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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.  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
3.  Effects of using structured templates for recalling chemistry experiments 
The way that we recall information is dependent upon both the knowledge in our memories and the conditions under which we recall the information. Electronic Laboratory Notebooks can provide a structured interface for the capture of experiment records through the use of forms and templates. These templates can be useful by providing cues to help researchers to remember to record particular aspects of their experiment, but they may also constrain the information that is recorded by encouraging them to record only what is asked for. It is therefore unknown whether using structured templates for capturing experiment records will have positive or negative effects on the quality and usefulness of the records for assessment and future use. In this paper we report on the results of a set of studies investigating the effects of different template designs on the recording of experiments by undergraduate students and academic researchers.
The results indicate that using structured templates to write up experiments does make a significant difference to the information that is recalled and recorded. These differences have both positive and negative effects, with templates prompting the capture of specific information that is otherwise forgotten, but also apparently losing some of the personal elements of the experiment experience such as observations and explanations. Other unexpected effects were seen with templates that can change the information that is captured, but also interfere with the way an experiment is conducted.
Our results showed that using structured templates can improve the completeness of the experiment context information captured but can also cause a loss of personal elements of the experiment experience when compared with allowing the researcher to structure their own record. The results suggest that interfaces for recording information about chemistry experiments, whether paper-based questionnaires or templates in Electronic Laboratory Notebooks, can be an effective way to improve the quality of experiment write-ups, but that care needs to be taken to ensure that the correct cues are provided.Graphical abstractScientists have traditionally recorded their research in paper notebooks, a format that provides great flexibility for capturing information. In contrast, Electronic Laboratory Notebooks frequently make use of forms or structured templates for capturing experiment records. Structured templates can provide cues that can improve record quality by increasing the amount of information captured and encouraging consistency. However, using the wrong cues can lead to a loss of personal elements of the experiment experience and frustrate users. This image shows two participants from one of our studies recording their experiment using a computer-based template
Electronic supplementary material
The online version of this article (doi:10.1186/s13321-016-0118-6) contains supplementary material, which is available to authorized users.
PMCID: PMC4759737  PMID: 26900406
Templates; Experiments; Experiment record; Context; ELN; User experience; Study
4.  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
5.  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
6.  Utilisation of internet resources for continuing professional development: a cross-sectional survey of general practitioners in Scotland 
BMC Medical Education  2016;16:24.
Participation in continuing professional development (CPD) is a professional and regulatory expectation of general practitioners (GPs). Traditionally, CPD activity was undertaken face-to-face in educational settings, but internet based formats have found increasing favour. The need for doctors to use the internet for service and educational purposes is growing, particularly in support of specialty training and appraisal. We aimed to determine how GPs in Scotland utilise online resources in support of their CPD. This involved identifying which resources are used and how frequently, along with their preferences as to how and why they access these resources.
A cross sectional study was undertaken using an online questionnaire to survey general practitioners across Scotland. Data were subjected to descriptive analysis and differences in attitudinal responses between groups and Fischer's exact tests were calculated.
Three hundred and eighty-three GP responses were received, with the majority being female (n = 232, 60.6 %) and GP partners (n = 236, 61.6 %). The majority used the internet on three or more working days per week or more frequently (n = 361, 94.3 %) with the three most common reasons being to obtain information for a patient (n = 358, 93.5 %), answering a clinical question (n = 357, 93.2 %) and CPD purposes (n = 308, 80.4 %). Of 37 online resources used by respondents, the top five were SIGN Guidelines (n = 303, 79.3 %), BMJ Learning (n = 279, 73.0 %), NICE Guidelines (n = 255, 66.8 %), GP Notebook (n = 243, 63.6 %) and Google (n = 234, 61.3 %). Low use of social media such as Facebook (n = 11, 2.9 %) and Twitter (n = 11, 2.9 %) was reported for CPD. A majority agreed that 'reading information online' (95.0 %) and 'completing online learning modules' (87.4 %) were the most valued online activities. Slow internet connections (n = 240, 62.7 %), website access restrictions (n = 177, 46.2 %) and difficulties logging into online CPD resources (n = 163, 42.6 %) were reported barriers. Significant response differences (P < 0.05) were found between groups based on high volume online usage, gender and age.
The majority of respondents had positive attitudes to using online resources for continuing professional development, and a preference for evidence-based and peer reviewed online resources. Information technology (IT) difficulties remain a barrier to effective utilisation. The findings have implications for future planning and design of online resources and IT infrastructure.
Electronic supplementary material
The online version of this article (doi:10.1186/s12909-016-0540-5) contains supplementary material, which is available to authorized users.
PMCID: PMC4721189  PMID: 26791566
Online resources; Internet; e-learning; Continuing professional development; General practice
7.  In Vivo Spinal Posture during Upright and Reclined Sitting in an Office Chair 
BioMed Research International  2013;2013:916045.
Increasing numbers of people spend the majority of their working lives seated in an office chair. Musculoskeletal disorders, in particular low back pain, resulting from prolonged static sitting are ubiquitous, but regularly changing sitting position throughout the day is thought to reduce back problems. Nearly all currently available office chairs offer the possibility to alter the backrest reclination angles, but the influence of changing seating positions on the spinal column remains unknown. In an attempt to better understand the potential to adjust or correct spine posture using adjustable seating, five healthy subjects were analysed in an upright and reclined sitting position conducted in an open, upright MRI scanner. The shape of the spine, as described using the vertebral bodies' coordinates, wedge angles, and curvature angles, showed high inter-subject variability between the two seating positions. The mean lumbar, thoracic, and cervical curvature angles were 29 ± 15°, −29 ± 4°, and 13 ± 8° for the upright and 33 ± 12°, −31 ± 7°, and 7 ± 7° for the reclined sitting positions. Thus, a wide range of seating adaptation is possible through modification of chair posture, and dynamic seating options may therefore provide a key feature in reducing or even preventing back pain caused by prolonged static sitting.
PMCID: PMC3794512  PMID: 24175307
8.  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
9.  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
10.  Influence of the Weight of a School Backpack on Spinal Curvature in the Sagittal Plane of Seven-Year-Old Children 
BioMed Research International  2015;2015:817913.
The aim of the paper was to determine a correlation between the weight of a child's backpack, their body weight, and certain features of their body posture. Material and Methods. The study group consisted of 109 children, all aged seven years. The parameters of body posture were determined using the Zebris Ultrasonic System. Results. The number of children carrying a school backpack in accordance with recommendations was 44 subjects (40.37%). Statistically significant changes were found in the total length of the spine (Z = 2.223, p = 0.026) and between backpack weight and changes in the following parameters: the total length of the spine (rs = −0.3999, p = 0.017), the length and the angle of the lumbar lordosis (rs = −0.3352, p = 0.049), the angle of the lumbar lordosis (rs = −0.5065, p = 0.002), and the sacral angle (rs = −0.4279, p = 0.010). Conclusions. Wearing a backpack heavier than 10% of one's body weight can cause shallowing of the lumbar lordosis and a tendency towards a vertical position of the sacrum. Monitoring the weight of children's school backpacks and enabling them to leave books and notebooks at school would probably be beneficial in reducing the daily burden put on children's spines.
PMCID: PMC4564613  PMID: 26413545
11.  Telemonitoring of home infusion technology 
The specialized registered nurses working in the technologic homecare team of our organization are highly qualified in technical nursing.
One component of their job is the intravenous administration of medication to patients in their own home by using an infusion pump.
In a hospital setting you can ask a colleague nurse to check the installation of the pump and the dose of medication. In the home situation of a patient this is not possible.
The Inspection for Healthcare in the Netherlands has mentioned this problem in a report about home infusion technology, for the absence of a double check means a higher risk of making mistakes.
This was a motivation to look for a safe solution for this problem by using telemonitoring.
To conceive this method we found an enthusiastic technical installation company (Focus Cura) to develop a portable telemonitoring device which can film and record. The device allows a colleague to receive the recorded pictures at the same time at another location.
After editing a list of requirements made together with the team of specialized nurses, Focus Cura made the first prototype of a portable suitcase with all the equipment. Four different methods of receiving the images have been examined.
The result is a portable suitcase with a camera that makes high quality video images, which are sent by a safe and protected connection to the notebook of a colleague at another location in the region. We have developed a protocol which describes the use of telemonitoring to aid home infusion technology.
Thus, specialized nurses working in an area of about 100 kilometres (62 miles) can reach each other in order of a safe double-check. A simple method which improves the safety of the patient and professional.
PMCID: PMC3031816
telemonitoring; infusion technology; home
12.  Automated Detection of Activity Transitions for Prompting 
Individuals with cognitive impairment can benefit from intervention strategies like recording important information in a memory notebook. However, training individuals to use the notebook on a regular basis requires a constant delivery of reminders. In this work, we design and evaluate machine learning-based methods for providing automated reminders using a digital memory notebook interface. Specifically, we identify transition periods between activities as times to issue prompts. We consider the problem of detecting activity transitions using supervised and unsupervised machine learning techniques, and find that both techniques show promising results for detecting transition periods. We test the techniques in a scripted setting with 15 individuals. Motion sensors data is recorded and annotated as participants perform a fixed set of activities. We also test the techniques in an unscripted setting with 8 individuals. Motion sensor data is recorded as participants go about their normal daily routine. In both the scripted and unscripted settings a true positive rate of greater than 80% can be achieved while maintaining a false positive rate of less than 15%. On average, this leads to transitions being detected within 1 minute of a true transition for the scripted data and within 2 minutes of a true transition on the unscripted data.
PMCID: PMC4805372  PMID: 27019791
Activity Recognition; Prompting Systems; Change-Point Detection; Smart Environments
13.  Prompting technologies: A comparison of time-based and context-aware transition-based prompting 
While advancements in technology have encouraged the development of novel prompting systems to support cognitive interventions, little research has evaluated the best time to deliver prompts, which may impact the effectiveness of these interventions.
This study examined whether transition-based context prompting (prompting an individual during task transitions) is more effective than traditional fixed time-based prompting.
Participants were 42 healthy adults who completed 12 different everyday activities, each lasting 1–7 minutes, in an experimental smart home testbed and received prompts to record the completed activities from an electronic memory notebook. Half of the participants were delivered prompts during activity transitions, while the other half received prompts every 5 minutes. Participants also completed Likert-scale ratings regarding their perceptions of the prompting system.
Results revealed that participants in the transition-based context prompting condition responded to the first prompt more frequently and rated the system as more convenient, natural, and appropriate compared to participants in the time-based condition.
Our findings suggest that prompting during activity transitions produces higher adherence to the first prompt and more positive perceptions of the prompting system. This is an important finding given the benefits of prompting technology and the possibility of improving cognitive interventions by using context-aware transition prompting.
PMCID: PMC4803438  PMID: 26409520
Prompting technology; cognitive intervention; assistive technology; cognitive aids
14.  A Flexible Three-in-One Microsensor for Real-Time Monitoring of Internal Temperature, Voltage and Current of Lithium Batteries 
Sensors (Basel, Switzerland)  2015;15(5):11485-11498.
Lithium batteries are widely used in notebook computers, mobile phones, 3C electronic products, and electric vehicles. However, under a high charge/discharge rate, the internal temperature of lithium battery may rise sharply, thus causing safety problems. On the other hand, when the lithium battery is overcharged, the voltage and current may be affected, resulting in battery instability. This study applies the micro-electro-mechanical systems (MEMS) technology on a flexible substrate, and develops a flexible three-in-one microsensor that can withstand the internal harsh environment of a lithium battery and instantly measure the internal temperature, voltage and current of the battery. Then, the internal information can be fed back to the outside in advance for the purpose of safety management without damaging the lithium battery structure. The proposed flexible three-in-one microsensor should prove helpful for the improvement of lithium battery design or material development in the future.
PMCID: PMC4481915  PMID: 25996509
lithium battery; micro-electro-mechanical systems; flexible three-in-one micro- sensor; internal monitoring
15.  Reflex control of the spine and posture: a review of the literature from a chiropractic perspective 
This review details the anatomy and interactions of the postural and somatosensory reflexes. We attempt to identify the important role the nervous system plays in maintaining reflex control of the spine and posture. We also review, illustrate, and discuss how the human vertebral column develops, functions, and adapts to Earth's gravity in an upright position. We identify functional characteristics of the postural reflexes by reporting previous observations of subjects during periods of microgravity or weightlessness.
Historically, chiropractic has centered around the concept that the nervous system controls and regulates all other bodily systems; and that disruption to normal nervous system function can contribute to a wide variety of common ailments. Surprisingly, the chiropractic literature has paid relatively little attention to the importance of neurological regulation of static upright human posture. With so much information available on how posture may affect health and function, we felt it important to review the neuroanatomical structures and pathways responsible for maintaining the spine and posture. Maintenance of static upright posture is regulated by the nervous system through the various postural reflexes. Hence, from a chiropractic standpoint, it is clinically beneficial to understand how the individual postural reflexes work, as it may explain some of the clinical presentations seen in chiropractic practice.
We performed a manual search for available relevant textbooks, and a computer search of the MEDLINE, MANTIS, and Index to Chiropractic Literature databases from 1970 to present, using the following key words and phrases: "posture," "ocular," "vestibular," "cervical facet joint," "afferent," "vestibulocollic," "cervicocollic," "postural reflexes," "spaceflight," "microgravity," "weightlessness," "gravity," "posture," and "postural." Studies were selected if they specifically tested any or all of the postural reflexes either in Earth's gravity or in microgravitational environments. Studies testing the function of each postural component, as well as those discussing postural reflex interactions, were also included in this review.
It is quite apparent from the indexed literature we searched that posture is largely maintained by reflexive, involuntary control. While reflexive components for postural control are found in skin and joint receptors, somatic graviceptors, and baroreceptors throughout the body, much of the reflexive postural control mechanisms are housed, or occur, within the head and neck region primarily. We suggest that the postural reflexes may function in a hierarchical fashion. This hierarchy may well be based on the gravity-dependent or gravity-independent nature of each postural reflex. Some or all of these postural reflexes may contribute to the development of a postural body scheme, a conceptual internal representation of the external environment under normal gravity. This model may be the framework through which the postural reflexes anticipate and adapt to new gravitational environments.
Visual and vestibular input, as well as joint and soft tissue mechanoreceptors, are major players in the regulation of static upright posture. Each of these input sources detects and responds to specific types of postural stimulus and perturbations, and each region has specific pathways by which it communicates with other postural reflexes, as well as higher central nervous system structures. This review of the postural reflex structures and mechanisms adds to the growing body of posture rehabilitation literature relating specifically to chiropractic treatment. Chiropractic interest in these reflexes may enhance the ability of chiropractic physicians to treat and correct global spine and posture disorders. With the knowledge and understanding of these postural reflexes, chiropractors can evaluate spinal configurations not only from a segmental perspective, but can also determine how spinal dysfunction may be the ultimate consequence of maintaining an upright posture in the presence of other postural deficits. These perspectives need to be explored in more detail.
PMCID: PMC1198239  PMID: 16091134
Cervical spine; Posture; Reflex
16.  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
17.  A pocket guide to electronic laboratory notebooks in the academic life sciences 
F1000Research  2016;5:2.
Every professional doing active research in the life sciences is required to keep a laboratory notebook. However, while science has changed dramatically over the last centuries, laboratory notebooks have remained essentially unchanged since pre-modern science. We argue that the implementation of electronic laboratory notebooks (eLN) in academic research is overdue, and we provide researchers and their institutions with the background and practical knowledge to select and initiate the implementation of an eLN in their laboratories. In addition, we present data from surveying biomedical researchers and technicians regarding which hypothetical features and functionalities they hope to see implemented in an eLN, and which ones they regard as less important. We also present data on acceptance and satisfaction of those who have recently switched from paper laboratory notebook to an eLN.  We thus provide answers to the following questions: What does an electronic laboratory notebook afford a biomedical researcher, what does it require, and how should one go about implementing it?
PMCID: PMC4722687  PMID: 26835004
Code of Federal Regulations Title 21; Documentation; Data storage; Good Scientific Practice; Good Laboratory Practice; Laboratory information management systems; Software
18.  Coordination of Hand Shape 
The neural control of hand movement involves coordination of the sensory, motor and memory systems. Recent studies have documented the motor coordinates for hand shape, but less is known about the corresponding patterns of somatosensory activity. To initiate this line of investigation, the present study characterized the sense of hand shape by evaluating the influence of differences in the amount of grasping or twisting force, and differences in forearm orientation. Human subjects were asked to use the left hand to report the perceived shape of the right hand. In Experiment 1, six commonly grasped items were arranged on the table in front of the subject: bottle, doorknob, egg, notebook, carton, pan. With eyes closed, subjects used the right hand to lightly touch, forcefully support or imagine holding each object, while 15 joint angles were measured in each hand with a pair of wired gloves. The forces introduced by supporting or twisting did not influence the perceptual report of hand shape, but for most objects, the report was distorted in a consistent manner by differences in forearm orientation. Subjects appeared to adjust the intrinsic joint angles of the left hand, as well as the left wrist posture, so as to maintain the imagined object in its proper spatial orientation. In a second experiment, this result was largely replicated with unfamiliar objects. Thus somatosensory and motor information appear to be coordinated in an object-based, spatial coordinate system, sensitive to orientation relative to gravitational forces, but invariant to grasp forcefulness.
PMCID: PMC3066006  PMID: 21389230
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.  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
21.  Building a Virtual Network in a Community Health Research Training Program 
Objective: To describe the experiences, lessons, and implications of building a virtual network as part of a two-year community health research training program in a Canadian province.
Design: An action research field study in which 25 health professionals from 17 health regions participated in a seven-week training course on health policy, management, economics, research methods, data analysis, and computer technology. The participants then returned to their regions to apply the knowledge in different community health research projects. Ongoing faculty consultations and support were provided as needed. Each participant was given a notebook computer with the necessary software, Internet access, and technical support for two years, to access information resources, engage in group problem solving, share ideas and knowledge, and collaborate on projects.
Measurements: Data collected over two years consisted of program documents, records of interviews with participants and staff, meeting notes, computer usage statistics, automated online surveys, computer conference postings, program Web site, and course feedback. The analysis consisted of detailed review and comparison of the data from different sources. NUD*IST was then used to validate earlier study findings.
Results: The ten key lessons are that role clarity, technology vision, implementation staging, protected time, just-in-time training, ongoing facilitation, work integration, participatory design, relationship building, and the demonstration of results are essential ingredients for building a successful network.
Conclusion: This study provides a descriptive model of the processes involved in developing, in the community health setting, virtual networks that can be used as the basis for future research and as a practical guide for managers.
PMCID: PMC61441  PMID: 10887165
22.  Informing Comprehensive HIV Prevention: A Situational Analysis of the HIV Prevention and Care Context, North West Province South Africa 
PLoS ONE  2014;9(7):e102904.
Building a successful combination prevention program requires understanding the community’s local epidemiological profile, the social community norms that shape vulnerability to HIV and access to care, and the available community resources. We carried out a situational analysis in order to shape a comprehensive HIV prevention program that address local barriers to care at multiple contextual levels in the North West Province of South Africa.
The situational analysis was conducted in two sub-districts in 2012 and guided by an adaptation of WHO’s Strategic Approach, a predominantly qualitative method, including observation of service delivery points and in-depth interviews and focus groups with local leaders, providers, and community members, in order to recommend context-specific HIV prevention strategies. Analysis began during fieldwork with nightly discussions of findings and continued with coding original textual data from the fieldwork notebooks and a select number of recorded interviews.
We conducted over 200 individual and group interviews and gleaned four principal social barriers to HIV prevention and care, including: HIV fatalism, traditional gender norms, HIV-related stigma, and challenges with communication around HIV, all of which fuel the HIV epidemic. At the different levels of response needed to stem the epidemic, we found evidence of national policies and programs that are mitigating the social risk factors but little community-based responses that address social risk factors to HIV.
Understanding social and structural barriers to care helped shape our comprehensive HIV prevention program, which address the four ‘themes’ identified into each component of the program. Activities are underway to engage communities, offer community-based testing in high transmission areas, community stigma reduction, and a positive health, dignity and prevention program for stigma reduction and improve communication skills. The situational analysis process successfully shaped key programmatic decisions and cultivated a deeper collaboration with local stakeholders to support program implementation.
PMCID: PMC4100930  PMID: 25028976
23.  MultiSeq: unifying sequence and structure data for evolutionary analysis 
BMC Bioinformatics  2006;7:382.
Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes.
Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins.
MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural visualization program for analyzing molecular dynamics simulations. Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5. The MultiSeq website has details on how to download and use the software:
PMCID: PMC1586216  PMID: 16914055
24.  Data Management in the Modern Structural Biology and Biomedical Research Environment 
Modern high-throughput structural biology laboratories produce vast amounts of raw experimental data. The traditional method of data reduction is very simple—results are summarized in peer-reviewed publications, which are hopefully published in high-impact journals. By their nature, publications include only the most important results derived from experiments that may have been performed over the course of many years. The main content of the published paper is a concise compilation of these data, an interpretation of the experimental results, and a comparison of these results with those obtained by other scientists.
Due to an avalanche of structural biology manuscripts submitted to scientific journals, in many recent cases descriptions of experimental methodology (and sometimes even experimental results) are pushed to supplementary materials that are only published online and sometimes may not be reviewed as thoroughly as the main body of a manuscript. Trouble may arise when experimental results are contradicting the results obtained by other scientists, which requires (in the best case) the reexamination of the original raw data or independent repetition of the experiment according to the published description of the experiment. There are reports that a significant fraction of experiments obtained in academic laboratories cannot be repeated in an industrial environment (Begley CG & Ellis LM, Nature 483(7391):531–3, 2012). This is not an indication of scientific fraud but rather reflects the inadequate description of experiments performed on different equipment and on biological samples that were produced with disparate methods. For that reason the goal of a modern data management system is not only the simple replacement of the laboratory notebook by an electronic one but also the creation of a sophisticated, internally consistent, scalable data management system that will combine data obtained by a variety of experiments performed by various individuals on diverse equipment. All data should be stored in a core database that can be used by custom applications to prepare internal reports, statistics, and perform other functions that are specific to the research that is pursued in a particular laboratory.
This chapter presents a general overview of the methods of data management and analysis used by structural genomics (SG) programs. In addition to a review of the existing literature on the subject, also presented is experience in the development of two SG data management systems, UniTrack and LabDB. The description is targeted to a general audience, as some technical details have been (or will be) published elsewhere. The focus is on “data management,” meaning the process of gathering, organizing, and storing data, but also briefly discussed is “data mining,” the process of analysis ideally leading to an understanding of the data. In other words, data mining is the conversion of data into information. Clearly, effective data management is a precondition for any useful data mining. If done properly, gathering details on millions of experiments on thousands of proteins and making them publicly available for analysis—even after the projects themselves have ended—may turn out to be one of the most important benefits of SG programs.
PMCID: PMC4086192  PMID: 24590705
Databases; Data management; Structural biology; LIMS; PSI; CSGID
25.  Innovation of High-risk Infants Follow-up Surveillance System in Iran 
Early childhood development is one of the most social determinants of health that must be notified in order to reducing social gap and inequity. In spite of increasingly developing intensive neonatal care wards and decreasing neonatal mortality rate, there is no follow-up surveillance system to identify high-risk infants (HRI) and their health problems for timely intervention after discharge. This study was carried out to design and pilot high-risk infant follow-ups (HRIFs) surveillance system, in Alzahra Hospital, a tertiary level center of Tabriz University of Medical Sciences (TUOMS), in 2012–2013.
In this qualitative research after studying international documents, consensus about criteria of HRIs accomplished by focus group discussion. Then, Delphi agreement technique was used to finalizing assessment timetable. In the second phase, we piloted the designed surveillance system in Alzahra Hospital, a tertiary level center of TUOMS. Pilot study was implemented by follow-up team organized in designed model at the first phase of the study. Then, the findings of the pilot study were being assessed by an expert panel. If the members agreed on made decisions, they were being placed on the agenda of the national committee of development care of newborns for final approval.
High-risk infants follow-up surveillance system was designed in following steps: Defining of evidence-based criteria of HRIs, organizing the follow-up team, regulating the organs and neurodevelopment assessment timetable, publishing a health certificate notebook for HRIs, and designing Access database software for data collection, report and evaluation.
We designed and piloted HRIFs surveillance system, so this system was institutionalized in Alzahra Hospital, finally. It can be prepared to apply in the whole country, after detecting the quantitative outcomes and developing the program in East Azarbijan.
PMCID: PMC4421883  PMID: 25969705
Follow-up; high-risk infants; Iran; surveillance system

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