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1.  Make it better but don't change anything 
With massive amounts of data being generated in electronic format, there is a need in basic science laboratories to adopt new methods for tracking and analyzing data. An electronic laboratory notebook (ELN) is not just a replacement for a paper lab notebook, it is a new method of storing and organizing data while maintaining the data entry flexibility and legal recording functions of paper notebooks. Paper notebooks are regarded as highly flexible since the user can configure it to store almost anything that can be written or physically pasted onto the pages. However, data retrieval and data sharing from paper notebooks are labor intensive processes and notebooks can be misplaced, a single point of failure that loses all entries in the volume. Additional features provided by electronic notebooks include searchable indices, data sharing, automatic archiving for security against loss and ease of data duplication. Furthermore, ELNs can be tasked with additional functions not commonly found in paper notebooks such as inventory control. While ELNs have been on the market for some time now, adoption of an ELN in academic basic science laboratories has been lagging. Issues that have restrained development and adoption of ELN in research laboratories are the sheer variety and frequency of changes in protocols with a need for the user to control notebook configuration outside the framework of professional IT staff support. In this commentary, we will look at some of the issues and experiences in academic laboratories that have proved challenging in implementing an electronic lab notebook.
PMCID: PMC2810290  PMID: 20098591
2.  Reduced inclination of cervical spine in a novel notebook screen system - implications for rehabilitation 
Professional working at computer notebooks is associated with high requirements on the body posture in the seated position. By the high continuous static muscle stress resulting from this position at notebooks, professionals frequently working at notebooks for long hours are exposed to an increased risk of musculoskeletal complaints. Especially in subjects with back pain, new notebooks should be evaluated with a focus on rehabilitative issues.
In a field study a new notebook design with adjustable screen was analyzed and compared to standard notebook position.
There are highly significant differences in the visual axis of individuals who are seated in the novel notebook position in comparison to the standard position. Also, differences are present between further alternative notebook positions. Testing of gender and glasses did not reveal influences.
This study demonstrates that notebooks with adjustable screen may be used to improve the posture. Future studies may focus on patients with musculoskeletal diseases.
PMCID: PMC3253038  PMID: 22118159
3.  From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks 
ZooKeys  2012;235-253.
Part diary, part scientific record, biological field notebooks often contain details necessary to understanding the location and environmental conditions existent during collecting events. Despite their clear value for (and recent use in) global change studies, the text-mining outputs from field notebooks have been idiosyncratic to specific research projects, and impossible to discover or re-use. Best practices and workflows for digitization, transcription, extraction, and integration with other sources are nascent or non-existent. In this paper, we demonstrate a workflow to generate structured outputs while also maintaining links to the original texts. The first step in this workflow was to place already digitized and transcribed field notebooks from the University of Colorado Museum of Natural History founder, Junius Henderson, on Wikisource, an open text transcription platform. Next, we created Wikisource templates to document places, dates, and taxa to facilitate annotation and wiki-linking. We then requested help from the public, through social media tools, to take advantage of volunteer efforts and energy. After three notebooks were fully annotated, content was converted into XML and annotations were extracted and cross-walked into Darwin Core compliant record sets. Finally, these recordsets were vetted, to provide valid taxon names, via a process we call “taxonomic referencing.” The result is identification and mobilization of 1,068 observations from three of Henderson’s thirteen notebooks and a publishable Darwin Core record set for use in other analyses. Although challenges remain, this work demonstrates a feasible approach to unlock observations from field notebooks that enhances their discovery and interoperability without losing the narrative context from which those observations are drawn.
“Compose your notes as if you were writing a letter to someone a century in the future.”
Perrine and Patton (2011)
PMCID: PMC3406479  PMID: 22859891
Field notes; notebooks; crowd sourcing; digitization; biodiversity; transcription; text-mining; Darwin Core; Junius Henderson; annotation; taxonomic referencing; natural history; Wikisource; Colorado; species occurrence records
4.  LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory 
PLoS ONE  2013;8(7):e67460.
The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research.
Methodology/Principal Findings
We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system.
LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.
PMCID: PMC3720848  PMID: 23935832
5.  Mediators between Theoretical and Practical Medieval Knowledge: Medical Notebooks from the Cairo Genizah and their Significance 
Medical History  2013;57(4):487-515.
This article presents a plethora of fragments from the medical notebooks found in the Cairo Genizah that comprise a unique source of historical data for scholarly study and for a better understanding of the ways in which medieval medical knowledge in Egypt was transferred from theory to practice and vice versa. These documents provide the most direct evidence we have for preferred practical medical recipes because they record the choices of medical practitioners in medieval Cairo. Since the language most commonly used in them was Judaeo-Arabic, they were evidently written by Jews. The medical genre in the notebooks was primarily pharmacopoeic, consisting of apparently original recipes for the treatment of various diseases. There are also a few notebooks on materia medica. The subject matter of the Genizah medical notebooks shows that they were mostly of an eclectic nature, i.e. the writers had probably learnt about these treatments and recipes from their teachers, applied them at the hospitals where they worked or copied them from the books they read. Foremost among the subjects dealt with were eye diseases, followed by skin diseases, coughs and colds, dentistry and oral hygiene, and gynaecological conditions. The writers of the Genizah notebooks apparently recorded the practical medical knowledge they wished to preserve for their future use as amateur physicians, students, traditional healers or professional practitioners.
PMCID: PMC3865955  PMID: 24069914
Cairo Genizah; History of Medicine; Jewish; Medieval Middle East; Middle Ages; Notebook
6.  A failure to communicate: patients with cerebral aneurysms and vascular neurosurgeons 
Objective: To assess communication between vascular neurosurgeons and their patients with unruptured cerebral aneurysms about treatment options and expected outcomes.
Methods: Vascular neurosurgeons and their patients with cerebral aneurysms were surveyed immediately following outpatient appointments in a neurosurgery clinic. Data collected included how well the patient understood their aneurysm treatment options, the risks of a poor outcome from various treatments, and the consensus "best" treatment. Patient and neurosurgeon responses were measured using Likert scales, multiple choice questions, and visual analogue scales. Agreement between patient and neurosurgeon was assessed with kappa scores. The Wilcoxon sign rank test was used to compare visual analogue scale responses.
Results: Data for 44 patient–neurosurgeon pairs were collected. Only 61% of patient–neurosurgeon pairs agreed on the best treatment plan for the patient's aneurysm (κ = 0.51, moderate agreement). Among the neurosurgeons, agreement with their patients ranged from 82% (κ = 0.77, almost perfect agreement) to 52% (κ = 0.37, fair agreement). Patients estimated much higher risks of stroke or death from surgical clipping, endovascular embolisation, or no intervention compared with the estimates offered by their neurosurgeons (surgical clipping: patient 36% v neurosurgeon 13%, p<0.001; endovascular embolisation: patient 35% v neurosurgeon 19%, p = 0.040; and no intervention: patient 63% v neurosurgeon 25%, p<0.001).
Conclusions: Following consultation with a vascular neurosurgeon, many patients with cerebral aneurysms have an inaccurate understanding of their aneurysm treatment plan and an exaggerated sense of the risks of aneurysmal disease and treatment.
PMCID: PMC1739590  PMID: 15774444
7.  eCAT: Online electronic lab notebook for scientific research 
eCAT is an electronic lab notebook (ELN) developed by Axiope Limited. It is the first online ELN, the first ELN to be developed in close collaboration with lab scientists, and the first ELN to be targeted at researchers in non-commercial institutions. eCAT was developed in response to feedback from users of a predecessor product. By late 2006 the basic concept had been clarified: a highly scalable web-based collaboration tool that possessed the basic capabilities of commercial ELNs, i.e. a permissions system, controlled sharing, an audit trail, electronic signature and search, and a front end that looked like the electronic counterpart to a paper notebook.
During the development of the beta version feedback was incorporated from many groups including the FDA's Center for Biologics Evaluation & Research, Uppsala University, Children's Hospital Boston, Alex Swarbrick's lab at the Garvan Institute in Sydney and Martin Spitaler at Imperial College. More than 100 individuals and groups worldwide then participated in the beta testing between September 2008 and June 2009. The generally positive response is reflected in the following quote about how one lab is making use of eCAT: "Everyone uses it as an electronic notebook, so they can compile the diverse collections of data that we generate as biologists, such as images and spreadsheets. We use to it to take minutes of meetings. We also use it to manage our common stocks of antibodies, plasmids and so on. Finally, perhaps the most important feature for us is the ability to link records, reagents and experiments."
By developing eCAT in close collaboration with lab scientists, Axiope has come up with a practical and easy-to-use product that meets the need of scientists to manage, store and share data online. eCAT is already being perceived as a product that labs can continue to use as their data management and sharing grows in scale and complexity.
PMCID: PMC2809322  PMID: 20334629
8.  An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook 
Lancet is a new, simulator-independent Python utility for succinctly specifying, launching, and collating results from large batches of interrelated computationally demanding program runs. This paper demonstrates how to combine Lancet with IPython Notebook to provide a flexible, lightweight, and agile workflow for fully reproducible scientific research. This informal and pragmatic approach uses IPython Notebook to capture the steps in a scientific computation as it is gradually automated and made ready for publication, without mandating the use of any separate application that can constrain scientific exploration and innovation. The resulting notebook concisely records each step involved in even very complex computational processes that led to a particular figure or numerical result, allowing the complete chain of events to be replicated automatically. Lancet was originally designed to help solve problems in computational neuroscience, such as analyzing the sensitivity of a complex simulation to various parameters, or collecting the results from multiple runs with different random starting points. However, because it is never possible to know in advance what tools might be required in future tasks, Lancet has been designed to be completely general, supporting any type of program as long as it can be launched as a process and can return output in the form of files. For instance, Lancet is also heavily used by one of the authors in a separate research group for launching batches of microprocessor simulations. This general design will allow Lancet to continue supporting a given research project even as the underlying approaches and tools change.
PMCID: PMC3874632  PMID: 24416014
IPython; pandas; reproducibility; workflow; simulation; batch computation; provenance; big data
9.  A novel collaborative e-learning platform for medical students - ALERT STUDENT 
BMC Medical Education  2014;14:143.
The increasing complexity of medical curricula would benefit from adaptive computer supported collaborative learning systems that support study management using instructional design and learning object principles. However, to our knowledge, there are scarce reports regarding applications developed to meet this goal and encompass the complete medical curriculum. The aim of ths study was to develop and assess the usability of an adaptive computer supported collaborative learning system for medical students to manage study sessions.
A study platform named ALERT STUDENT was built as a free web application. Content chunks are represented as Flashcards that hold knowledge and open ended questions. These can be created in a collaborative fashion. Multiple Flashcards can be combined into custom stacks called Notebooks that can be accessed in study Groups that belong to the user institution. The system provides a Study Mode that features text markers, text notes, timers and color-coded content prioritization based on self-assessment of open ended questions presented in a Quiz Mode. Time spent studying and Perception of knowledge are displayed for each student and peers using charts. Computer supported collaborative learning is achieved by allowing for simultaneous creation of Notebooks and self-assessment questions by many users in a pre-defined Group. Past personal performance data is retrieved when studying new Notebooks containing previously studied Flashcards. Self-report surveys showed that students highly agreed that the system was useful and were willing to use it as a reference tool.
The platform employs various instructional design and learning object principles in a computer supported collaborative learning platform for medical students that allows for study management. The application broadens student insight over learning results and supports informed decisions based on past learning performance. It serves as a potential educational model for the medical education setting that has gathered strong positive feedback from students at our school.
This platform provides a case study on how effective blending of instructional design and learning object principles can be brought together to manage study, and takes an important step towards bringing information management tools to support study decisions and improving learning outcomes.
PMCID: PMC4131539  PMID: 25017028
Medical education; Computer supported collaborative learning; E-learning; Information management; Memory retention; Computer-assisted instruction; Tailored learning; Student-centered learning; Spaced repetition
10.  Neurosurgery workforce in Canada, 1996 to 2011. Canadian Neurosurgical Society. 
OBJECTIVE. To determine the number of neurosurgeons in clinical practice in Canada on Jan. 1, 1996, and their practice profile and to determine requirements for 2001 and 2011. DESIGN. Telephone survey and national mail survey. SETTING. Canada. PARTICIPANTS. All 174 neurosurgeons in Canada engaged in active clinical practice on Jan. 1, 1996, and all residents enrolled in neurosurgery training programs in Canada during the 1995-96 academic year. OUTCOME MEASURES. Demographic characteristics, full-time equivalents, workload, attrition, reasons for exit, vacancies, supply and shortfall. RESULTS. All 174 neurosurgeons responded to the survey. There is a chronic shortage of 25 neurosurgeons in Canada. Sixty-two established neurosurgeons will have stopped practice by 2001 and 181 by 2011. They will need to be replaced, for a total requirement of 87 and 206 neurosurgeons by 2001 and 2011 respectively. Canadian neurosurgery training programs can currently generate only up to 69 and 177 graduates by 2001 and 2011 respectively. During the period 1985-95, 50% of neurosurgery graduates emigrated from Canada within 2 years of obtaining certification, creating potential deficits of up to 52 and 117 neurosurgeons by 2001 and 2011 respectively. CONCLUSIONS. Strategies need to be developed quickly to address not only the chronic shortfall but also the attrition of established neurosurgeons. Strategies to increase and retain the number of Canadian neurosurgery graduates are also needed.
PMCID: PMC1487860  PMID: 8673984
11.  Health Transformation Project and Defensive Medicine Practice among Neurosurgeons in Turkey 
PLoS ONE  2014;9(10):e111446.
The term “Defensive” medicine was coined in the early 1970′s and has been an important topic of scientific investigation and professional debate ever since.
The aim of this study was to investigate the characteristics of defensive medicine, its reasons, and the extent to which it is practiced in the Turkish health care system. This is the first national survey to study the practice of defensive medicine among neurosurgeons in Turkey.
The present cross-sectional study on defensive medicine assessed neurosurgeons registered at the Turkish Neurosurgical Society, who are actively working in various centers and hospitals within the Turkish health care system. A 40-question survey was adapted from existing measures described in the literature and was completed by a total of 404 neurosurgeons, representing 36.7% of the neurosurgeons registered at the Turkish Neurosurgical Society.
Seventy-two percent of the participants in the current study reported practicing defensive medicine. This practice was mainly reported among inexperienced neurosurgeons (74.4%). Most were younger than 40 years of age (75.2%), working in state hospitals/universities (72.7%), and living in the Marmara region (38%). Respondents reported engaging in defensive medicine by avoiding high-risk surgery (62.6%), ordering additional imaging studies (60.9%) and laboratory tests (33.7%), and referring patients to consultants (31.2%). Most participants consider every patient as a potential threat in terms of a medical lawsuit (68.3%) and do not believe the courts can distinguish malpractice from complications (89.6%).
Concerns and perceptions about medical liability lead neurosurgeons to practice defensive medicine. By avoiding high-risk surgery, ordering unnecessary diagnostic tests, and referring the patients to consultants, neurosurgeons try to minimize the risk of malpractice and protect themselves from legal risks, resulting in higher healthcare expenditure and longer treatment periods.
PMCID: PMC4205021  PMID: 25333736
12.  The benefits of integrated systems for managing both samples and experimental data: An opportunity for labs in universities and government research institutions to lead the way 
Currently most biomedical labs in universities and government funded research institutions use paper lab notebooks for recording experimental data and spreadsheets for managing sample data. One consequence is that sample management and documenting experiments are viewed as separate and distinct activities, notwithstanding that samples and aliquots are an integral part of a majority of the experiments carried out by these labs.
Various drivers are pushing labs towards integrated management of sample data and experimental data. These include the ever increasing amounts of both kinds of data, the increasing adoption of online collaborative tools, changing expectations about online communication, and the increasing affordability of electronic lab notebooks and sample management software. There is now an opportunity for smaller labs, which have been slow to move from paper to electronic record keeping, to leapfrog better resourced commercial labs and lead the way in adopting the new generation of tools which permit integrated management of samples and experimental data and a range of tangible benefits to conducting research, including:
1. Fewer lost and mislabelled samples
2. Clearer visualization of relationships between samples and experiments
3. Reduction of experimental error
4. More effective search
5. Productivity gains
6. More efficient use of freezers, leading to cost reduction and enhanced sustainability
7. Improved archiving and enhanced memory at the lab and institutional levels
PMCID: PMC3146905  PMID: 21707999
13.  The Memory Support System for Mild Cognitive Impairment: Randomized trial of a cognitive rehabilitation intervention 
Individuals with amnestic Mild Cognitive Impairment (MCI) have few empirically-based treatment options for combating their memory loss. This study sought to examine the efficacy of a calendar/notebook rehabilitation intervention, the Memory Support System (MSS), for individuals with amnestic MCI.
Forty individuals with single domain amnestic MCI and their program partners were randomized to receive the MSS, either with training or without (controls). Measures of adherence, activities of daily living, and emotional impact were completed at the first and last intervention session and again at 8-weeks and 6 months post intervention.
Training in use of a notebook/calendar system significantly improved adherence over those who received the calendars but no training. Functional ability and memory self efficacy significantly improved for those who received MSS training. Change in functional ability remained significantly better in the intervention group than in the control group out to 8 week follow up. Care partners in the intervention group demonstrated improved mood by 8 week and 6 month follow-up, while control care partners reported worse caregiver burden by 6 month follow up.
MSS training resulted in improvement in ADLs and sense of memory self efficacy for individuals with MCI. While ADL benefits were maintained out to 8 weeks post intervention, future inclusion of booster sessions may help extend the therapeutic effect out even further. Improved mood of care partners of trained individuals and worsening sense of caregiver burden over time for partners of untrained individuals further supports the efficacy of the MSS for MCI.
PMCID: PMC3766962  PMID: 22678947
Mild Cognitive Impairment; Rehabilitation; Behavioral Intervention; Activities of Daily Living; Quality of Life; Caregivers
14.  An Innovative Smartphone-Based Otorhinoendoscope and Its Application in Mobile Health and Teleotolaryngology 
The traditional otorhinoendoscope is widely used in the diagnosis of a variety of ear and nose diseases, but only one doctor can use it at a time. It is also very difficult to share observations from one doctor with another doctor. With advances in electronic health technology, the extended potential application of smartphones to support medical practice or mobile health has grown steadily.
The first phase of the study discussed how smartphones may be used for otorhinoscopic imaging and image management via an innovative adaptor. The second phase of the study was to evaluate the diagnostic capability of the smartphone-based otorhinoendoscope, as compared to the traditional otorhinoendoscope, and its application in mobile health and teleotolaryngology.
We designed a unique adaptor to connect the otorhinoendoscope and smartphone in order to perform smartphone-based otorhinoendoscopy. The main aim was to transform the smartphone into an otorhinoendoscope. We devised a method that would allow us to use the smartphone’s camera to capture otorhinoscopic images. Using a freely available Web-based real-time communication application platform and the 3G (or WIFI) network, the smartphone-based otorhinoendoscope could synchronize the smartphone-based otorhinoscopic image with smartphones, tablet PCs, computer notebooks, or personal computers.
We investigated the feasibility of telemedicine using a smartphone, tablet PC, and computer notebook. Six types of clinical otorhinoscopic images were acquired via the smartphone-based otorhinoendoscope from six patients, which were examined in this study. Three teleconsultants (doctors A, B, and C) reviewed the six types of clinical otorhinoscopic images and made a telediagnosis. When compared to the face-to-face diagnosis, which was made in-person via a traditional otorhinoendoscope, the three teleconsultants obtained scores of a correct primary telediagnosis 83% (5/6), 100% (6/6), and 100% (6/6) of the time, respectively. When the clinical data were provided, the three teleconsultants obtained a correct secondary telediagnosis score of 100% (6/6), 100% (6/6), and 100% (6/6) of the time, respectively.
The use of previously available technologies in the absence of any additional expensive devices could significantly increase the quality of diagnostics while lowering extraneous costs. Furthermore, this could also increase the connectivity between most isolated family doctors and remote referral centers.
PMCID: PMC3961810  PMID: 24590187
otorhinoendoscope; smartphone; mobile health; teleotolaryngology; telediagnosis
15.  Using tablets to support self-regulated learning in a longitudinal integrated clerkship 
Medical Education Online  2014;19:10.3402/meo.v19.23638.
The need to train physicians committed to learning throughout their careers has prompted medical schools to encourage the development and practice of self-regulated learning by students. Longitudinal integrated clerkships (LICs) require students to exercise self-regulated learning skills. As mobile tools, tablets can potentially support self-regulation among LIC students.
We provided 15 LIC students with tablet computers with access to the electronic health record (EHR), to track their patient cohort, and a multiplatform online notebook, to support documentation and retrieval of self-identified clinical learning issues. Students received a 1-hour workshop on the relevant features of the tablet and online notebook. Two focus groups with the students were used to evaluate the program, one early and one late in the year and were coded by two raters.
Students used the tablet to support their self-regulated learning in ways that were unique to their learning styles and increased access to resources and utilization of down-time. Students who used the tablet to self-monitor and target learning demonstrated the utility of tablets as learning tools.
LICs are environments rich in opportunity for self-regulated learning. Tablets can enhance students’ ability to develop and employ self-regulatory skills in a clinical context.
PMCID: PMC3955768  PMID: 24646438
mobile learning; self-regulated learning; clinical learning; longitudinal integrated clerkship; workplace learning
16.  Mobile education in autopsy conferences of pathology: presentation of complex cases 
Diagnostic Pathology  2006;1:42.
MeduMobile was a project to develop and evaluate learning scenarios for medical students and teachers by use of video communication and notebooks. Its core part was assigned to various medical routines, conferences or meetings such as doctor-patient bedside conversation. These were filmed by video teams and broadcasted live via the WLAN of the Charité campus to course participating students. One type of the learning arrangements was the autopsy conference as an on-call scenario.
Materials and methods
The MeduMobile project consisted of two main compartments: the regular seminar event which took place every week or month, and the on-call event. For an on-call event the students were informed two hours before the lesson's start. A mobile video team organised the video conference via a specific MeduMobile seminar system. This software offered the students to log. The MeduMobile seminar system is based on the Windows operating system and realises an extended video communication via WLAN. Thirteen access points were implemented at the Charité Campus Virchow Klinikum and Campus Mitte. A questionnaire was developed to investigate in the response and learning effect of the mobile seminar system.
During the MeduMobile project 42 video conferences with (cumulative) 145 participating students took place. Four autopsy conferences could be organised as on-call scenarios within this project. A prospective, not randomised follow-up study was included 25 students of the 1st – 6th clinical semester. According to the answers, professional reasoning, professional performance, sustainability, and the complexity were broadly accepted by the students.
In principle, the MeduMobile realised an interdisciplinary case presentation using video conference and web page. The evaluation indicates a high acception of such complex case presentation with multidisciplinary settings. The use of the notebooks in mobile learning enables an interconnective training and promotes a complex learning.
PMCID: PMC1654189  PMID: 17094805
17.  The Journey Project: a case study in providing health information to mitigate health disparities 
The Journey Project, part of the Virginia Commonwealth University Libraries' Social Work Information Specialist in Context Fellowship, was designed to merge social work and consumer health librarianship skills in order to improve the provision of health information to patients. A resource notebook was created encompassing the many dimensions of cancer health information. A social work informationist distributed the notebooks and provided individualized consultations with respect to patients' health information needs. Areas of congruence as well as key differences between social work and consumer health librarianship emerged during the course of the project. Merging the two professions into the role of a social work informationist increased the ability to attend holistically to clients' health information needs.
PMCID: PMC2605042  PMID: 19159008
18.  A Virtual Notebook for biomedical work groups. 
During the past several years, Baylor College of Medicine has made a substantial commitment to the use of information technology in support of its corporate and academic programs. The concept of an Integrated Academic Information Management System (IAIMS) has proved central in our planning, and the IAIMS activities that we have undertaken with funding from the National Library of Medicine have proved to be important extensions of our technology development. Here we describe our Virtual Notebook system, a conceptual and technologic framework for task coordination and information management in biomedical work groups. When fully developed and deployed, the Virtual Notebook will improve the functioning of basic and clinical research groups in the college, and it currently serves as a model for the longer-term development of our entire information management environment.
PMCID: PMC227118  PMID: 3046694
19.  iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis 
BMC Bioinformatics  2009;10:390.
In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques.
We have developed iLAP (Laboratory data management, Analysis, and Protocol development), a workflow-driven information management system specifically designed to create and manage experimental protocols, and to analyze and share laboratory data. The system combines experimental protocol development, wizard-based data acquisition, and high-throughput data analysis into a single, integrated system. We demonstrate the power and the flexibility of the platform using a microscopy case study based on a combinatorial multiple fluorescence in situ hybridization (m-FISH) protocol and 3D-image reconstruction. iLAP is freely available under the open source license AGPL from
iLAP is a flexible and versatile information management system, which has the potential to close the gap between electronic notebooks and LIMS and can therefore be of great value for a broad scientific community.
PMCID: PMC2789074  PMID: 19941647
20.  Variations in Practice Patterns among Neurosurgeons and Orthopaedic Surgeons in the Management of Spinal Disorders 
Asian Spine Journal  2011;5(4):208-212.
Study Design
This is a case series.
We wanted to identify variations in the practice patterns among neurosurgeons and orthopedic surgeons for the management of spinal disorders.
Overview of Literature
Spinal disorders are common in the clinical practice of both neurosurgeons and orthopedic surgeons. It has been observed that despite the availability of various guidelines, there is lack of consensus among surgeons about the management of various disorders.
A questionnaire was distributed, either directly or via e-mail, to the both the neurosurgeons and orthopedic surgeons who worked at 5 tertiary care centers within a single region of Korea. The surgeons were working either in private practice or in academic institutions. The details of the questionnaire included demographic details and the specialty (orthopedic/neurosurgeon). The surgeons were classified according to the level of experience as up to 5 years, 6-10 years and > 10 years. Questions were asked about the approach to lumbar discectomy (fragmentectomy or aggressive disc removal), using steroids for treating discitis, the fusion preference for spondylolisthesis, the role of an orthosis after fusion, the preferred surgical approach for spinal stenosis, the operative approach for spinal trauma (early within 72 hours or late > 72 hours) and the role of surgery in complete spinal cord injury. The data was analyzed using SPSS ver 16. p-values < 0.05 were considered to be significant.
Of the 30 surgeons who completed the questionnaire, 20 were neurosurgeons and 10 were orthopedic surgeons. Statistically significant differences were observed for the management of spinal stenosis, spondylolisthesis, using an orthosis after fusion, the type of lumbar discectomy and the value of surgical intervention after complete spinal cord injury.
Our results suggest that there continues to exist a statistically significant lack of consensus among neurosurgeons and orthopedic spine surgeons when considering using an orthosis after fusion, the type of discectomy and the value of intervention after complete spinal injury.
PMCID: PMC3230647  PMID: 22164314
Orthopedic surgeons; Neurosurgeons; Spinal trauma; Spinal stenosis; Complete cord injury
21.  Malpractice Liability and Defensive Medicine: A National Survey of Neurosurgeons 
PLoS ONE  2012;7(6):e39237.
Concern over rising healthcare expenditures has led to increased scrutiny of medical practices. As medical liability and malpractice risk rise to crisis levels, the medical-legal environment has contributed to the practice of defensive medicine as practitioners attempt to mitigate liability risk. High-risk specialties, such as neurosurgery, are particularly affected and neurosurgeons have altered their practices to lessen medical-legal risk. We present the first national survey of American neurosurgeons’ perceptions of malpractice liability and defensive medicine practices.
A validated, 51-question online-survey was sent to 3344 practicing U.S. neurosurgeon members of the American Association of Neurological Surgeons, which represents 76% of neurosurgeons in academic and private practices.
A total of 1028 surveys were completed (31% response rate) by neurosurgeons representing diverse sub-specialty practices. Respondents engaged in defensive medicine practices by ordering additional imaging studies (72%), laboratory tests (67%), referring patients to consultants (66%), or prescribing medications (40%). Malpractice premiums were considered a “major or extreme” burden by 64% of respondents which resulted in 45% of respondents eliminating high-risk procedures from their practice due to liability concerns.
Concerns and perceptions about medical liability lead practitioners to practice defensive medicine. As a result, diagnostic testing, consultations and imaging studies are ordered to satisfy a perceived legal risk, resulting in higher healthcare expenditures. To minimize malpractice risk, some neurosurgeons have eliminated high-risk procedures. Left unchecked, concerns over medical liability will further defensive medicine practices, limit patient access to care, and increase the cost of healthcare delivery in the United States.
PMCID: PMC3382203  PMID: 22761745
22.  Concussions: What a neurosurgeon should know about current scientific evidence and management strategies 
There has been a tremendous amount of interest focused on the topic of concussions over the past few decades. Neurosurgeons are frequently consulted to manage patients with mild traumatic brain injuries (mTBI) that have radiographic evidence of cerebral injury. These injuries share significant overlap with concussions, injuries that typically do not reveal radiographic evidence of structural injury, in the realms of epidemiology, pathophysiology, outcomes, and management. Further, neurosurgeons often manage patients with extracranial injuries that have concomitant concussions. In these cases, neurosurgeons are often the only “concussion experts” that patients encounter.
The literature has been reviewed and data have been synthesized on the topic including sections on historical background, epidemiology, pathophysiology, diagnostic advances, clinical sequelae, and treatment suggestions, with neurosurgeons as the intended target audience.
Neurosurgeons should have a fundamental knowledge of the scientific evidence that has developed regarding concussions and be prepared to guide patients with treatment plans.
PMCID: PMC3307233  PMID: 22439107
Concussion; management; mild traumatic brain injury; review
23.  Neurosurgeons’ management of lumbosacral radicular syndrome evaluated against a clinical guideline 
European Spine Journal  2004;13(8):719-723.
To establish to what extent neurosurgeons subscribe to the lumbosacral radicular syndrome (LRS) guideline, and to evaluate their current management of patients with LRS against the guideline. All active neurosurgeons in the Netherlands (n=92) were mailed a questionnaire about the guideline and data from 66 responders were analysed. Patients were recruited via seven of the participating neurosurgeons and were interviewed once by telephone. The medical records of the participating patients (n=163) were also examined. Of the 26 propositions in the LRS guideline, seven were not fully endorsed by the neurosurgeons. Three of these seven propositions may need updating based on “new evidence”. The time between the onset of the LRS episode and the actual moment of surgery was considerably longer than that recommended in the guideline. Based on their current management of LRS patients, the neurosurgeons largely adhere with the LRS guideline.
PMCID: PMC3454051  PMID: 15118898
Guideline adherence; Neurosurgeon; Lumbosacral radicular syndrome; Sciatica
24.  Quality and quantity of research publications by Iranian neurosurgeons: Signs of scientific progress over the past decades 
This is an analysis of papers published by Iranian neurosurgeons while working in Iran until the year 2010.
We collected bibliometric data and assigned a level of evidence (LOE) for each paper and compared neurosurgical research productivity across three time periods (before 1990, between 1991 and 2000, and after 2000). For further illustration, the annual growth rates of Iranian publications were calculated for all papers published after 1995.
We found a total of 1196 papers by 422 Iranian neurosurgeons. Five authors accounted for 22.9% of the papers. The average number of authors for each published manuscript was 3.48 and increased significantly from 2.0 to 4.0 across the three investigated periods (P < 0.001). 58.9% of Iranian papers were published in local journals only. A total of 74.6% articles were published after 2000, which was a significant increase compared with the decades before (P < 0.001). Original articles and case reports accounted for 63.8% and 31.1% of the publications, respectively. The proportion of case reports decreased while the proportion of original articles increased across the three time periods (P < 0.001). The adjusted growth rate for the total number of publications, original articles, case reports, clinical trials, and randomized clinical trials (RCTs) were 14.4%, 16.6%, 10.7%, 13.46%, and 14.7% per year, respectively. Overall, the four most frequently investigated topics were spine (27.3%), trauma (22.3%), tumor (19.1%), and vascular diseases (13.5%). The mean impact factor for journals publishing these studies and average number of citations for each paper (obtained from web of science) were found to be 1.2 and 5.46, respectively. A partitioning of these publications into assigned categories reflecting the LOE of each paper yielded the following LOE distribution for all assessed publications: Ib: 6.02%, Ic: 0.3%, IIa: 0.2%, IIb: 5.4%, IIc: 0.41%, IIIb: 4.8%, IV: 22.5%, and V: 1.2%. The relative number of publications categorized into higher LOE classes increased over the three investigated periods (P = 0.003). Based on growth curve model, the rate of increase in total numbers of publications following each position change from nonuniversity affiliated neurosurgeon to university affiliated and from university affiliated neurosurgeon to chairman university affiliated neurosurgeon was 81%.
A considerable increase in amount and quality of Iranian papers was observed during the past decade as reflected in a higher number of papers categorized in upper LOE classes.
PMCID: PMC3622377  PMID: 23607060
Iran; level of evidence; neurosurgery; publication
25.  Variations of endonasal anatomy: relevance for the endoscopic endonasal transsphenoidal approach 
Acta Neurochirurgica  2010;152(6):1015-1020.
The endoscopic endonasal transsphenoidal approach (EETA) to the pituitary is performed by ear, nose, and throat (ENT) surgeons in collaboration with neurosurgeons but also by neurosurgeons alone even though neurosurgeons have not been trained in rhinological surgery.
To register the frequency of endonasal anatomical variations and to evaluate whether these variations hinder the progress of EETA and require extra rhinological surgical skills.
A prospective cohort study of 185 consecutive patients receiving an EETA through a binostril approach was performed. All anatomical endonasal variations were noted and the relevance for the progress of surgery evaluated.
In 48% of patients, anatomical variations were recognized, the majority of which were spinae septi and septum deviations. In 5% of patients, the planned binostril approach had to be converted into a mononostril approach; whereas in 18% of patients with an anatomical variation, a correction had to be performed. There was no difference between the ENT surgeon and the neurosurgeon performing the approach. Complications related to the endonasal phase of the surgery occurred in 3.8%. Fluoroscopy or electromagnetic navigation has been used during 6.5% of the surgeries.
Although endonasal anatomical variations are frequent, they do not pose a relevant obstacle for EETA.
PMCID: PMC2872017  PMID: 20306338
Endoscopy; Endonasal; Transsphenoidal; Pituitary surgery; Anatomy

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