If the United States' Human Cloning Prohibition Act of 2003 (H.R. 534) becomes law, American researchers practicing any form of cloning could face up to ten years in prison and a minimum $1 million fine. The bill criminalizes a research procedure, called somatic cell nuclear transfer, that involves removing the DNA from a fertilized egg and replacing it with the DNA of a body (soma) cell. While the procedure could theoretically be used to clone a human being, used therapeutically its great promise lies in yielding a renewable source of stem cells to repair and regenerate tissue damaged by disease or injury. Embryonic stem cells appear most suited to this task, but some researchers are finding that adult stem cells could perform similar duties in certain tissues. And adult stem cells, it appears, are responsive to genetic manipulation. H.R. 534 does not threaten researchers working with adult stem cells.The precise origin of adult stem cells is unclear, though some propose that they are “set aside” during embryonic development and sequestered in mature tissue. These cells, which can make identical copies of themselves or give rise to specialized cells, serve primarily to replace damaged or injured cells. Skeletal muscle has a remarkable capacity to regenerate following exercise or injury and harbors two different types of adult stem cells to accomplish the job: satellite cells and adult stem cells that can be isolated as side population (SP) cells. Like embryonic stem cells, the adult cells commit to a certain fate once particular genes are activated.Pax7, plays a crucial role in directing the differentiation of these adult stem cells into skeletal muscle cells.It was thought that only satellite cells could mediate skeletal muscle regeneration until recently, when scientists found that adult stem cells not only participate in muscle tissue regeneration but also spawn satellite cells. A certain population of these stem cells, which are recognized by the cell surface proteins CD45 and Sca1 (stem cell antigen-1), is involved in normal muscle tissue repair, but is only triggered into the muscle cell development pathway by injury. The question then arises: what molecular factors turn these adult stem cells into muscle cells? Now Michael Rudnicki and colleagues have shown that one gene, Pax7 is required to turn adult stem cells into myogenic cells during regeneration. Here, the researchers worked with mouse models and in vitro experiments to investigate which cell populations Pax7 targets and how the gene initiates muscle cell formation in injured tissue. They show that CD45:Sca1 cells taken from regenerating muscle in mice lacking the Pax7 gene could not become muscle cells. And they show that by putting Pax7 back into CD45:Sca1 cells taken from uninjured muscle, they can generate a population of proliferating myoblasts that readily differentiate into muscle cells. When CD45:Sca1 cells engineered to express Pax7 proteins were injected into the muscles of mice lacking dystrophin (the protein defective in muscular dystrophy), the cells differentiated, forming dystrophin-expressing muscle cells in the defective muscle. This shows that engineered “donor cells” can differentiate in living tissue and help repair dystrophic muscle. When the researchers injected Pax7 (using a gene therapy virus) into the damaged muscle of mice lacking Pax7, they observed the production of muscle-forming cells that not only gave rise to differentiated muscle cells, but also aided in tissue repair.In previous studies, Rudnicki's group demonstrated that Pax7 as a key regulator of muscle cell differentiation in specific populations of adult stem cells during muscle tissue regeneration. If therapeutic strategies that activate Pax7 in adult stem cells can turn them into muscle cells, effectively replenishing injured or diseased muscle tissue, there's hope of reversing the debilitating effects of progressive muscle-wasting diseases. Though the clinical efficacy of such an approach will require intensive investigation, the results on these adult stem cells are encouraging—especially in this political climate.The researchers argue that these results “unequivocally establish”


Health professionals, says Herxheimer, must share their understanding of the benefits and harms of any treatment with patients and their families Everything that doctors and other health workers do involves communication about the benefits and harms to be expected from interventions—whether they are therapeutic, diagnostic, or prophylactic. As health-care professionals, we need to share our understanding and perceptions of benefits and harms with patients and their families as fully as we can. We also have to share them with other professionals. When we do so we have to remember that how we personally value particular benefits and harms may well differ from how another person values them.A clinician who recommends an intervention does so in the belief that its benefits outweigh the harms that it can cause. In most consultations there is little time in which to explain in detail what these benefits and harms are, or to find out what the patient thinks about them. Moreover, most clinicians are not trained or practised at describing and explaining benefits and harms clearly to patients, and much of the time they also lack important information about these aspects.The problems begin with the word “risk”. Very often people use it when they mean “harm”, and this causes ambiguities and confusion. The widely used expression “benefit/risk ratio” is meaningless—no such ratio exists. Before a decision is made to use an intervention, its benefits and harms must be weighed, ideally by the clinician and the patient together. Other advantages and disadvantages, such as convenience and cost, may also be relevant. This analysis requires use of the same dimensions for considering both benefits and harms. These dimensions have not been generally recognised or taught, though they seem obvious enough.In this context any benefit or harm has four dimensions (see sidebar). The clinician is expected to know or find out about the nature and probability of each benefit and harm, and how to maximise benefits and minimise harms. A great many clinicians do not meet this expectation, and often that is not their fault. But only patients can say how they regard the hoped for benefits and the possible harms, though they may need help to think clearly about them. Clinicians should identify how much the benefits matter to their patient—for example, are the benefits of taking a medicine or having an operation “worth the trouble”?—and whether a specific harm is particularly threatening or would be intolerable to that particular patient. People's fears, wishes, and priorities differ greatly and unpredictably.The deepening of the voice that occurs with long-term use of tamoxifen for breast cancer, and that is usually irreversible, is an example of a side effect that prescribers, manufacturers, and drug regulators have considered trivial and have largely ignored. While this side effect does not bother most women, for professional or keen amateur singers it is a disaster—it can rob them of what they enjoy most.A patient who is offered a treatment with serious implications needs time and encouragement to think, and to talk to other people, before making a decision. Three major issues are important in helping patients with decision-making: obtaining reliable information about benefits and harms, effectively communicating probabilities to the patient, and determining what to do to reverse or mitigate harmful effects when they occur.Innumeracy is very widespread. Many people cannot handle percentages, and most are unclear about the meaning of “relative risk”, “absolute risk”, “odds ratio”, and “number needed to treat”, including many clinicians who want to tell their patients about the likelihood of benefits or harms . Gigerennature, described by its quality, its intensity, and its time course .Its probability that it will occur.The importance to the person experiencing it.Its maximised, or the harm prevented or minimised.How the benefit can be www.cochrane.org). Nevertheless, there are huge gaps—we still lack reliable evidence about many important interventions.The effectiveness of an intervention  is most readily estimated from controlled clinical trials. With the rise of evidence-based medicine, there are now many more critical analyses, systematic reviews, and meta-analyses of the best evidence, as in the rapidly growing Cochrane Database of Systematic Reviews  can understand what to watch for and what to do if a problem arises. If not, or if examination or lab tests are necessary, then monitoring and follow-up by a nurse or doctor will need to be arranged.Here is a checklist of points for clinicians—and of course also drug regulators—to consider. (1) When an adverse effect occurs, should the dose be reduced, or the drug changed? (2) If reduced, by how much? (3) Is reducing the dose possible and practicable with the available preparations? (4) How and over what time should the effect of the change be observed and assessed? (5) Should the patient, as well as the clinician, keep the records of adverse effect(s) and their intensity and timing? Such notes can help both the patient and current and future doctors. Medication experiences can remain relevant for life. (6) Should an adverse effect be reported to a local or national adverse drug reaction register? .Effective communication about harms and risks is an essential component of care, and it requires learning, preparation, and rehearsal. The onus lies with professionals to persuade and to teach patients to play their part in coming to an informed decision about treatments.


Tuberculous meningitis (TBM) is a major global health problem, and it is sometimes difficult to perform a differential diagnosis of this disease from other diseases, particularly partially-treated pyogenic meningitis (PTPM). In an earlier study, we demonstrated the presence of a 30-kD protein antigen in cerebrospinal fluid (CSF) of TBM patients. We have also shown that lymphocytes from CSF of TBM patients respond differently to this antigen than do those from PTPM patients. The purpose of this study was to develop an assay that can discriminate between TBM and PTPM.We developed a cell enzyme-linked immunosorbant assay (Cell ELISA) to quantitatively measure production of antibodies against the 30-kD protein in B cells from CSF of TBM and PTPM patients.The cell ELISA yielded 92% (11/12) sensitivity and 92% (11/12) specificity for the differential diagnosis of TBM from PTPM.When induced with the 30-kD protein antigen, B cells derived from CSF of TBM patients respond to IgG production within 24 h while those derived from PTPM patients do not respond. Tuberculous meningitis (TBM) is an infection of the central nervous system (CNS) that is prevalent in both under-developed and developing countries. An increased incidence of TBM has occurred in recent years due to the growing number of people infected with human immunodeficiency virus (HIV). Diagnosis of TBM remains problematic despite many new, advanced diagnostic methods ,2. PreviClinical as well as CSF features are helpful for diagnosing TBM, but they cannot be used to differentiate TBM from other infectious and non-infectious disorders ,7. In paIn an earlier study, we reported the presence of a diagnostic 30-kD protein antigen in CSF of confirmed and suspected TBM patients . ImmunolCellular immune function is characterized by the existence of various types of lymphoid cells. As lymphocytes participate in the production of humoral immunity, they may respond to the 30-kD protein antigen in TBM and PTPM patients. We have developed a cell ELISA to study the response of B cells derived from CSF of TBM and PTPM cases following challenge with the 30-kD protein antigen. The purpose of the present study was to evaluate the antibody response to the 30-kD protein antigen in CSF of TBM and PTPM patients by cell ELISA and to determine whether this method may be used in differential diagnosis of TBM from PTPM.The Central India Institute of Medical Sciences (CIIMS), Nagpur, is a tertiary referral center. CSF was collected from patients who were suspected of having TBM or other infections before they received any treatment. For patients undergoing cranial surgery, analysis of CSF was performed if they were suspected of having meningitis. These patients were already on broad-spectrum antibiotics, such as third-generation cephalosporins and aminoglycosides.To establish a diagnosis of meningitis, 2–5 ml CSF was withdrawn from patients using a lumbar puncture. CSF was then subjected to routine biochemical analysis and pathological analysis including Gram staining, India ink staining, and AFB staining and culturing. One milliliter of CSF was used for the cell ELISA study, and 1 ml was used for detection of the 30-kD protein band by SDS-PAGE analysis in 12 randomly selected TBM and PTPM patients. Diagnosis of TBM and PTPM was based on the criteria described below.Presence of Mycobacterium tuberculosis in CSF by staining and/or culture, ORClinical meningitis with the following observations:A. Sub-acute or chronic fever with features of meningeal irritation such as headache, neck stiffness, and vomiting with or without other features of CNS involvementB. CSF findings showing increased proteins, decreased glucose (CSF:blood glucose ratio <0.5), and/or pleocytosis with lymphocytic predominanceC. Presence of the 30-kD protein band in CSF on SDS-PAGE analysisD. Good clinical response to antituberculous drugsNone of the 12 TBM patients had positive AFB staining.Presence of pathogenic bacteria in CSF by staining and/or culture, ORClinical meningitis with the following observations:A. Fever and/or signs of meningeal irritation , stroke, or head injury and who have received antibiotics), OR High fever and/or signs of meningeal irritation with or without CNS manifestations (patients who received broad-spectrum antibiotics)B. CSF findings showing increased proteins, decreased glucose (CSF:blood glucose ratio <0.2), and/or pleocytosis with a predominance of polymorphonuclear cells; CSF may resemble that of chronic meningitis patientsC. Absence of the 30-kD protein band in CSF on SDS-PAGE analysisD. Good clinical response to broad-spectrum antibioticsPeripheral blood samples from six healthy volunteers were also analyzed and included as negative controls.CSF samples obtained from confirmed and suspected TBM cases were subjected to SDS-PAGE. SDS-PAGE was performed with a vertical slab gel electrophoresis system  using the standard Laemmali method (10). A 4% stacking gel and 10% running gel were used. Electrophoresis was carried out at 250 volts/50 mAmps. Gels were developed by staining with Coomassie brilliant blue GR-250 and the protein profiles were then studied. Band size  was estimated using molecular weight markers  in a parallel lane.Following separation of proteins from CSF of confirmed TBM patients (AFB-positive) by SDS-PAGE, the 30-kD protein band was sliced out of the gel and pre-equilibrated in elution buffer  and then electro-eluted in a whole gel eluter system  for 90 min at 30 volts (11). The sample was then harvested from the unit and dialyzed against PBS and the protein content was measured using a Bio Lab KIT. Protein purity was checked using native PAGE and was then used to evaluate the antibody response of B cells derived from CSF of TBM and PTPM patients.One milliliter of CSF collected from TBM and PTPM patients was centrifuged at 400 rpm for approximately 20 min. The supernatant was then discarded and the cell pellet was washed two times with PBS and then diluted in RPMI 11640 tissue culture medium containing 10% fetal calf serum.Heparinized blood samples were obtained from six healthy volunteers. Peripheral blood mononuclear cells (PBMC) were isolated from heparinized blood by standard Ficoll-Hypaque gradient centrifugation. PBMCs were dissolved in PBS and centrifuged at 400 rpm for approximately 15–20 min, and the PBMCs were then diluted in RPMI 11640 tissue culture medium containing 10% fetal calf serum.2 in a carbon dioxide incubator. The following day, the plates were washed with PBS and horseradish peroxidase (HRP)-conjugated rabbit anti-human IgG  was then added to the plates. After a 2-hr incubation at 37°C, the plates were washed again with PBS and 100 μl tetramethylbenzidine (TMB)/H2O2 were added. The TMB/H2O2 served as a substrate for HRP. After a 15-min incubation, 100 μl stop solution (2.5 N sulphuric acid) were added and the plates were then read with an ELISA reader at 450 nm (12).Flat-bottomed, 96-well ELISA plates were coated with 10 μg 30-kD antigen/ml diluted in PBS (pH 7.2). Following overnight incubation, the plates were washed with PBS and then coated with 5% BSA-PBS for 4 h. The plates were then washed five times with PBS. Two-hundred μl of the cell preparation derived from CSF of patients with TBM or PTPM were then added to the wells and coated. Each sample was prepared in duplicate. Plates were maintained overnight at 37°C in 5% CODetailed clinical data for TBM and PTPM patients are presented in Table The ELISA absorbance values of IgG to the 30-kD protein antigen in CSF from TBM and PTPM patients are presented in Figure During the past decade, several conventional immunoassays including ELISA, dot immunobinding assays, immunoblot assays, and various molecular methods such as the polymerase chain reaction (PCR) have been reported as adjuncts in the diagnosis of TBM ,13-15. HM. tuberculosis and may be considered to be a diagnostic marker for TBM. In this study, we used this 30-kD protein antigen to evaluate the IgG antibody response of B cells derived from CSF of TBM and PTPM patients and from peripheral blood samples from six healthy volunteers. A cell ELISA was developed for the quantitative measurement of antibody production against the 30-kD protein antigen by these cells. Higher titers of IgG antibody production were observed in TBM patients compared to PTPM patients. The cells obtained from CSF of TBM patients gave an early response, presumably because they were already sensitized against the TBM antigen. However, when challenged with the 30-kD protein antigen, the cells obtained from PTPM patients and healthy volunteers gave a delayed response since they are not sensitized against this antigen. Therefore, an early response on this time scale is indicative of TBM.We previously used SDS-PAGE to demonstrate the presence of a 30-kD protein antigen in the CSF of TBM patients that is specific to M. tuberculosis (H37Rv strain) received from Colorado State University, Fort Collins USA (data not shown). The only limitation of this method is the time period (24–30 h) involved. However, the sensitivity of the test overcomes this drawback since it the only reported method that can discriminate TBM from PTPM.We have thus shown that cell ELISA is a sensitive technique for the differential diagnosis of TBM from PTPM. This method involves the demonstration of active antibody production by cells, particularly those derived from the affected site . PreviouThe sensitivity and specificity of IgG antibody in differential diagnosis of TBM from PTPM using the 30-kD protein antigen by cell ELISA was found to be 92% (11/12). We have also demonstrated that antibody production against the 30-kD protein antigen is higher in cells derived from CSF of TBM patients compared to PTPM patients.Various methods have been developed in our laboratory that yield a high specificity and sensitivity for diagnosis of TBM, but a small number of false positive results have been observed in pyogenic meningitis cases, particularly PTPM cases ,18. The The cell ELISA method for diagnosing TBM is based on the assumption that local synthesis of humoral antibodies against MTB antigen occurs. Various researchers have shown that CSF-derived cells have a significantly higher proliferation response to purified protein derivative (PPD) in patients with TBM, which is suggestive of an intrathecal immune response ,19.Our data can be summarized by the following observations: first, cell ELISA is a useful method for differentiating TBM from PTPM using the 30-kD protein antigen; second, the method of challenging B cells from CSF of suspected TBM patients with the 30-kD protein antigen can be helpful in confirming a TBM diagnosis; and third, the cell ELISA allows several samples to be analyzed simultaneously. Hence, the cell ELISA should be a very useful tool for the differential diagnosis of TBM from PTPM.M. tuberculosis. We have demonstrated that by using cell ELISA, we can differentiate TBM patients from PTPM patients, which should be helpful for diagnosing TBM. Additionally our results suggest that lymphocytes from CSF of TBM patients when challenged with 30 kD protein give a quick response by producing IgG antibodies when compared with that of PTPM and healthy volunteers. This may be because lymphocytes from TBM patients have already been exposed to 30 kD MTB antigens.The presence of a 30-kD protein antigen in CSF of TBM patients indicates that this protein carries the candidate marker antigen which is specific to The authors declare that they have no competing interests.RSK carried out the study design, data collection, statistical analysis, data interpretation, literature search, and manuscript preparation; NPA, RPK, and RMS assisted in data analysis collection; NHC assisted in data collection, statistical analysis, and data interpretation; HJP participated in the preparation of the manuscript, data interpretation, and study design; GMT provided assistance in preparation of the manuscript, data interpretation, study design, and funds collection; and HFD supervised the study design, statistical analysis, data interpretation, manuscript preparation, and literature search.The pre-publication history for this paper can be accessed here:


Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In recent times, improvement of existing progressing programs and implementation of new iterative algorithms have made a significant change in this field.We report an alignment algorithm that combines progressive dynamic algorithm, local substructure alignment and iterative refinement to achieve an improved, user-interactive tool. Large-scale benchmarking studies show that this FMALIGN server produces alignments that, aside from preservation of functional and structural conservation, have accuracy comparable to other popular multiple alignment programs.The FMALIGN server allows the user to fix conserved regions in equivalent position in the alignment thereby reducing the chance of global misalignment to a great extent. FMALIGN is available at  The advent of large genome projects has led to an explosion of sequence data in public databases. Analysis of protein families, understanding their evolutionary trends and detection of remote homologues are now the primary objectives. Genome annotation and analysis tools like fold prediction, homology modelling, protein-ligand docking and clustering algorithms rely heavily on accurate multiple alignments to provide a genome-wide perspective.The most popular approach for multiple sequence alignment has been the progressive alignment method . A multiIn this paper, we present an alignment algorithm that combines the properties of both progressive alignment methods and iterative refinement algorithms. This algorithm offers the user the selective advantage of guiding the course of alignment by simultaneous inputs of multiple conserved motif regions that in turn guarantees retention of structure/function in the final alignment. FMALIGN is an alignment server that provides the user to obtain a control over the alignment by providing important conserved regions as input to the alignment program to achieve a more structurally relevant and functionally useful alignment of protein sequences. It employs the sequential branching method to identify the closest pair of sequences and subsequently includes the next closest sequences to generate a guided tree using UPGMA , which iThe algorithm of FMALIGN (Fixed Motif ALIGNment) program combines three main criteria: (a) Progressive global alignment method, (b) substructure  conserved region fixation and (c) iterative refinement of alignment with identification of more conserved regions. The procedure involves three steps: (i) identification and fixing of the specified sequential conserved regions. This alignment method requires specific regions of the sequences to be aligned as anchor and these anchors are generally meant for sequentially conserved parts which do not undergo many changes. (ii) derivation of the progressive multiple sequence alignment guided by the tree. During this step, excluding the fixed anchored regions, the rest of the sequences are divided into several sub-segments that are aligned employing a dynamic alignment algorithm in a sequential order from N to C-terminus. The phylogenetic guide tree has been derived using Unweighted Pair Group Method with Arithmetic Mean (UPGMA)  which isFMALIGN server can accept amino acid patterns for multiple motifs provided by the user. It also provides option to the user to search motifs within their sequences using FINDMOTIF routine or to obtain them for the alignment by providing a link to SMoS , a strucTo assess the performance of FMALIGN in comparison to other programs, Sum-of-Pair-score (SPS) and Column-Score (CS) alignment scoring scheme  are applFMALIGN derived alignments retain high degree of conservation in secondary structures. Six members from the globin family were selected comprising a wide range of sequence identity between them (7% to 61%). Conserved regions for six aligned globin sequences were identified by the FINDMOTIF routine starting from CLUSTALX  alignmenIn order to evaluate the FMALIGN server, the results have been compared with 10 other alignment programs and objective criteria were employed to assess the quality of an alignment. We selected the BAliBASE benchmark alignment database  to compaReference 1 alignments consist of a small number of equidistant sequences of similar length, i.e. the percent residue identity (% ID) between any two sequences is within a specified range and no large extensions or insertions have been introduced.Reference 2 contains alignments of a family of closely related sequences with >25% ID, plus up to three 'orphan' sequences . It is designed to evaluate program accuracy according to two criteria: (i) the stability of the family alignment when orphans are introduced into the sequence set and (ii)the quality of the alignment of the orphan sequences.Reference 3 checks the ability of the programs to correctly align equidistant divergent families into a single alignment. The reference alignments consist of up to four families, with <25% ID between any two sequences from different families.Reference 4 and 5 contain alignments of upto 20 sequences including N/C-terminal extensions (upto 400 residues) and insertions (upto 100 residues), respectively.This dataset is designed to study the effect of sequence length and percentage identity on the performance of the alignment program and provides a basis for the remaining tests. The overall performance of FMALIGN server for this dataset is comparable to the two best performing alignment programs, like PRRP  and CLUSIt is possible to assess the performance of the methods to align divergent 'orphan' sequences (10–20% ID with the family and between orphans) with a family of highly related (>25% ID) sequences using this data set. It is also interesting to observe the disruption of the family alignment due to the introduction of orphans. Figure This allows the assessment of the programs to correctly align approximately equidistant divergent families (<20% ID) composed of highly related sequences (>25% ID) into a single multiple alignment. Figure This dataset includes large N/C-terminal extensions to investigate whether the programs are capable of aligning the core blocks flanking the extensions. No large internal insertions are introduced at this stage. Mostly local alignment strategies out-perform the global methods. PILEUP  is the only program based on a global alignment method which does reasonably well compared to other global methods. Performance of FMALIGN is comparable to the best three methods  are calculated using a standard program kindly provided by the authors of BAliBASE. The inter-motif regions are aligned in FMALIGN by normal progressive alignment using standard substitution matrices like BLOSUM62. The gap penalties used in this version of FMALIGN are all maintained according to standard multiple alignment parameters. Benchmarking at the superfamily level has also been done utilizing both structural and sequential conserved regions. The dataset is wide enough to include proteins from different structural classes and of different length. The average sequence identity for this dataset was less than 30% since the proteins are related at the superfamily level. The performance of FMALIGN has been tested against one of the best performing multiple sequence alignment (T-Coffee) as well as structure based alignment tool (COMPARER). Studies on large and different datasets revealed an overall better performance of FMALIGN server for all categories in BAliBASE benchmarking database. It works especially well at lower sequence identity range, such as superfamily level, where no two proteins are more than 25% identical to each other in comparison to other popular methods like CLUSTALX and T-Coffee. It is well-known that automatic multiple sequence alignments at poor sequence identity are often subject to careful manual validations and improvements to avoid offsets of critical functionally important residues. FMALIGN can sensitively address this issue to avoid manual intervention subsequent to final alignment. FMALIGN-derived alignments also show a high conservation of secondary structural elements and provide better alignments for comparative modelling. The implementation of this alignment algorithm can be used to include new members into an existing protein superfamily with the help of motif regions that provide a reliable approach to connect protein sequences with their structural homologues within a particular superfamily. FMALIGN is available via the following URL S.C. had carried out the benchmarking, was involved in the development of the server and has written the first draft of the manuscript. N.B. had written the initial part of the code and P.A. has written the latter part of the code and developed a web server. R.S. had initiated the idea, was involved in discussions and in the critical reading of the manuscript.Fixed Motif ALIGNmentFMALIGN SPS Sum-of-Pairs Score


Personal Digital Assistants (PDAS) are rapidly becoming popular tools in the assistance of managing hospitalized patients, but little is known about how often expert recommendations are available for the treatment of infectious diseases in hospitalized patients.To determine how often PDAs could provide expert recommendations for the management of infectious diseases in patients admitted to a general medicine teaching service.Prospective observational cohort studyInternal medicine resident teaching service at an urban hospital in Dayton, Ohio212 patients (out of 883 patients screened) were identified with possible infectious etiologies as the cause for admission to the hospital.Patients were screened prospectively from July 2002 until October 2002 for infectious conditions as the cause of their admissions. 5 PDA programs were assessed in October 2002 to see if treatment recommendations were available for managing these patients. The programs were then reassessed in January 2004 to evaluate how the latest editions of the software would perform under the same context as the previous year.PDAs provided treatment recommendations in at least one of the programs for 100% of the patients admitted over the 4 month period in the 2004 evaluation. Each of the programs reviewed improved from 2002 to 2004, with five of the six programs offering treatment recommendations for over 90% of patients in the study.Current PDA software provides expert recommendations for a great majority of general internal medicine patients presenting to the hospital with infectious conditions. PDAs  are becoming widely used in medicine. A survey done by the America College of Physician predicted that 67% of physicians would be using PDAs by the end of 2002 . These dOne medical specialty which has focused on PDA's application in medicine is infectious diseases . There aMiami Valley Hospital is an 827 bed secondary and tertiary referral center, in Dayton, Ohio. It is an urban hospital that averages over three-thousand patient admissions per month. The internal medicine resident teaching service consists of two teams, each team with 2 senior residents and 2 interns who are supervised by an attending physician. There is a senior resident and intern on call in the hospital at all times. Patients were eligible to be admitted to resident's service if they were established within the Medical-Surgical Health Center of Miami Valley Hospital, if they were uninsured or if they had insurance but were without a local physician (a.k.a. private unattached patients). The general medicine teaching service averages approximately eight admissions per twenty-four hour period.Mandell, Douglass and Bennett's Principles and Practice of Infectious Disease (PPID) (8) (Table The patients were screened prospectively over a four month period (July 2002 through October 2002). The admitting senior resident prospectively recorded the chief complaint and initial differential diagnosis for each patient. One of us (SDB), as the chief resident during these months, gathered the data during morning report. Patients were considered appropriate for the study if they had a leading diagnosis or active alternatives that suggested an infectious disease at the time of admission. Cases selected were then assigned categories based on the "major clinical syndromes" from 8) Table . Syndrom (SG) [ (JHABx) [) (5MID) [) (5MCC) [) (PMID) [) (QID) [A Sony Clie T615C  was the device used to access the software, but all programs evaluated were also available in the Pocket PC format . Five PDA programs were initially searched to determine if expert recommendations were available. Software was chosen based on its availability to both the Palm OS and the Pocket PC and at the time of the initial software evaluation were the primary infectious disease programs available (since 2002 numerous other titles have been released to address infectious diseases). The PDA programs included: Sanford's Guide to Antimicrobial Therapy  (SG) , John's ) (5MID) , 5-Minut) (5MCC) , and Poc) (PMID) . The ini[) (QID)  was alsoA minimum of three attempts were used to locate conditions within each program. Searching was done using either the disease name or clinical problem that had led to the patient's admission. Synonyms were used when appropriate to increase the possibility of locating a condition within each program . Programs that were organized according to organ system  were searched within the appropriate organ system, while programs that listed diagnoses alphabetically were searched accordingly. Expert recommendations were considered to be present and thus counted as a positive if the software had treatment recommendations present, whether related to antibiotic decision or "supportive care."In order to determine the change in software capabilities over a 14 month period, the same patient data set was used to assess software programs in January of 2004. A comparison of the programs was then performed comparing the availability of expert recommendations.The data was collected by a single physician (SDB) and then validated independently by a second physician (TEH). The data was analyzed using descriptive statistics with simple frequencies and the confidence intervals were calculated according to standard formulas.Over the four month period, from July through October of 2002, there were 883 patients admitted to the resident service, of whom 212 had syndromes that were suspected on admission to be infectious in etiology (202 of which could be assigned to the pre-defined categories)  familiar with both the PDA and the aforementioned software looking for management recommendations. This usually included antibiotic recommendations and occasionally recommendations regarding further evaluation. The possibility that we did not find recommendations which were indeed available seems unlikely because of the previously mentioned points as well as a systematic approach using multiple synonyms. Furthermore, the data was independently reviewed by a second physician and no inconsistencies were identified.A third potential limitation is that of reproducibility. Since searching was done by an experienced user, searching errors would be more likely with less experienced user(s). Many of the programs require persistent use to learn the nuances and style of the programs and how to best access information. Therefore, in order for others to duplicate our results, users will need to develop some profiency with the software and be willing to perform searches using multiple synonyms.Lastly, our study may have limits to its applicability. Our patients were admitted to an inpatient general internal medicine teaching service at an urban hospital in the United States. These data probably apply to similar inpatient services elsewhere within North America, but may not apply to either other specialty services  or hospitals in other parts of the world.While the limitations mentioned above apply to this study, they can also be expanded to include limitations in the software. No physician can access a software program for the first time and be expected to take full advantage of the recommendations available. It takes time and effort to maximize the clinical utility that is available on the PDA, which unfortunately, many clinicians do not accomplish. This paper was focused on treatment recommendations and did not evaluate the ability of the individual programs to assist with diagnosis. The diagnostic data and information other than treatment recommendations varies from program to program. This could be a topic for future research or may be available in other formats such as software reviews in PDA magazines.This study demonstrates that these infectious disease programs have improved over time table . The reaDespite these potential limitations, our data suggests that PDAs provide expert recommendations for the majority of infectious clinical conditions encountered in practice by non-infectious disease general physicians. Since a majority of patients admitted to the hospital receive care from clinicians who are not specialists in infectious diseases, PDA's have the potential to have an impact on the quality of initial care by guiding not only the choice of antibiotics but also diagnostic testing and when to involve infectious disease specialists. Further research is needed to examine the efficiency of use; evidence supporting the recommendations, and the clinical impact of the use of these resources.


Norwalk virus and related noroviruses cause a short but unpleasant illness known variously as stomach flu, viral gastroenteritis, and winter-vomiting disease. They are the major causative agent of epidemic gastroenteritis worldwide. Norwalk virus was first described in 1968 when teachers and pupils at a school in Norwalk, Ohio, succumbed to acute gastroenteritis. The causative agent was identified in 1972, and since then, many other Norwalk-like viruses have been recognized. Noroviruses are usually picked up from contaminated food or water but can also be spread by person-to-person contact. There are no cures for norovirus infections and no vaccines. Worse still, noroviruses survive freezing, heating to 60 °C, and the amounts of chlorine added to public water supplies. Little surprise, then, that around 23 million Americans get a norovirus infection annually.To reduce this disease burden, better prevention and control strategies for noroviruses are urgently needed. However, the development of such strategies has been hampered by the inability of scientists to find a way to grow noroviruses in cultured cells. Like all viruses, noroviruses replicate inside host cells, and they are choosy about which cells they will grow in. The discovery by Herbert Virgin and colleagues that a mouse norovirus can be grown inside dendritic cells and macrophages, two types of immune system cells, opens the door to a better understanding of norovirus biology and better disease control strategies.In 2003, Virgin's team discovered MNV-1, a mouse norovirus, and reported that the innate arm of the immune system (as opposed to the adaptive arm) was important in combating MNV-1 infection. The adaptive immune system involves cells that respond to a disease-causing bacterium or virus by making “adaptations” to their genomes that result in specific anti-pathogen responses. The innate immune system, on the other hand, contains cells that recognize general features of pathogens and rapidly attack them when they enter our bodies. It is our first line of defense against bacteria and viruses, and Virgin and coworkers found that mice with defective innate immune systems were particularly sensitive to MNV-1.Now, by examining tissues taken from mice infected with MNV-1 infection, the researchers show that in live animals the virus infects macrophages (cells that engulf and kill pathogens) and dendritic cells (cells that display pathogen proteins to the adaptive immune system). This observation provided the clue needed to grow a norovirus in cultured cells for the first time: when the researchers took uninfected dendritic cells or macrophages out of animals with defective innate immune systems and grew them in the laboratory, they found that MNV-1 could replicate within these cells. The researchers then used physical and biochemical techniques to verify that what they were growing in culture was indeed MNV-1 and also determined the cellular factors that control MNV-1 growth in culture, thereby confirming that the innate immune system is important for combating norovirus infection. Analysis of the sequence of a virus attenuated by growth in vitro identified an important part of the viral capsid that plays a role in MNV-1 virulence, potentially opening up an avenue to vaccination with attenuated viruses.The researchers speculate that dendritic cells in the gut may provide the route by which noroviruses gain access to cells deep within the lining of our guts and thus cause disease. The next step will be to see whether human noroviruses can also grow in macrophages and dendritic cells. If they do, researchers should at last be able to elucidate the lifecycle of human noroviruses and identify the cellular factors needed for their replication. Hopefully, this new knowledge will swiftly suggest ways to prevent and control the human diseases caused by noroviruses.


Plasmodium falciparum sporozoites, these antibodies are predominantly directed to the major repetitive epitope (Asn-Pro-Asn-Ala)n, (NPNA)n. In individuals immunized by the bites of irradiated Anopheles mosquitoes carrying P. falciparum sporozoites in their salivary glands, the anti-repeat response dominates and is thought by many to play a role in protective immunity.The circumsporozoite surface protein is the primary target of human antibodies against P. falciparum infected Anopheles stephensi was recapitulated in a phage display library. Following affinity based selection against (NPNA)3 antibody fragments that recognized the PfCSP repeat epitope were rescued.The antibody repertoire from a protected individual immunized by the bites of irradiated H3 and VκI families for heavy and light chain respectively with moderate affinity for the ligand.Analysis of selected antibody fragments implied the response was restricted to a single antibody fragment consisting of VH/VL pairing (PfNPNA-1). The affinity for the ligand was in the μM range. If anti-repeat antibodies are involved in the protective immunity elicited by exposure to radiation attenuated P. falciparum sporozoites, then high circulating levels of antibodies against the repeat region may be more important than intrinsic high affinity for protection. The ability to attain and sustain high levels of anti-(NPNA)n will be one of the key determinants of efficacy for a vaccine that relies upon anti-PfCSP repeat antibodies as the primary mechanism of protective immunity against P. falciparum.The dissection of the protective antibody response against the repeat epitope revealed that the response was apparently restricted to a single V Plasmodium sporozoites, the infective stage of the malaria parasite, confers protective immunity 2, R32tet32 [4 epitope contained within the hepatitis B virus nucleocapsid (C75CS2) [3C-BSA conjugate is probably due to the multivalent array of the capture ligand (i.e. multiple peptides coupled per BSA molecule), favouring more efficient retention of the antibody.Analysis of the fine specificity of the antibody PfNPNA-1 revealed weak binding to the repeat based [NVDP(NANP)R32tet32 , whilst C75CS2)  was stroCS2  was 6) sequences were subsequently transferred to the phage display vector. Panning with a functionally enhanced library resulted in very efficient enrichment and recovery. Previously it had been demonstrated that manipulating the conditions of phage production results in modulation of the density of antibody display on phage [The recombinant antibody library construction differed from conventional antibody phage display library assembly -13, a pron phage . The phaon phage  prior toP. falciparum sporozoite antibody response by combinatorial antibody library phage display would permit individual selected antibodies to be evaluated for protective potential and the information generated could be used in vaccine design. In particular, attention was focused on antibodies against the structural motif (NPNA)n. Despite using two different strategies for the elution of repeat region peptide specific antibodies (acid and peptide specific) it would appear that the anti-structural repeat response by this protected individual is restricted to a single VH/VL combination observed in the panel of selected phage (n = 25). Sequencing of randomly picked phage prior to panning revealed that a diverse range of VH and VL families were represented in the library as shown in Table H/VL was not represented in the sampling and was only detected after enrichment.Induction of protective immunity against sporozoite challenge by exposure to radiation attenuated malaria sporozoite has been demonstrated in humans ,7,22. PrP. falciparum sporozoites indicates that they recognize the repeat epitope(s) with equivalent affinities [H and VL genes suggesting antigen driven affinity maturation. Based on these observations, PfNPNA-1 may be a good candidate to develop and evaluate as a protective antibody.Comparison of the monovalent PfNPNA-1 molecule with the conventional bivalent murine mAb, such as the in vitro inhibitory 2A10 against finities . The seqP. falciparum sporozoites under natural conditions in the field, immunization with irradiated P. falciparum sporozoites induces in general higher levels of antibodies against the PfCSP repeats, and does induce sterile protective immunity [P. falciparum sporozoites. The generally accepted explanation for the lack of protection in the one volunteer is that the volunteer did not receive an adequate immunizing dose of irradiated sporozoites . Howeve bites )had signve bites ) H and VL domains for further in vitro and in vivo evaluation. The use of a human monoclonal antibody as a preventive measure against P. falciparum malaria, would be independent of factors which hinder active vaccination, such as adjuvant effects, the requirement to be effectively presented in a diverse range of human leukocyte class I and II molecules, and immunlogical antagonism [P. falciparum isolate that does not contain the (NPNA)n repeats on the PfCSP [P. falciparum. If this restricted antibody response to the repeat epitope plays a role in preventing P. falciparum infection, PfNPNA-1 may be a useful prophylactic agent. Moreover, if PfNPNA-1 is shown to be protective in passive immunization in humans or monkeys as previously demonstrated for anti-P. vivax CSP murine mAb, NVS3 [Efforts are being directed towards producing a fully human IgG based on the PfNPNA-1 Vtagonism ,44. In phe PfCSP , and theAb, NVS3 , it woulH/VL pairing, designated PfNPNA-1 encoded by VH3 and Vκ I families (with evidence of somatic mutations). The affinity for the ligand was in the μM range, which in the context of a whole antibody may be more than sufficient for retention on a polyvalent surface such as the P. falciparum CSP. It is speculated that the induction and the maintenance of high circulating levels of antibodies against the structural PfCSP repeat may be more important than intrinsic high affinity for the ligand for protection against P. falciparum infection. The absence of high affinity anti-repeat antibodies is in concordance with the expected response against a multivalent antigen (i.e. sporozoite surface). Under physiological conditions a whole IgG antibody and a multimeric ligand result in bivalent binding. Such complexes can have avidities estimated to be approaching the product of two independent monomeric interactions. In this case, the 1 × 10-6M monovalent affinity of PfNPNA-1 may approach a theoretical higher avidity (1 × 10-12 M) in the context of a whole antibody. This implies that further affinity maturation either in vivo or in vitro may not necessarily increase physiological effectiveness of the whole IgG antibody. Public health officials have acknowledged the urgency for development of an effective anti-P. falciparum malaria vaccine. One of the key criteria of such a putative vaccine may be the induction and maintenance of high levels of anti-(NPNA)n antibodies. The fully human PfNPNA-1 IgG could be used as a positive control in evaluating sera from immunized donors, or possibly be developed as a prophylactic agent that could be used alone or in combination with various vaccination strategies. One immediate hurdle for the development of such an antibody as a prophylactic would be the anticipated high cost of commercial manufacture in mammalian cells. However, advances in alternative antibody production technology may one day provide some more cost effective solutions [Over the past 25 years the antibody response against the PfCSP repeat epitope has been pursued as a target for active vaccination, with encouraging results . Our attolutions ,49.P. falciparum infected Anopheles mosquitoes, it should be possible to further dissect the antibody response against "other" sporozoite antigens [With the availability of an antibody phage display library constructed from a protected individual immunized via bites of irradiated antigens .JAC was the postdoctoral researcher on this project. WOR and SLH co-investigators. ASK was the PI and recipient of the Department of Army award. All authors read and approved the final manuscriptThe views and opinions expressed herein are those of the author and do not purport to reflect those of the U.S. Navy or the Department of Defense, Sanaria Inc or Avanir Pharmaceuticals Inc.


Autocoding (or automatic concept indexing) occurs when a software program extracts terms contained within text and maps them to a standard list of concepts contained in a nomenclature. The purpose of autocoding is to provide a way of organizing large documents by the concepts represented in the text. Because textual data accumulates rapidly in biomedical institutions, the computational methods used to autocode text must be very fast. The purpose of this paper is to describe the doublet method, a new algorithm for very fast autocoding.An autocoder was written that transforms plain-text into intercalated word doublets . Each doublet is checked against an index of doublets extracted from a standard nomenclature. Matching doublets are assigned a numeric code specific for each doublet found in the nomenclature. Text doublets that do not match the index of doublets extracted from the nomenclature are not part of valid nomenclature terms. Runs of matching doublets from text are concatenated and matched against nomenclature terms .The doublet autocoder was compared for speed and performance against a previously published phrase autocoder. Both autocoders are Perl scripts, and both autocoders used an identical text (a 170+ Megabyte collection of abstracts collected through a PubMed search) and the same nomenclature . In side-by-side comparison on the same computer, the doublet method autocoder was 8.4 times faster than the phrase autocoder . The doublet method codes 0.8 Megabytes of text per second on a desktop computer with a 1.6 GHz processor. In addition, the doublet autocoder successfully matched terms that were missed by the phrase autocoder, while the phrase autocoder found no terms that were missed by the doublet autocoder.The doublet method of autocoding is a novel algorithm for rapid text autocoding. The method will work with any nomenclature and will parse any ascii plain-text. An implementation of the algorithm in Perl is provided with this article. The algorithm, the Perl implementation, the neoplasm nomenclature, and Perl itself, are all open source materials. Autocoding is a specialized form of machine translation. The general idea behind machine translation is that computers have the patience, stamina and speed to quickly parse through gigabytes of text, matching text terms with equivalent terms from an external vocabulary. Human translators often scoff at the output of machine translators, noting the high rate of comical errors. An often cited, perhaps apocryphal, example of poor machine translation is the English to Russian transformation of "out of sight, out of mind" to the Russian equivalent of "invisible idiot."Despite limitations, machine translation is the only way to transform gigabytes and terabytes of text. As long as clinicians, pathologists, radiologists, nurses, and scientists continue to type messages, reports, manuscripts and notes into electronic documents, we will need computers to parse and organize the resulting text.One of the many problems in the field of machine translation is that expressions (multi-word terms) convey ideas that transcend the meanings of the individual words in the expression. Consider the following sentence:"The ciliary body produces aqueous humor."The example sentence has unambiguous meaning to anatomists, but each word in the sentence can have many different meanings. "Ciliary" is a common medical word, and usually refers to the action of cilia. Cilia are found throughout the respiratory and GI tract and have an important role locomoting particulate matter. The word "body" almost always refers to the human body. The term "ciliary body" should (but does not) refer to the action of cilia that move human bodies from place to place. The word "aqueous" always refers to water. Humor relates to something being funny. The term "aqueous humor" should (but does not) relate to something that is funny by virtue of its use of water (as in squirting someone in the face with a trick flower). Actually, "ciliary body" and "aqueous humor" are each examples of medical doublets whose meanings are specific and contextually constant . Furthermore, the meanings of the doublets cannot be reliably determined from the individual words that constitute the doublet, because the individual words have several different meanings. Basically, you either know the correct meaning of the doublet, or you don't.Any sentence can be examined by parsing it into an array of intercalated doublets:"The ciliary, ciliary body, body produces, produces aqueous, aqueous humor."The important concepts in the sentence are contained in two doublets (ciliary body and aqueous humor). A nomenclature containing these doublets would allow us to extract and index these two medical concepts. A nomenclature consisting of single words might miss the contextual meaning of the doublets.What if the term were larger than a doublet? Consider the tumor "orbital alveolar rhabdomyosarcoma." The individual words can be misleading. This orbital tumor is not from outer space, and the alveolar tumor is not from the lung. The 3-word term describes a sarcoma arising from the orbit of the eye that has a morphology characterized by tiny spaces of a size and shape as may occur in glands . The term "orbital alveolar rhabdomyosarcoma" can be parsed as "orbital alveolar, alveolar rhabdomyosarcoma" Why is this any better than parsing the term into individual words, as in "orbital, alveolar, rhabdomyosarcoma"? The doublets, unlike the single words, are highly specific terms that are unlikely to occur in association with more than a few specific concepts.Very few medical terms are single words. In "The developmental lineage classification and taxonomy of neoplasms" there are 102,271 unique terms for neoplasms. All but 252 of these terms are multi-word terms see  see Add[1]. Of tMedical autocoding can be considered a specialized form of machine translation. Medical autocoders transform text into an index of coded nomenclature terms . Several innovative approaches to autocoding have used the higher information content of multiword terms  to match terms in text with terms in vocabularies or to enhance the content of vocabularies by identifying n-grams occurring in text that qualify as new nomenclature terms -4. UnlikThe purpose of this paper is to describe a novel algorithm for autocoding based on finding runs of word-doublets that match a list of doublets extracted from a medical nomenclature. Using the same hardware and the same nomenclature, the speed and accuracy of the doublet method can be compared with another fast lexical parser.The nomenclature used is neocl.xml, previously described by the author and currently designated as "The developmental lineage classification and taxonomy of neoplasms". In the An example of the variety of synonyms encountered for a single tumor is shown for "adenocarcinoma of the colon." There are 44 synonyms listed in the taxonomy. These are: adenoca arising from colon, adenoca arising in colon, adenoca of colon, adenocarcinoma arising from colon, adenocarcinoma arising from large intestine, adenocarcinoma arising from the colon, adenocarcinoma arising from the large intestine, adenocarcinoma arising in colon, adenocarcinoma arising in large intestine, adenocarcinoma arising in the colon, adenocarcinoma arising in the large intestine, adenocarcinoma of colon, adenocarcinoma of large intestine, ca arising from colon, ca arising in colon, ca of colon, cancer arising from colon, cancer arising in colon, cancer of colon, carcinoma arising from colon, carcinoma arising in colon, carcinoma of colon, colon adenoca, colon adenocarcinoma, colon ca, colon cancer, colon cancers, colon carcinoma, colon carcinomas, colon with adenoca, colon with adenocarcinoma, colon with ca, colon with cancer, colon with carcinoma, colonic adenoca, colonic adenocarcinoma, colonic adenocarcinomas, colonic ca, colonic cancer, colonic cancers, colonic carcinoma, colonic carcinomas, large intestine adenocarcinoma, large intestine with adenocarcinoma.The input file was created by a PubMed query on "pathology [ad] AND neoplasm [all]", at the U.S. government website . The queThe doublet autocoder is supplied as an open source Perl script (doubcode.pl) with this manuscript see . Perl itThe algorithm used by the doublet autocoder is described:1. Each phrase (term) in the nomenclature (neocl.xml) is converted into intercalated doublets, and each doublet is assigned a consecutive number.2. Each nomenclature phrase is assigned the concatenated list of numbers that represent the ordered doublets composing the phrase.3. Every text record (pubmed abstract in this case) is split into an array consisting of the consecutive words in the text record.4. The text array is parsed as intercalated doublets. Intercalated doublets from the text that match doublets found anywhere in the nomenclature are assigned their numeric values (from the doublet index created for the nomenclature). Runs of consecutive doublets from the text that match doublets from the nomenclature are built into concatenated strings of doublet values. The occurrence of a text doublet that does not match any doublet in the nomenclature cannot possibly be part of a nomenclature term. Such text doublets serve as "stop" doublets between candidate runs of text doublets that match nomenclature doublets.5. The runs of matching doublets are tested to see if they match any of the runs of doublets that compose nomenclature terms or if they contain any subsumed terms that match nomenclature terms.6. The array of doublet runs extracted from the text that match nomenclature terms are cached in an external file.The phrase autocoding script, phrase.pl is included as supplementary file with this article see . The scrThe speed of both coders was compared using a 170+ Megabyte text. The doublet method coded the entire text in 211 seconds compared with 1,766 seconds required for the phrase method. Therefore the doublet method coded 8.4 times faster than the phrase method. The text coding rate for the doublet method is 0.8 Megabytes per second on a desktop computer with a modest 1.6 GHz Pentium processor.Both the phrase method and the doublet method coders used the same Programming Language, the same nomenclature, and the same data structure for the nomenclature (a simple associative array). Both coders grab sequentially occurring chunks of text, each chunk delimited by a double-newline delimiter  and place the grabbed text chunk into a temporary scalar variables.The difference between the two coders occurs when the chunks of text are parsed. The phrase coder takes the text and creates an array of every ordered combination of 1,2,3,4 and 5-word phrases contained in the record. This number of elements in the phrase array is about 5 times larger than the number of words in the record. The doublet coder parses the record into the set of all ordered doublet terms. This number of elements in the array of doublets is about the same as the number of words in the record. The phrase coder must try to match about 5 times as many terms as the doublet coder. Also, the phrase coder tries to match each phrase in the record array against the entire nomenclature. The doublet coder tries to match each doublet encountered in the input text against the collection of doublet terms extracted from the nomenclature. Because doublets of text, unlike individual words, tend to have unique meanings, only a small subset of the doublets encountered in the input text will match the set of doublets extracted from the nomenclature. Text doublets that do not match any doublets in the nomenclature are "skipped." Text doublets that match doublets from the nomenclature are concatenated to consecutive matching doublets until a non-matching doublet is encountered. The length of matching doublets sets the length of the candidate term. The algorithmic strength of the doublet method is that it eliminates the need to create and match [against a nomenclature] an array of all possible phrases of all possible lengths found in a textual record.The output of the doublet method and phrase method autocoders are provided as supplemental files with this manuscript see  see Add. The anaThe two autocoder methods parsed a text exceeding 170 megabytes in length. The doublet method coded 4807 different [sometimes called unique] terms. The total number of matching term encountered (which includes replicate matches of terms within a record) by the doublet method is 467,391 terms. The phrase method coded 4557 different terms. There were 250 terms that the doublet method matched and the phrase method missed. There were zero terms that the phrase method matched and the doublet method missed.The improved performance of the doublet coder is accounted for by its ability to match terms of any length, while the phrase coder is limited to match terms that are no more than 5 words in length. Because the phrase coder parses chunks of input text into all allowed phrase size combinations, the performance of the phrase coder is slowed dramatically when the allowed phrase length is large. For instance, if the theoretical maximum phrase size were permitted for a text chunk 100 words in length, the phrase parser would need to create an array of a size equal to 100 × 100 or 10,000 phrases, matching each phrase against nomenclature. If the phrase size were restricted to 5 words, then the phrase parser would only need to create a phrase array of size 5 × 100 or 500. It is reasonable to restrict the allowed length of coded term phrases if it is known that the number of nomenclature terms with length exceeding the allowed limit is small. It is also reasonable to restrict the allowed length of coded term phrases is it is believed that terms of long length can be successfully represented by subsumed terms within the longer term.For example, "Refractory anemia with excess blasts in transformation" will be captured as a single term by the doublet method. The phrase method will miss the 7-word term but will code the subsumed terms, "refractory anemia" and "refractory anemia with excess blasts". In this specific instance, the doublet coder outperformed the phrase coder. However, few cancer terms actually exceed 5 words in length, and longer terms almost always contain modifying phrases  that add little to the fundamental meaning of the term.The following terms are examples of neoplasms extracted by the doublet method and missed by the phrase method. All of the listed terms exceed 5 words in length. "Acute myelogenous leukemia with minimal differentiation, acute myeloid leukemia with minimal differentiation, adenocarcinoma arising in the parotid gland, adenoid cystic carcinoma of submandibular gland, aids-related primary central nervous system lymphoma, atypical glandular cells of undetermined significance, atypical squamous cells of uncertain significance, carcinoid tumor arising from meckel diverticulum, extranodal marginal zone b-cell lymphoma of mucosa-associated lymphoid tissue, giant cell tumor of tendon sheath, giant cell tumour of tendon sheath, glandular malignant peripheral nerve sheath tumor, high-grade malignant peripheral nerve sheath tumor, hurthle cell carcinoma arising from thyroid, hyalinizing spindle cell tumor with giant rosettes, interdigitating dendritic cell sarcoma arising from the spleen, intermediate-grade b-cell non-hodgkin lymphoma, intraductal papillary mucinous neoplasm of pancreas, intraductal papillary-mucinous tumor with moderate dysplasia, kaposi sarcoma arising in the heart, large cell calcifying sertoli cell tumor, leiomyosarcoma arising from the pulmonary artery, low grade cervical glandular intraepithelial neoplasia, low-grade malignant peripheral nerve sheath tumor, lymphoma arising in the thyroid gland, malignant epithelioid peripheral nerve sheath tumor, malignant tumor of peripheral nervous system, malt lymphoma arising in the stomach, metanephric adenosarcoma in a young adult, monomorphic clear cell adenocarcinoma of salivary glands, ovarian serous borderline tumor with micropapillary and cribriform patterns, ovarian serous tumor of low malignant potential, paraganglioma arising in the cauda equina, perineurial malignant peripheral nerve sheath tumor, philadelphia chromosome negative chronic myeloid leukemia, phosphaturic mesenchymal tumor mixed connective tissue variant, pineal parenchymal tumor of intermediate differentiation, pleomorphic adenoma of minor salivary glands, polymorphous low-grade adenocarcinoma of minor salivary gland, polymorphous low-grade adenocarcinoma of minor salivary glands, polymorphous low-grade adenocarcinoma of salivary gland, poorly differentiated malignant peripheral nerve sheath tumor, porokeratotic eccrine ostial and dermal duct nevus, primary cutaneous anaplastic large cell lymphoma, primary gastric diffuse large b-cell lymphoma, primary signet-ring cell carcinoma of lung, primitive neuroectodermal tumor arising in the pancreas, pulmonary immunocytoma with massive crystal storing histiocytosis, rhabdoid transformation of tumor cells in meningioma, serous ovarian tumor of low malignant potential, sex cord tumor with annular tubules, signet ring cell adenocarcinoma of prostate, signet-ring cell mucin-producing adenocarcinoma of minor salivary glands, sinonasal desmoplastic small round cell tumor, smooth muscle tumor of uncertain malignant potential, smooth muscle tumor with an uncertain malignant potential, splenic lymphoma with circulating villous lymphocytes, squamous cell carcinoma of fallopian tube, submandibular gland carcinoma ex pleomorphic adenoma, tall cell variant of papillary carcinoma of thyroid, testicular large cell calcifying sertoli cell tumor, uterine tumor resembling ovarian sex cord tumor."The long terms found by the doublet coder and missed by the phrase coder represent a very small percentage of the different terms found by either coder in the long 170+ Megabyte text (250/4807 = 5%). A cursory review of these terms indicates that they represent rare lesions or rare variants of common lesions.Developers of medical autocoders seldom publish manuscripts. It is the author's perception, based on many years of activity in this field, that most autocoders are proprietary products produced for a very specific type of job. The author has never encountered any autocoder vendors who revealed the speed of their autocoders or shared any primary data that measures the performance of their autocoders. There really has never been any publication where one autocoder was compared against another. This is unfortunate because software developers may defer implementing brilliant ideas for autocoders, if they are uncertain whether better autocoders already exist. Even if competing software developers were to share performance data, there are no widely accepted standards for measuring the performance of medical autocoders. One of the purposes of this paper is to provide open access to algorithms, software, performance methodology and performance outcome data.The performance of autocoders is always a contentious issue. The reflexive approach to measuring autocoder performance usually involves selecting a small corpus of text and allowing a human expert in a language domain to carefully read through the lines of the text, creating a so-called gold standard against which the autocoder can be compared. The problems with this seemingly straightforward approach are many and have been explained by myself and others. The many limitations of "precision and recall" as measurements of indexing performance have been reviewed elsewhere ,10.It would be a useful exercise to re-examine what autocoding performance means to different people in contrast to what autocoding performance means within the context of lexical parsers ,12. FirsFinally, some coders seek to create "concept signatures" from text. A concept signature is the list of the concepts contained in a section of text. The relationship of one section of text to another section of text is determined by a quantitative representation of how closely their signatures match. Concept signatures are used to retrieve or organize related documents, not specific concepts .Lexical coders are, in a sense, perfect autocoders because they don't use grammatic rules, they have no "exception" lists, and they never guess or interpret text. The only thing that lexical parsers do is to parse text, examining strings to see if they contain exact matches to terms from a nomenclature. When well-constructed, they do not make mistakes. If they miss a valid term that is present in the text, it is because the term was missing from the nomenclature. Developers of lexical autocoders place enormous demands on the curators of nomenclatures.The most common cause of missed terms arises when the text contains a modifying word that breaks the term into a phrase that no longer matches anything found in the nomenclature. For instance, "adenocarcinoma of the left lung," would be missed by a lexical parser if the nearest term in its terminology list is "adenocarcinoma of the lung." A rule-based parser or a semantic parser may have successfully teased out the "left" from the term and found the match. In this instance, the nomenclature failed the lexical parser because it did not list terms that indicated tumor laterality. Lexical parsers do not match terms that are absent from the text . False-positive terms are possible in rule-based and semantic parsers if they create word patterns not present in the original text. Also, since lexical parsers strictly match phrases in text with phrases in nomenclatures, it is possible to achieve accurate results of dubious value. For instance, a lexical parser would parse "adenocarcinoma of the lung is not seen" and find a match against the neoplasm term, "adenocarcinoma of the lung." The concept is present in the text, even if though it is absent from the patient. It is a misleading but "true" positive.The doublet autocoder creates a string of words from a chunk of text. In the case of the example corpus (PubMed abstracts), all of the sentences from the abstract are squeezed into a single string of words, obliterating sentence boundaries. This means that if a sequence of words crossing a sentence boundary happens to match a term in the reference nomenclature, the coder will register a "pseudo-positive" term. Empirical evidence suggests that this theoretical error in the doublet autocoder simply does not occur. A 4 megabyte collection of abstracts chunked as whole abstracts or as chunked sentences (delimited by period-space-space) contained no instances of pseudo-terms created by the obliteration of sentence boundaries in the whole-abstract text chunks. For fastidious developers who wish to ensure that their parsers respect sentence boundaries, it is possible to pre-process text into sentences with a sentence parser ,15.Lexical parsers can be modified to provide an output that preserves the intended sense of the term as used in its context. For example, if the text includes the sentence, "Adenocarcinoma of the lung is not present." The "sensible" lexical parser may be modified to tag the "adenocarcinoma of the lung" with a negation modifier, preserving the intended sense of the term. The author has previously published an "in place" method of inserting codes directly into sentences, preserving modifier terms (including negations) .The two lexical parsers used the same programming language (Perl), the same nomenclature, the same data structure to hold the nomenclature, the same text corpus, and the same method for breaking the complete text into text chunks. Differences between the performance of the two autocoding methods were accounted for entirely by the algorithmic processes by which chunks of text are parsed into phrases that are matched against the common nomenclature. It is easy to compare speeds. The doublet parser required 211 seconds to parse the 170+ Megabyte file, while the phrase parser required 1,776 seconds. Three algorithmic properties contribute to the speed advantage of the doublet coder over the phrase coder: 1) The doublet coder parses text into a number of phrases that is 5-fold smaller than the number of phrases produced by the phrase coder; 2) Doublets that are not found in any of the nomenclature terms can be quickly excluded, 3) Successive text doublets that match doublets from the nomenclature can be quickly concatenated and tested for matches in the nomenclature. These are the algorithmic differences between the phrase coder and the doublet coder and presumably account for the improved speed of the doublet method.Comparing coding accuracy is somewhat trickier. As discussed, lexical parsers have no "false positive" matches. Lexical parsers, unlike natural language processors, do not construct context-based new word phrases from native text. Lexical parsers only match exact phrases found in text with exact nomenclature terms. Therefore, neither the doublet coder nor the phrase coder have false-positive term matches. Coding output was compared by examining the different terms matched by the two coders. The number of different terms found by the doublet method was 4,807, compared with 4,557 terms found by the phrase method. There were no terms found by the phrase method and missed by the doublet method. There were 250 terms missed by the phrase method and found by the doublet method (about 5% of the number of different terms found by the doublet method). For the most part, these terms represented rare neoplasms with pre-coordinated modifiers. The reason that such rare terms were encountered is due to the large size of the text (exceeding 170 Megabytes). When the doublet and phrase methods are judged by their ability to extract nomenclature from text, their output would be similar for small text sizes or when the primary purpose of the coding is to extract and count commonly occurring terms.The doublet method is a novel approach to autocoding. It can autocode 0.8 Megabytes of text per second on desktop computer using a modest 1.6 GHz processor. For this manuscript, the doublet autocoder was tested on a corpus of medical text that exceeded 170 Megabytes in length and used a publicly available nomenclature of neoplasia containing 102,271 unique terms. In a side-by-side comparison with a publicly available fast lexical autocoder, the doublet method was 8.4-fold faster. The doublet algorithm is generalizable to any type or length of plain-text using any nomenclature. The algorithm and the Perl implementation script are available as open source documents.The autocoding scripts are short programs written in Perl. Perl is a freely available open source programming language. Perl interpreters for virtually any operating system are available from several sites on the web ,7. TheseThe Perl scripts (doublet.pl and phrase.pl) will work without modification using the current version of "The developmental lineage classification and taxonomy of neoplasms," which is provided with this manuscript see  see Add.None declared.The work expresses the opinion of the author and does not represent policy of the U.S. government.The pre-publication history for this paper can be accessed here:Neocl.xml is the developmental lineage classification and taxonomy of neoplasms, in XML format. Because neocl.xml exceeds 7 Megabytes when uncompressed, a gzipped version of the file is provided (neoclxml.gz). After downloading from the biomedcentral site, the filename should be provided with a .gz suffix (if absent from the filename as downloaded). After decompressing the file, the file shoud be renamed "neocl.xml". The file can be viewed on current web browsers, but experience has shown that many browsers lack sufficient memory to display the entire file. Otherwise, the file can be viewed on a wordprocessor or an ascii editor.Click here for fileNeoself.gz is the ascii flat-file version of the neocl.xml file. The file exceeds 16 Megabytes when expanded. Each line-record of the file consists of the numbered name of a different term, its code value, and the hierarchical list of its ancestral [class] terms from the developmental lineage classification and taxonomy of neoplasms.Click here for fileDoubcode.pl is a Perl script that implements the doublet method for text autocoding and expects an external file named tumor.txt as the source corpus and a file named neocl.xml as the reference nomenclature.Click here for filePhrase.pl is a Perl script that implements the doublet method for text autocoding and expects an external file named tumor.txt as the source corpus and a file named neocl.xml as the reference nomenclature.Click here for fileDoub.out is the plain-text output of the doublet method for text autocoding (i.e. output of doubcode.pl).Click here for fileQuickcan.txt is the plain-text output file for phrase method for text autocoding (i.e. output of phrase.pl).Click here for fileDoubcomp.pl is the Perl script comparing the output files produced by doubcode.pl and phrase.pl.Click here for fileDoubcomp.txt is the plain-text output of doubcomp.pl.Click here for file