bluuebunny/crossref_metadata_2025 huggingface dataset:
DETERMINATION OF DRB ALLELES USING PCR AMPLIFICATION AND ALLELE‐SPECIFIC PRIMERS
Authors: Lepage V. , Schaeffer V. , Mallet C. , Ivanova R. , & I. Khalil , Charron D.
Published: April 2007

HLA class‐II allelic diversity is commonly defined using polymerase chain reaction (PCR) in combination with sequence‐specific oligotyping (PCR‐SSO) or the combination of PCR and restriction fragment length polymorphism methods (PCR‐RFLP). Nevertheless, the identification of the DRB polymorphism by PCR‐SSO is a time‐consuming procedure and the PCR‐RFLP is cumbersome. A rapid technique which allows a precise and extensive HLA‐DRB typing is required, particularly in order to study the role of class‐II matching in organ transplantation. A DRB typing method based on the detection and length of PCR products amplified using combination of allele specific primers has been developed. Thirty‐four DRB alleles (29 DRB1, 4DRB3, 1DRB4) can be detected using 29 primers distributed into 19 amplification mixtures.
DRB, DQA, DQB AND DPB NUCLEOTIDE SEQUENCES OF SANGUINUS OEDIPUS B95‐8
Authors: Bidwell J. L. , Lu P. , Wang Y. , Zhou. K. , Clay T. M. , Bontrop R. E.
Published: April 2007

We present eight new nucleotide sequences derived from the second exons of class II genes within the major histocompatibility complex of Sanguinus oedipus (cotton‐top tamarin). These comprise two DRB alleles (Saoe‐DRB3*0504, ‐DRB*w1203), two DQA1 alleles (Saoe‐DQA1*2501, ‐DQA1*2502), two DQB1 alleles (Saoe‐DQB1*2201, ‐DQB1*2301), one DQB2 allele (Saoe‐DQB2*0101) and one DPB1 allele (Saoe‐DPB1*0101).
FREQUENCY OF HLA‐DPB1 ALLELES IN A SPANISH POPULATION: THEIR CONTRIBUTION TO RHEUMATOID ARTHRITIS SUSCEPTIBILITY
Authors: Yélamos J. , Garcéa‐Lozano J.R. , Moreno I. , Romero M. , Garcéa A. , Sánchez B.
Published: April 2007

HLA‐DPB1 allele frequencies in 181 unrelated control individuals and 70 rheumatoid factor‐positive RA patients from Seville (Spain) were determined using oligonucleotide typing methods. All frequencies shown concern the percentage of individuals positive for a certain allele. HLA‐DPB1*0401 was the most common DPB1 allele in the healthy individuals, possessed by 65.7% of them. In addition to HLA‐DPB1 *0401, only the following alleles were found in normal subjects at frequencies greater than 10%: DPB1*0101 (15.5%), DPB1*0201 (12.2%), DPB1*0301 (16.6), and DPB1*0402 (29.3%). When HLA‐DPB1 allelic frequencies were compared between seropositive RA patients and controls, a negative association for DPB1*0301 and DPB1*0401 was found in RA patients, although it failed to reach statistical significance after correction for the number of comparisons made. The other DPB1 alleles exhibited almost identical frequencies in both groups. However, when only DR4+ patients and controls were considered, the decrease in the frequency of the DPB1*0301 and DPB1*0401 alleles lacked statistical significance. On the other hand, when DR4‐ RA patients and controls were compared, the frequency of DPB1*0301 was found decreased significantly again, even more than in the whole group of patients.
DISTRIBUTION OF HLA‐A*28 ALLELES IN A SPANISH POPULATION
Authors: Yélamos J. , González M. F. , Garcéa‐Lozano J. R. , Sánchez B.
Published: April 2007

DNA oligotyping was used to determine HLA‐A28 subtypes in 25 unrelated Caucasian individuals living in or around Seville, Spain. Results showed that HLA‐A*6802 was the most frequent allele, found in 14 individuals (53.8%), followed by HLA‐68.3, which was present in eight subjects (30.8%), and both combined represented 84.6% of A28+ individuals in the area. The HLA‐A*6801 allele was found in three individuals (11.5%), whereas HLA‐A*6901 was present in one subject only (3.8%). Results indicate that the distribution of HLA‐A28 alleles can vary among different Caucasoid populations. In this way, the high frequency obtained for A*6802 supports previous studies suggesting that the HLA‐A*6802 allele was prevalent in people of the Mediterranean basin, in contrast to A*6801, prevalent in northern European populations.
A WILD‐TYPE μs C‐TERMINAL GENE IS EXPRESSED IN BLOOM'S SYNDROME CELLS
Authors: Ozawa T. , Kondo N. , Kato Y. , Motoyoshi F. , Suzuki Y. , Shimozawa N. , & K. Kasahara , Orii T.
Published: April 2007

Selective IgM deficiency is found commonly in patients with Bloom's syndrome (BS). Serum IgM concentrations were low though serum IgG and IgA concentrations were normal in both patients with BS included in the study. In a previous study the authors showed that selective IgM deficiency in BS is due to an abnormality in the maturation of surface IgM‐bearing cells into IgM‐secreting cells and a failure of secreted μ (μ s) mRNA synthesis. The membrane‐bound μ (μ m) and μ s mRNA are produced from transcripts of a single immunoglobulin μ gene by alternative RNA processing pathways. The control of μ s mRN A synthesis depends on the addition of poly(A) to μ s C‐terminal segment. The study described here demonstrated that there was no mutation or deletion in the sequence including μ s C‐terminal coding sequence, the RNA splice site (GG/TAAAC) at the 5’ end of μ s C‐terminal segment, and the AATAAA poly(A) signal sequence, and second GT‐rich element immediately down‐stream of the cleavage site in both patients.
HLA‐DPB1 DNA POLYMORPHISM IN THE SWISS POPULATION: LINKAGE DISEQUILIBRIUM WITH OTHER HLA LOCI AND POPULATION GENETIC AFFINITIES
Authors: Grundschober C. , Sanchez‐Mazas A. , Excoffier L. , Langaney A. , Jeannet M. , Tiercy J.‐M.
Published: April 2007

Allelic diversity at the HLA‐DPB1 locus was determined by PCR‐oligotyping in a sample of 125 healthy Swiss individuals. A total of 17 alleles were detected among which four main alleles (DPB 1*0401, *0201, *0301, *0402) reached a cumulative frequency of 74.8%. HLA‐A and ‐B (by serology) and HLA‐DRB1 (by oligotyping) allelic polymorphisms were analysed also. HLA‐B and HLA‐DRB1 loci were highly polymorphic with 25 and 28 alleles respectively and similar heterozygosity levels of 0.93 and 0.92. These two loci were found to be more polymorphic than expected under neutrality, while lower heterozygosity levels were found for HLA‐A (0.87) and DPB1 (0.81) loci. This paper presents also a global comparison of DPB1 allelic frequencies among 15 populations from four continents. As opposed to the DRB1 locus, overall DPB1 is shown to have a lower level of polymorphism and may be considered as neutral in all tested populations. DPB 1 genetic diversity is correlated significantly with geography also, as found previously for DRB1. Two‐ and four‐locus haplotype frequencies were determined and the significance of their linkage disequilibrium tested by an original non‐parametric method. A significant positive linkage disequilibrium was found for 11 A‐B, 16 B‐DRB1, 7 DRB1‐DPB1 and 3 A‐B‐DRB1‐DPB1 haplotypes. The overall linkage disequilibrium between DRB1 and DPB1 was much lower than expected from the physical distance and lower than for A‐B and B‐DRB1 pairs. The implications of these results for bone marrow transplantation and for the evolution of HLA loci are discussed.
COMPLEXITY OF THE BOVINE MHC CLASS‐II SPECIFICITY DW3 AS DEFINED BY ALLOANTISERA
Authors: Nilsson Ph. R. , Van't Klooster J. W. , Van Der Poel J. Y. , Davis W. C. , Schreuder G. M. T.
Published: April 2007

Alloantisera related to the bovine major histocompatibility complex (MHC) class‐II specificity Dw3 were investigated by cross‐absorption experiments and by application of the monoclonal antibody‐specific immobilization of lymphocyte antigen assay (MAILA). The absorption study revealed antibodies specific for an antigenic determinant shared by all Ds03 (Dw3)‐positive animals, and several other antibody populations recognizing the locally defined specificites Ds10, Ds11 and Ds15, that are closely associated with Ds03. The results of the MAILA‐assay indicate that the Ds03 specificity is probably encoded by DQ, whereas specificities Ds10 and Ds11 are more closely associated with DR molecules. The data presented here provide the first evidence that bovine DR and DQ specificities can be identified separately by serological methods using alloimmune antisera.
GENOMIC STRUCTURE AND ORGANIZATION OF A Q‐LIKE GENE IN THE GRC‐GIC REGION OF THE RAT
Authors: Rushton J. J. , Misra D. N. , Kunz H. W. , Cortese Hassett A. L. , Gill T. J.
Published: April 2007

In the rat homologue of the mouse Q/TL region, grc‐G/C, a TL‐like gene (RT1.N) has been identified recently. This paper reports on a Q‐like gene, designated RT1.0, that maps in the same region. It contains a 5’ untranslated region (UT), signal peptide, α3 domain, transmembrane region, cytoplasmic domain (three exons) and 3′ UT region. Comparison with mouse class‐I genes shows that the greatest similarity is to the H‐2Q, K, D and L genes; it is very different from the TL genes of the mouse and rat. A sequence that includes many CT repeats occurs in the 3′UT region of RT1.0 and in three to five other class I‐hybridizing fragments. Thus, the MHC‐linked region of the rat contains both Q‐like and TL‐like class‐I genes.
POLYMORPHISM OF BOVINE MHC CLASS II GENES. JOINT REPORT OF THE FIFTH INTERNATIONAL BOVINE LYMPHOCYTE ANTIGEN (BOLA) WORKSHOP, INTERLAKEN, SWITZERLAND, 1 AUGUST 1992
Authors: Davies C. J. , Joosten I. , Andersson L. , Arriens M. A. , Bernoco D. , Bissumbhar B. , Byrns G. , van Eijk M. J. T. , Kristensen B. , Lewin H. A. , Mikko S. , Morgan A. L. G. , Muggli‐Cockett N. E. , Nilsson Ph. R. , Oliver R. A. , Park C. A. , Van Der Poel J. J. , Polli M. , Spooner R. L. , Stewart J. A.
Published: April 2007

Polymorphism of the bovine DRB, DQA, DQB, DYA, DOB and DIB genes was investigated using restriction fragment length polymorphism (RFLP) analysis, isoelectric focusing (IEF), class II serology and polymerase chain reaction (PCR) based typing techniques. The simultaneous application of multiple typing techniques and the characterization of multiple genes resulted in a greatly enhanced picture of the bovine class II regions. Thirty‐eight class IIa (DR‐DQ) and 5 class lib (DYA‐DOB‐DIB) haplotypes were defined. It was found that IEF types were associated with DRB3 polymorphism defined by DRB3 PCR‐RFLP and DRB3 microsatellite PCR. Serologically defined polymorphism was associated with distinct molecular/IEF motifs and, therefore, DR and DQ specificities could be tentatively distinguished. Although the DR and DQ genes are tightly linked, neither DR nor DQ typing defined all of the class IIa region polymorphism. Furthermore, even the most powerful DRB3 typing technique, DRB3 PCR‐RFLP, failed to detect all expressed DRB3 polymorphism. All detected DRB3 polymorphism could, however, be distinguished with a combination of two molecular techniques: DRB3 PCR‐RFLP and DRB3 microsatellite PCR. RFLP typing with transmembrane probes detected significantly less polymorphism than typing with cDNA or exon probes. However, the transmembrane probes were useful because they were locus specific. The presence of only 5 of 12 possible class lib haplotypes was unexpected and indicates that the DYA, DOB and DIB genes are tightly linked.
THE FIRST HLA ANTHROPOLOGICAL STUDY IN THE KUWAITI POPULATION
Authors: Al‐Harbi S. , Fouad F. , Kaaba S.A.
Published: April 2007

HLA antigens of the Kuwaiti population are not as well characterized as those of other international ethnic groups. We present results for HLA typing of Kuwaiti individuals using commercial Biotest sera. Six hundred and seventy one Kuwaiti were typed for HLA‐A, ‐B, ‐C antigens and 399 were typed for HLA‐DR, ‐DQ antigens. Antigen frequency and gene frequency were computed for each phenotype observed. The antigens with the highest frequencies were HLA‐A2, A1 and A3; B5, B12 and B7; Cw″4 and Cw‐l; DR52, DR5, DR3 and DR7; DQ1 and DQ2. HLA haplotypes with strong linkage disequilibrium and characteristic of Kuwaiti population are A2‐B5, A1‐B8, B7‐DR7 and B8‐DR3. A comparison study with other populations is presented.
RAPID DNA CROSSMATCH ANALYSIS OF HLA CLASS II GENOTYPIC POLYMORPHISMS BY TEMPERATURE GRADIENT GEL ELECTROPHORESIS IN UNRELATED BONE MARROW DONOR SELECTION
Authors: Uhrberg M. , & J. Enczmann , Wernet P.
Published: April 2007

The present paper demonstrates the usefulness of the temperature gradient gel electrophoresis (TGGE) as a precise method for the rapid identification of HLA‐DR full matched donors by molecular crossmatch analysis. The resulting TGGE fingerprints are highly diverse for different HLA‐DR genotypes and identical for samples with identical HLA‐DR type, as shown for a panel of 25 randomly selected PCR‐SSO pretyped DNA samples. In addition, TGGE analysis of a panel of homozygous typing cell lines (HTCs) established, that even subtle differences in the DR4 subtypes are detectable by TGGE crossmatch analysis. Furthermore, TGGE crossmatch analysis of unrelated donor/patient pairs demonstrated, that only HLA‐DR identical patient/donor combinations showed identical TGGE patterns. Thus crossmatch analysis by TGGE presents a novel basis for a rapid and safe unrelated bone marrow donor selection strategy. Only HLA class I identical donors which also show HLA‐DR identity in the TGGE crossmatch test are selected for the final confirmation of the HLA class II genes by a suitable DNA subtyping method.
Gm and Km PHENOTYPE FREQUENCIES IN CHILDREN WITH CHRONIC ACTIVE HEPATITIS (CAH) B VIRUS INFECTION
Authors: Kacprzak‐Bergman I. , Halasa J.
Published: April 2007

Patients with CAH, extrahepatic HBV manifestation and healthy children were studied for presence of Gm 1,2,3,10,21 factors and Km 1 factor. Significantly higher frequency of Gm (1, 2, 3, 10, 21) phenotype was shown in CAH group as compared with the other two groups. Relationship between Km factors and examined groups was not found.
GENOMIC ANALYSIS OF THE F SUBTYPES OF HUMAN COMPLEMENT FACTOR B
Authors: Jahn I. , Mejéa J. E. , Thomas M. , Darke C. , Schröder H. , Geserick G. , Hauptmann G.
Published: April 2007

Factor B of human complement is encoded within the Major Histocompatibility Complex (MHC) and is polymorphic, with up to 30 alleles defined by electrophoretic mobility. One of the most common alleles, BF*F, is subdivided into the FA and FB subtypes, which differ at the gene level by non‐synonymous base substitutions in the seventh codon. We have found at this position a new restriction site polymorphism, as a Bsl I site absent from the FB allele. Using this restriction polymorphism, we have developed a method for BF F subtype determination, based on amplification by polymerase chain reaction of the 5’ end of the BF gene, and digestion with Bsl I. This new method has been applied to a panel of 29 selected BF F individuals. A single strand DNA conformation analysis of the same region of the gene allowed us to confirm the above DNA‐based BF F subtyping. During this study, two BF*F1 alleles showed discrepancies between protein and DNA typing, which were confirmed by our sequencing data. These were identical, in the 5’ region, to BF*S and BF*FB genes, respectively. In a comparison with two protein subtyping methods, identical results were found for only one third of the selected samples. The conflicting results may arise, in part, from previously undescribed molecular heterogeneity within BF F subtypes, or from the presence of a null allele. Our new method allows RF*F subtyping to be used with confidence in the definition of disease‐associated MHC haplotypes.
PCR SSCP REVEALS HAPLOTYPE RELATED POLYMORPHISM OF PERB 1: A NEW MARKER FOR MHC β BLOCK TYPING
Authors: Leelayuwat C. , Degli‐Esposti M. A. , Taylor E. , Abraham L. J. , Dawkins R. L.
Published: April 2007

Many new Major Histocompatibility Complex (MHC) genes have been discovered in the last 5 years. Defining the polymorphism of these new genes may elucidate their function and their relevance to diseases with MHC associations. Polymerase chain reaction and single stranded conformation polymorphism (PCR SSCP) analyses were used to detect sequence polymorphisms of PERB1 demonstrated by comparing the available genomic sequence of four haplotypes. This study showed that PCR SSCP of PERB 1 is reproducible. In addition, PERB1 alleles segregate within families together with MHC haplotypes. Typing results from the Forth Asia and Oceania Histocompatibility Workshop (4AOHW) cell panel indicate that the identified polymorphisms of PERB 1 are ‘haplotypic’, i.e., unrelated individuals carrying the same MHC ancestral haplotypes carry the same PERB1 SSCP pattern. Interestingly, PERB1 SSCP patterns allow the distinction of ancestral haplotypes which share HLA‐B serological specificities, such as HLA‐B44 and therefore this analysis can be used to further define MHC haplotypes and thus to improve our understanding of the evolution of this complex.
TNF Nco‐I RFLP IS NOT AN INDEPENDENT RISK FACTOR IN RHEUMATOID ARTHRITIS
Authors: Campbell D. A. , Nelson S. , Madhok R. , Field M. , Gallagher G.
Published: April 2007

The human TNF genes are located within the MHC class‐III region on chromosome 6. The presence or absence of an Nco‐I restriction site in the 5’ non‐coding sequence of the TNFβ gene defines two alleles (TNFB*1 and TNFB*2). The segregation of these alleles has been associated with levels of TNFα or TNFβ production in systemic lupus erythematosis (SLE), insulin‐dependent diabetes mellitus (IDDM) and in healthy control individuals.

Rheumatoid arthritis (RA) is characterized by high levels of TNFα within the synovial fluid and to address the question of whether this could be brought about by a genetic predisposition to high TNF production by RA individuals, we examined the distribution of this Nco‐I polymorphism in 98 healthy volunteers and 123 patients with active rheumatoid arthritis. No difference was observed between the normal and RA groups with respect to haplotype segregation or allelic frequency. Furthermore, no difference was observed between DR4+ or DR4‐ individuals in the control or RA groups.

These data demonstrate that the high level of TNFα seen in the joints of RA patients is unlikely to be due to a genetic predisposition of these patients to high TNFα production, as defined by the TNF Nco‐I restriction fragment length polymorphism (RFLP).
ANTIGENIC CHARACTERISTICS AND cDNA SEQUENCES OF HLA‐B73
Authors: Hoffmann H.J. , Kristensen T.J. , Jensen T.G. , Graugaard B. , Lamm L.U.
Published: April 2007

The cDNA sequence and serological data for HLA‐B73 are reported. Anti‐B73 sera are found relatively frequently, considering the rarity of the antigen. It was noted early that in some cases the antibodies in sera of multiparous women did not react with the eliciting cells (fathers) and thus all behaved as a naturally occurring antibody. We report on 18 B73 antisera found during the screening of 55000 Danish sera. Only one of the 17 stimulators typed also had the B73 tissue type. Ten of the stimulators had antigens from the B7 CREG (B7, B22, B27, B42, B67, B73), whereas none of the responders had such tissue types. In seven cases the serum was not able to react with the stimulator's lymphocytes in a cytotoxicity assay and in four cases the stimulator lymphocytes could not deplete the anti‐B73 activity from the serum in absorption experiments. The cDNA of B73 was expressed correctly in COS cells and was recognized on the cell surface by a monospecific serum. The α1α2 domains of B73 are most similar to those of the HLA‐B22 family. Interestingly, the α3 and transmembrane domains of HLA‐B73 are not standard human domains, but are most similar to the corresponding domains of some gorilla and chimpanzee HLA‐B genes.
IMMUNOPRINTING EXCLUDES MANY POTENTIAL SUSCEPTIBILITY GENES AS PREDISPOSING TO EARLY ONSET PAUCIARTICULAR JUVENILE CHRONIC ARTHRITIS EXCEPT HLA CLASS II AND TNF
Authors: Epplen C. , Rumpf H. , Albert E. , Haas P. , Truckenbrodt H. , Epplen J. T.
Published: April 2007

DNA profiles (immunoprints) were generated for 120 patients suffering from early onset pauciarticular chronic arthritis (EOPA‐JCA) and <500 healthy controls utilizing highly polymorphic microsatellites in the vicinity of immunorelevant genes. Six T cell receptor (TCR) markers for the CD3D, TCRDVAJ, TEA, TCRBV6S1, BV6S3, BV6S7 and BV13S2 genes were analysed. Furthermore markers for the cell surface molecule CD40L, for cytokine genes (IL‐1A, IL‐2, IFN‐α, FGF‐α, TNF‐α), the chromosomal region of the 1RF2 and the cytokine receptor gene IL5RA were studied as well as two polymorphisms within the promotor region of the TNF‐α gene. Coding region polymorphisms were evidenced indirectly by repeat length variation or they were predicted from the microsatellite distribution profiles and then confirmed by direct sequence analysis. Statistical evaluations were performed with respect to known predispositions, predominance of females (<80%) and HLA‐DR and ‐DQ haplo‐types. Cell surface molecules (TCR, CD40L, IL5RA) as well as almost all cytokines (IL‐1 A, IFNα, FGFA, IRF2 region) were excluded as predisposing in our JCA panel. The TNF‐a microsatellite alleles (GT)10–12 contribute considerably to manifestation of the disease, in HLA‐DRB1*11(12) individuals (RR = 12.8). The TNF‐α allele is not found in linkage disequilibrium with HLA‐DRB1*11(12) and may be present on either chromosome 6. Thus, a novel susceptibility factor probably within the TNFAITNFB gene region has been identified via linkage with the TNF‐α microsatellite allele. Apparently complex compositions of the genetic background rather than single genes provide the precondition for manifestation of the autoimmune disease EOPA‐JCA. Immunoprinting unravels the variability of the immunological genome via the semi‐directed microsatellite approach efficiently.
ANALYSIS OF THE MAJOR HISTOCOMPATIBILITY COMPLEX MICROSATELLITE CL1 IN DIFFERENT HUMAN HAPLOTYPES
Authors: Ulgiati D. , Grimsley G. , Leelayuwat C. , Abraham L.J.
Published: April 2007

Characterization of the region between HLA‐B and the TNF loci in the human MHC revealed the presence of duplicated loci, named CL1 and CL2, that included repeat sequences. Development and use of a PCR typing methodology that amplified both CL microsatellites simultaneously indicated that PCR product patterns analysed on native agarose gels were allelic (Abraham et al., 1992). The purpose of the current study was to determine the molecular explanation for the unique patterns achieved. Sequence analysis of the CL1 locus from 32 chromosomes representing 10 ancestral haplotypes indicated that six alleles were present. The CL microsatellites also provided an opportunity to study the evolutionary relationships between MHC haplotypes from different racial groups. Sequence comparison of closely related ancestral haplotypes from different racial groups suggested that the CL1 microsatellite has not changed in the period since divergence.
HLA‐DPB 1 POLYMORPHISM IN SEVEN SOUTH AMERICAN INDIAN TRIBES IN COLOMBIA
Authors: Briceno I. , Gomez A. , Bernal J. E. , Papiha S. S.
Published: April 2007

HLA‐DPB 1 allele frequencies were investigated in seven geographically and linguistically distinct Amerindian tribes of Colombia. Allele *1301 was found only in the Embera tribe living along the Pacific coast, while allele *0101 was found only in two individuals of the Wayuu tribe inhabiting the Guajira desert. Significant geographical variation was observed in the other two alleles (*1401 and *0402), which were found in all seven tribal groups. The possible reasons for this restricted polymorphism and the genetic diversity found in the investigation are discussed.
EXPRESSION AND FUNCTION OF HLA‐DQ8 (DQA1*0301/DQB1*0302) GENES IN TRANSGENIC MICE
Authors: Cheng S. , Baisch J. , Krco C. , Savarirayan S. , Hanson J. , Hodgson K. , Smart M. , David C.
Published: April 2007

Transgenic mice expressing HLA‐DQA1*0301 and HLA‐DQB1*0302 genes (DQ8) were produced. The transgenes were then transferred into mouse (Ab°) class II negative mice: the only class II molecules expressed in these animals were therefore coded by the HLA‐DQ8 genes. Good expression of HLA‐DQ molecules was found. Both CD4+ T cells and DQ8‐specific T‐cell receptor Vβ expressing cells were positively selected in these mice. The HLA‐DQ8 molecules expressed in these animals can present various foreign and self antigens and induce T‐cell proliferation in vitro. These mice will be invaluable in future studies of the structure and function of HLA‐DQ8 genes.
DEVELOPMENTAL EXPRESSION OF THE MOUSE MHC Q GENES
Authors: Wang Q. , Flaherty L.
Published: April 2007

To investigate the role of class lb genes in the Q region of the mouse major histocompatibility complex (MHC), the developmental expression and foetal tissue distribution of the Q genes were studied in the C57BL/6 mouse. Using RNase protection assays, we examined Q gene expression in a wide spectrum of foetal tissues at different stages of gestation. Q4, Q6 and Q8 were widely expressed in a variety of tissues. In contrast, the expression of Q1 was restricted to the thymus and intestinal epithelium.
AN APPARENT FUNCTIONAL CORRELATION BETWEEN VARIATIONS IN AMINO ACID RESIDUES IN HLA‐DR 4.1 AND 4.2 SEROLOGICAL SUBTYPES AND OLIGONUCLEOTIDE CHARACTERIZATION*
Authors: Lee. T. D. , Lee. A. , Lai S. , Huang R. , Yan L. , Lee G.
Published: April 2007

HLA‐DR4 can be subdivided serologically into two specificities, DR4.1 and DR4.2, using well‐defined monospecific alloantisera used in the 11th International Histocompatibility Workshop. In this study, a total of 1095 random DR4‐positive individuals from several ethnic groups were tested first for serotype DR4.1/4.2 and then for DRB1 *04 alleles using polymerase chain reaction (PCR) followed by sequence‐specific oligonucleotide probe hybridization (SSOPH). An almost 100% correlation between samples testing positive for DR4.1 and the presence of alanine at position 74 was observed, while samples testing positive for DR4.2 correlated with the presence of glutamic acid at position 74. DRB 1*04 alleles 0401, 0402, 0404, 0405, 0408, 0409 and 0410 are aligned in functional groups which coincide with the serological subtype of DR4.1. DRB 1*04 alleles 0403, 0406, 0407 and 0411 coincide with subtype DR4.2. Amino acid substitutions at positions 57, 71 and 86 indicate other significant variations between alleles within the serological subgroup of DR4.1 and define five minor subgroups. The serologic and oligonucleotide allelic subgroups are in turn correlated with recognized cellular Dw antigens. While sequence data provide evidence of structural differences, data on cellular antigens support a functional association between these designated groups and their significance in transplantation and GVHD. Testing results are categorized by ethnic group in order to establish frequency data for donor selection criteria.
The Use of Portfolios in Coordinated School Health Programs: Benefits and Challenges to Implementation
Authors: Barnes Seraphine Pitt , Torrens Anna , George Valerie , Brown Kelli McCormack
Published: April 2007

Background:  Coordinated school health programs (CSHP) frequently struggle with how to adequately evaluate implementation. The CSHP framework provides flexibility in how it is implemented; however, this flexibility makes it a challenge to effectively evaluate. Portfolios have been used as a technique for evaluating progress and achievement. This article describes the development and implementation of a CSHP portfolio and examines the perceptions of school personnel who have used CSHP portfolios.

Methods:  This study employed content analysis and key informant interviews. Two elementary, 4 middle, and 2 high schools in Florida participated.

Results:  Portfolios (N = 5) contained rich descriptions and program artifacts documenting each school’s CSHP goals and activities. Key informant interviews (N = 14) revealed that school personnel found value in completing CSHP portfolios. CSHP portfolios were described as helpful in assessing progress, facilitating transition with new members, and building support for their efforts. Barriers to portfolio development included lack of time, money, and human resources.

Conclusions:  This study found the use of portfolios in documenting the implementation of the CSHP feasible and useful for school personnel. Portfolios provide a rich description of CSHP activities that may not be apparent through traditional program reports used for evaluation. As portfolios continue to be used in implementing CSHP, they may be viewed as a best process for CSHP implementation and a key element in the evaluation of CSHP.
Social Influences, and Attitudes and Beliefs Associated With Smoking Among Border Latino Youth
Authors: Chalela Patricia , Velez Luis F. , Ramirez Amelie G.
Published: April 2007

Background:  Adolescent smoking rates have declined among all ethnic groups since the late 1990s. However, despite the recent declines and intervention efforts, today smoking remains a serious problem among youth, with a quarter of adolescents being current smokers by the time they complete 12th grade. This problem is particularly prevalent among Latino youth, who have among the highest rates of lifetime and past‐30‐day use. The purpose of this study was to examine the association between psychosocial factors and the smoking behavior of Latino youth living along the Mexico‐US border.

Methods:  A convenient sample of 2471 middle and high school Latino students was surveyed in fall 2000. Logistic regression analysis was used to examine the association between study risk factors and youth smoking behavior.

Results:  The strongest predictor of lifetime and past‐30‐day smoking was peer influence; however, the strength of the association was greater with recent use. There were also differences in the influence of family and attitudes and beliefs between the 2 groups.

Conclusions:  These differences need to be taken into consideration to guide development of tailored prevention and control interventions aimed at this specific group. These efforts should address social influences to smoke, particularly those from peers; promote changes in attitudes and beliefs toward smoking; increase understanding of the addictive nature of nicotine; and provide development of skills young people need to resist social and environmental pressures to smoke. Strict control and enforcement measures are needed to completely eliminate the sale of cigarettes to minors.
Multiplex PCR to Assay the Effect of Nucleic Acid‐Based Inhibitors on Prothrombin Transcript Level
Authors: Böhl Markus , Schwenzer Bernd
Published: April 2007

We compared an antisense‐oligodeoxynucleotide and four DNAzymes directed to the prothrombin mRNA for their efficiency to reduce prothrombin transcript level in HepG2 cells. The DNAzymes have different binding arm symmetry and cleavage sites, but are directed to the identical target site of the antisense‐oligodeoxynucleotide. The nucleic acid‐based inhibitors were transfected into HepG2 cells and prothrombin transcript level was quantified and normalized to the β‐actin transcript level by multiplex PCR. All nucleic acid‐based inhibitors reduced prothrombin transcript level and the effect was in almost all cases, strongest 24 h after transfection, but still remarkable up to 68 h after transfection. The antisense‐oligodeoxynucleotide was more effective than the DNAzymes tested.
Shear wave speed recovery using moving interference patterns obtained in sonoelastography experiments
Authors: McLaughlin Joyce , Renzi Daniel , Parker Kevin , Wu Zhe
Published: April 2007

Two new experiments were created to characterize the elasticity of soft tissue using sonoelastography. In both experiments the spectral variance image displayed on a GE LOGIC 700 ultrasound machine shows a moving interference pattern that travels at a very small fraction of the shear wave speed. The goal of this paper is to devise and test algorithms to calculate the speed of the moving interference pattern using the arrival times of these same patterns. A geometric optics expansion is used to obtain Eikonal equations relating the moving interference pattern arrival times to the moving interference pattern speed and then to the shear wave speed. A cross-correlation procedure is employed to find the arrival times; and an inverse Eikonal solver called the level curve method computes the speed of the interference pattern. The algorithm is tested on data from a phantom experiment performed at the University of Rochester Center for Biomedical Ultrasound.
Quantifying the uncertainty of geoacoustic parameter estimates for the New Jersey shelf by inverting air gun data
Authors: Jiang Yong-Min , Chapman N. Ross , Badiey Mohsen
Published: April 2007

This paper describes geoacoustic inversion of low frequency air gun data acquired during an experiment on the New Jersey shelf. Hybrid optimization and Bayesian inversion techniques based on matched field processing were applied to multiple shots from three air gun data sets recorded by a vertical line array in a long-range shallow water geometry. For the Bayesian inversions, full data error covariance matrix was estimated from a set of consecutive shots that had high temporal coherence and small spatial variation in source position. The effect of different data error information on the geoacoustic parameter uncertainty estimates was investigated by using the full data error covariance matrix, a diagonalized version of the full error covariance, and a diagonal matrix with identical variances. The comparison demonstrated that inversion using the full data error information provided the most reliable parameter uncertainty estimates. The inversions were highly sensitive to the near sea floor geoacoustic parameters, including sediment attenuation, of a simple single-layer geoacoustic model. The estimated parameter values of the model were consistent with depth averaged values (over wavelength scales) of a high resolution geoacoustic model developed from extensive ground truth information. The interpretation of the frequency dependence of the estimated attenuation is also discussed.
Beamforming using spatial matched filtering with annular arrays
Authors: Kim Kang-Sik , Liu Jie , Insana Michael F.
Published: April 2007

A linear array beamforming method for ultrasonic B-mode imaging using spatial matched filtering (SMF) and a rectangular aperture geometry was recently proposed Kim et al., [J. Acoust. Soc. Am. 120, 852–861 (2006)]. This letter extends those results to include circularly symmetric apertures. SMF applied to annular arrays can improve the lateral resolution and echo signal-to-noise ratio as compared with conventional dynamic-receive delay-sum beamforming. At high frequencies, where delay and sum beamforming is problematic, SMF showed greatly improved target contrast over an extended field of view.
Time course of speech changes in response to unanticipated short-term changes in hearing state
Authors: Perkell Joseph S. , Lane Harlan , Denny Margaret , Matthies Melanie L. , Tiede Mark , Zandipour Majid , Vick Jennell , Burton Ellen
Published: April 2007

The timing of changes in parameters of speech production was investigated in six cochlear implant users by switching their implant microphones off and on a number of times in a single experimental session. The subjects repeated four short, two-word utterances, ∕dV1n♯SV2d∕ (S=∕s∕ or /ʃ/), in quasi-random order. The changes between hearing and nonhearing states were introduced by a voice-activated switch at V1 onset. “Postural” measures were made of vowel sound pressure level (SPL), duration, F0; contrast measures were made of vowel separation (distance between pair members in the formant plane) and sibilant separation (difference in spectral means). Changes in parameter values were averaged over multiple utterances, lined up with respect to the switch. No matter whether prosthetic hearing was blocked or restored, contrast measures for vowels and sibilants did not change systematically. Some changes in duration, SPL and F0 were observed during the vowel within which hearing state was changed, V1, as well as during V2 and subsequent utterance repetitions. Thus, sound segment contrasts appear to be controlled differently from the postural parameters of speaking rate and average SPL and F0. These findings are interpreted in terms of the function of hypothesized feedback and feedforward mechanisms for speech motor control.
Theoretical foundations of apparent-damping phenomena and nearly irreversible energy exchange in linear conservative systems
Authors: Carcaterra A. , Akay A.
Published: April 2007

This paper discusses a class of unexpected irreversible phenomena that can develop in linear conservative systems and provides a theoretical foundation that explains the underlying principles. Recent studies have shown that energy can be introduced to a linear system with near irreversibility, or energy within a system can migrate to a subsystem nearly irreversibly, even in the absence of dissipation, provided that the system has a particular natural frequency distribution. The present work introduces a general theory that provides a mathematical foundation and a physical explanation for the near irreversibility phenomena observed and reported in previous publications. Inspired by the properties of probability distribution functions, the general formulation developed here is based on particular properties of harmonic series, which form the common basis of linear dynamic system models. The results demonstrate the existence of a special class of linear nondissipative dynamic systems that exhibit nearly irreversible energy exchange and possess a decaying impulse response. In addition to uncovering a new class of dynamic system properties, the results have far-reaching implications in engineering applications where classical vibration damping or absorption techniques may not be effective. Furthermore, the results also support the notion of nearly irreversible energy transfer in conservative linear systems, which until now has been a concept associated exclusively with nonlinear systems.
The measurement problem in level discrimination
Authors: Shepherd Daniel , Hautus Michael J.
Published: April 2007

There is disagreement among theorists over the exact measure to be used to quantify auditory level discrimination. It has been proposed that, for level discrimination tasks, the measure that is most linearly related to the sensitivity index, d′, will be the correct measure. The level difference (ΔL) and the Weber fraction (Θ) are both candidates, though the latter is sensitive to the physical unit in which it is expressed (e.g., pressure or intensity) while the former is not. Psychometric functions for level discrimination were obtained at a number of pedestal levels for 10-ms sinusoids (either 1000 or 6500Hz) and broadband noise bursts. These functions were used to assess which of three measures: ΔL, Θ=Δp∕p, or Θ=ΔI∕I, is most nearly linearly related to d′. The results suggest that Δp∕p is the measure that comes closest to being linearly related to d′.
Periodic orbit theory in acoustics: spectral fluctuations in circular and annular waveguides
Authors: Wright M. C. M. , Ham C. J.
Published: April 2007

Formulas based on the theory of Weyl are widely used to obtain the average number of modes at or below a given frequency in acoustic and vibrational waveguides. These formulas are valid at asymptotically high frequencies; at finite frequencies they are subject to some error, due to fluctuations in the mode count, which depend on the shape of the waveguide. The periodic orbit theory of semiclassical physics is used to give estimates of the variance of these fluctuations and these results are compared with numerical estimates based on eigenvalues obtained by root-finding. The comparison is good but shows errors that can be related to the nature of the periodic orbit theory. Engineering formulas are provided that give an accurate approximation without significant computational cost. The results are valid for membranes, ducts, and thin plates with clamped and/or simply supported boundary conditions.
The effect of impedance on interaural azimuth cues derived from a spherical head model
Authors: Treeby Bradley E. , Paurobally Roshun M. , Pan Jie
Published: April 2007

Recent implementations of binaural synthesis have combined high-frequency pinna diffraction data with low-frequency acoustic models of the head and torso. This combination ensures that the salient cues required for directional localization in the horizontal plane are consistent with psychophysical expectations, regardless of the accuracy or match of the high-frequency cues, or the fidelity of experimental low-frequency information. This paper investigates the effect of a nonrigid boundary condition on the surface pressure and the resulting interaural cues used for horizontal localization. These are derived from an analytical single sphere diffraction model assuming a locally reacting and uniformly distributed impedance boundary condition. Decreasing the magnitude of a purely resistive surface impedance results in an overall decrease in the sphere surface pressure level, particularly in the posterior region. This produces nontrivial increases in both the interaural level and time difference, especially for sound source directions near the interaural axis. When the surface impedance contains a reactive component the interaural cues exhibit further changes. The basic impedance characteristics of human hair and their incorporation into the sphere diffraction model are also discussed.
Optical and acoustic monitoring of bubble cloud dynamics at a tissue-fluid interface in ultrasound tissue erosion
Authors: Xu Zhen , Hall Timothy L. , Fowlkes J. Brian , Cain Charles A.
Published: April 2007

Short, high-intensity ultrasound pulses have the ability to achieve localized, clearly demarcated erosion in soft tissue at a tissue-fluid interface. The primary mechanism for ultrasound tissue erosion is believed to be acoustic cavitation. To monitor the cavitating bubble cloud generated at a tissue-fluid interface, an optical attenuation method was used to record the intensity loss of transmitted light through bubbles. Optical attenuation was only detected when a bubble cloud was seen using high speed imaging. The light attenuation signals correlated well with a temporally changing acoustic backscatter which is an excellent indicator for tissue erosion. This correlation provides additional evidence that the cavitating bubble cloud is essential for ultrasound tissue erosion. The bubble cloud collapse cycle and bubble dissolution time were studied using the optical attenuation signals. The collapse cycle of the bubble cloud generated by a high intensity ultrasound pulse of 4–14μs was ∼40–300μs depending on the acoustic parameters. The dissolution time of the residual bubbles was tens of ms long. This study of bubble dynamics may provide further insight into previous ultrasound tissue erosion results.
Loudness changes induced by a proximal sound: Loudness enhancement, loudness recalibration, or both?
Authors: Oberfeld Daniel
Published: April 2007

The effect of a forward masker on the loudness of a target tone in close temporal proximity was investigated. Loudness matches between a target and a comparison tone at the same frequency were obtained for a wide range of target and masker levels. Contrary to the hypothesis by Scharf, Buus, and Nieder [J. Acoust. Soc. Am. 112, 807–810 (2002)], these matches could not be explained by an effect of the masker on the comparison loudness, which was measured by loudness matches between the comparison and a fourth tone separated in frequency from the comparison and the masker. The data thus demonstrate that a forward masker has an effect on the loudness of a proximal target. The results are compatible with the suggestion by Arieh and Marks [J. Acoust. Soc. Am. 114, 1550–1556 (2003)] that the masker triggers two processes. The data indicate that the effect of the slower-decaying process resulting in a reduction in the loudness of a following tone saturates at masker-target level differences of 10–20dB. The faster-decaying process causing loudness enhancement or loudness decrement has the strongest effect at a masker-target level difference of approximately 30dB. A model explaining this mid-difference hump is proposed.
Perception of roughness by listeners with sensorineural hearing loss
Authors: Tufts Jennifer B. , Molis Michelle R.
Published: April 2007

The perception of auditory roughness presumably results from imperfect spectral or temporal resolution. Sensorineural hearing loss, by affecting spectral resolution, may therefore alter roughness perception. In this study, normal-hearing and hearing-impaired listeners estimated the roughness of amplitude-modulated tones varying in carrier frequency, modulation rate, and modulation depth. Their judgments were expected to reflect effects of impaired spectral resolution. Instead, their judgments were similar, in most respects, to those of normally-hearing listeners, except at very slow modulation rates. Results suggest that mild-to-moderate sensorineural hearing loss increases the roughness of slowly fluctuating signals.
Statistical modeling of natural auditory source event perception
Authors: Pastore Richard , Flint Jesse , Gaston Jeremy
Published: April 2007

Challenges to understanding auditory source perception can be understood by contrast with classic psychophysics. Psychophysics studies the relationship between properties of sound and perception; by mapping changes in a single perceptual dimension as a function of controlled, systematic variation in a single acoustic property. This severely limits the degrees of freedom for both the listeners strategy and the investigators interpretation of the complex, often nonlinear, sound-perception relationships. Source perception investigation not only adds the original event as an analysis stage, but also multiple levels of complexity to every component in the analysis stages. Natural source events are complex and, although acoustic properties must reflect source event structure, variation in many acoustic dimensions of the produced sounds is determined both separately and interactively by attributes that vary with all source properties, including the one(s) investigated. Furthermore, physical acoustic dimensions seldom map directly to perceptual dimensions. Finally, listeners have many degrees of freedom in assigning importance weighting to the multitude of sound attributes, differ in their weightings, and are seldom optimal. The current paper discusses statistical modeling approaches for developing a systematic understanding of the relationships among the source-sound-perception components to event perception. [Work supported by NSF grant BCS-0213666.]
Clinical presentation and incidence of complications in patients with coeliac disease diagnosed by relative screening
Authors: Sundar Neela , Crimmins Rosemary , Swift Gillian L
Published: April 2007

Background

There is an increased prevalence of coeliac disease (CD) among relatives of those with the disease.

Aims

To compare the clinical features in patients with CD detected via family screening with those in patients diagnosed routinely.

Methods

Information on screening was provided to relatives of patients. Those who wished to be screened were tested for endomysial and/or tissue transglutaminase antibodies. Duodenal biopsy was performed in those with positive antibodies. The clinical details of the relative screening group were compared with those of 105 patients diagnosed routinely.

Results

183 relatives underwent screening, of whom 32 had positive serology, 24 had histology diagnostic of CD, six had normal biopsies and two declined duodenal biopsy. Patients in the relative screening group were younger with a median age of 33 years (range 17–72 years) compared to the routine group which had a median age of 54 years (range 25–88 years). In the relative screening group, there was a male preponderance (M:F ratio 16:8), anaemia at presentation was significantly less common (13% v 58%; p<0.001) and osteoporosis was less frequent (9% v 22%; p<0.244) compared with the routine group. 65% of the relative screening group had gastrointestinal symptoms or anaemia at diagnosis.

Conclusions

Patients detected by family screening are younger with a male preponderance, but fewer had anaemia and osteoporosis.