Consequences of intra-canopy and top LED lighting for uniformity of light distribution in a tomato crop

In the past decade, the potential of positioning LED lamps in between the canopy (intra-canopy) to enhance crop growth and yield has been explored in greenhouse cultivation. Changes in spatial heterogeneity of light absorption that come with the introduction of intra-canopy lighting have not been thoroughly explored. We calibrated and validated an existing functional structural plant model (FSPM), which combines plant morphology with a ray tracing model to estimate light absorption at leaflet level. This FSPM was used to visualize the light environment in a tomato crop illuminated with intra-canopy lighting, top lighting or a combination of both. Model validation of light absorption of individual leaves showed a good fit (R² = 0.93) between measured and modelled light absorption of the canopy. Canopy light distribution was then quantified and visualized in three voxel directions by means of average absorbed photosynthetic photon flux density (PPFD) and coefficient of variation (CV) within that voxel. Simulations showed that the variation coefficient within horizontal direction was higher for intra-canopy lighting than top lighting (CV=48% versus CV= 43%), while the combination of intra-canopy lighting and top lighting yielded the lowest CV (37%). Combined intra-canopy and top lighting (50/50%) had in all directions a more uniform light absorption than intra-canopy or top lighting alone. The variation was minimal when the ratio of PPFD from intra-canopy to top lighting was about 1, and increased when this ratio increased or decreased. Intra-canopy lighting resulted in 8% higher total light absorption than top lighting, while combining 50% intra-canopy lighting with 50% top lighting, increased light absorption by 4%. Variation in light distribution was further reduced when the intra-canopy LEDs were distributed over strings at four instead of two heights. When positioning LED lamps to illuminate a canopy both total light absorption and light distribution have to be considered.

Genomic diversity of the human pathogen Paracoccidioides across the South American continent

Paracoccidioidomycosis (PCM) is a life-threatening systemic mycosis widely reported in the Gran Chaco ecosystem. The disease is caused by different species from the genus Paracoccidioides, which are all endemic to South and Central America. Here, we sequenced and analyzed 31 isolates of Paracoccidioides across South America, with particular focus on isolates from Argentina and Paraguay. The de novo sequenced isolates were compared with publicly available genomes. Phylogenetics and population genomics revealed that PCM in Argentina and Paraguay is caused by three distinct Paracoccidioides genotypes, P. brasiliensis (S1a and S1b) and P. restrepiensis (PS3). P. brasiliensis S1a isolates from Argentina are frequently associated with chronic forms of the disease. Our results suggest the existence of extensive molecular polymorphism among Paracoccidioides species, and provide a framework to begin to dissect the connection between genotypic differences in the pathogen and the clinical outcomes of the disease.

The role of magnetic resonance imaging in assessing residual disease and pathologic complete response in breast cancer patients receiving neoadjuvant chemotherapy: a systematic review

OBJECTIVES

This systematic review aimed to assess the role of magnetic resonance imaging (MRI) in evaluating residual disease extent and the ability to detect pathologic complete response (pCR) after neoadjuvant chemotherapy for invasive breast cancer.

METHODS

PubMed, the Cochrane Library, MEDLINE, and Embase databases were searched for relevant studies published until 1 July 2012. After primary selection, two reviewers independently assessed the content of each eligible study using a standardised extraction form and pre-defined inclusion and exclusion criteria.

RESULTS

A total of 35 eligible studies were selected. Correlation coefficients of residual tumour size assessed by MRI and pathology were good, with a median value of 0.698. Reported sensitivity, specificity, positive predictive value and negative predictive value for predicting pCR with MRI ranged from 25 to 100 %, 50-97 %, 47-73 % and 71-100 %, respectively. Both overestimation and underestimation were observed. MRI proved more accurate in determining residual disease than physical examination, mammography and ultrasound. Diagnostic accuracy of MRI after neoadjuvant chemotherapy could be influenced by treatment regimen and breast cancer subtype.

CONCLUSIONS

Breast MRI accuracy for assessing residual disease after neoadjuvant chemotherapy is good and surpasses other diagnostic means. However, both overestimation and underestimation of residual disease extent could be observed.

MAIN MESSAGES

• Breast MRI accuracy for assessing residual disease is good and surpasses other diagnostic means. • Correlation coefficients of residual tumour size assessed by MRI and pathology were considered good. • However, both overestimation and underestimation of residual disease were observed. • Diagnostic accuracy of MRI seems to be affected by treatment regimen and breast cancer subtype.

Disability rating with the IFMSS scales

The long-term continuous care program of the Göttingen MS Information and Counseling Unit is described. In 120 patients, analysis of environmental situation showed that 1/3 of the patients had endangered family situations, 2/3 were unemployed or pensioned and 2/3 were unable to do housework. 1/3 had unsatisfactory financial situations, 1/3 were in need of better housing, 2/3 required daily personal assistance, and in 1/3 transportation was possible only in special vehicles. An attempt is made to qualify the effort and cost/benefit relation to the unit. A summary of the performance-limiting disturbances showed that there were several severe and frequently occurring disturbances which are difficult to document with the IFMSS systems. To deal with this problem, clinical profiles were developed, examples of which are given.

HLA-DRB1*0403 is associated with dominant protection against IDDM in the general Dutch population and subjects with high-risk DQA1*0301-DQB1*0302/DQA1*0501-DQB1*0201 genotype

Insulin-dependent (Type 1) diabetes mellitus (IDDM) is a genetically controlled T-cell mediated autoimmune disease. Recently, subtyping of HLA-DRB1*04 identified the HLA-DRB1*0403 allele to be associated with protection in Caucasoids with the highest risk heterozygous genotype DQA1*0301-DQB1*0302/DQA1*0501-DQB1*0201. Some studies confirmed this finding, but other reports were not consistent with a dominantly protective trait. We here report the frequency of HLA-DRB1*0403 in a large cohort (n=200) of Dutch patients with IDDM, their first-degree family members (n=370), and random controls (n=420) of the general population in The Netherlands. We found that HLA-DRB1*0403 is strongly associated with dominant protection against development of IDDM in unrelated subject, even in the context of the highest risk HLA-DQ phenotypes and HLA-DR4-DQB1*0302 (P < 0.0001).

HLA and elephantiasis revisited

A recent case-control study in Indonesia suggested that the course of Brugian filariasis and in particular resistance to the development of elephantiasis was associated with certain HLA class II alleles. In order to see whether these data could be confirmed we conducted a similar study in another Indonesian population from South Sulawesi. We could not confirm our earlier results and therefore concluded that HLA-DR and -DQ alleles are at least not strongly associated with progression to elephantiasis in Brugian filariasis. The complete data are presented also for anthropological reference purposes.

Human T cell repertoire generation in the absence of MHC class II expression results in a circulating CD4+CD8- population with altered physicochemical properties of complementarity-determining region 3

In this study, we have investigated the impact of deficient MHC class II expression on the use of TCRBV6 and TCRBJ gene elements, and on the pattern of amino acid incorporation exhibited in the N1-D-N2 segments of the third complementarity-determining region (CDR3) of these TCRBV6 rearrangements. To this end, we have analyzed circulating T cells from three, nonrelated MHC class II-deficient (bare lymphocyte syndrome (BLS)) patients and three MHC class II-expressing family members. The patients and healthy controls exhibited similar, nonrandom usage profiles of TCRBV6 and TCRBJ gene elements in both the CD4+CD8- and the CD4-CD8+ subsets of peripheral blood T cells. No statistically significant differences between patients and controls were detected in the length of CDR3, or in the amount of non-germline modification at the sites of recombination. However, detailed analysis of the TCRBV6 rearrangements derived from the CD4+CD8- subsets from the BLS patients revealed patterns of amino acid incorporation into the N1-D-N2 region of CDR3 that resulted in altered charge and hydropathicity properties of the presumed Ag binding site. In this way, we have been able to demonstrate that human T cell repertoire development in the absence of MHC class II expression results in a circulating CD4+CD8- T cell population bearing TCRs with altered CDR3 profiles. Such altered profiles are likely to be a direct reflection of the lack of MHC class II-mediated selection processes in these BLS patients.

Mismatches of minor histocompatibility antigens between HLA-identical donors and recipients and the development of graft-versus-host disease after bone marrow transplantation

BACKGROUND

Graft-versus-host disease (GVHD) can be a major complication of allogeneic bone marrow transplantation even when the donor and recipient are siblings and share identical major histocompatibility antigens. The explanation may be a mismatch of minor histocompatibility antigens. We previously characterized five minor histocompatibility antigens, HA-1, 2, 3, 4, and 5, that are recognized by T cells in association with the major histocompatibility antigens HLA-A1 an A2.

METHODS

We collected peripheral-blood leukocytes from 148 bone marrow recipients and their sibling donors, who were genotypically HLA identical. Fifty pairs were positive for HLA-A1, 117 were positive for HLA-A2, and 19 were positive for both. The pairs were typed with cytotoxic-T-cell clones specific for minor histocompatibility antigens HA-1, 2, 3, 4, and 5.

RESULTS

Mismatches of HA-3 were equally distributed among recipients in whom GVHD developed and those in whom it did not. By contrast, a mismatch of only HA-1 was significantly correlated with GVHD of grade II or higher (odds ratio, infinity; P = 0.02) in adults. One or more mismatches of HA-1, 2, 4, and 5 were also significantly associated with GVHD (odds ratio, infinity; P = 0.006) in adults. These associations were not observed in children.

CONCLUSIONS

A mismatch of minor histocompatibility antigen HA-1 can cause GVHD in adult recipients of allogeneic bone marrow from HLA-identical donors. Prospective HA-1 typing may improve donor selection and identify recipients who are at high risk for GVHD.

Human T cell repertoire generation in the absence of MHC class II expression results in a circulating CD4+CD8- population with altered physicochemical properties of complementarity-determining region 3

In this study, we have investigated the impact of deficient MHC class II expression on the use of TCRBV6 and TCRBJ gene elements, and on the pattern of amino acid incorporation exhibited in the N1-D-N2 segments of the third complementarity-determining region (CDR3) of these TCRBV6 rearrangements. To this end, we have analyzed circulating T cells from three, nonrelated MHC class II-deficient (bare lymphocyte syndrome (BLS)) patients and three MHC class II-expressing family members. The patients and healthy controls exhibited similar, nonrandom usage profiles of TCRBV6 and TCRBJ gene elements in both the CD4+CD8- and the CD4-CD8+ subsets of peripheral blood T cells. No statistically significant differences between patients and controls were detected in the length of CDR3, or in the amount of non-germline modification at the sites of recombination. However, detailed analysis of the TCRBV6 rearrangements derived from the CD4+CD8- subsets from the BLS patients revealed patterns of amino acid incorporation into the N1-D-N2 region of CDR3 that resulted in altered charge and hydropathicity properties of the presumed Ag binding site. In this way, we have been able to demonstrate that human T cell repertoire development in the absence of MHC class II expression results in a circulating CD4+CD8- T cell population bearing TCRs with altered CDR3 profiles. Such altered profiles are likely to be a direct reflection of the lack of MHC class II-mediated selection processes in these BLS patients.

HLA and elephantiasis in lymphatic filariasis

Lymphatic filariasis presents a spectrum of manifestations with infection-free asymptomatics at one end and elephantiasis at the other. In order to determine if any HLA antigens are associated with the development of elephantiasis, we compared the HLA frequencies in 55 elephantiasis patients with those in 40 controls consisting of individuals older than 45 years of age without any signs of elephantiasis. The only significant difference in class I antigen frequencies was observed for B27, which was present in 11% of the patients and absent in the controls. More differences were observed in HLA class II antigen frequencies. Both DR3 and the 2B3 epitope (on DQ6, DQ8, and DQ9 molecules) were significantly decreased in patients with elephantiasis whereas the DQ5 frequency was significantly higher in patients than in controls. Analysis of specific antibody isotype profiles revealed that DQ5-positive individuals had increased levels of antifilarial IgG3, an isotype known to be involved in tissue damage. These data suggest that HLA class II genes may control the course of Brugian filariasis by influencing the T-cell-dependent antibody repertoire.

Striking changes in smoking behaviour and lung cancer incidence by histological type in south-east Netherlands, 1960-1991

Changes in lung cancer incidence in south-east Netherlands between 1960 and 1991 were analysed, using data from the Eindhoven Cancer Registry, and related to previous changes in smoking habits. Male lung cancer incidence rates increased markedly from birth cohorts 1890-1899 to 1910-1919, followed by a decline. The peak incidences for both squamous cell carcinoma and small cell carcinoma were reached in 1978, while for adenocarcinoma it was 1985. A rising trend in female lung cancer incidence up to 1988 was found for each successive birth cohort and for every histological type. These changes in lung cancer incidence rates are most likely related to the pattern of past smoking habits: the percentage of male adult smokers in the southern part of the Netherlands decreased from 95% in 1960 to 40% in 1981 and the percentage of female adult smokers increased from 27% in 1960 to 40% in 1967, slightly decreasing only after 1979. In view of the trends in smoking behaviour, the incidence rates for male lung cancer will decline further, whereas female lung cancer incidence may decrease after the year 2000.

A computer program for predicting possible cytotoxic T lymphocyte epitopes based on HLA class I peptide-binding motifs

Vaccination with peptides recognized by antigen-specific CTLs can prevent lethal virus infections and tumor growth. In order to avoid the synthesis and testing of the numerous overlapping peptide of long AA sequences of proteins of interest, we developed a computer program which utilizes the rules, "motifs" which govern how peptides bind to HLA class I molecules, to derive a predicted binding score for each overlapping peptide. Correlations between the predicted and actual binding results to HLA-A*0201 for 100 peptides selected from six early and two late protein sequences of human papillomavirus type 1a revealed an acceptable level (61%) of concordance. The program is very flexible with regard to the input of protein sequences and motif definitions and is able to handle various motif and peptide lengths.

Insertion of N-linked glycosylation sites in the variable regions of the human immunodeficiency virus type 1 surface glycoprotein through AAT triplet reiteration

Variable regions with sequence length variation in the human immunodeficiency virus type 1 envelope exhibit an unusual pattern of codon usage with AAT, ACT, and AGT together composing > 70% of all codons used. We postulate that this distribution is caused by insertion of AAT triplets followed by point mutations and selection. Accumulation of the encoded amino acids (asparagine, serine, and threonine) leads to the creation of new N-linked glycosylation sites, which helps the virus to escape from the immune pressure exerted by virus-neutralizing antibodies.

Down syndrome phenotypes: the consequences of chromosomal imbalance

Down syndrome (DS) is a major cause of mental retardation and congenital heart disease. Besides a characteristic set of facial and physical features, DS is associated with congenital anomalies of the gastrointestinal tract, an increased risk of leukemia, immune system defects, and an Alzheimer-like dementia. Moreover, DS is a model for the study of human aneuploidy. Although usually caused by the presence of an extra chromosome 21, subsets of the phenotypic features of DS may be caused by the duplication of small regions of the chromosome. The physical map of chromosome 21 allows the molecular definition of the regions duplicated in these rare cases of partial trisomy. As a first step in identifying the genes responsible for individual DS features and their pathophysiology, a panel of cell lines derived from 16 such individuals has been established and the molecular break points have been determined using fluorescence in situ hybridization and Southern blot dosage analysis of 32 markers unique to human chromosome 21. Combining this information with detailed clinical evaluations of these patients, we have now constructed a "phenotypic map" that includes 25 features and assigns regions of 2-20 megabases as likely to contain the genes responsible. This study provides evidence for a significant contribution of genes outside the D21S55 region to the DS phenotypes, including the facies, microcephaly, short stature, hypotonia, abnormal dermatoglyphics, and mental retardation. This strongly suggests DS is a contiguous gene syndrome and augurs against a single DS chromosomal region responsible for most of the DS phenotypic features.

T-cell receptor V-gene usage in synovial fluid lymphocytes of patients with chronic arthritis

In this study we analyzed the usage frequencies of the TCR V-gene segments by alpha beta+ T cells present in synovial fluid of 17 patients with chronic arthritis, including rheumatoid arthritis. The results of this study, obtained from semiquantitative PCR analyses, showed that in all patients most of the TCR V alpha- and V beta-gene segments could be detected both in fresh PBMCs and in fresh SFMCs. The relative frequencies of use of these V-region genes were variable between the different patients. Although there was some skewing of increased usage frequencies of particular TCR V alpha and V beta genes among SFMC-derived TCRs when compared with PBMCs, we could not correlate such increased TCR V-gene usage with the inflammation in the joints as a disease-specific marker.

A personal computer program for large-scale comparisons of related nucleotide sequences

A personal computer program (COMPSEQ) has been developed which can present an informative listing of pre-aligned exonic nucleotide sequences and of their translations to amino acid sequences as well run triplet-oriented analyses on these sequences in a given reading frame. The sequence listing focuses on the differences between related sequences by suppressing the concordances between them.

Mhc-DRB diversity of the chimpanzee (Pan troglodytes)

Fifty-four chimpanzee Patr-DRB and five human HLA-DRB second exons were cloned and sequenced from thirty-five chimpanzees and four human B-cell lines and compared with known Mhc-DRB sequences of these two species. Equivalents of the HLA-DRB1*02, -DRB1*03, -DRB1*07 allelic lineages and the HLA-DRB3, -DRB4, -DRB5, -DRB6, and -DRB7 loci were all found in the chimpanzee. In addition, two chimpanzee Patr-DRB lineages (Patr-DRBX and -DRBY) were found for which no human counterparts have been described. None of the Patr-DRB sequences is identical to known HLA-DRB sequences. The Patr-DRB1*0702 and HLA-DRB1*0701 alleles are the most similar sequences in a comparison between the two species and differ by only two nucleotides out of 246 sequenced. Equivalents of the HLA-DRB1*01, -DRB1*04, and -DRB1*09 alleles were not found in our sample of chimpanzees. A per locus comparison of the number of Patr-DRB alleles with the HLA-DRB alleles shows that the Patr-DRB3, -DRB4, -DRB5, and -DRB6 locus are, thus far, more polymorphic than their human homologs. The polymorphism of the Patr-DRB1 locus seems to be less extensive than that reported for the HLA-DRB1 locus. Nevertheless, the Patr-DRB1 locus seems to be the most polymorphic of the Patr-DRB loci. Phylogenetic analyses indicate that the HLA-DRB1*09 allele may have originated from a recombination between a Mhc-DRB5 allele and the DRB1 allele of a Mhc-DR7 haplotype. Although recombination seems to increase the diversity of the Patr-DRB alleles, its contribution to the generation of Patr-DRB variation is probably low. Hence, most Patr-DRB diversity presumably accumulated via recurrent point mutations. Finally, two distinct Patr-DRB haplotypes are deduced, one of which (the chimpanzee equivalent of the HLA-DR7 haplotype) is probably older than 6-8 million years.

DNATYPE--a personal computer program for HLA-DR typing based upon restriction fragment length polymorphisms

The use of specific cDNA probes and selected combinations of restriction endonucleases makes it possible to characterize specific antigens by the molecular weights of the hybridized restriction enzyme digests of DNA. We have developed a simple program suitable for personal computers which utilizes such results to deduce HLA-DR phenotypes of any nucleated cell from which DNA may be extracted.

[The resorption of cotrimoxazol from preparations produced by different manufacturies (author's transl)]

In a pharmacokinetic study with healthy test persons we compared the forte-tablet form of cotrimoxazol produced by 4 different manufacturers. We were able to show that 3 of the tested products (2 well known standard products I and II as well as a new comparative product) achieved nearly equal high serum concentrations of sulfamethoxazole and trimethoprim. The serum concentrations of a fourth product, a generic product, were lower for sulfamethoxazole and trimethoprim. As the difference is of no statistical significance and the serum concentrations of the last product are within the therapeutic range this product is also qualified for therapeutic use. When the dose is given after a standard breakfast the serum values of sulfamethoxazole were slightly higher than if given on an empty stomach. However, the serum values of trimethoprim given on an empty stomach were higher.