IN SILICO ANALYSIS TECHNIQUES (BIOINFORMATICS) - LITERATURE RESEARCHES

Reading a newspaper on a personal digital assistant (PDA) rather than as traditional newsprint reduces the amount of CO2 pumped into the atmosphere by a factor of between 32 and 140, and cuts emissions of oxides of nitrogen and sulphur by several orders of magnitude. And business delegates can reduce all 3 emissions by up to 1,000-folds if they teleconference instead of travelling to overseas meetingsref.

  • medical writing
  • publication ethics
  • online periodic journals on general medicine
  • search-engines for official medical literature
  • free online medical books
  • online book-sellers
  • search-engines for non-official medical literature
  • open text mining interface (OTMI)
  • image archives
  • softwares for literature gestion
  • author profiles
  • bibliographies
  • statistical analysis software
  • aggregators
  • document delivery services
  • bookmarks
  • publishers

  • medical writing
  • Web resources :
  • Publication ethics:
  • Web resources : Scientific and engineering publications between 1997 and 2001 :
  • Online periodic journals on general medicine (specialistic journals are listed under respective sections; journals regarding immunology are listed in Journals on basic immunology; see also Publishers section)
  • Search-engines for official medical literature
  • Free online medical books
  • Online book-sellers
  • Open text mining interface (OTMI) was first presented at the Life Sciences Conference and Expo in Boston in April 2006. The proposal would make coded text freely available to all. If all publishers were to adopt this or some similar standard, the entire literature would become accessible for mining. OTMI is a software that explores open 'text bases', especially the PubMed database. They scan many publications in order to discover relationships based on phrases or sentences that, when analysed in combination, cumulatively link one object (such as a disease) to another (such as a molecule)
  • At the University of California, Berkeley, the BioText project is being used to explore apoptosis, for example
  • At the University of Illinois in Chicago, the Arrowsmith software explores the causes of disease
  • At the European Bioinformatics Institute near Cambridge, UK, the EBIMed retrieval engine explores protein–protein interactions
  • Search-engines for non-official medical literature
  • Image archives
  • Softwares for literature gestion
  • the digital object identifier (DOI) system is an identification system for intellectual property in the digital environment. Developed by the International DOI Foundation on behalf of the publishing industry, its goals are to provide a framework for managing intellectual content, link customers with publishers, facilitate electronic commerce, and enable automated copyright management. Publishing on the Internet requires new tools for managing content. Where traditional printed texts such as books and journals provided a title page or a cover for specific identifying information, digital content needs its own form of unique identifier. This is important for both internal management of content within a publishing house and for dissemination on electronic networks. In the fast-changing world of electronic publishing, there is the added problem that ownership of information changes, and location of electronic files changes frequently over the life of a work. Technology is needed that permits an identifier to remain persistent although the links to rights holders may vary with time and place. The network environment creates an expectation among users that resources can be linked and that these links should be stable. The DOI system provides a way to identify related materials and to link the reader or user of content to them. DOI has wide applicability to all forms of intellectual content and can therefore be applied to all forms of related materials, such as articles, books, classroom exercises, supporting data, videos, electronic files, and so on. DOI provides a basis for work now in progress to develop automated means of processing routine transactions such as document retrieval, clearinghouse payments, and licensing. Publishers and users are being encouraged to experiment with DOI usage, and to commonly develop guidelines for DOI scope and rules for usage. The DOI system has 2 main parts (the identifier, and a directory system) and a third logical component, a database.
  • The DOI can also serve as an agent. In the future, the DOI will also be used to automate transactions. The DOI is being further developed to incorporate functionality which could enable the user to associate a function with the DOI.
  • Although many clinical journals publish high-quality, clinically relevant and important original studies and systematic reviews, the articles for each discipline studied are concentrated in a small subset of journals. This subset varied according to healthcare discipline; however, many of the important articles for all disciplines in this study were published in broad-based healthcare journals rather than subspecialty or discipline-specific journalsref.
  • Libraries :
  • Author profiles :
  • Bibliographies : citation managers
  • EndNote 9 by Thomson ISI ResearchSoft [trial version]
  • Reference Manager v11 by Thomson ISI ResearchSoft [trial version]
  • ProCite by Thomson ISI ResearchSoft [trial version]
  • BibTeX
  • MEDLARS format
  • Statistical analysis software
  • JMP has replaced Staview
  • SPSS
  • SigmaStat
  • language-editing servicesref
  • Professional Editing Services
  • Boston BioEdit : English language editing services for biological scientists
  • International Science Editing
  • Asia Science Editing
  • Science Editing : scientific editing and proofreading services
  • BiomEditor : international bioscience consultants
  • Online English proofreading and editorial services
  • Aggregators : services that provide a single point of online access to multiple full-text publications, aggregate online access to the publications of multiple publishers and/or providers.
  • Document delivery services :
  • Bookmarks
  • Personal digital assistants (PDAs) are capable of changing how health care is delivered in the future, since they aim to merge and integrate this functionality in one device that is versatile, customisable, and portable. According to polls, the worldwide PDA market had 10.5 million devices in 2003. Clinicians are rapidly adopting PDAs into their daily practice (Medicine on the move. PDAs and tablet PCs make the rounds with doctors and nurses. Postgrad Med 2004; 115 (suppl): i-vi). In one study, > 50% of all doctors younger than 35 years in developed countries used a PDA in 2003ref. In a survey from the University of California (San Francisco, CA, USA) 40–50% of all US physicians and junior doctors (also referred to as residents in the USA) use or can use a PDAref. In 2005, the proportion of US doctors using PDAs is expected to be well above 50% and rising. This Review provides an overview of current PDA technologies, applications relevant to medical education and clinical practice, a guide to medical software, safety and security, a personal perspective, current limitations, and a future outlook. In the past, hand-held computing was restricted to sophisticated programmable calculators with or without a data storage option. By comparison, most PDAs currently run on the mobile operating systems of either Palm OS (PalmSource Inc, Sunnyvale, CA, USA) or Microsoft Windows (Microsoft Corp, Redmond, WA, USA) that, in addition to their intrinsic functionality, allow customisation by the installation of third-party software applications. Furthermore, some Palm OS or Windows mobile-based PDAs have a Java (Sun Microsystems, Santa Carla, CA, USA) runtime that allows the use of platform-independent, Java-based applications. Other platforms such as Newton (Apple Computer, Cupertino, CA, USA), Psion (Psion Teklogix, Mississauga, ON, Canada), BeOS (PalmSource Inc), Symbian OS (Symbian, London, UK), and Blackberry (Research in Motion, Waterloo, ON, Canada), currently have no major role in the health-care market. In 1996, Palm Inc introduced the Pilot 1000 and Pilot 5000 products running the Palm OS operating system (PalmSource Inc) that led the resurgence of hand-held computing. In 1999, the company added advanced wireless communications capabilities to the Palm OS platform to address the demand for mobile information appliances. Their company policy to provide registered developers with access to the source code of the Palm operating system led to the development of more than 40000 software applications, to run on > 36 million Palm OS devices sold, unmatched by any other hand-held operating system so farref1, ref2. Microsoft Windows mobile is Microsoft's most recent operating system for hand-held devices. Its source code is proprietary and only available to professional-device and software manufacturersref. Although Palm Inc still markets its own line of devices directly, both Palm OS and Windows mobile-based PDAs and smartphones (devices with a mobile phone and PDA combined) are also designed, manufactured, and distributed by several major computer manufacturers. PDAs are shirt-pocket-sized devices with a touch-sensitive screen, a dedicated input area or keyboard, customisable application buttons, and a multiway (button or mini joystick) navigator to browse information on the screen. Depending on the brand and model, some devices feature an expansion slot for memory cards or accessories, a built-in camera, headphone jacks, speaker, microphone, ports for infrared, Bluetooth, or Wi-Fi (Wireless Fidelity), and even built-in GPS (global positioning system) receivers. PDAs are now generally equipped with a comprehensive suite of personal information management software or the option to integrate with common brands of such software, note-taking applications, and contact databases. PDAs can connect to desktop computers and wireless local area networks (W-LAN) using infrared, Bluetooth (first developed by Telefonaktiebolaget L M Ericsson, Stockholm, Sweden, now Bluetooth Special Interest Group [SIG], Delaware, DE, USA), or Wi-Fi communication technology. The desktop synchronisation software or additional add-on applications provide compatibility with popular office file formats. Most devices feature an e mail application to integrate with current office suites, which allows users not only to carry critical files when travelling, but also to synchronise important files quickly and easily between desktop and hand-held devices. Smartphones enhance the basic PDA functionality with wireless communication properties, including instant messaging, e mail, web browsing, data synchronisation with remote servers and networks, and even video conferencing, if used in the coverage of commercial cellular telephone networks. Basic PDA functionality of a sample main application screen on Palm OS 6.1 :

    Physicians, nurses, dieticians, medical students and trainees, and other health-care professionals must review an ever-increasing amount of constantly changing information about their patients several times a day and correlate the data with the most recent diagnostic and therapeutic recommendations and management options to make sound decisions. Traditionally, health-care professionals consulted meticulously collected personal notebooks and article cut-outs, white-coat-pocket manuals, subscription journals, medical reference books, or electronic references on desktop computers. The wealth of information and its constant changes due to the accelerated pace in translational research in biomedical science mean that these traditional resources are very difficult to keep up to date. Fast approval and propagation of newly discovered therapies by regulatory agencies such as the FDA (US Food and Drug Administration) or EMEA (European Medicines Agency) can also lead to more frequent recalls of drugs, medical products, and devices (as well as newly issued warnings); labelling changes; and novel interactions with existing compounds. Additionally, with the advent of overzealous documentation, coding, and billing requirements in managed care, constantly overworked health-care professionals cause an increasing number of treatment and management errors, because the time available to spend with patients is sadly diminishing. PDAs can help to overcome some of these problems. The education of medical students now relies heavily on computer technology, beginning with the replacement of animal experiments by computer simulations in basic science laboratories, multimedia study programmes and exercises, and the abolition of paper-and-pencil board examinations for fully computerised systems in the USA and other countries. PDAs fit very well with these concepts, and the fact that medical students were among the earliest adopters of PDA use is unsurprisingref. Many medical schools require students to acquire basic clinical skills in clerkships. Faculty staff and students generally complete lengthy assessment forms at the end of the respective rotation, which do not always allow for a timely feedback and balanced learning experience. Electronic records of patient encounter and procedure logs maintained by the students on their PDAs, which are synchronised with either a central database or the mentor's desktop system, provide an interesting new approach. This concept has been assessed by several academic medical centres for rotations in internal medicine, family medicine, and emergency medicine in surveys. Medical students thought the logs were convenient to use. This system generally increased the number of patient encounters and recorded diagnoses, helped improve history-taking skills by alerting students to under-addressed issues such as women's health, improved overall computer literacy, allowed to immediately identify large gaps in basic clinical skills, and provided an easy mutual feedback with faculty staff during clinical clerkshipsref1, ref2, ref3, ref4 (Lee JS, Sineff SS, Sumner W. Validation of electronic student encounter logs in an emergency medicine clerkship. Proc AMIA Symp 2002; 425-429; Denton GD, Williams RW, Pangaro L. Core problems reported by students in a palm OS and Internet-based problem entry system predicts performance on the third-year internal medicine clerkship. AMIA Annu Symp Proc 2003; 827; Bakken S, Sheets CS, Curtis L, Soupios M, Curran C. Informatics competencies pre-and post-implementation of a Palm-based student clinical log and informatics for evidence-based practice curriculum. AMIA Annu Symp Proc 2003; 41-45). The early use of a clinical management approach to evidence-based medicine is a worthy goal in undergraduate medical education. 2 studies were undertaken to investigate whether PDAs could assist this approach at the point of care. In both studies, medical students were given PDAs preloaded with either university-developed clinical-decision support software (CDSS) or a bundle of commercial-decision support applications commonly used by clinicians. Multivariable regression analysis showed that improved perceived usefulness of PDAs with CDSS was associated with supportive faculty attitudes, good knowledge of evidence-based medicine, enhanced computer literacy skills. Greater satisfaction with the CDSS than with commercial-decision support devices was associated with increased use in a clinical setting and improved success in search ratesref. In the second study, pre-orientation and post-orientation questionnaires and a post-rotation assessment measured students' comfort levels, and the perceived usefulness of PDAs with CDSS and ratings of programmes on their PDAs were analysed. PDAs almost always enhanced the clerkship experience, although the outcome measures were not as clearly defined as those in the first studyref. The education effectiveness of evidence-based-medicine learning was investigated objectively in a randomised controlled trial, in which students' use of a PDA with CDSS was compared with the use of a pocket card containing guidelines and controls. Main outcome measures were factored and individual item scores from a validated questionnaire on personal, current, and future use of evidence-based medicine; use of evidence during and after the clerking of patients; frequency of discussions on the role of evidence during teaching rounds; and self-perceived confidence in clinical decision-making. The PDA showed significant improvements in all outcome scores, with the largest change in students' educational experience with evidence-based medicine. No substantial deterioration was seen in the improvements even after the withdrawal of PDAs during an 8-week washout period, which suggested at least short-term sustainability of PDA effectsref. PDAs can also assist in telementoring and multimedia learning. 2 studies have shown the feasibility of live wireless transmissions of laparoscopic surgical procedures to PDAs. One of these studies also compared the recognition of anatomical landmarks on PDA screens with that of standard computer monitors during the procedure and showed significant improvementsref1, ref2. PDAs could also help enhance the classroom learning experience. In a pilot study, a histology class teacher polled the students about effectiveness, student interest, and comprehension with Bluetooth-equipped PDAs. End-of-class survey results indicated that students were enthusiastic about the polling deviceref. Overall, current data lend support to the potential usefulness of PDAs in medical education. However, large randomised controlled trials with comparisons of PDA with non-PDA groups and with objective outcome measures, such as performance in in-house or board examinations, are needed to substantiate these early observations. Another important aspect of hand-held computer-assisted learning is the integration of faculty staff, who are traditionally more reluctant to adopt new technology than studentsref. Several programmes for junior doctors at leading US academic institutions (such as Harvard Medical School, Boston, MA; Columbia College of Physicians and Surgeons, New York, NY; or Georgetown University Medical School, Washington, DC), have been early adopters of hand-held computers and provide their junior doctors with PDAs and software bundles. Training programme accreditation authorities and medical specialty boards demand an ever-increasing documentation of patient exposure and procedural performance, to maintain and improve training standards. Apart from log cards, no simple and reliable mechanisms currently exist for directors of junior doctor programmes to assess how well their trainees are being exposed to teaching in their specialties and what curriculum weaknesses need to be addressed. Several studies in specialties such as anaesthesia, emergency medicine, family practice, general surgery, internal medicine, neurology, obstetrics and gynaecology, radiology, and urology, have demonstrated the usefulness of PDAs to simplify data collection and assess doctor and programme performanceref1, ref2, ref3, ref4, ref5, ref6 (Sequist TD, Singh S, Pereira A, Pearson SD. On Track: a database for evaluating the outpatient clinical experience of internal medicine residency training. AMIA Annu Symp Proc 2003; 1002). A larger survey in junior doctors of six training programmes in family practice, internal medicine, neurology, paediatrics, radiology, and surgery concluded that, as advantages, many junior doctors readily adapted their personal organisers to help keep track of their clinical tasks and keep in touch with patients, and that commercial medical references were used most by the surveyed residents to answer immediate medical questions. The perceived drawbacks included: calculators and patients' trackers were not clearly able to be tailored to residents' needs (eg, to restrict and modify types of calculations to just those actually used), the physical size (both too small for display and too bulky overall), and several junior doctors mentioned a concern of becoming too dependent on one source of information, which was viewed as being too easy to lose or break. PDAs were widely used across the spectrum of specialties, irrespective of encouragement by the training programmeref. PDAs can also assist in assessing the performance of clinical educators and students in objective structured clinical examinations (OSCE)ref (McGowan JJ, Bangert M, Ballinger SH, Highbaugh S. Implementing wireless evaluation in a hospital-based OSCE center. AMIA Annu Symp Proc 2003; 930). The available data suggest the potential usefulness of PDAs in junior physician education. However, as concluded for medical student education, larger randomised controlled trials and surveys are needed to compare PDA-assisted training with traditional training in institutions and specialties by use of objective outcome measures, such as performance in in-house or board examinations, to define the role of PDAs in postgraduate medical education. PDAs are widely used among health-care professionals across all major specialties. A study of 2130 paediatricians selected randomly from the American Medical Associations' Physician Masterfile (American Medical Association, Chicago, IL, USA) aimed to calculate the percentage of paediatricians using PDAs, deduce the perceived strengths and weaknesses of PDAs, and explore characteristics associated with beliefs and use. The most commonly used applications were for drug reference (80%), followed by scheduling (67%), medical calculations (61%), prescription writing (8%), and billing (4%). PDA users were significantly more likely to be male, come from an urban community, have recently graduated from medical school, and work in non-private practice. Users were also more likely to believe that PDAs could reduce medical error, but often complained about memory capacity, although small screen size and system speed were not problemsref. With 35–40% of respondents using a PDA, this study is a good example for mainstream hand-held computer use by physicians in many clinical specialties. PDAs can replace bulky drug reference books and help with the selection and comparison of drugs, identification of dosing schedules, and dose adjustment when drug excretion is impaired. A major advantage of PDA use over paper-based drug references are drug interaction checks and—if updated (synchronised) with an institutional or commercial server regularly—the most up-to-date drug information and immediate access to alerts or recalls from regulatory or government agencies, such as the FDA or CDC (Centers for Disease Control, Atlanta, GA, USA). The usefulness of PDA-based drug references, including parenteral nutrition, blood products, and chemotherapy, and drug interaction checks has been established in several different studiesref1, ref2, ref3, ref4, ref5, ref6, ref7. The effect of PDA use on medication safety can be even greater if use is extended to nursing staff and combined with patient identification systems. To improve patient safety in hospitals by reducing drug treatment and treatment errors, the FDA has published a final rule about bar code label requirements for human drugs and biological products, in February, 2004ref. Bar codes are now required on most prescription drugs, blood, blood products, and specific over-the-counter drugs. This system begins when a patient is admitted to the hospital. The hospital gives the patient a bar-coded identification bracelet to link to his or her computerised medical record. As required by the FDA rule, most prescription drugs and specific over-the-counter drugs would have a bar code on their labels. The health-care team uses PDA-based bar-code scanners that are linked to the hospital's computer system of electronic medical records. Before a health-care worker gives a drug to the patient, the health-care worker scans the patient's bar code, which allows the computer to access the patient's computerised medical record. The health-care worker then scans the drug that the hospital pharmacy has provided for treatment. This scan informs the computer which drug is being given. The computer then compares the patient's medical record with the drug being given to ensure that they match. Therefore some of the following problems (unfortunately not uncommon) could be easily avoided: wrong patient, wrong dose of drug, wrong drug, and wrong time to administer the drug. The technology is available and has already been implemented in some multisite facilities in the USA with some successref1, ref2, ref3, ref4, ref5, ref6. Daily writing of progress notes with patients' data interpretation, management plans, and coding of medical treatments and procedures are crucial clinician responsibilities. However, the quality and legibility of notes are often inadequate. The following studies illustrate how the quality of medical records can be enhanced with PDA use. In a paediatric critical-care unit, researchers recorded documentation discrepancies in 60% of daily-progress notes. Therefore, they undertook a before-and-after trial to determine whether a point-of-care, PDA-based patient record and charting system could reduce discrepancies in progress note documentation by junior doctors in a neonatal intensive-care unit. They recorded significantly fewer documentation discrepanciesref. Another randomised study investigated whether hand-held computer-based documentation could improve both the quantitative and qualitative aspects of medical records in orthopaedic surgery. The electronic documentation consisted of a specially designed software package on a hand-held computer for bedside use with structured decision trees for examination, access to a history, and coding. In the control group, chart notes were compiled on standard paper forms and were subsequently entered into the hospital's information system. The number of documented ICD (International Classification of Diseases) diagnoses was the primary endpoint for sample size calculations. All patients' charts were reread by an expert panel, which assigned quality ratings to the different documentation systems by scrutinising the extent and accuracy of patients' histories and physical findings assessed by daily chart notes. Documentation with the hand-held computer significantly increased the median number of diagnoses per patients from four to nine, but it produced some over-coding for false or redundant items. Documentation quality ratings improved significantly with the introduction of the hand-held device with respect to the correct assessment of a patient's progress and translation into ICD diagnoses. Various learning curve effects were recorded with different operators (Stengel D, Bauwens K, Walter M, Kopfer T, Ekkernkamp A. Comparison of handheld computer-assisted and conventional paper chart documentation of medical records. A randomized, controlled trial. J Bone Joint Surg Am 2004; 86-A: 553-560). These findings were confirmed by another orthopaedic surgery study in outpatientsref. A study among anaesthesiologists investigated their experience of using acute pain assessment software on a PDA for patient management. PDA assessments were more likely to contain documentation regarding pain and side-effects than paper assessments. The median time of the assessment period during the patient encounter was longer with the PDA than with paper; however, the median period for the total encounter time (chart review, assessment, documentation) was significantly shorter with the PDA than with paperref. The battle between health insurers and physicians about claims is not overref. Claims are frequently denied or delayed on technicalities such as over-coding or under-coding, which PDA use could help in the future. Many clinicians have difficulty determining the appropriate code for current procedural terminology (CPT) or evaluation and management (E&M) to assign to the type and intensity of patient care they provide. Several surveys reported PDA-based charge capture and billing programmes were more accurate than paper. The reimbursement advantage was estimated to be 20%ref1, ref2, ref3. Quality assessment and outcomes research in large medical associations require the acquisition, analysis of, and response to point-of-care data. Although most hospitals now process much of their clinical and administrative data electronically, data acquisition from the actual care providers and patients during encounters are still accomplished with an intermediate paper process. PDAs have the potential to simplify and accelerate this. Several studies, particularly in procedure-oriented specialties, have shown feasibility and measurable benefits of PDA-based data collection, because they allowed the quick modification of the study design, rapid data acquisition, and processing, to enable immediate effect of the results on clinical and administrative daily practice. This type of data collection increased performance almost instantly. Data were obtained with PDAs from either providers or patients to assess patient-perceived outcomesref1, ref2, ref3, ref4, ref5 (Astrahan MA. HDR quality assurance methods for personal digital assistants. Med Dosim 2004; 29: 166-172). Quality of care can be improved with the implementation of CDSSref, evidence-based medicineref, or other critically appraised publications and with alerting systems in hand-held computers. In a survey of 1538 health-sciences faculty staff and junior doctors, most responders indicated that they would like to learn more about clinical resources for PDAsref. Although many health-care professionals already rely on various sources of medical reference applicationsref, their effect on the quality of care is currently under-explored. Pilot studies in which users either assessed an interface to access institution-provided, critically appraised topics or headlines delivered to their PDAs alerting them to new books, National Guideline Clearinghouse guidelines, Cochrane reviews, and National Institute of Health (NIH) Clinical Alerts, as well as updated content in UpToDate (UptoDate, Waltham, MA, USA), Harrison's Online (McGraw Hill, Princeton, NJ, USA), Scientific American Medicine (now renamed ACP Medicine; American College of Physicians, Philadelphia, PA, USA), and Clinical Evidence. Participants could request additional information for any of the headlines, and the information that was delivered via e mail during their next synchronisation was perceived as helpfulref1, ref2, ref3, ref4. Example of PDA-based software for clinical decision support. MedCalc sample equation to calculate the Ranson's score to assist in the management of acute pancreatitisref :

    Example of a guideline reference application :

    Sample screen of the Shots 2005 application, developed by the Society of Teachers of Family Medicine and based on guidelines of the CDC National Immunization Programref. Reproduced with permission of Dr Richard K Zimmerman, University of Pittsburgh, PA, USA on behalf of the Group of Immunisation Education, Society of Teachers of Family Medicine. The Lister Hill National Center for Biomedical Communications (Bethesda, MD, USA), a research and development division of the National Library of Medicine (NLM) of the NIH, has undertaken a project to discover and implement design principles for point-of-care delivery of clinical support information. PubMed on Tap is an application for PDAs that retrieves MEDLINE citations directly from the PDA through a wireless connection to the internet. PubMed on Tap features include several PubMed search options, a history of previous queries, the ability to save citations to an electronic memo pad, two clustered results options, and links to journal websitesref. The National Cancer Institute (NCI; Bethesda, MD, USA), another NIH branch, has also recognised the need for new information delivery methods and is currently undertaking a research study that investigates how health-care professionals use cancer information on hand-held wireless devices. The AvantGo Enterprise 4.2 Solution (iAnywhere Solutions, Dublin, CA, USA) provided the platform to deliver the website content of NCI's cancer information service (CIS) onto hand-held devices. Several obstacles still need to be overcome before this service will be available to the general publicref. Other clinical settings where PDA-based decision support devices have been reported to be useful or advantageous include: emergency and mass casualty triage, data management of transplantation patients, management of patients with stroke, infection control, and enforcement of institution-specific, rational antibiotic useref1, ref2, ref3, ref4, ref5, ref6. (Ray HN, Boxwala AA, Anantraman V, Ohno-Machado L. Providing context-sensitive decision-support based on WHO guidelines. Proc AMIA Symp 2002; 637-641; Quaglini S, Caffi E, Boiocchi L, Panzarasa S, Cavallini A, Micieli G. Web-based data and knowledge sharing between stroke units and general practitioners. AMIA Annu Symp Proc 2003; 534-538; Chang P, Hsu Y, Tzeng Y, Hou IC, Sang YY. Development and pilot evaluation of user acceptance of advanced mass-gathering emergency medical services PDA support systems. Medinfo 2004; 1421-1425). Although these concepts undoubtedly have potential, no study so far has compared this approach with existing methods of information delivery or performance of users in board examinations or re-certifications. Most patients feel comfortable with their physicians using a PDA in daily clinical practice (Houston TK, Ray MN, Crawford MA, Giddens T, Berner ES. Patient perceptions of physician use of handheld computers. AMIA Annu Symp Proc 2003; 299-303). However, their use is not restricted to health-care providers. PDAs can serve as electronic patient diaries and prediction devices in diseases that are intermittently flaring, such as asthma or urticaria. The successful use of PDAs in diabetes care to improve glycaemia in patients with insulin pumps has been reported. PDAs can also help migraine patients to predict attacksref1, ref2, ref3, ref4, ref5, ref6 (Kerkenbush NL. A comparison of self-documentation in diabetics: electronic versus paper diaries. AMIA Annu Symp Proc 2003; 88. Kwak M, Han SB, Kim G, et al. The knowledge modeling for chronic urticaria assessment in clinical decision support system with PDA. AMIA Annu Symp Proc 2003; 902). The new use of PDAs in patients has also been recognised by government agencies such as the US Public Health Service (USPHS), which released an interactive programme for Palm PDAs to help patients quit smoking. The programme is distributed through the Agency for Healthcare Research and Quality (AHRQ) and is available on their website.ref In addition to these professional applications, the internet is replete with software of the fitness, wellness, and personal health-care categories, such as menstrual calendars, diet, weight, calorie, and workout management applications, among others. PDAs could help patients with brain dysfunction or injury as cognitive-behavioural orthosesref1, ref2. A frequent outcome in these patients is memory impairment. One group of researchers designed and tested a mobile-distributed care system in a cognitive neurology day-care clinic of an academic medical centreref. A PDA-based speech synthesiser for speech-impaired patients has also been reportedref. With an extended bandwidth of cellular telephone networks (eg, universal mobile telecommunications system or UMTS) and high-speed institutional wireless networks, teleradiology on hand-held computers may become a reality. Pilot studies have shown promising data, such as CT scans that have been transmitted in the industry standard format of DICOM (digital image and communications in medicine) and that have been assessed remotely by radiologists. Echocardiograms have also been successfully read on PDAsref1, ref2 (Raman B, Raman R, Raman L, Beaulieu CF. Radiology on handheld devices: image display, manipulation, and PACS integration issues. Radiographics 2004; 24: 299-310). International, randomised, multicentre clinical trials usually need the collection, storage, and processing of large amounts of data. Data collection by investigators and study coordinators is traditionally done with specifically designed paper forms in clinical research files or complex telephone interview systems. Most trials also need the repeated completion of patient questionnaires to calculate standardised disease activity or quality-of-life scores. Unfortunately, paper-based, self-administered instruments remain inefficient for data collection because of missing information, respondent error, and slow data analysis due to processing delay from paper-to-computer file conversion. The advantages of PDAs to improve trial efficacy, quicken data analysis, and even improve patient safety due to earlier availability of results of interim analyses, among others, are obvious. Text and photo data capture, transmission feasibility, and visual analogue scales have been validatedref1, ref2, ref3, ref4 (Sellors JW, Hayward R, Swanson G, et al. Comparison of deferral rates using a computerized versus written blood donor questionnaire: a randomized, cross-over study [ISRCTN84429599]. BMC Public Health 2002; 2: 14). PDA appliances can record, store, and transmit virtual electrocardiograms and electrochemical dataref1, ref2. There are comprehensive PDA-based data recorders that, in combination with a sensor vest, continuously encrypt and store patients' physiological data (ie, blood pressure, blood oxygen saturation, electroencephalograms, electro-oculograms, periodic leg movement, core body temperature, skin temperature, end tidal CO2, and cough) on a memory card. Patients could also record time-stamped symptoms, moods, activities, and other endpoint-specific information in the recorder's digital diary. These features allow researchers to correlate multiple physiological indices that can be objectively measured with subjective inputref. Clinical research organisations have already discovered the advantages of PDA-based data collection in clinical trials. One such organisation and a major PDA manufacturer reported record sales of customised electronic diaries in 2004. This clinical research organisation has deployed 40000 electronic diaries in 46 languages to 48 countries for use in clinical trials since 2000ref.
    Several thousands of medical software applications and documents are available for health-care professionals to use. Medical software can be grouped into major categories: standard medical textbooks and manuals adapted for PDAs, PDA-designed medical references, medical dictionaries, drug reference and interaction check programmes, medical calculators, medical prediction rule applets (a Java software component), document readers, medical image viewers, software for medical evidence retrieval, subscription platforms to electronic newsletters or journal digests, educational programmes for medical students, and medical alerting messaging; comprehensive medical enterprise solutions integrating with electronic medical records, patient management and scheduling systems, and electronic order, prescribing and pharmacy-dispensing systems, coding, billing and file-sharing. Software and content are available from commercial suppliers, shareware and freeware distributors, health-care organisations, and PDA enthusiasts. The quality of medical software applications varies greatly and depends heavily on accessibility of the information. Initially, most suppliers offered static translations of traditional textbooks that were difficult to navigate. The market has now become more sophisticated, demanding more dynamic content with frequent updates taking advantage of the implementation of wireless networking protocols in PDAs. Internet websites are available to link users to sites dedicated to medical PDA use : General use or non-medical programmes (applications) for PDA users : .... guidelines from professional societies or health-care agencies ... : ..., and helpful programmes for general PDA use : Additionally, some medical journals such as the Journal of the American Medical Association (JAMA) regularly announce and discuss novel hand-held computer software titles. Examples of common medical software :

    A personal perspective
    As an internist and gastroenterologist, I face the same challenges that all academic physicians do: attending on the wards, clinics, critical care units, and emergency rooms; doing consultations for other specialties; dealing with numerous conferences, administrative work, lecturing, and bedside teaching; being an investigator in clinical trials; mentoring doctoral students; and running a basic science research laboratory, which often hardly fit into those 24 hours, unless one is very organised. I perceived the arrival of the Palm Pilot (Palm Inc, Sunnyvale, CA, USA) in 1996 as a blessing; it quickly changed how I organised my day, kept abreast of the ever-changing specialties of medicine and biomedical science, obtained and accessed medical information, and taught students. My old spiral notebook is retired now. On a typical day, my PDA wakes up 30 minutes before I do, logs on to my notebook as well as the internet, and synchronises and updates all PDA applications. Not only are contacts, appointments, and medical references kept up to date in this way, but my PDA e mail application is also programmed to retrieve exclusive e mails such as electronic tables of contents from medical journals, alerts from the FDA Medwatch system, and other resources in my e mail inbox. On the way to work I can review, mark, and erase these e mails. Once at the hospital, my PDA reminds me of conferences, meetings, and displays a to-do list for the day. When I see patients, I rely on drug reference and interaction applications, institutional microbial spectra databases, medical calculators, prediction rules, and specific topics in PDA editions of popular medical reference manuals. Additionally, I have many guidelines from our institution, professional organisations, and agencies, as well as pdf excerpts from journal articles stored in my memory card. I do not believe PDA versions of large medical textbooks are helpful, because they are often difficult to navigate. I am currently investigating the usefulness of the new PubMed on Tap programme, whenever I have access to the institutional W-LAN. Our department receives a fair amount of patients with gastrointestinal cancers. Staging of uncommon cancers is easy with a TNM (tumour, node, metastasis) staging programme. I can customise and print actual chemotherapy protocols with a shareware application. An add-on to this shareware application allows me to programme and print protocols for rare cancers. At ward rounds with students, I take full advantage of the multimedia capabilities of my PDA: I can display images from my personal medical image library or other PDA reference materials, play heart murmur or lung sound recordings, and use the screen to quickly sketch something to make a teaching point. I can carry and share with students (via infrared) a self-created collection of text notes, customised to the patients we see together. In clinics where I see many patients enrolled in clinical trials, I quickly enter, access, and sort essential data on spreadsheets. The spreadsheets were created with my notebook spreadsheet application, transferred to and updated on my PDA with a commercial programme. This software also helps me to review and store my presentations for lectures and talks. New versions of PDAs can also act as USB memory sticks. At the end of the day, my PDA synchronises and backs up the day's data with my notebook before it charges for the night
    PDA safety and security
    Information recording and interchange always raise the question of security and privacy. Overall, PDA security hazards are probably similar to other computers used in hospitals and elsewhere. Catastrophic data loss can only be prevented with regular backups. PDA viruses have been reported for the mobile operating system from Microsoft Windows and also, to a lesser degree, for the Palm operating system. Major security firms are addressing this problem with the development of commercial antivirus products for hand-held devices. In the USA, PDA-based patient data processing and storage must comply with the Health Information Portability and Accountability Act (HIPAA) of 1996. The Centers of Medicare and Medicaid Services (CMS) of the US Department of Health and Human Services provide information technology professionals and the general public with extensive resources to address the issues on their information security programme websiteref. In addition to a general policy manual, the CMS has outlined fundamental regulations as well as system architecture and security requirements for the acquisition, storage, management, and transmission of patient data. As a general rule, these policies are developed to provide a defence-in-depth security structure, along with a least-privilege approach and a need-to-know basis for all information access. Developers can download security threat identification resources based on their occurrence and importance in the current CMS environment. Before approval, applications have to pass the contractor assessment security tool (CAST) test to record their compliance with the CMS. Several specific new risks and vulnerabilities arise with wireless networks. Bluejacking (ie, unauthorised accessing of Bluetooth-enabled devices) in airports and other public places is advancing to a new hacker sport. These problems need to be addressed by hardware and software makers with improved encryption and authentication technology. Currently, no evidence shows that wireless-enabled PDAs interfere with the functioning of implanted cardiac pacemakers or defibrillatorsref1, ref2, ref3 (Chen D, Soong SJ, Grimes GJ, Orthner HF. Wireless local area network in a prehospital environment. BMC Med Inform Decis Mak 2004; 4: 12)
    Challenges of current PDA technology and future outlook
    Evidence of PDA use and dominance in medical education, clinical practice, and research is still evolving. Most studies available so far have not been randomised, controlled, or are multicentric in design. The fact that physicians can carry an entire shelf of medical reference textbooks on a hand-held computer's memory card does not automatically mean that physicians know their contents or can apply their knowledge appropriately in clinical practice. The increasing incidence of the so-called palmomental reflex by residents and medical students should remind clinical educators that PDAs are not peripheral brains and are a poor substitute for ad-hoc clinical knowledgeref. At a time when governments, health-care organisations, and insurers worldwide cannot stop entertaining the themes of necessity assessment, cost saving, and down-sizing, we need convincing arguments that the extra expenses of investment into PDA technology can actually improve quality of care, save lives, and ultimately save health-care costsref. The IT industry has recognised health care as the next big marketref1, ref2. It will be up to health-care professionals who depend on PDAs to inform PDA manufacturers of users' true needs, do the necessary research, and actively direct the development of new hardware and software. The future of information exchange in medicine is digital and wirelessref. What will a medical PDA look like in 2015? It will probably be housed in a ceramic or lightweight alloy case, and hopefully be no larger but substantially lighter than current shirt-pocket-sized devices. New semiconductor technology will allow hand-held computers to be equipped with processors that can handle much more work than the best desktop systems that are currently available, while consuming less power to extend battery life. Memory will no longer be an issue, because data will be mainly kept in network storage systems. Manual data entry is still a problem in current versions of PDAs. In the future, authorised, secure logons to the PDA and data entry will be done with combined speech and fingerprint recognition by sophisticated audio hardware and a new high-resolution generation of touch-sensitive screens. Graffiti 2 (PalmSource Inc) characters will be further developed into true handwriting recognition. Speech processing will also be a reality, replacing many dictation methods currently used. Very high network speeds will provide immediate access to clinical and administrative data, including imaging information such as procedural movies; three-dimensional ultrasonography; CT, MRI, or PET scans; histological slides; microbial cultures; and institutional and remote reference systems at any place and time. Medical applications will go beyond organisation and storage of information. PDAs could evolve into expert systems that access information from many sources (ie, classic textbook style references, data from basic and clinical research and genome scans, environmental and public-health information, and results from ongoing clinical trials, match the information with the patient's medical records from current or past admissions or visits, apply prediction rules, calculate clinical equations, and integrate all the data into an overall information package for clinicians. Users will be able to obtain and share opinions on patients with colleagues and international experts with ad-hoc medical multimedia conferencing. PDA-based medical information management could even have an environmental effect that goes beyond paper-saving. The environmental effects of two applications of wireless technologies were compared with those of conventional technologiesref. Compared with the use of a newspaper, users receiving the news on a PDA resulted in the release of 32–140 times less CO2, several orders of magnitude less NOx and SOx, and the use of 26–67 times less water than the use of newspapers. Wireless teleconferencing resulted in one to three orders of magnitude less CO2, NOx, and SO2 emissions than those from business travel. Is this future scenario widely off the mark? Perhaps so, but critics should remember that many theoretical predictions of the future have inspired the design of devices used today. However, it is still certain that no computer system can ever replace dedicated, experienced clinicians and their empathic interaction with patients and familiesref.

    Enhanced Network Accessibility for the Blind and Visually Impaired (ENABLED)
    Creative Commons : if you are interested in licensing software documentation or other supporting text for a piece of code, we recommend the GNU Free Documentation License.
    Counting Online Usage of NeTworked Electronic Resources (COUNTER)
    Tools for searching literature covering a particular topic are listed in the section related to such topic (e.g. Cancer)

    Having doubled between 1998 and 2003, the NIH budget is expected to be $28.6 billion for fiscal year 2007, a 0.1% decrease from last year (Office of Budget. FY 2007 budget in brief: advancing the health, safety, and well-being of our people. Washington, D.C.: Department of Health and Human Services, 2006), or a 3.8% decrease after adjustment for inflation — the first true budgeted reduction in NIH support since 1970. Whereas national defense spending has reached approximately $1,600 per capita, federal spending for biomedical research now amounts to about $97 per capita — a rather modest investment in "advancing the health, safety, and well-being of our people."1 Annualized growth rates (adjusted for inflation) of the NIH budget, 1971 to 2005 :

    Meanwhile, for > 10 years, the pharmaceutical industry has been investing larger amounts in research and development than the federal government — $51.3 billion in fiscal year 2005ref, for instance, or 78% more than NIH funding that year. Korn and colleagues have argued that stability and quality can be ensured by maintaining overall funding at an annual growth rate of 8 to 9 percent (unadjusted for inflation)ref. The annual required growth rate should rather be 5-6% real growth plus inflation: the annual growth rate over the past 30 years has been approximately 10%, which reflects an annual average real growth rate of 5.2% and an average inflation rate of 4.8% (ranging from 1.1 to 13.3%)ref.

    Web resources : companies offering products for modeling, databases, data mining and analysis : Accelrys, Agilent Technologies, Ariadne Genomics, BG Medicine, Bioanalytics Group, Biomax Informatics, BioSieve, CambridgeSoft, CLC bio, Entelos, Genedata, GeneGo, Genomatica, Genomatix, Genstruct, Invitrogen, InforSense, Ingenuity Systems, Innetics, Insightful, InSilico discovery, Integrated Genomics, Jubilant Biosys, Lion Bioscience, MathWorks, Medicel Ltd, Microsoft, Numerica technology, Ocimum Biosolutions, Oracle, Physiomics, Premier Biosoft, Protein Lounge, SoftBerry, Spotfire, Stratagene, Teranode Corp, Wolfram Research


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