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1.  An immunohematological ‘Wet’ workshop 
A practical workshop on ‘Immunohematology’ was conducted in conjunction with the Indian Society of Blood Transfusion and Immunohaematology annual scientific program. The participants, from many parts of India, were able to obtain valuable practice in key areas of blood group serology and by the end of the workshop were able to carry out ‘tube’ techniques for antibody detection and identification. Column agglutination methods were also demonstrated. A preliminary questionnaire was completed by participants. Results showed a wide variety in types of pretransfusion (serologic) testing being performed. Less than half of the participants had encountered hemolytic transfusion reactions. The program was rated as excellent by most participants in response to a postworkshop evaluation questionnaire, with requests for longer and more frequent workshops. Safety of blood for transfusion depends on maintenance of high standards of both microbiological and immunohematological performance by the blood bank staff.
PMCID: PMC3168125  PMID: 21938238
Blood group serology; education; immunohematology
2.  Virtual blood bank 
Virtual blood bank is the computer-controlled, electronically linked information management system that allows online ordering and real-time, remote delivery of blood for transfusion. It connects the site of testing to the point of care at a remote site in a real-time fashion with networked computers thus maintaining the integrity of immunohematology test results. It has taken the advantages of information and communication technologies to ensure the accuracy of patient, specimen and blood component identification and to enhance personnel traceability and system security. The built-in logics and process constraints in the design of the virtual blood bank can guide the selection of appropriate blood and minimize transfusion risk. The quality of blood inventory is ascertained and monitored, and an audit trail for critical procedures in the transfusion process is provided by the paperless system. Thus, the virtual blood bank can help ensure that the right patient receives the right amount of the right blood component at the right time.
doi:10.4103/2153-3539.76155
PMCID: PMC3046379  PMID: 21383930
Computer crossmatch; laboratory information system; virtual blood bank
3.  Participation in proficiency programs and promotion of quality in transfusion services of Minas Gerais 
Objective
This study aimed at identifying associations between the participation of transfusion services in immunohematology external quality control programs and their accuracy in immunohematology testing and adaptation to technical and legal operational procedures.
Methods
From 2007 to 2009, a cross-sectional study was conducted in 219 transfusion services of the State of Minas Gerais who participated in this investigation by responding to a questionnaire and conducting a proficiency test comprising: ABO and RhD phenotyping, irregular RBC antibody screening and cross-matching. Frequencies and bivariate analysis followed by binary logistic regression were used for statistical analysis.
Results
Transfusion services who participated in external quality control programs (32.4%) and those that did not (67.6%) obtained worrying error percentages in proficiency tests which may significantly increase blood transfusion risks. Shortfalls related to the establishment of protocols, standards and internal quality control were also significant. On comparing the two groups, transfusion services that participated in these programs had a 2.35 times higher chance of correct results in the proficiency panel testing, a 3.16 higher chance of having transfusional records and a 2.81 higher chance of performing preventive maintenance of equipment.
Conclusion
The study showed that independent factors associated to participation in external quality control programs suggest that more investment in internal quality control procedures is necessary and that more attention should be paid to current legislation.
doi:10.5581/1516-8484.20120009
PMCID: PMC3459603  PMID: 23049379
Quality control; Blood banks; Blood transfusion; Quality assurance, health care; Program evaluation
4.  Assessment of performance of professionals in immunohematology proficiency tests of the public blood bank network of the state of Minas Gerais 
Background
Despite significant advances, the practice of blood transfusion is still a complex process and subject to risks. Factors that influence the safety of blood transfusion include technical skill and knowledge in hemotherapy mainly obtained by the qualification and training of teams.
Objective
This study aimed to investigate the relationship between professional categories working in transfusion services of the public blood bank network in the State of Minas Gerais and their performance in proficiency tests.
Methods
This was an observational cross-sectional study (2007-2008) performed using a specific instrument, based on evidence and the results of immunohematology proficiency tests as mandated by law.
Results
The error rates in ABO and RhD phenotyping, irregular antibody screening and cross-matching were 12.5%, 9.6%, 43.8% and 20.1%, respectively. When considering the number of tests performed, the error rates were 4.6%, 4.2%, 26.7% and 11.0%, respectively. The error rates varied for different professional categories: biochemists, biologists and biomedical scientists (65.0%), clinical pathology technicians (44.1%) and laboratory assistants, nursing technicians and assistant nurses (74.6%). A statistically significant difference was observed when the accuracy of clinical pathology technicians was compared with those of other professionals with only high school education (p-value < 0.001). This was not seen for professionals with university degrees (p-value = 0.293).
Conclusion
These results reinforce the need to invest in training, improvement of educational programs, new teaching methods and tools for periodic evaluations, contributing to increase transfusion safety and improve hemotherapy in Brazil.
doi:10.5581/1516-8484.20120027
PMCID: PMC3459385  PMID: 23049397
Blood banks/standards; Blood transfusion; Security measures; Training courses; Evaluation; Quality control
5.  Transfusion management using a remote-controlled, automated blood storage 
Blood Transfusion  2008;6(2):101-106.
Background
Generally, the safety of transfusion terapies for patients depends in part on the distribution of the blood products. The prevention of adverse events can be aided by technological means, which, besides improving the traceability of the process, make errors less likely. In this context, the latest frontier in automation and computerisation is the remote-controlled, automated refrigerator for blood storage.
Materials and methods
Computer cross-matching is an efficient and safe method for assigning blood components, based on Information Technology applied to typing and screening. This method can be extended to the management of an automated blood refrigerator, the programme of which is interfaced with the Transfusion Service’s information system. The connection we made in our Service between EmoNet® and Hemosafe® enables real-time, remote-controlled management of the following aspects of blood component distribution: a) release of autologous and allogeneic units already allocated to a patient, b) release of available units, which can be allocated by remote-control to known patients, in the presence of a valid computer cross-match, c) release of O-negative units of blood for emergencies.
Results
Our system combines an information database, which enables computer cross-matching, with an automated refrigerator for blood storage with controlled access managed remotely by the Transfusion Service. The effectiveness and safety of the system were validated during the 4 months of its routine use in the Transfusion Service’s outpatient department.
Conclusions
The safety and efficiency of the distribution of blood products can and must be increased by the use of technological innovations. With the EmoNet®/Hemosafe® system, the responsibility for the remote-controlled distribution of red blood cell concentrates remains with the chief of the Transfusion Services, through the use of automated computer procedures and supported by continuous training of technicians and nursing staff.
doi:10.2450/2008.0029-06
PMCID: PMC2626845  PMID: 18946954
transfusion safety; remote-control; computer cross-match
6.  DNA-Based Methods in the Immunohematology Reference Laboratory 
Although hemagglutination serves the immunohematology reference laboratory well, when used alone, it has limited capability to resolve complex problems. This overview discusses how molecular approaches can be used in the immunohematology reference laboratory. In order to apply molecular approaches to immunohematology, knowledge of genes, DNA-based methods, and the molecular bases of blood groups are required. When applied correctly, DNA-based methods can predict blood groups to resolve ABO/Rh discrepancies, identify variant alleles, and screen donors for antigen-negative units. DNA-based testing in immunohematology is a valuable tool used to resolve blood group incompatibilities and to support patients in their transfusion needs.
doi:10.1016/j.transci.2010.12.011
PMCID: PMC3058268  PMID: 21257350
Antibody identification; blood group antigens; molecular methods; DNA testing; blood groups; identification of blood groups
7.  Canine Dal Blood Type: A Red Cell Antigen Lacking in Some Dalmatians 
Background
Based upon alloantibodies produced after sensitizing dogs with transfused blood, more than a dozen blood group systems have been recognized thus far, and some have been classified as dog erythrocyte antigens (DEA).
Hypothesis
A new canine red cell antigen was suspected, based on the development of specific alloantibodies in a Dalmatian previously sensitized by blood transfusions.
Animals
Twenty-six Dalmatians (including 1 Dalmatian in need of blood compatibility studies); 55 canine blood donors.
Methods
Serologic tests, including blood typing, crossmatching, and direct Coombs’ test were performed by standard tube techniques and a novel gel column technology adapted from human blood banking.
Results
By day 40 after transfusion of an anemic Dalmatian, all major crossmatch tests to 55 non-Dalmatian dogs were incompatible. The 2 initial donors, who were compatible before transfusion, were also now incompatible, suggesting the development of an alloantibody to a common red cell antigen. No siblings were available, but 4 of 25 unrelated Dalmatians were crossmatch compatible, suggesting that they were missing the same red cell antigen. The patient was blood typed DEA 1.1, 3, 4, and 5 positive, but DEA 7 negative. Further blood typing and crossmatching results did not support an association to any of these known blood types. The alloantibodies produced were determined to be of the immunoglobulin G class.
Conclusions and Clinical Importance
Based upon the identification of an acquired alloantibody in a Dalmatian, a presumably new common blood type named Dal was identified. Dalmatians lacking the Dal antigen are likely at risk of delayed and acute hemolytic transfusion reactions.
PMCID: PMC3132505  PMID: 17427389
Alloantibody; Blood compatibility; Crossmatch; Dog erythrocyte antigen; Transfusion
8.  The evolution of immunohematology in South Asian countries 
Many factors have resulted in the slow development of transfusion services in some South Asian countries. Despite difficulties, there have been some excellent developments and the outlook for the future is very positive. The biggest problems relate to the availability of the truly voluntary altruistic blood donors and considerable work is still needed to upgrade this aspect of the work. Screening for transfusion transmissible diseases is now widespread although there is still a requirement to enhance quality assurance procedures and to improve statistical definitions and collection. Other factors that have affected the evolution of immunohematology are outlined and there is now optimism for the future.
doi:10.4103/0973-6247.53881
PMCID: PMC2920469  PMID: 20808656
Immunohematology; blood donors; blood donation
9.  Clinical informatics: 2000 and beyond. 
Healthcare has begun to flounder in the mounting flood of data available from automated monitoring equipment, microprocessor controlled life-support equipment, such as ventilators, ever more sophisticated laboratory tests, and the myriad of minor technological wonders that every hospital and clinic seem to collect. It is no longer enough to merely display the data in a large spreadsheet or on a complex, colorful time-sequence graph. The next generation of healthcare information systems must help the clinician to assimilate the myriad of data and to make fast and effective decisions. The following is a list of features that the next generation of computer systems will have to include if they are to have a significant impact on the quality of patient care: data acquisition, data storage, information display, data processing, and decision support. By automating or streamlining repetitive or complex tasks, correlating and presenting complex and potentially confusing data, and tracking patient outcomes, the computer can augment clinicians' skills to improve patient care.
PMCID: PMC2232766  PMID: 10566431
10.  Automated processing of whole blood units: operational value and in vitro quality of final blood components 
Blood Transfusion  2012;10(1):63-71.
Background
The Community Transfusion Centre in Madrid currently processes whole blood using a conventional procedure (Compomat, Fresenius) followed by automated processing of buffy coats with the OrbiSac system (CaridianBCT). The Atreus 3C system (CaridianBCT) automates the production of red blood cells, plasma and an interim platelet unit from a whole blood unit. Interim platelet unit are pooled to produce a transfusable platelet unit. In this study the Atreus 3C system was evaluated and compared to the routine method with regards to product quality and operational value.
Materials and methods
Over a 5-week period 810 whole blood units were processed using the Atreus 3C system. The attributes of the automated process were compared to those of the routine method by assessing productivity, space, equipment and staffing requirements. The data obtained were evaluated in order to estimate the impact of implementing the Atreus 3C system in the routine setting of the blood centre. Yield and in vitro quality of the final blood components processed with the two systems were evaluated and compared.
Results
The Atreus 3C system enabled higher throughput while requiring less space and employee time by decreasing the amount of equipment and processing time per unit of whole blood processed. Whole blood units processed on the Atreus 3C system gave a higher platelet yield, a similar amount of red blood cells and a smaller volume of plasma.
Discussion
These results support the conclusion that the Atreus 3C system produces blood components meeting quality requirements while providing a high operational efficiency. Implementation of the Atreus 3C system could result in a large organisational improvement.
doi:10.2450/2011.0008-11
PMCID: PMC3258991  PMID: 22044958
whole blood processing; automation; Atreus 3C system; blood components; operational value
11.  Contemporary issues in transfusion medicine informatics 
The Transfusion Medicine Service (TMS) covers diverse clinical and laboratory-based services that must be delivered with accuracy, efficiency and reliability. TMS oversight is shared by multiple regulatory agencies that cover product manufacturing and validation standards geared toward patient safety. These demands present significant informatics challenges. Over the past few decades, TMS information systems have improved to better handle blood product manufacturing, inventory, delivery, tracking and documentation. Audit trails and access to electronic databases have greatly facilitated product traceability and biovigilance efforts. Modern blood bank computing has enabled novel applications such as the electronic crossmatch, kiosk-based blood product delivery systems, and self-administered computerized blood donor interview and eligibility determination. With increasing use of barcoding technology, there has been a marked improvement in patient and specimen identification. Moreover, the emergence of national and international labeling standards such as ISBT 128 have facilitated the availability, movement and tracking of blood products across national and international boundaries. TMS has only recently begun to leverage the electronic medical record to address quality issues in transfusion practice and promote standardized documentation within institutions. With improved technology, future growth is expected in blood bank automation and product labeling with applications such as radio frequency identification devices. This article reviews several of these key informatics issues relevant to the contemporary practice of TMS.
doi:10.4103/2153-3539.74961
PMCID: PMC3046378  PMID: 21383927
Blood bank; barcode; computer; donor; electronic crossmatch; FDA; informatics; transfusion medicine; virtual
12.  Microcomputer Systems in Solo and Small Group Medical Practices 
Technological developments of microprocessors and microcomputers will facilitate transferring the advantages of larger computer installations to solo and small group medical practices. A series of powerful forces will create the need for computer assistance, helping to overcome earlier restraints. Surveys show the physician is anxious for the help, and manufacturers have the needed advanced components under development. A typical advanced system for physical examination and clerical transactions (ASPECT) has been synthesized from the identified components at attractive economies of scale. More orderly and faster patient processing, lower costs for in-office laboratory tests, high quality, comparative diagnostic protocols, processing more patients at lower unit costs, automated administrative procedures and interface with emerging data banks are a few of the many potential benefits to the patient, the practitioner and society. Effective demonstration programs, triggering modified manufacturing and marketing patterns, are pragmatic priorities before the arsenal of these benefits can be effectively arrayed against today's greatest health care adversary - “the inflation crunch.”
PMCID: PMC2231720
13.  Performance and diagnostic usefulness of commercially available enzyme linked immunosorbent assay and rapid kits for detection of HIV, HBV and HCV in India 
Virology Journal  2012;9:290.
Background
HIV, HBV and HCV pose a major public health problem throughout the world. Detection of infection markers for these agents is a major challenge for testing laboratories in a resource poor setting. As blood transfusion is an important activity saving millions of live every year, it also carries a risk of transfusion transmissible infections caused by these fatal blood borne pathogens if the quality of testing is compromised. Conventional ELISA is regarded as the mostly used screening technique but due to limitations like high cost, unavailability in many blood banks and testing sites, involvement of costly instruments, time taking nature and requirement of highly skilled personnel for interpretation, rapid tests are gaining more importance and warrants comparison of performance.
Results
A comparative study between these two techniques has been performed using commercially available diagnostic kits to assess their efficacy for detection of HIV, HBV and HCV infections. Rapid kits were more efficient in specificity with synthetic antigens along with high PPV than ELISA in most cases. Comparison between different ELISA kits revealed that Microlisa HIV and Hepalisa (J. Mitra & Co. Pvt. Ltd.); ERBA LISA HIV1 + 2, ERBA LISA Hepatitis B and ERBA LISA HCV (Transasia Bio-medicals Ltd.) gives uniform result with good performance in terms of sensitivity, specificity, PPV, NPV and efficiency, whereas, Microlisa HCV (J. Mitra & Co. Pvt. Ltd.), Microscreen HBsAg ELISA and INNOVA HCV (Span Diagnostics Ltd.) did not perform well. Rapid kits were also having high degree of sensitivity and specificity (100%) except in HIV Comb and HCV Comb (J. Mitra & Co. Pvt. Ltd.). The kit efficiency didn’t vary significantly among different companies and lots in all the cases except for HCV ELISA showing statistically significant variation (p < 0.01) among three kit types.
Conclusions
ELISA is a good screening assay for markers of HIV, HBV and HCV infections. Rapid tests are useful for further detection of false positive samples. ELISA seems the appropriate assay in blood bank. For availability of quality commercial diagnostic assays, evaluation of kit may be helpful.
doi:10.1186/1743-422X-9-290
PMCID: PMC3568713  PMID: 23181517
Kit evaluation; HIV; HBV; HCV; Sera panel; ELISA; Rapid assay; Sensitivity; Specificity
14.  An Automatic Refolding Apparatus for Preparative-Scale Protein Production 
PLoS ONE  2012;7(9):e45891.
Protein refolding is an important process to recover active recombinant proteins from inclusion bodies. Refolding by simple dilution, dialysis and on-column refolding methods are the most common techniques reported in the literature. However, the refolding process is time-consuming and laborious due to the variability of the behavior of each protein and requires a great deal of trial-and-error to achieve success. Hence, there is a need for automation to make the whole process as convenient as possible. In this study, we invented an automatic apparatus that integrated three refolding techniques: varying dilution, dialysis and on-column refolding. We demonstrated the effectiveness of this technology by varying the flow rates of the dilution buffer into the denatured protein and testing different refolding methods. We carried out different refolding methods on this apparatus: a combination of dilution and dialysis for human stromal cell-derived factor 1 (SDF-1/CXCL12) and thioredoxin fused-human artemin protein (Trx-ARTN); dilution refolding for thioredoxin fused-human insulin-like growth factor I protein (Trx-IGF1) and enhanced fluorescent protein (EGFP); and on-column refolding for bovine serum albumin (BSA). The protein refolding processes of these five proteins were preliminarily optimized using the slowly descending denaturants (or additives) method. Using this strategy of decreasing denaturants concentration, the efficiency of protein refolding was found to produce higher quantities of native protein. The standard refolding apparatus configuration can support different operations for different applications; it is not limited to simple dilution, dialysis and on-column refolding techniques. Refolding by slowly decreasing denaturants concentration, followed by concentration or purification on-column, may be a useful strategy for rapid and efficient recovery of active proteins from inclusion bodies. An automatic refolding apparatus employing this flexible strategy may provide a powerful tool for preparative scale protein production.
doi:10.1371/journal.pone.0045891
PMCID: PMC3459974  PMID: 23029296
15.  Application of Molecular Diagnostic Techniques for Viral Testing 
The Open Virology Journal  2012;6:104-114.
Nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. These techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. The increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. This technology has reduced the use of some other techniques such as viral culture based methods and serological assays in the clinical virology laboratory. Moreover, nucleic acid amplification techniques are now the methods of reference and also the most useful assays for the diagnosis in several diseases. The introduction of these techniques and their automation provides new opportunities for the clinical laboratory to affect patient care. The main objectives in performing nucleic acid tests in this field are to provide timely results useful for high-quality patient care at a reasonable cost, because rapid results are associated with improvements in patients care. The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. This review is an up-to-date of the main nucleic acid techniques and their clinical applications, and special challenges and opportunities that these techniques currently provide for the clinical virology laboratory.
doi:10.2174/1874357901206010104
PMCID: PMC3522074  PMID: 23248732
Automation methods; molecular diagnosis; molecular microbiology; nucleic acid techniques; PCR techniques; viral laboratory diagnosis.
16.  Electrical properties of the red blood cell membrane and immunohematological investigation 
Hemagglutination is widely used in transfusion medicine and depends on several factors including antigens, antibodies, electrical properties of red blood cells and the environment of the reaction. Intermolecular forces are involved in agglutination with cell clumping occurring when the aggregation force is greater than the force of repulsion. Repulsive force is generated by negative charges on the red blood cell surface that occur due to the presence of the carboxyl group of sialic acids in the cell membrane; these charges create a repulsive electric zeta potential between cells. In transfusion services, specific solutions are used to improve hemagglutination, including enzymes that reduce the negative charge of red blood cells, LISS which improves the binding of antibodies to antigens and macromolecules that decrease the distance between erythrocytes. The specificity and sensitivity of immunohematological reactions depend directly on the appropriate use of these solutions. Knowledge of the electrical properties of red blood cells and of the action of enhancement solutions can contribute to the immunohematology practice in transfusion services.
doi:10.5581/1516-8484.20110080
PMCID: PMC3415751  PMID: 23049321
Zeta potential; Erythrocytes; Optical tweezers; Agglutination
17.  Automatic and manual latex agglutination tests for measurement of cholera toxin and heat-labile enterotoxin of Escherichia coli. 
Automated and manual latex agglutination methods were employed to measure cholera toxin (CT), heat-labile enterotoxin (LT) of Escherichia coli, and their subunits A and B. Dow polystyrene latex particles (diameter, 0.22 microns) and polystyrene-chlorostyrene latex particles (diameter, 1 micron) were sensitized by rabbit-specific immunoglobulin for each antigen and used as the reagents of the automated and manual agglutination tests, respectively. Automated agglutination was performed by a nephelometric assay system measuring time-dependent differences of light scattering due to agglutination, and manual latex agglutination was carried out in microtiter plates. As low as 1,000 and 31 pg of CT per ml were estimated by the automated and manual agglutination tests, respectively. Using these methods, the amount of CT and LT was measured in several clinical isolates of Vibrio cholerae and E. coli. Furthermore, it was discovered that cyclic AMP is not essential for the production of CT by measuring the amount of the toxin in numbers of cyclic AMP-dependent mutants of V. cholerae (with the agglutination tests).
PMCID: PMC272564  PMID: 6298275
18.  MAGNETIC RESONANCE IMAGING COMPATIBLE ROBOTIC SYSTEM FOR FULLY AUTOMATED BRACHYTHERAPY SEED PLACEMENT 
Urology  2006;68(6):1313-1317.
Objectives
To introduce the development of the first magnetic resonance imaging (MRI)-compatible robotic system capable of automated brachytherapy seed placement.
Methods
An MRI-compatible robotic system was conceptualized and manufactured. The entire robot was built of nonmagnetic and dielectric materials. The key technology of the system is a unique pneumatic motor that was specifically developed for this application. Various preclinical experiments were performed to test the robot for precision and imager compatibility.
Results
The robot was fully operational within all closed-bore MRI scanners. Compatibility tests in scanners of up to 7 Tesla field intensity showed no interference of the robot with the imager. Precision tests in tissue mockups yielded a mean seed placement error of 0.72 ± 0.36 mm.
Conclusions
The robotic system is fully MRI compatible. The new technology allows for automated and highly accurate operation within MRI scanners and does not deteriorate the MRI quality. We believe that this robot may become a useful instrument for image-guided prostate interventions.
doi:10.1016/j.urology.2006.08.1089
PMCID: PMC3100553  PMID: 17169653
19.  Anemia in the preterm infant: Erythropoietin versus erythrocyte transfusion — It’s not that simple 
Clinics in perinatology  2009;36(1):111-123.
SYNOPSIS
Since the late 1980s recombinant human erythropoietin (r-Epo) has been studied as an alternative to packed red blood cell (RBC) transfusion for the treatment of anemia of prematurity in very low birth weight (VLBW, <1500 grams) infants. Initial trials and reports focused on r-Epo’s ability to prevent or treat anemia of prematurity with the goal of eliminating RBC transfusion, but achieved limited success. Reduced volumes of blood sampling for laboratory tests and improved blood banking techniques have decreased the need for RBC transfusion. New concerns about the safety of r-Epo administration have emerged. Past cost-benefit analyses of r-Epo administration versus transfusion for the treatment of anemia of prematurity have been nearly balanced. Autologous transfusion, blood-sparing technologies, changes in RBC transfusion technique and safety, and further elucidation of the risk-benefit ratio of r-Epo therapy may change the cost-benefit analysis. The jury is still out with regard to the role of r-Epo therapy in the VLBW population.
doi:10.1016/j.clp.2008.09.009
PMCID: PMC2683173  PMID: 19161869
erythropoietin; transfusion; very low birth weight; infant; premature
20.  Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology 
PLoS ONE  2012;7(11):e47768.
Many genomes have been sequenced to high-quality draft status using Sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. However, even the best draft genomes contain gaps and other imperfections due to limitations in the input data and the techniques used to build draft assemblies. Sequencing biases, repetitive genomic features, genomic polymorphism, and other complicating factors all come together to make some regions difficult or impossible to assemble. Traditionally, draft genomes were upgraded to “phase 3 finished” status using time-consuming and expensive Sanger-based manual finishing processes. For more facile assembly and automated finishing of draft genomes, we present here an automated approach to finishing using long-reads from the Pacific Biosciences RS (PacBio) platform. Our algorithm and associated software tool, PBJelly, (publicly available at https://sourceforge.net/projects/pb-jelly/) automates the finishing process using long sequence reads in a reference-guided assembly process. PBJelly also provides “lift-over” co-ordinate tables to easily port existing annotations to the upgraded assembly. Using PBJelly and long PacBio reads, we upgraded the draft genome sequences of a simulated Drosophila melanogaster, the version 2 draft Drosophila pseudoobscura, an assembly of the Assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the Sooty mangabey. With 24× mapped coverage of PacBio long-reads, we addressed 99% of gaps and were able to close 69% and improve 12% of all gaps in D. pseudoobscura. With 4× mapped coverage of PacBio long-reads we saw reads address 63% of gaps in our budgerigar assembly, of which 32% were closed and 63% improved. With 6.8× mapped coverage of mangabey PacBio long-reads we addressed 97% of gaps and closed 66% of addressed gaps and improved 19%. The accuracy of gap closure was validated by comparison to Sanger sequencing on gaps from the original D. pseudoobscura draft assembly and shown to be dependent on initial reference quality.
doi:10.1371/journal.pone.0047768
PMCID: PMC3504050  PMID: 23185243
21.  Haemagglutination kinetics using a continuous-flow system. 
Journal of Clinical Pathology  1980;33(9):885-887.
An automated technique for measuring haemagglutination kinetics is described. Equipment used in this test is very simple and already present in most blood transfusion centres. This method may be used with advantage to differentiate homozygous and heterozygous subjects in Rhesus, MNSs, and Kell systems, and to study antigen variations, especially in genetic investigations.
PMCID: PMC1146252  PMID: 6776159
22.  Organizing research data 
Acta Veterinaria Scandinavica  2011;53(Suppl 1):S2.
Research relies on ever larger amounts of data from experiments, automated production equipment, questionnaries, times series such as weather records, and so on. A major task in science is to combine, process and analyse such data to obtain evidence of patterns and correlations.
Most research data are on digital form, which in principle ensures easy processing and analysis, easy long-term preservation, and easy reuse in future research, perhaps in entirely unanticipated ways. However, in practice, obstacles such as incompatible or undocumented data formats, poor data quality and lack of familiarity with current technology prevent researchers from making full use of available data.
This paper argues that relational databases are excellent tools for veterinary research and animal production; provides a small example to introduce basic database concepts; and points out some concerns that must be addressed when organizing data for research purposes.
doi:10.1186/1751-0147-53-S1-S2
PMCID: PMC3194121  PMID: 21999359
23.  Automation of environmental ELISAs 
ELISAs for pesticides and herbicides in environmental and agricultural samples are becoming very important in screening applications [1-3]. Traditional chromatographic methods are expensive and results need long turnaround times, making them incompatible with rapid on-site decision making. ELISA methods have been shown to meet or exceed the performance of gas chromatography—they offer rapid low-cost analysis, thereby increasing the frequency of sampling and enhancing data quality. Automated ELISA workstations allow the full benefit of these kits to be realized. Sample preparation, reagent pipetting, incubation, and photometric evaluation can be performed without user intervention. Reliability is increased through the elimination of operator error, better accuracy and precision, and often higher speed. Much larger batch sizes are possible and these systems can provide sample tracking with report generation for documentation requirements. In this paper the manual procedures and ELISA methods are compared and some critical aspects of automating these ELISA kits are discussed.
doi:10.1155/S146392469400026X
PMCID: PMC2548040  PMID: 18924993
24.  Sequence-Based Typing of Human Blood Groups 
Summary
In the last two decades, all but one of the genes encoding the 30 blood group systems present on red blood cells have been identified. This body of knowledge has permitted the application of molecular techniques to characterize the common blood group antigens and to elucidate the background for some of the variant phenotypes. DNA sequencing methodology was developed in the late 1970s and has become one of the most widely used techniques in molecular biology. In the field of immunohematology, this method is currently used by specialized laboratories to elucidate the molecular basis of unusual blood group phenotypes that cannot be defined by serology and genotyping. Because of the heterogeneity of the blood groups on both the antigen and the genetic level, special knowledge of the biology of blood group systems is needed to design sequencing strategies and interpret sequence data. This review summarizes the technical and immunohematologic expertise that is required when applying sequence-based typing for characterization of human blood groups.
doi:10.1159/000217322
PMCID: PMC2980529  PMID: 21113262
Blood group; Sequencing; ABO; Rhesus; Genotyping
25.  Accuracies of β-Lactam Susceptibility Test Results for Pseudomonas aeruginosa with Four Automated Systems (BD Phoenix, MicroScan WalkAway, Vitek, and Vitek 2)▿  
Journal of Clinical Microbiology  2007;45(4):1339-1342.
Contemporary clinical isolates and challenge strains of Pseudomonas aeruginosa were tested by four automated susceptibility testing systems (BD Phoenix, MicroScan WalkAway, Vitek, and Vitek 2; two laboratories with each) against six broad-spectrum β-lactams, and the results were compared to reference broth microdilution (BMD) and to consensus results from three validated methods (BMD, Etest [AB Biodisk, Solna, Sweden], and disk diffusion). Unacceptable levels of error (minor, major, and very major) were detected, some with systematic biases toward false susceptibility (piperacillin-tazobactam and imipenem) and others toward false resistance (aztreonam, cefepime, and ceftazidime). We encourage corrective action by the system manufacturers to address test biases, and we suggest that clinical laboratories using automated systems should consider accurate alternative methods for routine use.
doi:10.1128/JCM.01716-06
PMCID: PMC1865858  PMID: 17229867

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