bluuebunny/crossref_metadata_2025 huggingface dataset:
Balancing Between Privacy and Patient Needs for Health Information in the Age of Participatory Health and Social Media: A Scoping Review
Authors: Househ Mowafa , Grainger Rebecca , Petersen Carolyn , Bamidis Panagiotis , Merolli Mark
Published: April 2018

Objectives: With the increased use of participatory health enabling technologies, such as social media, balancing the need for health information with patient privacy and confidentiality has become a more complex and immediate concern. The purpose of this paper produced by the members of the IMIA Participatory Health and Social Media (PHSM) working group is to investigate patient needs for health information using participatory health enabling technologies, while balancing their needs for privacy and confidentiality.

Methods: Six domain areas including media sharing platforms, patient portals, web-based platforms, crowdsourcing websites, medical avatars, and other mobile health technologies were identified by five members of the IMIA PHSM working group as relevant to participatory health and the balance between data sharing and patient needs for privacy and confidentiality. After identifying the relevant domain areas, our scoping review began by searching several databases such as PubMed, MEDLINE, Scopus, and Google Scholar using a variety of key search terms.

Results: A total of 1,973 studies were identified, of which 68 studies met our inclusion criteria and were included in the analysis. Results showed that challenges for balancing patient needs for information and privacy and confidentiality concerns included: cross-cultural understanding, clinician and patient awareness, de-identification of data, and commercialization of patient data. Some opportunities identified were patient empowerment, connecting participatory health enabling technologies with clinical records, open data sharing agreement, and e-consent.

Conclusion: Balancing between privacy and patient needs for health information in the age of participatory health and social media offers several opportunities and challenges. More people are engaging in actively managing health through participatory health enabling technologies. Such activity often includes sharing health information and with this comes a perennial tension between balancing individual needs and the desire to uphold privacy and confidentiality. We recommend that guidelines for both patients and clinicians, in terms of their use of participatory health-enabling technologies, are developed to ensure that patient privacy and confidentiality are protected, and a maximum benefit can be realized.
Five Years of Clinical Informatics Board Certification for Physicians in the United States of America
Authors: Lehmann Christoph , Gundlapalli Adi , Williamson Jeffrey , Fridsma Douglas , Hersh William , Krousel-Wood Marie , Ondrula Christopher , Munger Benson
Published: April 2018

Objectives: To review the highlights of the new Clinical Informatics subspecialty including its history, certification requirements, development of and performance on the certification examination in the United States.

Methods: We reviewed processes for the development of a subspecialty. Data from board certification examinations were collated and analyzed. We discussed eligibility requirements in the fellowship as well as practice pathways.

Results: Lessons learned from the development of the Clinical Informatics subspecialty, opportunities, challenges, and future directions for the field are discussed.

Conclusions: There remains a need for fellowship programs and creation and maintenance of a professional home for the subspecialty with the American Medical Informatics Association. Ongoing attention to the currency of the core content is required to maintain an examination designed to test the key concepts within the field of Clinical Informatics.
The Datafication of Everything — Even Toilets
Authors: Lun Kwok-Chan
Published: April 2018

Health informatics has benefitted from the development of Info-Communications Technology (ICT) over the last fifty years. Advances in ICT in healthcare have now started to spur advances in Data Technology as hospital information systems, electronic health and medical records, mobile devices, social media and Internet Of Things (IOT) are making a substantial impact on the generation of data. It is timely for healthcare institutions to recognize data as a corporate asset and promote a data-driven culture within the institution. It is both strategic and timely for IMIA, as an international organization in health informatics, to take the lead to promote a data-driven culture in healthcare organizations. This can be achieved by expanding the terms of reference of its existing Working Group on Data Mining and Big Data Analysis to include (1) data analytics with special reference to healthcare, (2) big data tools and solutions, (3) bridging information technology and data technology and (4) data quality issues and challenges.
Terminology Services: Standard Terminologies to Control Health Vocabulary
Authors: González Bernaldo de Quirós Fernán , Otero Carlos , Luna Daniel
Published: April 2018

Healthcare Information Systems should capture clinical data in a structured and preferably coded format. This is crucial for data exchange between health information systems, epidemiological analysis, quality and research, clinical decision support systems, administrative functions, among others. Structured data entry is an obstacle for the usability of electronic health record (EHR) applications and their acceptance by physicians who prefer to document patient EHRs using “free text”. Natural language allows for rich expressiveness but at the same time is ambiguous; it has great dependence on context and uses jargon and acronyms. Although much progress has been made in knowledge and natural language processing techniques, the result is not yet satisfactory enough for the use of free text in all dimensions of clinical documentation. In order to address the trade-off between capturing data with free text and at the same time coding data for computer processing, numerous terminological systems for the systematic recording of clinical data have been developed. The purpose of terminology services consists of representing facts that happen in the real world through database management in order to allow for semantic interoperability and computerized applications. These systems interrelate concepts of a particular domain and provide references to related terms with standards codes. In this way, standard terminologies allow the creation of a controlled medical vocabulary, making terminology services a fundamental component for health data management in the healthcare environment. The Hospital Italiano de Buenos Aires has been working in the development of its own terminology server. This work describes its experience in the field.
The Privacy and Security Implications of Open Data in Healthcare
Authors: Kobayashi Shinji , Kane Thomas , Paton Chris
Published: April 2018

Objective: The International Medical Informatics Association (IMIA) Open Source Working Group (OSWG) initiated a group discussion to discuss current privacy and security issues in the open data movement in the healthcare domain from the perspective of the OSWG membership.

Methods: Working group members independently reviewed the recent academic and grey literature and sampled a number of current large-scale open data projects to inform the working group discussion.

Results: This paper presents an overview of open data repositories and a series of short case reports to highlight relevant issues present in the recent literature concerning the adoption of open approaches to sharing healthcare datasets. Important themes that emerged included data standardisation, the inter-connected nature of the open source and open data movements, and how publishing open data can impact on the ethics, security, and privacy of informatics projects.

Conclusions: The open data and open source movements in healthcare share many common philosophies and approaches including developing international collaborations across multiple organisations and domains of expertise. Both movements aim to reduce the costs of advancing scientific research and improving healthcare provision for people around the world by adopting open intellectual property licence agreements and codes of practice. Implications of the increased adoption of open data in healthcare include the need to balance the security and privacy challenges of opening data sources with the potential benefits of open data for improving research and healthcare delivery.
Benefit-risk of Patients' Online Access to their Medical Records: Consensus Exercise of an International Expert Group
Authors: Liyanage Harshana , Liaw Siaw-Teng , Konstantara Emmanouela , Mold Freda , Schreiber Richard , Kuziemsky Craig , Terry Amanda , de Lusignan Simon
Published: April 2018

Background: Patients' access to their computerised medical records (CMRs) is a legal right in many countries. However, little is reported about the benefit-risk associated with patients' online access to their CMRs.

Objective: To conduct a consensus exercise to assess the impact of patients' online access to their CMRs on the quality of care as defined in six domains by the Institute of Medicine (IoM), now the National Academy of Medicine (NAM).

Method: A five-round Delphi study was conducted. Round One explored experts' (n = 37) viewpoints on providing patients with access to their CMRs. Round Two rated the appropriateness of statements arising from Round One (n = 16). The third round was an online panel discussion of findings (n = 13) with the members of both the International Medical Informatics Association and the European Federation of Medical Informatics Primary Health Care Informatics Working Groups. Two additional rounds, a survey of the revised consensus statements and an online workshop, were carried out to further refine consensus statements.

Results: Thirty-seven responses from Round One were used as a basis to initially develop 15 statements which were categorised using IoM's domains of care quality. The experts agreed that providing patients online access to their CMRs for bookings, results, and prescriptions increased efficiency and improved the quality of medical records. Experts also anticipated that patients would proactively use their online access to share data with different health care providers, including emergencies. However, experts differed on whether access to limited or summary data was more useful to patients than accessing their complete records. They thought online access would change recording practice, but they were unclear about the benefit-risk of high and onerous levels of security. The 5-round process, finally, produced 16 consensus statements.

Conclusion: Patients' online access to their CMRs should be part of all CMR systems. It improves the process of health care, but further evidence is required about outcomes. Online access improves efficiency of bookings and other services. However, there is scope to improve many of the processes of care it purports to support, particularly the provision of a more effective interface and the protection of the vulnerable.
History of Romanian Medical Informatics: Learning from the Past to Reshape the Future
Authors: Mihalas George , Stoicu-Tivadar Lacramioara
Published: April 2018

Objectives: The paper presents a review of the history of medical informatics in Romania, starting from the pioneering works, relating the present, and foreseeing the future.

Methods: Major milestones of the development of this field have not been simply enumerated, but described within the specific socio-political frame, grasping the entire context over the last four decades in Romania. Two main perspectives have been traced: education and training in medical informatics and implementations in healthcare.

Results: Four distinctive historical periods are identified and the major events of each period are described in a critical manner. The history of the Romanian Society of Medical Informatics is presented in a separate chapter. The last section is dedicated to the present state of the field in Romania.

Conclusion: The history of Romanian Medical Informatics spans many years and is rich in content. The Romanian Society of Medical Informatics is mainly the result of the efforts undertaken by an enthusiastic and sound professional community, trying to continue the tradition, to achieve new goals, and to work as an active member of the international biomedical/health informatics community.
Middle East and North African Health Informatics Association (MENAHIA): Building Sustainable Collaboration
Authors: Al-Shorbaji Najeeb , Househ Mowafa , Taweel Adel , Alanizi Abdullah , Mohammed Bennani , Abaza Haitham , Bawadi Hala , Rasuly Hamayon , Alyafei Khalid , Fernandez-Luque Luis , Shouman Mohamed , El-Hassan Osama , Hussein Rada , Alshammari Riyad , Mandil Salah , Shouman Sarah , Taheri Shahrad , Emara Tamer , Dalhem Wasmiya , Al-Hamdan Zaid , Serhier Zineb
Published: April 2018

There has been a growing interest in Health Informatics applications, research, and education within the Middle East and North African Region over the past twenty years. People of this region share similar cultural and religious values, primarily speak the Arabic language, and have similar health care related issues, which are in dire need of being addressed. Health Informatics efforts, organizations, and initiatives within the region have been largely under-represented within, but not ignored by, the International Medical Informatics Association (IMIA). Attempts to create bonds and collaboration between the different organizations of the region have remained scattered, and often, resulted in failure despite the fact that the need for a united health informatics collaborative within the region has never been more crucial than today. During the 2017 MEDINFO, held in Hangzhou, China, a new organization, the Middle East and North African Health Informatics Association (MENAHIA) was conceived as a regional non-governmental organization to promote and facilitate health informatics uptake within the region endorsing health informatics research and educational initiatives of the 22 countries represented within the region. This paper provides an overview of the collaboration and efforts to date in forming MENAHIA and displays the variety of initiatives that are already occurring within the MENAHIA region, which MENAHIA will help, endorse, support, share, and improve within the international forum of health informatics.
Significant Hypo-Responsiveness to GPVI and CLEC-2 Agonists in Pre-Term and Full-Term Neonatal Platelets and following Immune Thrombocytopenia
Authors: Hardy Alexander , Palma-Barqueros Verónica , Watson Stephanie , Malcor Jean-Daniel , Eble Johannes , Gardiner Elizabeth , Blanco José , Guijarro-Campillo Rafael , Delgado Juan , Lozano María , Teruel-Montoya Raúl , Vicente Vicente , Watson Steve , Rivera José , Ferrer-Marín Francisca
Published: April 2018

Neonatal platelets are hypo-reactive to the tyrosine kinase-linked receptor agonist collagen. Here, we have investigated whether the hypo-responsiveness is related to altered levels of glycoprotein VI (GPVI) and integrin α2β1, or to defects in downstream signalling events by comparison to platelet activation by C-type lectin-like receptor 2 (CLEC-2). GPVI and CLEC-2 activate a Src- and Syk-dependent signalling pathway upstream of phospholipase C (PLC) γ2. Phosphorylation of a conserved YxxL sequence known as a (hemi) immunotyrosine-based-activation-motif (ITAM) in both receptors is critical for Syk activation. Platelets from human pre-term and full-term neonates display mildly reduced expression of GPVI and CLEC-2, as well as integrin αIIbβ3, accounted for at the transcriptional level. They are also hypo-responsive to the two ITAM receptors, as shown by measurement of integrin αIIbβ3 activation, P-selectin expression and Syk and PLCγ2 phosphorylation. Mouse platelets are also hypo-responsive to GPVI and CLEC-2 from late gestation to 2 weeks of age, as determined by measurement of integrin αIIbβ3 activation. In contrast, the response to G protein-coupled receptor agonists was only mildly reduced and in some cases not altered in neonatal platelets of both species. A reduction in response to GPVI and CLEC-2, but not protease-activated receptor 4 (PAR-4) peptide, was also observed in adult mouse platelets following immune thrombocytopenia, whereas receptor expression was not impaired. Our results demonstrate developmental differences in platelet responsiveness to GPVI and CLEC-2, and also following immune platelet depletion leading to reduced Syk activation. The rapid generation of platelets during development or following platelet depletion is achieved at the expense of signalling by ITAM-coupled receptors.
Interpolation framework to speed up near-surface wind simulations for data-driven wildfire applications
Authors: Rios O. , Jahn W. , Pastor E. , Valero M. M. , Planas E.
Published: April 2018

Local wind fields that account for topographic interaction are a key element for any wildfire spread simulator. Currently available tools to generate near-surface winds with acceptable accuracy do not meet the tight time constraints required for data-driven applications. This article presents the specific problem of data-driven wildfire spread simulation (with a strategy based on using observed data to improve results), for which wind diagnostic models must be run iteratively during an optimisation loop. An interpolation framework is proposed as a feasible alternative to keep a positive lead time while minimising the loss of accuracy. The proposed methodology was compared with the WindNinja solver in eight different topographic scenarios with multiple resolutions and reference – pre-run– wind map sets. Results showed a major reduction in computation time (~100 times once the reference fields are available) with average deviations of 3% in wind speed and 3° in direction. This indicates that high-resolution wind fields can be interpolated from a finite set of base maps previously computed. Finally, wildfire spread simulations using original and interpolated maps were compared showing minimal deviations in the fire shape evolution. This methodology may have an important effect on data assimilation frameworks and probabilistic risk assessment where high-resolution wind fields must be computed for multiple weather scenarios.
Automated location of active fire perimeters in aerial infrared imaging using unsupervised edge detectors
Authors: Valero M. M. , Rios O. , Pastor E. , Planas E.
Published: April 2018

A variety of remote sensing techniques have been applied to forest fires. However, there is at present no system capable of monitoring an active fire precisely in a totally automated manner. Spaceborne sensors show too coarse spatio-temporal resolutions and all previous studies that extracted fire properties from infrared aerial imagery incorporated manual tasks within the image processing workflow. As a contribution to this topic, this paper presents an algorithm to automatically locate the fuel burning interface of an active wildfire in georeferenced aerial thermal infrared (TIR) imagery. An unsupervised edge detector, built upon the Canny method, was accompanied by the necessary modules for the extraction of line coordinates and the location of the total burned perimeter. The system was validated in different scenarios ranging from laboratory tests to large-scale experimental burns performed under extreme weather conditions. Output accuracy was computed through three common similarity indices and proved acceptable. Computing times were below 1 s per image on average. The produced information was used to measure the temporal evolution of the fire perimeter and automatically generate rate of spread (ROS) fields. Information products were easily exported to standard Geographic Information Systems (GIS), such as GoogleEarth and QGIS. Therefore, this work contributes towards the development of an affordable and totally automated system for operational wildfire surveillance.
Relationships between mature trees and fire fuel hazard in Australian forest
Authors: Wilson Nicholas , Cary Geoffrey J. , Gibbons Philip
Published: April 2018

Increasing density of mid-storey vegetation since European settlement has been observed in forests and woodlands in several parts of the world and may result in greater fire fuel hazard. This phenomenon is often attributed to a longer interval between fires since European settlement, but may also be influenced by tree removal during the same period. We hypothesised that the number of mature trees in a stand reduces mid-storey vegetation cover and the associated fire fuel hazard through competition. To test this hypothesis, we examined associations between mid-storey cover and fire fuel hazard and the mean diameter of trees within stands of open forest and woodland in south-eastern Australia, a region prone to wildfires. We found that vegetation cover between 2 and 4 m and 4 and 6 m above the ground and two measures of fire fuel hazard were negatively associated with the quadratic mean tree diameter. Our results suggested that the removal of mature trees since European settlement may have triggered tree and shrub regeneration, resulting in higher mid-storey cover and fire fuel hazard. Thus, managing stands for the persistence and replacement of mature trees may contribute to long-term fuel reduction in Australian forests and woodlands.
Use of ordinary kriging and Gaussian conditional simulation to interpolate airborne fire radiative energy density estimates
Authors: Klauberg C. , Hudak A. T. , Bright B. C. , Boschetti L. , Dickinson M. B. , Kremens R. L. , Silva C. A.
Published: April 2018

Fire radiative energy density (FRED, J m−2) integrated from fire radiative power density (FRPD, W m−2) observations of landscape-level fires can present an undersampling problem when collected from fixed-wing aircraft. In the present study, the aircraft made multiple passes over the fire at ~3 min intervals, thus failing to observe most of the FRPD emitted as the flame front spread. We integrated the sparse FRPD time series to obtain pixel-level FRED estimates, and subsequently applied ordinary kriging (OK) and Gaussian conditional simulation (GCS) to interpolate across data voids caused by the undersampling. We compared FRED interpolated via OK and GCS with FRED estimated independently from ground measurements of biomass consumed from five prescribed burns at Eglin Air Force Base, Florida, USA. In four of five burns considered where undersampling prevailed, OK and GCS effectively interpolated FRED estimates across the data voids, improving the spatial distribution of FRED across the burning event and its overall mean. In a fifth burn, the burning characteristics were such that undersampling did not present a problem needing to be fixed. We also determined where burning and FRPD sampling characteristics merited applying OK and CGS only to the highest FRED estimates to interpolate more accurate FRED maps.
Pyramiding Quantitative Resistance with a Major Resistance Gene in Apple: From Ephemeral to Enduring Effectiveness in Controlling Scab
Authors: Lasserre-Zuber Pauline , Caffier Valérie , Stievenard René , Lemarquand Arnaud , Le Cam Bruno , Durel Charles-Eric
Published: April 2018

Genetic resistance is a useful strategy to control plant disease, but its effectiveness may be reduced over time due to the emergence of pathogens able to circumvent the defenses of the plant. However, the pyramiding of different resistance factors in the same plant can improve the effectiveness and durability of the resistance. To investigate the potential for this approach in apple to control scab disease we surveyed scab incidence in two experimental orchards located at a distance of more than 300 km planted with apple genotypes carrying quantitative resistance and major gene resistance alone or in combination. Our results showed that the effectiveness of pyramiding in controlling scab was dependent on the site and could not be completely explained by the effectiveness level of the resistances alone.
Remediation in Practicing Physicians: Current and Alternative Conceptualizations
Authors: Bourgeois-Law Gisèle , Teunissen Pim W. , Regehr Glenn
Published: April 2018

Suboptimal performance in practicing physicians is a decades-old problem. The lack of a universally accepted definition of remediation, the paucity of research on best remediation practices, and the ongoing controversy regarding the institutional responsibility for enacting and overseeing the remediation of physicians suggest that it is not merely a difficult problem to solve but a problem that the community does not grapple with meaningfully. Undoubtedly, logistical and political considerations contribute to this state of affairs; however, other underlying conceptual issues may also play a role in the medical profession’s difficulties in engaging with the challenges around remediation.

Through a review of the medical education and other literatures, the authors examined current conceptualizations of both reme-diation itself and the individual being remediated, as well as how the culture of medicine influences these conceptions. The authors explored how conceptualizations of remediation and the surrounding culture might affect not only the medical community’s ability to support but also its willingness to engage with physicians in need of remediation.

Viewing remediation as a means of supporting practice change—rather than as a means of redressing gaps in knowledge and skill—might be a useful alternative conceptualization, providing a good place to start exploring new avenues of research. However, moving forward will require more than simply a reconceptualization of remediation; it will also necessitate a change in how the community views its struggling members and a change in the medical culture that currently positions professional autonomy as the foundational premise for individual practice improvement.
Temporal Sensitivity Measured Shortly After Cochlear Implantation Predicts 6-Month Speech Recognition Outcome
Authors: Erb Julia , Ludwig Alexandra Annemarie , Kunke Dunja , Fuchs Michael , Obleser Jonas
Published: April 2018

Objectives:

Psychoacoustic tests assessed shortly after cochlear implantation are useful predictors of the rehabilitative speech outcome. While largely independent, both spectral and temporal resolution tests are important to provide an accurate prediction of speech recognition. However, rapid tests of temporal sensitivity are currently lacking. Here, we propose a simple amplitude modulation rate discrimination (AMRD) paradigm that is validated by predicting future speech recognition in adult cochlear implant (CI) patients.

Design:

In 34 newly implanted patients, we used an adaptive AMRD paradigm, where broadband noise was modulated at the speech-relevant rate of ~4 Hz. In a longitudinal study, speech recognition in quiet was assessed using the closed-set Freiburger number test shortly after cochlear implantation (t

0
) as well as the open-set Freiburger monosyllabic word test 6 months later (t

6
).

Results:

Both AMRD thresholds at t

0
(r = –0.51) and speech recognition scores at t

0
(r = 0.56) predicted speech recognition scores at t

6
. However, AMRD and speech recognition at t

0
were uncorrelated, suggesting that those measures capture partially distinct perceptual abilities. A multiple regression model predicting 6-month speech recognition outcome with deafness duration and speech recognition at t

0
improved from adjusted R2
= 0.30 to adjusted R2
= 0.44 when AMRD threshold was added as a predictor.

Conclusions:

These findings identify AMRD thresholds as a reliable, nonredundant predictor above and beyond established speech tests for CI outcome. This AMRD test could potentially be developed into a rapid clinical temporal-resolution test to be integrated into the postoperative test battery to improve the reliability of speech outcome prognosis.
Factors Associated With Gaps in Medicaid Enrollment Among People With HIV and the Effect of Gaps on Viral Suppression
Authors: Monroe Anne K. , Myint Leslie , M. Rutstein Richard , Aberg Judith , L. Boswell Stephen , L. Agwu Allison , A.Gebo Kelly , D. Moore Richard ,   for the HIV Research Network
Published: April 2018

Introduction:

Gaps in Medicaid enrollment may affect HIV outcomes. We evaluated factors associated with Medicaid enrollment gaps and their effect on viral suppression (VS) within the HIV Research Network.

Methods:

We used a combined data set with Medicaid enrollment files from 2006 to 2010 and HIV Research Network demographic and clinical data. A gap was defined as ≥1 month without Medicaid and gap length was determined. We used multivariable logistic regression to determine factors associated with a gap and multivariable logistic regression with generalized estimated equations to evaluate factors associated with VS after gap.

Results:

Of 5836 participants, the majority were male, of black race, and aged 25–50 years. More than half had a gap in Medicaid. Factors associated with a gap included male sex [adjusted odds ratio (aOR) 1.79, (1.53, 2.08)] and younger age (aORs ranging from 1.50 to 4.13 comparing younger age groups to age >50, P < 0.05 for all). About a quarter of gaps had VS information before and after gap. Of those, 53.7% had VS both before and after gap and 25.8% were unsuppressed both before and after gap. The strongest association with VS after gap was VS before gap [aOR 15.76 (10.48, 23.69)]. Transition into Ryan White HIV/AIDS Program coverage during Medicaid gaps was common (28% of all transitions).

Conclusions:

Gaps in Medicaid enrollment were common and many individuals with pre-gap VS maintained VS after gap, possibly due to accessing other sources of antiretroviral therapy coverage. Implementing initiatives to maintain Medicaid enrollment and to expedite Medicaid reenrollment and having alternate resources available in gaps are important to ensure continuous antiretroviral therapy to optimize HIV outcomes.
High cholesterol diet modulates macrophage polarization and liver inflammation during early hepatocellular carcinoma progression in zebrafish
Authors: de Oliveira Sofia , Houseright Ruth A. , Graves Alyssa L. , Golenberg Netta , Korte Benjamin G. , Miskolci Veronika , Huttenlocher Anna
Published: April 2018

Diabetes and obesity have been associated with nonalcoholic fatty liver disease (NAFLD)/nonalcoholic steatohepatitis (NASH) and increased incidence of hepatocellular carcinoma (HCC). Here we use optically transparent zebrafish to visualize liver inflammation and disease progression in a NAFLD/NASH-HCC model. We combined a high-cholesterol diet (HCD) with a transgenic zebrafish HCC model induced by hepatocyte-specific activated β-catenin and found that diet induced an increase in liver size and enhanced angiogenesis and neutrophil infiltration in the liver. Although macrophage number was not affected by diet, HCD induced changes in macrophage morphology and polarization with an increase in liver associated TNFα-positive macrophages. Treatment with metformin altered macrophage polarization and reduced liver size in NAFLD/NASH-associated HCC larvae. Moreover, ablation of macrophages limited progression in NAFLD/NASH-associated HCC larvae but not in HCC alone. These findings suggest that HCD alters macrophage polarization and exacerbates the liver inflammatory microenvironment and cancer progression in a zebrafish model of NAFLD/NASH-associated HCC.
Pattern of severe injuries in Spanish children: boys and falls are alarmingly overrepresented
Authors: Benito Sergio , López-Parellada Rosa , Esteban Elisabeth , Hemández-Platero Lluïsa , Prat Salvi , Esparza Mireia , José Cambra Francisco , Esther Esteban Maria
Published: April 2018

Background: Taking into account that injury is one of the main causes of child fatalities in developed countries, and that boys are more likely to suffer it than girls, we have explored a database of pediatric patients with severe injuries to determine whether sex and age influence the pattern of these fatalities, and the magnitude of this.

Method: Observational study of the demographic and clinical characteristics of 227 patients from a Spanish pediatric reference hospital, all of them admitted with a diagnosis of trauma.

Result: Falls are the most frequent type of trauma (60.7%), followed by pedestrian traffic collisions (15%). Boys are over-represented in falls (72% vs 28% in girls) and pedestrian traffic injuries (61% vs 39 %). In boys, falls are mainly observed in public roads and during leisure activities (53.8%) whereas in girls at home (55.2%). In a logistic regression, sex and age are statistically significant predictors of severe trauma, boys (OR = 1.59) and the adolescent age group (OR = 3.7) showed the highest odds.

Conclusion: We have observed a clear gender-biased pattern of injury-related events: falls are the leading cause of injuries, with 2.5 boys for every girl. Falls mostly happened during outdoor leisure activities in boys and at home in girls. Pedestrian traffic injuries also show significant differences between sexes, emphasizing the role of cognitive and cultural factors in children’s behavior.
Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics
Authors: McInnes Gregory , Tanigawa Yosuke , DeBoever Chris , Lavertu Adam , Olivieri Julia Eve , Aguirre Matthew , Rivas Manuel
Published: April 2018

Large biobanks linking phenotype to genotype have led to an explosion of genetic association studies across a wide range of phenotypes. Sharing the knowledge generated by these resources with the scientific community remains a challenge due to patient privacy and the vast amount of data. Here we present Global Biobank Engine (GBE), a web-based tool that enables the exploration of the relationship between genotype and phenotype in large biobank cohorts, such as the UK Biobank. GBE supports browsing for results from genome-wide association studies, phenome-wide association studies, gene-based tests, and genetic correlation between phenotypes. We envision GBE as a platform that facilitates the dissemination of summary statistics from biobanks to the scientific and clinical communities. GBE currently hosts data from the UK Biobank and can be found freely available at biobankengine.stanford.edu.
Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements
Authors: Tsueng Ginger , Kumar Arun , Nanis Steven M. , Su Andrew I
Published: April 2018

Citizen science is the participation in scientific research by members of the public, and it is an increasingly valuable tool for both scientists and educators. For researchers, citizen science is a means of more quickly investigating questions which would otherwise be time-consuming and costly to study. For educators, citizen science offers a means to engage students in actual research and improve learning outcomes. Since most citizen science projects are usually designed with research goals in mind, many lack the necessary educator materials for successful integration in a formal science education (FSE) setting. In an ideal world, researchers and educators would build the necessary materials together; however, many researchers lack the time, resources, and networks to create these materials early on in the life of a citizen science project. For resource-poor projects, we propose an intermediate entry point for recruiting from the educational setting: community service or service learning requirements (CSSLRs). Many schools require students to participate in community service or service learning activities in order to graduate. When implemented well, CSSLRs provide students with growth and development opportunities outside the classroom while contributing to the community and other worthwhile causes. However, CSSLRs take time, resources, and effort to implement well. Just as citizen science projects need to establish relationships to transition well into formal science education, schools need to cultivate relationships with community service organizations. Students and educators at schools with CSSLRs where implementation is still a work in progress may be left with a burdensome requirement and inadequate support. With the help of a volunteer fulfilling a CSSLR, we investigated the number of students impacted by CSSLRs set at different levels of government and explored the qualifications needed for citizen science projects to fulfill CSSLRs by examining the explicitly-stated justifications for having CSSLRs, surveying how CSSLRs are verified, and using these qualifications to demonstrate how an online citizen science project, Mark2Cure, could use this information to meet the needs of students fulfilling CSSLRs.
Automated delineation of non-small cell lung cancer
Authors: Saad Maliazurina
Published: April 2018

Purpose

The tendencies of non-small cell lung cancers (NSCLC) to be large-sized, irregularly shaped, and to grow against the surrounding structures can cause even expert clinicians to experience difficulty with accurate segmentation.

Methods

An automated delineation tool based on spatial analysis was developed and studied on 25 sets of CT scans of primary NSCLCs with diverse radiological characteristics (sizes, shapes, contouring, localization, and microenvironment). Manual and automated gross delineations of the gross tumor were compared using a specific metric built based on spatially overlapping pixels.

Results

The proposed algorithm exhibited robustness in terms of the tumor size (5.32–18.24 mm), shape (spherical or non-spherical), contouring (lobulated, spiculated, or cavitated), localization (solitary, pleural, mediastinal, endobronchial, or tagging), and microenvironment (left or right lobe), with sensitivity, specificity, and accuracy rates of 80–98%, 85–99%, and 84–99%, respectively.

Conclusions

Small discrepancies were observed between the manual and automated delineations. These might have risen from the variability in the practitioners’ definitions of ROIs or from imaging artifacts that reduced the tissue resolution.
How thalamic relays might orchestrate supervised deep training and symbolic computation in the brain
Authors: Hayworth Kenneth J. , Marblestone Adam H.
Published: April 2018

The thalamus appears to be involved in the flexible routing of information among cortical areas, yet the computational implications of such routing are only beginning to be explored. Here we create a connectionist model of how selectively gated cortico-thalamo-cortical relays could underpin both symbolic and sub-symbolic computations. We first show how gateable relays can be used to create a Dynamically Partitionable Auto-Associative Network (DPAAN) (Hayworth, 2012) consisting of a set of cross-connected cortical memory buffers. All buffers and relays in a DPAAN are trained simultaneously to have a common set of stable attractor states that become the symbol vocabulary of the DPAAN. We show via simulations that such a DPAAN can support operations necessary for syntactic rule-based computation, namely buffer-to-buffer copying and equality detection. We then provide each DPAAN module with a multilayer input network trained to map sensory inputs to the DPAAN’s symbol vocabulary, and demonstrate how gateable thalamic relays can provide recall and clamping operations to train this input network by Contrastive Hebbian Learning (CHL) (Xie and Seung, 2003). We suggest that many such DPAAN modules may exist at the highest levels of the brain’s sensory hierarchies and show how a joint snapshot of the contents of multiple DPAAN modules can be stored as a declarative memory in a simple model of the hippocampus. We speculate that such an architecture might first have been ‘discovered’ by evolution as a means to bootstrap learning of more meaningful cortical representations feeding the striatum, eventually leading to a system that could support symbolic computation. Our model serves as a bridging hypothesis for linking controllable thalamo-cortical information routing with computations that could underlie aspects of both learning and symbolic reasoning in the brain.
Software-assisted manual review of clinical NGS data: an alternative to routine Sanger sequencing confirmation with equivalent results in >15,000 hereditary cancer screens
Authors: Muzzey Dale , Kash Shera , Johnson Jillian I. , Melroy Laura M. , Kaleta Piotr , Pierce Kelly A. , Ready Kaylene , Kang Hyunseok P. , Haas Kevin R.
Published: April 2018

Clinical genomic tests increasingly utilize a next generation sequencing (NGS) platform due in part to the high fidelity of variant calls, yet rare errors are still possible. In hereditary cancer screening, failure to correct such errors could have serious consequences for patients, who may follow an unwarranted screening or surgical-management path. It has been suggested that routine orthogonal confirmation via Sanger sequencing is required to verify NGS results, especially low-confidence positives with depressed allele fraction (<30% of alternate allele). We evaluated whether an alternative method of confirmation—software-assisted manual call review—performed comparably to Sanger confirmation in >15,000 samples. Licensed reviewers manually inspected both raw and processed data at the batch-, sample-, and variant-level, including raw NGS read pileups. Of ambiguous variant calls with <30% allele fraction (1,707 total calls at 38 unique sites), manual call review classified >99% (1,701) as true positives (enriched for long insertions or deletions (“indels”) and homopolymers) or true negatives (often conspicuous NGS artifacts), with the remaining <1% (6) being mosaic. Critically, results from software-assisted manual review and retrospective Sanger sequencing were concordant for samples selected from all ambiguous sites. We conclude that the confirmation required for high confidence in NGS-based germline testing can manifest in different ways: a trained NGS expert operating platform-tailored review software achieves quality comparable to routine Sanger confirmation.
Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development
Authors: Madissoon Elo , Damdimopoulos Anastasios , Katayama Shintaro , Krjutškov Kaarel , Einarsdottir Elisabet , Mamia Katariina , De Groef Bert , Hovatta Outi , Kere Juha , Damdimopoulou Pauliina
Published: April 2018

Pleomorphic adenoma gene 1 (PLAG1) is a transcription factor involved in cancer and growth. We discovered a de novo DNA motif containing a PLAG1 binding site in the promoters of genes activated during zygotic genome activation (ZGA) in human embryos. This motif was located within an Alu element in a region that was conserved in the murine B1 element. We show that maternally provided Plag1 is essential for timely mouse preimplantation embryo development. Heterozygous mouse embryos lacking maternal Plag1 showed disrupted regulation of 1,089 genes, spent significantly longer time in the 2-cell stage, and started expressing Plag1 ectopically from the paternal allele. The de novo PLAG1 motif was enriched in the promoters of the genes whose activation was delayed in the absence of Plag1. Further, these mouse genes showed a significant overlap with genes upregulated during human ZGA that also contain the motif. By gene ontology, the mouse and human ZGA genes with de novo PLAG1 motifs were involved in ribosome biogenesis and protein synthesis. Collectively, our data suggest that PLAG1 affects embryo development in mice and humans through a conserved DNA motif within Alu/B1 elements located in the promoters of a subset of ZGA genes.
The effect of acquisition resolution on orientation decoding from V1: comparison of 3T and 7T
Authors: Sengupta Ayan , Speck Oliver , Yakupov Renat , Kanowski Martin , Tempelmann Claus , Pollmann Stefan , Hanke Michael
Published: April 2018

Previously published results indicate that the accuracy of decoding visual orientation from 7 Tesla fMRI data of V1 peaks at spatial acquisition resolutions that are routinely accessible with more conventional 3 Tesla scanners. This study directly compares the decoding performance between a 3 Tesla and a 7 Tesla dataset that were acquired using the same stimulation paradigm by applying an identical analysis procedure. The results indicate that decoding models built on 3 Tesla data are comparatively impaired. Moreover, we found no evidence for a strong coupling of BOLD signal change magnitude or temporal signal to noise ratio (tSNR) with decoding performance. Direct enhancement of tSNR via multiband fMRI acquisition at the same resolution did not translate into improved decoding performance. Additional voxel selection can boost 3 Tesla decoding performance to the 7 Tesla level only at a 3 mm acquisition resolution. In both datasets the BOLD signal available for orientation decoding is spatially broadband, but, consistent with the size of the BOLD point-spread-function, decoding models at 3 Tesla utilize spatially coarser image components.
Virtual navigation tested on a mobile app is predictive of real-world wayfinding navigation performance
Authors: Coutrot A. , Schmidt S. , Coutrot L. , Pittman J. , Hong L. , Wiener J. M. , Hölscher C. , Dalton R.C. , Hornberger M. , Spiers H. J.
Published: April 2018

Virtual reality environments presented on tablets and smartphones have potential to aid the early diagnosis of conditions such as Alzheimer’s dementia by quantifying impairments in navigation performance. However, it is unclear whether performance on mobile devices can predict navigation errors in the real world. We compared the performance of 60 participants (30 females, 18-35 years old) at wayfinding and path integration tasks designed in our mobile app ‘Sea Hero Quest’ with their performance at similar tasks in a real-world environment. We first performed this experiment in the streets of London (UK) and replicated it in Paris (France). In both cities, we found a significant correlation between virtual and real-world wayfinding performance and a male advantage in both environments, although smaller in the real world (Cohen’s d in the game = 0.89, in the real world = 0.59). Results in London and Paris were highly similar, and controlling for familiarity with video games did not change the results. The strength of the correlation between real world and virtual environment increased with the difficulty of the virtual wayfinding task, indicating that Sea Hero Quest does not merely capture video gaming skills. The fact that the Sea Hero Quest wayfinding task has real-world ecological validity constitutes a step toward controllable, sensitive, safe, low-cost, and easy to administer digital cognitive assessment of navigation ability.