bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blood group antigens and immune responses–detailed knowledge is necessary to prevent immunization and to follow up immunized individuals
Authors: Husebekk A. , Ahlen M. T. , Killie M. K. , Tiller H. , Eksteen M. , Killie I. L. , Heide G. , Kjeldsen‐Kragh J. , Skogen B. , Stuge T. B. 
Published: June 2010

Background The immune system is educated to detect and react with foreign antigens and to tolerate self‐antigen. Transfusion of blood cells and plasma and pregnancies challenge the immune system by the introduction of foreign antigens. The antigens may cause an immune response, but in many instances this is not the case and the individual is not immunised after exposure of blood group antigens.Aims The aim of the presentation is to dissect some immune responses to blood group antigens in order to understand the mechanism of immunisation.Methods The results of immune responses to blood group antigens can be detected by the presence of antibodies to the antigens. If the antibodies are of IgG class, the activated B cells have received help from antigen specific T cells. Both antibodies, B cells and T cells can be isolated from immunised individuals and studied in the laboratory. Also B‐cell receptors and T‐cell receptors as well as MHC molecules on antigen presenting cells can be studied and models of the immune synapses can be created in vitro.Results The most classic immune responses in transfusion medicine and in incompatible pregnancies are immune responses to the RhD antigen on red cells, HLA class I molecules on white cells and platelets and human platelet antigens. The nature of these antigens are different; RhD antigens are part of a large complex, present on red cells from RhD positive individuals and completely lacking on red cells from RhD negative individuals. It is likely that many peptides derived from this antigen complex may stimulate T cells and B cells. HLA antigens are highly polymorphic and the antigens are known to induce strong alloimmune responses. The HPA antigens are created by one amino acid difference in allotypes based on a single nucleotide polymorphism at the genetic level. HPA 1a induce immune responses in 10% of HPA 1b homozygote pregnant women. The result of these immune responses is destruction of blood cells with clinical consequences connected to the effect of transfusions or the outcome of pregnancies.Summary/Conclusions Even though there is emerging knowledge about the immune responses to some of the blood group antigens, more information must be gained in order to understand the complete picture. The action of the innate immune response initiating the adaptive immune response to blood group antigens is not well understood. A detailed understanding of both the innate ad the adaptive part of the immune response is necessary to identify individuals at risk for immunisation and to prevent immunisation to blood group antigens.
Multicomponent apheresis
Authors: Zingsem Jürgen 
Published: June 2010

Introduction:  An increasing demand for blood components is opposed by a decreasing donor availability for the collection of the required blood components. Furthermore, current stem cell transplantation regiments require the collection of more than one similar or different component from one donor or patient. One strategy for maintaining the patients’ supply with the required blood components can be the concurrent collection of more than one component from one donor by apheresis, thus multicomponent apheresis.Scope of multicomponent combinations:  Combinations are possible for nearly every kind of blood components. In one session it is possible – depending on the apheresis device – to collect up to four plasma units alone, one or more plasma units and one or two red blood cell (RBC) units, one or more plasma units and one or more platelet units, one or more plasma units and one or two RBC units and one or more platelet units, one or two RBC units and one or more platelet units, two RBC units alone, one or more platelet units.Also in leucocytapheresis the collection of more than one blood component has become a routine procedure. Performing allogeneic stem cell apheresis can lead to a cell dose for two transplantations or to one unit of PBSCs and concurrently collected and frozen mononuclear cells used for donor lymphocyte infusions therapy. Autologous mononuclear cell products (e.g. PBSCs or monocytes for dendritic cell generation) usually are cryoconserved before use and require additional plasmaproteins for cryoconservation. The latter can be obtained by the concurrent collection of plasma during leucocytapheresis. Thus, the combination of cell and plasma units or of cell units of different dose or for different purpose are further examples for the implementation of multicomponent apheresis in tumor therapy.Conclusions:  The understanding of apheresis technologies facilitates the use of multicomponent apheresis in the vast application field for tailoring the kind, quantity, and quality of blood components for patient care.
Volunteer safer than replacement donor blood: a myth revealed by evidence
Authors: Allain J.‐P. 
Published: June 2010

The dogma that volunteer non‐remunerated blood donors (VNRD) are safer has been a cornerstone of world transfusion, including developing countries, for WHO and other major transfusion organizations although the data supporting this dogma has never been convincing. It was supported by data collected without regard for the basic rule of epidemiology, which is to compare what is comparable. In this case, first‐time and repeat VNRD were amalgamated, and genuine replacement/family donors (R/F) were mixed with paid donors. In sub‐Saharan Africa (SSA), VNRD and R/F donors have a median age of < 20 and around 30, respectively. In VNRD, the proportion of females is considerably higher than in R/F donors further distorting the comparisons. In epidemiological terms, only first‐time VNRD can be validly compared to R/F donors.When such valid approach is taken, as published by three SSA countries (Cameroon, Ghana and Guinea), no significant difference in the prevalence of anti‐HIV and HBsAg is apparent. In each study, first‐time VNRD > 20 years of age have higher prevalence of HBsAg and sometimes of anti‐HIV than R/F donors. These confirmed preliminary data strongly suggest that first‐time VNRD and R/F donors are epidemiologically undistinguishable and equally safe for viral infections.This collective data should directly impact three critical factors: the cost of blood, the availability of blood and the efforts put in recruiting repeat donors. R/F blood costs 2–5 times less than VNRD blood, and collecting R/F blood should no longer be discouraged. VNRD‐only policy not only costs more but also limits blood availability for acute anaemia, potentially endangering patients’ lives. Collecting R/F blood as a legitimate supplement to VNRD blood may help reaching 10 units/1000 inhabitants, a level considered adequate for developing countries’ blood supply.Only repeat donation significantly improves blood viral safety. As a result, not only first‐time VNRD but also R/F donors should be actively encouraged to repeat donation. Evidence should take precedence over a moribund myth.
Sources of variability in greenhouse gas and energy balances for biofuel production: a systematic review
Authors: WHITAKER JEANETTE , LUDLEY KATHERINE E. , ROWE REBECCA , TAYLOR GAIL , HOWARD DAVID C. 
Published: June 2010

AbstractAcross the energy sector, alternatives to fossil fuels are being developed, in response to the dual drivers of climate change and energy security. For transport, biofuels have the greatest potential to replace fossil fuels in the short‐to medium term. However, the ecological benefits of biofuels and the role that their deployment can play in mitigating climate change are being called into question. Life Cycle Assessment (LCA) is a widely used approach that enables the energy and greenhouse gas (GHG) balance of biofuel production to be calculated. Concerns have nevertheless been raised that published data show widely varying and sometimes contradictory results. This review describes a systematic review of GHG emissions and energy balance data from 44 LCA studies of first‐ and second‐generation biofuels. The information collated was used to identify the dominant sources of GHG emissions and energy requirements in biofuel production and the key sources of variability in published LCA data. Our analysis revealed three distinct sources of variation: (1) ‘real’ variability in parameters e.g. cultivation; (2) ‘methodological’ variability due to the implementation of the LCA method; and (3) ‘uncertainty’ due to parameters rarely included and poorly quantified. There is global interest in developing a sustainability assessment protocol for biofuels. Confidence in the results of such an assessment can only be assured if these areas of uncertainty and variability are addressed. A more defined methodology is necessary in order to allow effective and accurate comparison of results. It is also essential that areas of uncertainty such as impacts on soil carbon stocks and fluxes are included in LCA assessments, and that further research is conducted to enable a robust calculation of impacts under different land‐use change scenarios. Without the inclusion of these parameters, we cannot be certain that biofuels are really delivering GHG savings compared with fossil fuels.
Threshold choice and the analysis of protein marking data in long‐distance dispersal studies
Authors: Sivakoff Frances S. , Rosenheim Jay A. , Hagler James R. 
Published: June 2010

Summary1. A valuable technique in the study of insect movement is protein marking, a quantitative method where individuals are categorized as marked or unmarked based on the amount of foreign protein detected by an enzyme‐linked immunosorbent assay (ELISA).2. Whether individuals are considered marked or not is dependent on a threshold value chosen by the experimenter. The traditional method of choosing the threshold accepts some risk of false positives, wherein unmarked individuals are misclassified as marked. The error rate associated with this method, adopted from the rubidium marking literature, relies on assumptions violated by most ELISA data.3. We critically examined the effect of violating these assumptions on the false positive rate. In long‐distance dispersal studies where the ratio of unmarked to marked insects is high, false positives can seriously bias estimates of insect movement abilities.4. Simulations demonstrated that the conventional method for choosing a threshold (i) masks the presence of false positives, (ii) results in a 10‐fold higher than expected false positive rate, and (iii) relies on assumptions of normality that are rarely satisfied; non‐normality produces further increases in false positive rates.5. We provide some solutions by introducing a new procedure for choosing a threshold that decreases the incidence of false positives and allows data to be corrected for anticipated rates of false positives. This methodology should enhance researcher confidence in the data generated from dispersal studies using protein marking techniques.
Resampling Approach for Determination of the Method for Reference Interval Calculation in Clinical Laboratory Practice
Authors: Pavlov Igor Y. , Wilson Andrew R. , Delgado Julio C. 
Published: June 2010

ABSTRACTReference intervals (RI) play a key role in clinical interpretation of laboratory test results. Numerous articles are devoted to analyzing and discussing various methods of RI determination. The two most widely used approaches are the parametric method, which assumes data normality, and a nonparametric, rank-based procedure. The decision about which method to use is usually made arbitrarily. The goal of this study was to demonstrate that using a resampling approach for the comparison of RI determination techniques could help researchers select the right procedure. Three methods of RI calculation—parametric, transformed parametric, and quantile-based bootstrapping—were applied to multiple random samples drawn from 81 values of complement factor B observations and from a computer-simulated normally distributed population. It was shown that differences in RI between legitimate methods could be up to 20% and even more. The transformed parametric method was found to be the best method for the calculation of RI of non-normally distributed factor B estimations, producing an unbiased RI and the lowest confidence limits and interquartile ranges. For a simulated Gaussian population, parametric calculations, as expected, were the best; quantile-based bootstrapping produced biased results at low sample sizes, and the transformed parametric method generated heavily biased RI. The resampling approach could help compare different RI calculation methods. An algorithm showing a resampling procedure for choosing the appropriate method for RI calculations is included.
Identification of Immunologically Relevant Proteins ofChlamydophila abortusUsing Sera from Experimentally Infected Pregnant Ewes
Authors: Marques P. X. , Souda Puneet , O'Donovan J. , Gutierrez J. , Gutierrez E. J. , Worrall S. , McElroy M. , Proctor A. , Brady C. , Sammin D. , Basset H. F. , Whitelegge Julian P. , Markey B. E. , Nally J. E. 
Published: June 2010

ABSTRACTChlamydophila abortusis an intracellular pathogen and the etiological agent of enzootic abortion of ewes (EAE).C. abortushas a biphasic development cycle; extracellular infectious elementary bodies (EB) attach and penetrate host cells, where they give rise to intracellular, metabolically active reticulate bodies (RB). RB divide by binary fission and subsequently mature to EB, which, on rupture of infected cells, are released to infect new host cells. Pregnant ewes were challenged with 2 × 106inclusion forming units (IFU) ofC. abortuscultured in yolk sac (comprising both EB and RB). Serum samples were collected at 0, 7, 14, 21, 27, 30, 35, 40, and 43 days postinfection (dpi) and used to identify antigens ofC. abortusexpressed during disease. Additionally, sera from fetal lambs were collected at 30, 35, 40, and 43 dpi. All serum samples collected from experimentally infected pregnant ewes reacted specifically with several antigens of EB as determined by one-dimensional (1-D) and 2-D gel electrophoresis; reactive antigens identified by mass spectrometry included the major outer membrane protein (MOMP), polymorphic outer membrane protein (POMP), and macrophage infectivity potentiator (MIP) lipoprotein.
Genome-Wide Single Nucleotide Polymorphism Typing Method for Identification of
Bacillus anthracis
Species and Strains among
B. cereus
Group Species
Authors: Kuroda Makoto , Serizawa Masakuni , Okutani Akiko , Sekizuka Tsuyoshi , Banno Satomi , Inoue Satoshi 
Published: June 2010

ABSTRACT

As an issue of biosecurity, species-specific genetic markers have been well characterized. However,
Bacillus anthracis
strain-specific information is currently not sufficient for traceability to identify the origin of the strain. By using genome-wide screening using short read mapping, we identified strain-specific single nucleotide polymorphisms (SNPs) among
B. anthracis
strains including Japanese isolates, and we further developed a simplified 80-tag SNP typing method for the primary investigation of traceability. These 80-tag SNPs were selected from 2,965 SNPs on the chromosome and the pXO1 and pXO2 plasmids from a total of 19
B. anthracis
strains, including the available genome sequences of 17 strains in the GenBank database and 2 Japanese isolates that were sequenced in this study. Phylogenetic analysis based on 80-tag SNP typing showed a higher resolution power to discriminate 12 Japanese isolates rather than the 25 loci identified by multiple-locus variable-number tandem-repeat analysis (MLVA). In addition, the 80-tag PCR testing enabled the discrimination of
B. anthracis
from other
B. cereus
group species, helping to identify whether a suspected sample originates from the intentional release of a bioterrorism agent or environmental contamination with a virulent agent. In conclusion, 80-tag SNP typing can be a rapid and sufficient test for the primary investigation of strain origin. Subsequent whole-genome sequencing will reveal apparent strain-specific genetic markers for traceability of strains following an anthrax outbreak.
Specific Detection of Unamplified Mycobacterial DNA by Use of Fluorescent Semiconductor Quantum Dots and Magnetic Beads
Authors: Gazouli M. , Liandris E. , Andreadou M. , Sechi L. A. , Masala S. , Paccagnini D. , Ikonomopoulos J. 
Published: June 2010

ABSTRACT

Here we present the development of a specific DNA detection method using fluorescent semiconductor quantum dots (QDs) and magnetic beads (MBs) for fast detection of
Mycobacterium
spp., dispensing with the need for DNA amplification. Two biotinylated oligonucleotide probes were used to recognize and detect specific complementary mycobacterial target DNA through a sandwich hybridization reaction. Cadmium selenite QDs conjugated with streptavidin and species-specific probes were used to produce a fluorescent signal. MBs conjugated with streptavidin and a genus-specific probe were used to isolate and concentrate the DNA targets. The application of the proposed method to isolated bacteria produced the expected result in all cases. The minimum detection limit of the assay was defined as 12.5 ng of DNA diluted in a sample volume of 20 μl. In order to obtain an indication of the method's performance with clinical samples, we applied the optimized assay to the detection of
Mycobacterium tuberculosis
in DNA isolated from bronchoalveolar lavage specimens from patients with tuberculosis and
Mycobacterium avium
subsp.
paratuberculosis
in DNA isolated from feces and paraffin-embedded tissues in comparison with culture, Ziehl-Neelsen staining, and real-time PCR. The concordance of these methods compared to the proposed method with regard to positive and negative samples varied between 53.84% and 87.23% and between 84.61% and 100%, respectively. The overall accuracy of the QD assay compared to real-time PCR was 70 to 90% depending on the type of clinical material. The proposed diagnostic assay offers a simple, rapid, specific, and cost-effective method for direct detection and identification of mycobacterial DNA in clinical samples.
Mitochondrial DNA Targets Increase Sensitivity of Malaria Detection Using Loop-Mediated Isothermal Amplification
Authors: Polley Spencer D. , Mori Yasuyoshi , Watson Julie , Perkins Mark D. , González Iveth J. , Notomi Tsugunori , Chiodini Peter L. , Sutherland Colin J. 
Published: June 2010

ABSTRACT

Loop-mediated isothermal amplification (LAMP) of DNA offers the ability to detect very small quantities of pathogen DNA following minimal tissue sample processing and is thus an attractive methodology for point-of-care diagnostics. Previous attempts to diagnose malaria by the use of blood samples and LAMP have targeted the parasite small-subunit rRNA gene, with a resultant sensitivity for
Plasmodium falciparum
of around 100 parasites per μl. Here we describe the use of mitochondrial targets for LAMP-based detection of any
Plasmodium
genus parasite and of
P. falciparum
specifically. These new targets allow routine amplification from samples containing as few as five parasites per μl of blood. Amplification is complete within 30 to 40 min and is assessed by real-time turbidimetry, thereby offering rapid diagnosis with greater sensitivity than is achieved by the most skilled microscopist or antigen detection using lateral flow immunoassays.
Clinical Relevance and Diversity of Two Homologous Genes Encoding Glycosyltransferases inHelicobacter pylori
Authors: Oleastro Mónica , Santos Andrea , Cordeiro Rita , Nunes Baltazar , Mégraud Francis , Ménard Armelle 
Published: June 2010

ABSTRACTHelicobacter pyloriis known to be a major cause of peptic ulceration. Thejhp0562gene, encoding a glycosyltransferase involved in the synthesis of the lipopolysaccharide, was associated with peptic ulcer disease (PUD) in children. The β-(1,3)-galactosyltransferase [β-(1,3)GalT] gene (jhp0563), involved in Lewis (Le) antigen expression, is highly similar tojhp0562. The clinical significance and diversity of both genes were examined by PCR and sequencing of clinical strains (n= 117) isolated from children with PUD (n= 57) and nonulcer dyspepsia (NUD;n= 60). The prevalence of thejhp0562gene was significantly higher in strains with a more-virulent profile (strains positive for thecagpathogenicity island [PAI],vacAsl allele,babA,homB, phase-variable geneoipA“on” [i.e., functional], andhopQI allele). The distribution of genotypes according to clinical outcome showed that the presence ofjhp0562represented one of the greatest risks for the development of PUD. Moreover, the triple-positive genotype for thecagPAI,jhp0562, andhomBprovided the best discriminatory model for distinguishing PUD and NUD outcomes in children. Sequence andin vitroexpression analyses ofjhp0562showed the presence of a complete open reading frame, while the β-(1,3)GalT gene was shown to be a phase-variable gene. The regular presence ofjhp0562in strains with a truncated β-(1,3)GalT gene suggests thatjhp0562may also be implicated in the regulation of Le antigen expression. Overall, the results of this study suggest that thejhp0562gene is of great clinical relevance, being a useful comarker for severeH. pylori-related disease and contributing to host adaptation.
Comparative Study on Genotypic and Phenotypic Second-Line Drug Resistance Testing of
Mycobacterium tuberculosis
Complex Isolates
Authors: van Ingen Jakko , Simons Sami , de Zwaan Rina , van der Laan Tridia , Kamst-van Agterveld Miranda , Boeree Martin J. , van Soolingen Dick 
Published: June 2010

ABSTRACT

The mycobacterium growth indicator tube (MGIT960) automated liquid medium testing method is becoming the international gold standard for second-line drug susceptibility testing of multidrug- and extensively drug-resistant
Mycobacterium tuberculosis
complex isolates. We performed a comparative study of the current gold standard in the Netherlands, the Middlebrook 7H10 agar dilution method, the MGIT960 system, and the GenoType MTBDR
sl
genotypic method for rapid screening of aminoglycoside and fluoroquinolone resistance. We selected 28 clinical multidrug- and extensively drug-resistant
M. tuberculosis
complex strains and
M. tuberculosis
H37Rv. We included amikacin, capreomycin, moxifloxacin, prothionamide, clofazimine, linezolid, and rifabutin in the phenotypic test panels. For prothionamide and moxifloxacin, the various proposed breakpoint concentrations were tested by using the MGIT960 method. The MGIT960 method yielded results 10 days faster than the agar dilution method. For amikacin, capreomycin, linezolid, and rifabutin, results obtained by all methods were fully concordant. Applying a breakpoint of 0.5 μg/ml for moxifloxacin led to results concordant with those of both the agar dilution method and the genotypic method. For prothionamide, concordance was noted only at the lowest and highest MICs. The phenotypic methods yielded largely identical results, except for those for prothionamide. Our study supports the following breakpoints for the MGIT960 method: 1 μg/ml for amikacin, linezolid, and clofazimine, 0.5 μg/ml for moxifloxacin and rifabutin, and 2.5 μg/ml for capreomycin. No breakpoint was previously proposed for clofazimine. For prothionamide, a division into susceptible, intermediate, and resistant seems warranted, although the boundaries require additional study. The genotypic assay proved a reliable and rapid method for predicting aminoglycoside and fluoroquinolone resistance.