published: November 2016

Abstract

The benefits of solving problems have been widely acknowledged by literature. Its implementation in eâ€“learning platforms can make easier its management and the learning process itself. However, its implementation can also become a very timeâ€“consuming task, particularly when the number of problems to generate is high. In this tutorial we describe a methodology that we have developed aiming to alleviate the workload of producing a great deal of problems in Moodle for an undergraduate business course. This methodology follows a six-step process and allows evaluating studentâ€™s skills in problem solving, minimizes plagiarism behaviors and provides immediate feedback. We expect this tutorial encourage other educators to apply our six steps process, thus benefiting themselves and their students of its advantages.

Keywords: Learning management systems; problem generation; randomization; cloze questions
Design Based Research: the Way of Developing and Implementing Educational Innovation
Authors: Štemberger Tina , Cencič Majda 
Published: November 2016

Abstract
The appropriate implementation of innovation is a crucial factor in improving educational practice. In the implementation process, there is, however, often a lack of interaction between designers and practitioners that would enable the latter to become competent enough to implement theoretical knowledge into practice and to have an ongoing support from designers. Design-based research is based on close cooperation between researchers, practitioners and designers which consequently allows greater integration of research and practice in education. In the present paper, the beginnings, development, basic characteristics, advantages, disadvantages and the research process of design-based research are reviewed and an example of design-based research is presented.

Keywords: design-based research; educational research; educational innovation; mixed methods research; educational improvement