bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic elimination of dopamine vesicular stocks in the nigrostriatal pathway replicates Parkinson’s disease motor symptoms without neuronal degeneration in adult mice
Authors: Isingrini Elsa , Guinaudie Chloé , C Perret Léa , Rainer Quentin , Moquin Luc , Gratton Alain , Giros Bruno 
Published: September 2017

AbstractThe type 2 vesicular monoamine transporter (VMAT2), by regulating the storage of monoamines transmitters into synaptic vesicles, has a protective role against their cytoplasmic toxicity. Increasing evidence suggests that impairment of VMAT2 neuroprotection contributes to the pathogenesis of Parkinson’s disease (PD). Several transgenic VMAT2 mice models have been developed, however these models lack specificity regarding the monoaminergic system targeting. To circumvent this limitation, we created VMAT2-KO mice specific to the dopamine (DA) nigrostriatal pathway to analyze VMAT2’s involvement in DA depletion-induced motor features associated to PD and examine the relevance of DA toxicity in the pathogenesis of neurodegeneration. Adult VMAT2 floxed mice were injected in the substancia nigra (SN) with an adeno-associated virus (AAV) expressing the Cre-recombinase allowing VMAT2 removal in DA neurons of the nigrostriatal pathway solely. VMAT2 deletion in the SN induced both DA depletion exclusively in the dorsal striatum and motor dysfunction. At 16 weeks post-injection, motor symptoms were accompanied with a decreased in food and water consumption and weight loss. However, despite an accelerating death, degeneration of nigrostriatal neurons was not observed in this model during this time frame. This study highlights a non-cytotoxic role of DA in our genetic model of VMAT2 deletion exclusively in nigrostriatal neurons.
Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem
Authors: Zhang Kai , Sun Yongge , Cui Zhisong , Yu Di , Zheng Li , Liu Peng , Lv Zhenmei 
Published: September 2017

AbstractIn this study, time-series samples were taken from a gravel beach to ascertain whether a periodic oil input induced by tidal action at the early stage of an oil spill can be a trigger to stimulate the development of hydrocarbon-degrading bacteria under natural in situ attenuation. High-throughput sequencing shows that the microbial community in beach sediments is characterized by the enrichment of hydrocarbon-degrading bacteria, including Alcanivorax, Dietzia, and Marinobacter. Accompanying the periodic floating-oil input, dynamic successions of microbial communities and corresponding fluctuations in functional genes (alkB and RDH) are clearly indicated in a time sequence, which keeps pace with the ongoing biodegradation of the spilled oil. The microbial succession that accompanies tidal action could benefit from the enhanced exchange of oxygen and nutrients; however, regular inputs of floating oil can be a trigger to stimulate an in situ “seed bank” of hydrocarbon-degrading bacteria. This leads to the continued blooming of hydrocarbon-degrading consortia in beach ecosystems. The results provide new insights into the beach microbial community structure and function in response to oil spills.
Sensor, Signal, and Imaging Informatics
Authors: Hsu W. , Park S. , Kahn Charles 
Published: September 2017

Summary
Objective: To summarize significant contributions to sensor, signal, and imaging informatics published in 2016.
Methods: We conducted an extensive search using PubMed® and Web of Science® to identify the scientific contributions published in 2016 that addressed sensors, signals, and imaging in medical informatics. The three section editors selected 15 candidate best papers by consensus. Each candidate article was reviewed by the section editors and at least two other external reviewers. The final selection of the six best papers was conducted by the editorial board of the Yearbook.
Results: The selected papers of 2016 demonstrate the important scientific advances in management and analysis of sensor, signal, and imaging information.
Conclusion: The growing volume of signal and imaging data provides exciting new challenges and opportunities for research in medical informatics. Evolving technologies provide faster and more effective approaches for pattern recognition and diagnostic evaluation. The papers selected here offer a small glimpse of the high-quality scientific work published in 2016 in the domain of sensor, signal, and imaging informatics.
Clinical Research Informatics: Contributions from 2016
Authors: Daniel C. , Choquet R. 
Published: September 2017

Summary
Objectives: To summarize key contributions to current research in the field of Clinical Research Informatics (CRI) and to select the best papers published in 2016.
Methods: A bibliographic search using a combination of MeSH and free terms on CRI was performed using PubMed, 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 organized to finally conclude on the selection of best papers.
Results: Among the 452 papers published in 2016 in the various areas of CRI and returned by the query, the full review process selected four best papers. The authors of the first paper utilized a comprehensive representation of the patient medical record and semi-automatically labeled training sets to create phenotype models via a machine learning process. The second selected paper describes an open source tool chain securely connecting ResearchKit compatible applications (Apps) to the widely-used clinical research infrastructure Informatics for Integrating Biology and the Bedside (i2b2). The third selected paper describes the FAIR Guiding Principles for scientific data management and stewardship. The fourth selected paper focuses on the evaluation of the risk of privacy breaches in releasing genomics datasets.
Conclusions: A major trend in the 2016 publications is the variety of research on “real-world data” - healthcare-generated data, person health data, and patient-reported outcomes -highlighting the opportunities provided by new machine learning techniques as well as new potential risks of privacy breaches.
Capturing the Patient’s Perspective: a Review of Advances in Natural Language Processing of Health-Related Text
Authors: Gonzalez-Hernandez G. , Sarker A. , O’Connor K. , Savova G. 
Published: September 2017

Summary
Background: Natural Language Processing (NLP) methods are increasingly being utilized to mine knowledge from unstructured health-related texts. Recent advances in noisy text processing techniques are enabling researchers and medical domain experts to go beyond the information encapsulated in published texts (e.g., clinical trials and systematic reviews) and structured questionnaires, and obtain perspectives from other unstructured sources such as Electronic Health Records (EHRs) and social media posts.
Objectives: To review the recently published literature discussing the application of NLP techniques for mining health-related information from EHRs and social media posts.
Methods: Literature review included the research published over the last five years based on searches of PubMed, conference proceedings, and the ACM Digital Library, as well as on relevant publications referenced in papers. We particularly focused on the techniques employed on EHRs and social media data.
Results: A set of 62 studies involving EHRs and 87 studies involving social media matched our criteria and were included in this paper. We present the purposes of these studies, outline the key NLP contributions, and discuss the general trends observed in the field, the current state of research, and important outstanding problems.
Conclusions: Over the recent years, there has been a continuing transition from lexical and rule-based systems to learning-based approaches, because of the growth of annotated data sets and advances in data science. For EHRs, publicly available annotated data is still scarce and this acts as an obstacle to research progress. On the contrary, research on social media mining has seen a rapid growth, particularly because the large amount of unlabeled data available via this resource compensates for the uncertainty inherent to the data. Effective mechanisms to filter out noise and for mapping social media expressions to standard medical concepts are crucial and latent research problems. Shared tasks and other competitive challenges have been driving factors behind the implementation of open systems, and they are likely to play an imperative role in the development of future systems.
Health Data for Public Health: Towards New Ways of Combining Data Sources to Support Research Efforts in Europe
Authors: Burgun A. , Bernal-Delgado E. , Kuchinke W. , van Staa T. , Cunningham J. , Lettieri E. , Mazzali C. , Oksen D. , Estupiñan F. , Barone A. , Chène G. 
Published: September 2017

Summary
Objectives: To present the European landscape regarding the re-use of health administrative data for research. Methods: We present some collaborative projects and solutions that have been developed by Nordic countries, Italy, Spain, France, Germany, and the UK, to facilitate access to their health data for research purposes.
Results: Research in public health is transitioning from siloed systems to more accessible and re-usable data resources. Following the example of the Nordic countries, several European countries aim at facilitating the re-use of their health administrative databases for research purposes. However, the ecosystem is still a complex patchwork, with different rules, policies, and processes for data provision.
Conclusion: The challenges are such that with the abundance of health administrative data, only a European, overarching public health research infrastructure, is able to efficiently facilitate access to this data and accelerate research based on these highly valuable resources.
On Contributing to the Progress of Medical Informatics as Publisher
Authors: Haux R. , Geissbuhler A. , Holmes J. , Jaulent M.-C. , Koch S. , Kulikowski C. A. , Lehmann C. U. , McCray A. T. , Séroussi B. , Soualmia L. F. , van Bemmel J. H. 
Published: September 2017

Summary
May 1st, 2017, will mark Dieter Bergemann’s 80th birthday. As Chief Executive Officer and Owner of Schattauer Publishers from 1983 to 2016, the biomedical and health informatics community owes him a great debt of gratitude. The past and present editors of Methods of Information in Medicine, the IMIA Yearbook of Medical Informatics, and Applied Clinical Informatics want to honour and thank Dieter Bergemann by providing a brief biography that emphasizes his contributions, by reviewing his critical role as an exceptionally supportive publisher for Schattauer’s three biomedical and health informatics periodicals, and by sharing some personal anecdotes. Over the past 40 years, Dieter Bergemann has been an influential, if behind-the-scenes, driving force in biomedical and health informatics publications, helping to ensure success in the dissemination of our field’s research and practice.
Secondary Use and Analysis of Big Data Collected for Patient Care
Authors: Martin-Sanchez F. J. , Aguiar-Pulido V. , Lopez-Campos G. H. , Peek N. , Sacchi L. 
Published: September 2017

Summary
Objectives: To identify common methodological challenges and review relevant initiatives related to the re-use of patient data collected in routine clinical care, as well as to analyze the economic benefits derived from the secondary use of this data. Through the use of several examples, this article aims to provide a glimpse into the different areas of application, namely clinical research, genomic research, study of environmental factors, and population and health services research. This paper describes some of the informatics methods and Big Data resources developed in this context, such as electronic phenotyping, clinical research networks, biorepositories, screening data banks, and wide association studies. Lastly, some of the potential limitations of these approaches are discussed, focusing on confounding factors and data quality.
Methods: A series of literature searches in main bibliographic databases have been conducted in order to assess the extent to which existing patient data has been repurposed for research. This contribution from the IMIA working group on “Data mining and Big Data analytics” focuses on the literature published during the last two years, covering the timeframe since the working group’s last survey.
Results and Conclusions: Although most of the examples of secondary use of patient data lie in the arena of clinical and health services research, we have started to witness other important applications, particularly in the area of genomic research and the study of health effects of environmental factors. Further research is needed to characterize the economic impact of secondary use across the broad spectrum of translational research.
The IMIA History Working Group: Inception through the IMIA History Taskforce, and Major Events Leading Up to the 50th Anniversary of IMIA
Authors: Kulikowski C. A. , Mihalas G. , Greenes R. A. , Yacubsohn V. , Park H.-A. 
Published: September 2017

Summary
Background: The 50th Anniversary of IMIA will be celebrated in 2017 at the World Congress of Medical Informatics in China. This takes place 50 years after the International Federation of Information Processing (IFIP) Societies approved the formation of a new Technical Committee (TC) 4 on Medical Information Processing, which was the predecessor of IMIA, under the leadership of Dr. Francois Grémy. The IMIA History Working Group (WG) was approved in 2014 to document and write about the history of the field and its organizations.
Objectives: The goals of this paper are to describe how the IMIA History WG arose and developed, including its meetings and projects, leading to the forthcoming 50th Anniversary of IMIA.
Methods: We give a chronology of major developments leading up to the current work of the IMIA History WG and how it has stimulated writing on the international history of biomedical and health informatics, sponsoring the systematic compilation and writing of articles and stories from pioneers and leaders in the field, and the organization of workshops and panels over the past six years, leading towards the publication of the contributed volume on the 50th IMIA Anniversary History as an eBook by IOS Press.
Conclusions: This article leads up to the IMIA History eBook which will contain original autobiographical retrospectives by pioneers and leaders in the field, together with professional organizational histories of the national and regional societies and working groups of IMIA, with commentary on the main themes and topics which have evolved as scientific and clinical practices have changed under the influence of new insights, technologies, and the changing socio-economic, cultural and professional circumstances around the globe over the past 50 years.
Added Value from Secondary Use of Person Generated Health Data in Consumer Health Informatics
Authors: Hsueh P.-Y. , Cheung Y.-K. , Dey S. , Kim K. K. , Martin-Sanchez F. J. , Petersen S. K. , Wetter T. 
Published: September 2017

Summary
Introduction: Various health-related data, subsequently called Person Generated Health Data (PGHD), is being collected by patients or presumably healthy individuals as well as about them as much as they become available as measurable properties in their work, home, and other environments. Despite that such data was originally just collected and used for dedicated predefined purposes, more recently it is regarded as untapped resources that call for secondary use.
Method: Since the secondary use of PGHD is still at its early evolving stage, we have chosen, in this paper, to produce an outline of best practices, as opposed to a systematic review. To this end, we identified key directions of secondary use and invited protagonists of each of these directions to present their takes on the primary and secondary use of PGHD in their sub-fields. We then put secondary use in a wider perspective of overarching themes such as privacy, interpretability, interoperability, utility, and ethics.
Results: We present the primary and secondary use of PGHD in four focus areas: (1) making sense of PGHD in augmented Shared Care Plans for care coordination across multiple conditions; (2) making sense of PGHD from patient-held sensors to inform cancer care; (3) fitting situational use of PGHD to evaluate personal informatics tools in adaptive concurrent trials; (4) making sense of environment risk exposure data in an integrated context with clinical and omics-data for biomedical research.
Discussion: Fast technological progress in all the four focus areas calls for a societal debate and decision-making process on a multitude of challenges: how emerging or foreseeable results transform privacy; how new data modalities can be interpreted in light of clinical data and vice versa; how the sheer mass and partially abstract mathematical properties of the achieved insights can be interpreted to a broad public and can consequently facilitate the development of patient-centered services; and how the remaining risks and uncertainties can be evaluated against new benefits. This paper is an initial summary of the status quo of the challenges and proposals that address these issues. The opportunities and barriers identified can serve as action items individuals can bring to their organizations when facing challenges to add value from the secondary use of patient-generated health data.
IMIA Accreditation of Biomedical and Health Informatics Education: Current State and Future Directions
Authors: Jaspers M. W. , Mantas J. , Borycki E. , Hasman A. 
Published: September 2017

Summary
Objectives: The educational activities initiated by the International Medical Informatics Association (IMIA) have had global impacts and influenced national societies and local academic programs in the field of Biomedical and Health Informatics (BMHI). After the successful publication and dissemination of its educational recommendations, IMIA launched an accreditation procedure for educational programs in BMHI. The accreditation procedure was pilot tested by several BMHI academic programs in different countries and continents to obtain a global perspective.
Methods: This paper presents an overview of IMIA quality assurance and accreditation procedures along with feedback on issues and problems which emerged during the pilot.
Results: It appears that IMIA quality assurance and procedures worked quite well in different countries of Europe, the Middle East, South America, and Asia. These first experiences provided adequate information for adapting, modifying, and optimizing the procedures and finally for the planning of future activities.
Conclusions: IMIA accreditation framework comprises a single set of standards that apply at various levels to both academic and professional BMHI programs. The pilot phase confirmed the robustness and generalizability of quality assurance standards and associated procedures on which IMIA accreditation is based at an international level.
Surgical Emergencies in Intestinal Venous Malformations
Authors: Bueno Alba , De La Torre Carlos , Cerezo Vanesa , Rebolledo Bryant , Cervantes Manuel , Dore Mariela , Gomez Javier , Santamaria Manuel , Martinez Leopoldo , Lopez-Gutierrez Juan , Romo Muñoz Martha 
Published: September 2017

Background Venous malformations (VMs) can occur in any part of the body; however, the gastrointestinal tract is a frequent location. These are usually asymptomatic, thus, representing a challenge to diagnosis. Intestinal location of VMs can be associated with severe complications that ultimately require an emergency surgery. Our aim was to analyze all patients with an intestinal VM with special focus on those who required emergency surgery.
Materials and Methods A retrospective study of patients presenting complication caused by intestinal VM was performed. Clinical records, associated anomalies, physical findings, and treatment were assessed.
Results Twenty-one patients had a diagnosis of intestinal VM, 16 (76%) were associated to blue rubber bleb nevus syndrome (BRBNS) and 5 (24%) were isolated. Only four (19%) of the total cases presented an episode of acute abdomen with hemodynamic instability that required an emergency surgery. Findings included two gastrointestinal bleedings, one volvulus, and one intussusception of small bowel. All patients underwent an uneventful recovery and are presently doing well.
Conclusion Intestinal VM can be challenging to diagnose in emergency situations, such as gastrointestinal situation or acute abdomen. The complications associated with it must be kept in mind, regardless of its low incidence.
Outcomes of Esophageal Replacement: Gastric Pull-Up and Colonic Interposition Procedures
Authors: Sloan Keren , Morandi Anna , Lakshminarayanan Bhanumathi , Cox Sharon , Millar Alastair , Numanoglu Alp , Lakhoo Kokila , Bradshaw Catherine 
Published: September 2017

Aim No consensus exists about the optimal surgical technique for esophageal replacement. This study reports the surgical outcomes for the gastric pull-up and the colonic interposition procedures.
Materials and Methods A retrospective review of children undergoing esophageal replacement surgery between January 2001 and June 2015 across four different pediatric surgery centers was conducted. Data collected included indications, epidemiology, surgical technique, complications, and outcomes. Patients were divided into group A, those that had a gastric pull-up procedure and group B, those that had a colonic interposition procedure.
Results In total, 50 patients were included; 29 in group A and 21 in group B. Indications included esophageal atresia, caustic ingestion, and infective esophageal stricture. The median age at the time of surgery was 13 months. The mean length of follow-up was 5.2 years. Three patients died giving a mortality rate of 6%; 2 in group A and 1 in group B.In both groups, early postoperative complications included infective complications, such as wound infections, sepsis, and pneumonia (11), anastomotic leak (7), and respiratory complications (7). Late complications included adhesive bowel obstruction (2), anastomotic strictures (4), redundancy (1), and jejunostomy problems (1). Septic complications and anastomotic strictures occurred more frequently in group B. Further surgery was needed in eight patients; this was significantly higher in group B. Full oral feeding was achieved within 6 months in 91.5%.
Conclusion The gastric pull-up and colonic interposition have comparable mortality and outcomes. The colonic interposition was associated with a higher rate of early septic complications, anastomotic strictures, and need for further surgery.