cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5104645.v1
title: Supplementary Material for: Exclusion of <i>NFYB </i>as candidate gene for congenital splay leg in piglets and radiation hybrid mapping of further five homologous porcine genes from human chromosome 12 (HSA12)

description: Nuclear transcription factor Y, beta (<i>NFYB)</i> was evaluated as candidate gene for congenital splay leg in piglets based on data from differential display and QTL analysis. We mapped <i>NFYB</i> to pig chromosome 5 (SSC5). By assigning further five porcine genes from the corresponding region on human chromosome (HSA) 12q23.3→ q24.11 to SSC5 and 14 we could confine an evolutionary breakpoint from an interval of more than 10 Mb to less than 400 kb. Comparative sequence analysis of the coding region of <i>NFYB</i> in healthy and splay leg piglets revealed no polymorphism. Inter-species conservation of the codons ranges from 87% to 95% between pig, human, cow, dog, rat and mouse, respectively. The expression of <i>NFYB</i> in M. biceps femoris was not different between healthy and splay leg piglets. However, healthy male piglets had a significantly higher expression than females. Our results exclude <i>NFYB</i> as candidate gene for congenital splay leg but provide a basis for selection of further candidates for the disease from SSC5.
DOI: 10.6084/m9.figshare.5104639.v1
title: Supplementary Material for: Recombinant Major Urinary Proteins of the Mouse in Specific IgE and IgG Testing

description: <i>Background:</i> Recombinant allergens are preferred over natural allergen extracts in measuring antibodies. We tested the use of recombinant variants of the major mouse allergen Mus m 1 in detection of mouse-specific antibodies in sera of laboratory animal workers and children. <i>Methods:</i> Six recombinant major urinary proteins (MUPs) were produced and antibody-binding capacity was compared to natural Mus m 1 and to mouse urine extract. In a specific subset, cross-reactivity of MUP with Mus m 1 and between the different recombinant MUPs was determined. <i>Results:</i> For IgE antibodies, MUP8 showed high cross-reactivity with Mus m 1. MUP8-specific IgE was found in 55% of the mouse urine IgE-positive sera. Specific IgG and IgG4 antibodies against natural Mus m 1 correlated strongly with antibodies against recombinant MUP8 and were cross-reactive. IgG4 levels against MUP8 and mouse urine extract correlated, but detection of mouse urine-specific IgG4 in the absence of MUP-specific IgG4 was not uncommon. Cross-reactivity of IgG antibodies between MUP8 and Mus m 1 as well as between the different MUPs was high and inhibition varied between 54 and 99%. <i>Conclusion:</i> The mouse allergen Mus m 1 can be replaced in antibody testing by recombinant MUP8. Other MUPs, except MUP4, are interchangeable with MUP8. However, mouse urine extract showed better detection of both mouse-specific IgE and IgG4 levels. Other components in the mouse urine, like mouse albumin and other yet unidentified components, also induce IgE and IgG(4) antibodies.
DOI: 10.6084/m9.figshare.5104648.v1
title: Supplementary Material for: Assessment of Suitability of Thrombolysis in Middle Cerebral Artery Infarction: A Proof of Concept Study of a Stereologically-Based Technique

description: <i>Background:</i> The extent of cerebral ischemia, assessed by the Alberta Stroke Program Early CT Score (ASPECTS) method and unaided visual determination of the CT Summit Criterion, correlates with increased risk of intracerebral hemorrhage following rt-PA administration. Concerns about the accuracy of the unaided visual assessment in the estimation of infarct size and the conservative nature of the ASPECTS method led us to develop a new method (MCAGrid) based on stereological grid counting and a digital atlas of the middle cerebral artery (MCA) infarct territory. <i>Methods:</i> We tested the hypotheses that the stereological method increases the accuracy of infarct estimation and that the number of patients deemed eligible for thrombolysis is greater with this method than with existing methods. Four experienced radiologists with extensive neuroradiological experience examined the CT images of 19 patients with MCA territory stroke and determined patient eligibility for thrombolysis by: unaided visual determination of the CT Summit Criterion, MCAGrid, and the ASPECTS score. The χ<sup>2</sup> test was used to compare the differences in the number of patients deemed ‘eligible’ for thrombolysis by the 3 imaging methods. Further, the unaided visual assessment and MCAGrid were compared with volumes calculated following manual segmentation of infarct, and the sensitivity, specificity and positive and negative likelihood ratios for these techniques were calculated. <i>Results:</i> In general, MCAGrid was better than unaided visual assessment in the prediction of &gt;1/3 involvement of the MCA territory by infarct. The number of patients considered as ‘eligible’ for thrombolysis based on imaging criteria was significantly lower when ASPECTS criteria (15/76) were used than when unaided visual determination of the CT Summit Criterion (32/76; p &lt; 0.01) or MCAGrid (59/76; p &lt; 0.001) criteria were used. <i>Conclusion:</i> The choice of methods for rating infarct extent affects the number of patients ‘eligible’ for thrombolysis significantly. Furthermore, MCAGrid increased the accuracy with which infarct extent was estimated. These results provide justification for a prospective study of this technique in the setting of acute stroke.
DOI: 10.6084/m9.figshare.5104627
title: Supplementary Material for: Topo-Proteomic in situ Analysis of Psoriatic Plaque under Efalizumab Treatment

description: In a pilot study 6 psoriasis patients were treated over 12 weeks with efalizumab targeting the CD11a subunit of LFA-1. The treatment was well tolerated. Five of these patients proved to be responders with an average decrease in psoriasis area and severity index (PASI) from 21.3 ± 5.4 (day 0) to 3.9 ± 0.6 (week 12). The nonresponder was subsequently successfully treated with cyclosporin. Skin biopsies were taken before and after efalizumab treatment and subjected to Multi-Epitope Ligand Cartography (MELC) robot microscopy. A MELC library of 46 antibodies including FITC-labeled efalizumab was chosen focusing upon inflammatory epitopes. Quantification of marker expression was performed using a special adaptation to the needs of skin tissue in terms of pixel events normalized to a standardized horizontal skin width of 100 µm. The before-versus-after comparison for the responders revealed at the ‘single epitope level’ of MELC analysis a significant decrease (p &lt; 0.05) in epidermal thickness (represented by pan-cytokeratin, CD71, CD138), of the expression of common leukocyte antigen (CD45), T-cell markers (CD2, CD4, CD8, CD45R0), CD11a, efalizumab binding site (EfaBS), and CD58. At the ‘EfaBS-centered, double colocation level’ a corresponding decrease was observed for CD2, CD3, CD4, CD8, CD11a, CD13, CD26, CD44, CD45, CD45R0, CD54, CD62L, HLA-DR, and TIA-1. MELC analysis at the ‘multicombinatorial level’ revealed predominant combinatorial molecular phenotype (CMP) motifs, which showed an efalizumab treatment-dependent significant decrease. These CMP motifs were defined as toponomic combinations of lead markers for (i) leukocytes in general (CD45), (ii) T cells (CD2, CD3, CD4, CD45R0, CD45RA), (iii) macrophages (CD68), (iv) cell activation (CD13, CD26, HLA-DR), and (v) cell adhesion (CD11a, EfaBS). Thirty-five of the most relevant 50 CMP motifs were directly related to the T-cell type. A descriptive statistical analysis of the nonresponder before treatment showed a below-responder range degree of expression for CD4, CD8, CD44 (H-CAM), CD56, CD62L, HLA-DQ, and also for these epitopes in colocation with EfaBS. In the nonresponder and before treatment we observed an above-responder range degree of expression for CD54 (ICAM-1) as LFA-1 ligand. In conclusion, the topo-proteomic data provide new diversified insights into the pleiotropic cellular dynamics in psoriatic skin lesions under effective efalizumab treatment. Moreover, the data may be relevant to the future development of possible strategies for individual prediction of efalizumab treatment response or nonresponse.
DOI: 10.6084/m9.figshare.5104633
title: Supplementary Material for: Patterns of Linkage Disequilibrium between SNPs in a Sardinian Population Isolate and the Selection of Markers for Association Studies

description: <i>Objective:</i> In isolated populations, ‘background’ linkage disequilibrium (LD) has been shown to extend over large genetic distances. This and their reduced environmental and genetic heterogeneity has stimulated interest in their potential for association mapping. We compared LD unit map distances with pair-wise measurements of LD in a dense single nucleotide polymorphism (SNP) set. <i>Methods:</i> We genotyped 771 SNPs in an 8 Mb segment of chromosome 22 on 101 individuals from the isolated village of Talana, Sardinia, and compared with outbred European populations. <i>Results:</i> Heterozygosity was remarkably similar in both populations. In contrast, the extent of LD observed was quite different. The decay of LD with distance is slower in the isolate. The differences in LD map lengths suggest that useful LD extends up to three times farther in the Sardinian population; smaller differences are seen with pairwise LD metrics. While LD map length slightly decreases with average relatedness, cryptic relatedness does not explain the decrease in LD map length. Haplotypes, block boundaries, and patterns of LD are similar in both populations, suggesting a shared distribution of recombination hotspots. <i>Conclusions:</i> About 15% fewer haplotype tagging SNPs need to be genotyped in the isolate, and possibly 70% fewer if selecting SNPs evenly spaced on the metric LD map.
DOI: 10.6084/m9.figshare.5104636.v1
title: Supplementary Material for: The Phylogeography of African Brazilians

description: <i>Background/Aims:</i> Approximately four million Africans were taken as slaves to Brazil, where they interbred extensively with Amerindians and Europeans. We have previously shown that while most White Brazilians carry Y chromosomes of European origin, they display high proportions of African and Amerindian mtDNA lineages, because of sex-biased genetic admixture. <i>Methods:</i> We studied the Y chromosome and mtDNA haplogroup structure of 120 Black males from Sao Paulo, Brazil. <i>Results:</i> Only 48% of the Y chromosomes, but 85% of the mtDNA haplogroups were characteristic of sub-Saharan Africa, confirming our previous observation of sexually biased mating. We mined literature data for mtDNA and Y chromosome haplogroup frequencies for African native populations from regions involved in Atlantic Slave Trade. Principal Components Analysis and Bayesian analysis of population structure revealed no genetic differentiation of Y chromosome marker frequencies between the African regions. However, mtDNA examination unraveled considerable genetic structure, with three clusters at Central-West Africa, West Africa and Southeast Africa. A hypothesis is proposed to explain this structure. <i>Conclusion:</i> Using these mtDNA data we could obtain for the first time an estimate of the relative ancestral contribution of Central-West (0.445), West (0.431) and Southeast Africa (0.123) to African Brazilians from Sao Paulo. These estimates are consistent with historical information.
DOI: 10.6084/m9.figshare.5104624
title: Supplementary Material for: Postlaryngectomy Vocal Rehabilitation: Assessment Using a Validated Questionnaire in 51 Patients

description: <i>Background:</i> This study aimed to assess valved speech and related issues in total laryngectomy patients with the help of the validated Voice Prosthesis Questionnaire (VPQ). <i>Patients and Methods:</i> We identified 61 patients who had undergone a surgical voice restoration with a valve following total laryngectomy and who were sent the VPQ by mail. <i>Results:</i> Fifty-one patients (37 males) completed the questionnaire giving a response rate of 83.6%. Fifty-three percent of the patients (n = 27) were fully aware of the dimensions of their valve including the length and diameter, whilst 25% (n = 13) were aware of only one of the two. There was a strong correlation between the patient’s perception of tone and their gender with the tone scores significantly lower in women as compared to men (Mann-Whitney test, p = 0.04). Ten patients (19.6%) had had leakage-related issues during the previous 7 days. <i>Conclusions:</i> This questionnaire provided a significant amount of valuable data. Based on our experience, we recommend the VPQ for prospective use in the serial monitoring and audit of total laryngectomy patients.
DOI: 10.6084/m9.figshare.5104627.v1
title: Supplementary Material for: Topo-Proteomic in situ Analysis of Psoriatic Plaque under Efalizumab Treatment

description: In a pilot study 6 psoriasis patients were treated over 12 weeks with efalizumab targeting the CD11a subunit of LFA-1. The treatment was well tolerated. Five of these patients proved to be responders with an average decrease in psoriasis area and severity index (PASI) from 21.3 ± 5.4 (day 0) to 3.9 ± 0.6 (week 12). The nonresponder was subsequently successfully treated with cyclosporin. Skin biopsies were taken before and after efalizumab treatment and subjected to Multi-Epitope Ligand Cartography (MELC) robot microscopy. A MELC library of 46 antibodies including FITC-labeled efalizumab was chosen focusing upon inflammatory epitopes. Quantification of marker expression was performed using a special adaptation to the needs of skin tissue in terms of pixel events normalized to a standardized horizontal skin width of 100 µm. The before-versus-after comparison for the responders revealed at the ‘single epitope level’ of MELC analysis a significant decrease (p &lt; 0.05) in epidermal thickness (represented by pan-cytokeratin, CD71, CD138), of the expression of common leukocyte antigen (CD45), T-cell markers (CD2, CD4, CD8, CD45R0), CD11a, efalizumab binding site (EfaBS), and CD58. At the ‘EfaBS-centered, double colocation level’ a corresponding decrease was observed for CD2, CD3, CD4, CD8, CD11a, CD13, CD26, CD44, CD45, CD45R0, CD54, CD62L, HLA-DR, and TIA-1. MELC analysis at the ‘multicombinatorial level’ revealed predominant combinatorial molecular phenotype (CMP) motifs, which showed an efalizumab treatment-dependent significant decrease. These CMP motifs were defined as toponomic combinations of lead markers for (i) leukocytes in general (CD45), (ii) T cells (CD2, CD3, CD4, CD45R0, CD45RA), (iii) macrophages (CD68), (iv) cell activation (CD13, CD26, HLA-DR), and (v) cell adhesion (CD11a, EfaBS). Thirty-five of the most relevant 50 CMP motifs were directly related to the T-cell type. A descriptive statistical analysis of the nonresponder before treatment showed a below-responder range degree of expression for CD4, CD8, CD44 (H-CAM), CD56, CD62L, HLA-DQ, and also for these epitopes in colocation with EfaBS. In the nonresponder and before treatment we observed an above-responder range degree of expression for CD54 (ICAM-1) as LFA-1 ligand. In conclusion, the topo-proteomic data provide new diversified insights into the pleiotropic cellular dynamics in psoriatic skin lesions under effective efalizumab treatment. Moreover, the data may be relevant to the future development of possible strategies for individual prediction of efalizumab treatment response or nonresponse.
DOI: 10.6084/m9.figshare.5104630
title: Supplementary Material for: ‘Mini-Gauge’ Pars Plana Vitrectomy: ‘Inside-Out View’ with the GRIN Solid Rod Endoscope

description: <i>Purpose:</i> To stimulate the discussion about ‘mini-gauge’ pars plana vitrectomy. <i>Methods:</i> Gradient index high-resolution endoscopy to analyze the 23- or 25-gauge access into the vitreous cavity. A total number of 66 pars plana interventions (almost 200 cannulas) were performed and recorded with the gradient index solid rod endoscope as well as through the microscope. <i>Results:</i> Five main ‘inside-out’ observations were made through the endoscope. Some very slight rotating movement of the trocar was required to achieve a safe cannula implantation. Rotating the cannula too much could result in some unwanted side effects. The major amount of vitreous incarceration occurs during the implantation of cannulas. Incarcerated vitreous causes significant anterior-posterior vitreous traction. Intraocular cleaning of the port with the suction cutter releases the anterior-posterior traction without increasing the postoperative rate and degree of hypotony. Side effects like bleeding of the wound are likely to occur due to any sort of manipulation to the outside of the sclerotomy (i.e. cotton tips) other than the essential replacement of the conjunctiva. <i>Discussion:</i> Surgeons who are considering the conversion to mini-gauge pars plana vitrectomy systems may be aided by endoscopic observations.
DOI: 10.6084/m9.figshare.5104633.v1
title: Supplementary Material for: Patterns of Linkage Disequilibrium between SNPs in a Sardinian Population Isolate and the Selection of Markers for Association Studies

description: <i>Objective:</i> In isolated populations, ‘background’ linkage disequilibrium (LD) has been shown to extend over large genetic distances. This and their reduced environmental and genetic heterogeneity has stimulated interest in their potential for association mapping. We compared LD unit map distances with pair-wise measurements of LD in a dense single nucleotide polymorphism (SNP) set. <i>Methods:</i> We genotyped 771 SNPs in an 8 Mb segment of chromosome 22 on 101 individuals from the isolated village of Talana, Sardinia, and compared with outbred European populations. <i>Results:</i> Heterozygosity was remarkably similar in both populations. In contrast, the extent of LD observed was quite different. The decay of LD with distance is slower in the isolate. The differences in LD map lengths suggest that useful LD extends up to three times farther in the Sardinian population; smaller differences are seen with pairwise LD metrics. While LD map length slightly decreases with average relatedness, cryptic relatedness does not explain the decrease in LD map length. Haplotypes, block boundaries, and patterns of LD are similar in both populations, suggesting a shared distribution of recombination hotspots. <i>Conclusions:</i> About 15% fewer haplotype tagging SNPs need to be genotyped in the isolate, and possibly 70% fewer if selecting SNPs evenly spaced on the metric LD map.
DOI: 10.6084/m9.figshare.5104612
title: Supplementary Material for: Extent of linkage disequilibrium in chicken

description: Many of the economically important traits in chicken are multifactorial and governed by multiple genes located at different quantitative trait loci (QTLs). The optimal marker density to identify these QTLs in linkage and association studies is largely determined by the extent of linkage disequilibrium (LD) around them. In this study, we investigated the extent of LD on two chromosomes in a white layer and two broiler chicken breeds. Pairwise levels of LD were calculated for 33 and 36 markers on chromosomes 10 and 28, respectively. We found that useful LD (i.e. an r<sup>2</sup> value higher than 0.3) in Nutreco chicken breed E5 (inbred) can extend to around 1 cM on chromosomes 10 and 28, although in a second region on chromosome 28 it extends to about 2.5 cM. The extent in breed Nutreco E3 (outbred) was very short in chromosome 10 (15 kb) but very much larger on chromosome 28, particularly in one region of depressed heterozygosity. The layer breed E2 (inbred) showed an extent of useful LD up to 4 cM on chromosome 10; the extent on chromosome 28 could not be assessed due to an erratic pattern of LD on that chromosome, although in one region LD appears to be in the order of 0.8 cM. This indicates that there may be very large differences in patterns of LD between different chicken breeds and different genomic regions.
DOI: 10.6084/m9.figshare.5104615
title: Supplementary Material for: Supportive Evidence for the Anticancerous Potential of Alternative Medicine against Hepatocarcinogenesis in Mice

description: The present study examines if Lycopodium 200 (Lyco-200) has demonstrable anti-cancer activities in mice which are chronically fed carcinogens, p-dimethylaminoazobenzene (p-DAB) and phenobarbital (PB) to induce liver cancer. Materials and Methods: Mice in 5 different groups were chronically fed for varying periods of time: group I: normal diet; group II: normal diet + alcohol 200); group III: p-DAB + PB; group IV: p-DAB + PB + alcohol 200 (vehicle of Lyco-200 being ethyl alcohol); group V: p-DAB + PB + Lyco-200. They were sacrificed at day 7, 15, 30, 60, 90 or 120, and the following parameters were assessed: cytogenetic endpoints like chromosome aberrations, micronuclei, mitotic index and sperm-head anomaly; toxicity biomarkers like acid and alkaline phosphatases, alanine and aspartate amino transferase, glutathione reductase, succinate dehydrogenase and catalase activities, lipid peroxidation and reduced glutathione content. Additionally, scanning and transmission electron microscopic analyses of liver tissues were made at day 90 and 120, and immunodetection of p53 protein as well as gelatin zymography for matrix metalloproteinases in liver tissue were performed. Furthermore, studies were conducted on blood glucose, hemoglobin and cholesterol, estradiol, testosterone and cortisol, and lymphocyte and hepatic cell viabilities. Physical properties of Lyco-200 and potentized alcohol 200 were analyzed by using methods such as UV, Fourier Transform Infrared Spectroscopy (FTIR), Fluorescence Spectroscopy, <sup>1</sup>H-NMR and<sup> 13</sup>C-NMR (Nuclear Magnetic Resonance Spectroscopy). Results: Lyco-200 reduced cytogenetic damages yielding positive modulations of all biochemical, pathological and other risk factors, cell viability and expression of p53 protein and matrix metalloproteinases as compared to controls. Conclusion: Studies on other mammals are recommended to further investigate the potential of Lyco-200 in liver cancer.
DOI: 10.6084/m9.figshare.5104621
title: Supplementary Material for: Analyses of the <i>vrl</i> Gene Cluster in <i>Desulfococcus multivorans</i>: Homologous to the Virulence-Associated Locus of the Ovine Footrot Pathogen <i>Dichelobacter nodosus</i> Strain A198

description: Major parts of the virulence-associated<i> vrl</i> locus known from the gammaproteobacterium <i>Dichelobacter nodosus</i>, the causative agent of ovine footrot, were analyzed in the genome of the sulfate-reducing deltaproteobacterium <i>Desulfococcus multivorans</i>. In the genome of <i>D. multivorans</i> 13 of the 19 <i>vrl</i> genes described for <i>D. nodosus</i> are present and highly conserved with respect to gene sequence and order. The <i>vrl</i> locus and its flanking regions suggest a bacteriophage-mediated transfer into the genome of <i>D. multivorans</i>. Comparative analysis of the deduced Vrl proteins reveals a wide distribution of parts of the virulence-associated <i>vrl</i> locus in distantly related bacteria. Horizontal transfer is suggested as driving mechanism for the circulation of the <i>vrl</i> genes in bacteria. Except for the <i>vrlBMN</i> genes <i>D. multivorans</i> and <i>Desulfovibrio desulfuricans</i> G20 together contain all <i>vrl</i> genes displaying a high degree of similarity. For <i>D. multivorans</i> it could be shown that guanine plus cytosine (GC) content, GC skew, di-, tri- or tetranucleotide distribution did not differ between the<i> vrl </i>locus and its flanking sequences. This could be a hint that the <i>vrl</i> locus originated from a related organism or at least a genome with similar characteristics. The conspicuous high degree of conservation of the analyzed <i>vrl</i> genes may result from a recent transfer event or reflect a function of the <i>vrl</i> genes, which is still unknown and not necessarily disease associated. The latter is supported by the evidence for expression of the <i>vrl</i> genes in <i>D. multivorans</i>, which has not been described as pathogen or to be associated to any disease pattern before.