cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5104624.v1
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.5104630.v1
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.5104606
title: Supplementary Material for: Sequencing and genomic annotation of the chicken <i>(Gallus gallus)</i> Hox clusters, and mapping of evolutionarily conserved regions

description: Hox genes encode transcription factors that are involved in the regulation of normal development and are mutated in some diseases and malformations. Chicken <i>HOX</i> genes have been extensively studied in the chick limb and other developmental models. To date while the chicken <i>HOXA </i>cluster has been completely sequenced many other chicken <i>HOX</i> genes are known only from partial mRNAs or unfinished genome assemblies. Furthermore, although a finished sequence of the <i>HOXA</i> cluster is available, the sequence has not yet been annotated. We have therefore manually annotated the available <i>HOX</i> sequences and improved the sequences by sequencing PCR fragments that bridge existing gaps in the genome sequences. These sequences complement the published sequences, including the currently incomplete WashUC Gallus_gallus-2.1 build, to give an improved coverage of the cluster. We used phylogenetic footprinting to map the genomic location of 398 Ultra Conserved Regions in the<i> HOX</i> complex 248 of which do not overlap with any known annotated coding exon. These included the hox-related microRNAs miR-10 and miR-196. The chicken <i>HOX</i> clusters appear to be broadly comparable to their human counterparts. A few human orthologues were not recovered from the chicken, presumably because of incomplete sequence.
DOI: 10.6084/m9.figshare.5104609
title: Supplementary Material for: Characterising alternate splicing and tissue specific expression in the chicken from ESTs

description: Alternate splicing is believed to produce the greatest diversity in transcriptional complexity and function in eukaryotic species. In this study, we present an analysis of alternative splicing events that occur in the chicken, using the recently sequenced genomic sequence and over 580,000 EST sequences mapped back to the genome. A carefully controlled EST-to-genome mapping pipeline is presented, based around the EXONERATE program using the est2genome model, which also considers several quality control steps to filter out erroneous matches. The data is then used to estimate the level of alternate splicing events with respect to Ensembl predicted transcripts. The EST-genome mappings are characterised at the exon level, in order to classify individual splicing events and provide estimates of novel transcripts not currently annotated by the Ensembl genome database. This is the first large scale analysis of this kind in an avian species, and suggests that chicken displays a similar level of alternate splicing as that found in other higher vertebrates such as human and mouse, both in terms of the number of genes that undergo alternate splicing events, and the average number of transcripts produced per gene. The EST data suggests alternate splicing may occur in some 50–60% of the chicken gene set and with an average of around 2.3 transcripts per gene which undergo this process. The EST data is also used to look at gene and transcript usage in the tissues sequenced in embryonic and adult libraries. Genes which display notable biases were analysed in more detail, including twinfilin-2 and embryonic heavy chain myosin. This also highlights several as yet functionally un-annotated genes which appear to be important in embryonic tissues and also undergo alternate splicing events. The analysis also demonstrates some of the difficulties involved in using EST-based data to annotate transcriptional activity in eukaryotic genes, where a broad spectrum of tissues and a large number of sequenced transcripts are required in order to fully characterise alternate splicing and differential expression.
DOI: 10.6084/m9.figshare.5104612.v1
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.v1
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.5104600
title: Supplementary Material for: A high-resolution linkage map for the Z chromosome in chicken reveals hot spots for recombination

description: A comprehensive linkage map for chicken chromosome Z was constructed as the result of a large-scale screening of single nucleotide polymorphisms (SNPs). A total of 308 SNPs were assigned to Z based on the genotype distribution among 182 birds representing several populations. A linkage map comprising 210 markers and spanning 200.9 cM was established by analyzing a small Red junglefowl/White Leghorn intercross. There was excellent agreement between the linkage map for Z and a recently released assembly of the chicken genome (May 2006). Almost all SNPs assigned to chromosome Z in the present study are on Z in the new genome assembly. The remaining 12 loci are all found on unassigned contigs that can now be assigned to Z. The average recombination rate was estimated at 2.7 cM/Mb but there was a very uneven distribution of recombination events with both cold and hot spots of recombination. The existence of one of the major hot spots of recombination, located around position 39.4 Mb, was supported by the observed pattern of linkage disequilibrium. Thirteen markers from unassigned contigs were shown to be located on chromosome W. Three of these contigs included genes that have homologues on chromosome Z. The preliminary assignment of three more genes to the gene-poor W chromosome may be important for studies on the mechanism of sex determination and dosage compensation in birds.
DOI: 10.6084/m9.figshare.5104594
title: Supplementary Material for: A Proteomic Study to Identify Soya Allergens – The Human Response to Transgenic versus Non-Transgenic Soya Samples

description: <i>Background:</i> In spite of being among the main foods responsible for allergic reactions worldwide, soybean <i>(Glycine max)</i>-derived products continue to be increasingly widespread in a variety of food products due to their well-documented health benefits. Soybean also continues to be one of the elected target crops for genetic modification. The aim of this study was to characterize the soya proteome and, specifically, IgE-reactive proteins as well as to compare the IgE response in soya-allergic individuals to genetically modified Roundup Ready soya® versus its non-transgenic control. <i>Methods:</i> We performed two-dimensional gel electrophoresis of protein extracts from a 5% genetically modified Roundup Ready flour sample and its non-transgenic control followed by Western blotting with plasma from 5 soya-sensitive individuals. We used peptide tandem mass spectrometry to identify soya proteins (55 protein matches), specifically IgE-binding ones, and to evaluate differences between transgenic and non-transgenic samples. <i>Results:</i> We identified 2 new potential soybean allergens – one is maturation associated and seems to be part of the late embryogenesis abundant proteins group and the other is a cysteine proteinase inhibitor. None of the individuals tested reacted differentially to the transgenic versus non-transgenic samples under study. <i>Conclusion:</i> Soybean endogenous allergen expression does not seem to be altered after genetic modification. Proteomics should be considered a powerful tool for functional characterization of plants and for food safety assessment.
DOI: 10.6084/m9.figshare.5104597
title: Supplementary Material for: Prospective Controlled Cohort Studies on Long-Term Therapy of Cervical Cancer Patients with a Mistletoe Preparation (Iscador®)

description: Mistletoe preparations such as Iscador are commonly used in complementary medication for many cancer indications, particularly solid cancers. The efficacy of this complementary therapy is still controversial. Objective: Does longterm therapy with Iscador show any effect on survival, tumor progression and psychosomatic self-regulation of patients with cervical cancer? Patients and Methods: Prospective recruitment and long-term follow-up was carried out in 3 controlled cohort studies: In a randomized matched-pair study (19 pairs), cervical cancer patients with distant metastases and no mistletoe therapy were matched for prognostic factors. By paired random allocation, one of the patients was recommended mistletoe therapy by the attending physician. In 2 non-randomized matched-pair studies, cervical cancer patients without (102) and with (66) metastases, who already received mistletoe therapy, were matched with control patients without Iscador therapy. Results: For survival, the non-randomized studies showed significant effects in favor of Iscador therapy: hazard ratio (HR) estimate and 95% confidence interval (CI): 0.23 (0.14-0.39) and 0.37 (0.17-0.80), respectively. An effect of long-term Iscador therapy on tumor progression was not seen. Psychosomatic self-regulation in the Iscador group improved significantly within 12 months compared with the control group in the randomized as well as in 1 non-randomized study (cervical cancer without metastases): estimate of the median difference and 95% CI: 0.70 (0.15-1.05) and 0.25 (0.15-0.35), respectively. Conclusion: Iscador may have the effect of prolonging overall survival of cervical cancer patients. In the short term, psychosomatic self-regulation increases more markedly under complementary Iscador therapy than under conventional therapy alone.
DOI: 10.6084/m9.figshare.5104585
title: Supplementary Material for: Knowledge and Understanding of Disease Process, Risk Factors and Treatment Modalities in Patients with a Recent TIA or Minor Ischemic Stroke

description: <i>Background:</i> Patients with acute stroke often have a striking lack of knowledge of causes, warning signs, and risk factors. Lack of knowledge may lead to inappropriate secondary prevention behavior. We investigated the knowledge of patients with a TIA or minor stroke about specific aspects of their disease 3 months after the event. <i>Methods:</i> Patients with a TIA or minor stroke who participated in a randomized controlled trial of the effect of health education by an individualized multimedia computer program (IMCP) were included. All patients received information about their disease from their treating neurologist and half of the patients received extra information through the IMCP. The patients’ knowledge was tested after 3 months by means of a questionnaire that contained items on pathogenesis, warning signs, vascular diseases, risk factors, lifestyle and treatment. The highest possible score was 71 points. <i>Results:</i> The 57 patients had a mean total score of 41.2 points (SD 10.4) of the maximum 71. Only 15 (26%) correctly identified the brain as the affected organ in stroke and TIA, and only 21 (37%) could give a correct description of a TIA or stroke. In contrast, 80–90% of the patients identified hypertension and/or obesity as vascular risk factors. Knowledge of various treatment modalities of hypertension, hypercholesterolemia and obesity was moderate to high (40–91% adequate responses).<i> Conclusion:</i> The vast majority of patients with TIA or stroke lack specific knowledge about their disease, but they do have a reasonable knowledge of general vascular risk factors and treatment. This suggests that counseling by neurologists of patients with a TIA or stroke can be improved.
DOI: 10.6084/m9.figshare.5104597.v1
title: Supplementary Material for: Prospective Controlled Cohort Studies on Long-Term Therapy of Cervical Cancer Patients with a Mistletoe Preparation (Iscador®)

description: Mistletoe preparations such as Iscador are commonly used in complementary medication for many cancer indications, particularly solid cancers. The efficacy of this complementary therapy is still controversial. Objective: Does longterm therapy with Iscador show any effect on survival, tumor progression and psychosomatic self-regulation of patients with cervical cancer? Patients and Methods: Prospective recruitment and long-term follow-up was carried out in 3 controlled cohort studies: In a randomized matched-pair study (19 pairs), cervical cancer patients with distant metastases and no mistletoe therapy were matched for prognostic factors. By paired random allocation, one of the patients was recommended mistletoe therapy by the attending physician. In 2 non-randomized matched-pair studies, cervical cancer patients without (102) and with (66) metastases, who already received mistletoe therapy, were matched with control patients without Iscador therapy. Results: For survival, the non-randomized studies showed significant effects in favor of Iscador therapy: hazard ratio (HR) estimate and 95% confidence interval (CI): 0.23 (0.14-0.39) and 0.37 (0.17-0.80), respectively. An effect of long-term Iscador therapy on tumor progression was not seen. Psychosomatic self-regulation in the Iscador group improved significantly within 12 months compared with the control group in the randomized as well as in 1 non-randomized study (cervical cancer without metastases): estimate of the median difference and 95% CI: 0.70 (0.15-1.05) and 0.25 (0.15-0.35), respectively. Conclusion: Iscador may have the effect of prolonging overall survival of cervical cancer patients. In the short term, psychosomatic self-regulation increases more markedly under complementary Iscador therapy than under conventional therapy alone.
DOI: 10.6084/m9.figshare.5104588
title: Supplementary Material for: <i>DTNBP1 (Dystrobrevin Binding Protein 1)</i> and Schizophrenia: Association Evidence in the 3′ End of the Gene

description: <i>Objectives:</i><i>Dysbindin</i> (<i>DTNBP1</i>) has been identified as a susceptibility gene for schizophrenia (SZ) through a positional approach. However, a variety of single nucleotide polymorphisms (SNPs) and haplotypes, in different parts of the gene, have been reported to be associated in different samples, and a precise molecular mechanism of disease remains to be defined. We have performed an association study with two well-characterized family samples not previously investigated at the <i>DTNBP1</i> locus. <i>Methods:</i> We examined 646 subjects in 136 families with SZ, largely of European ancestry (EA), genotyping 26 SNPs in <i>DTNBP1</i>. <i>Results:</i> Three correlated markers (rs875462, rs760666, and rs7758659) at the 3′ region of <i>DTNBP1 </i>showed evidence for association to SZ (p = 0.004), observed in both the EA (p = 0.031) and the African American (AA) subset (p = 0.045) with the same over-transmitted allele. The most significant haplotype in our study was rs7758659-rs3213207 (global p = 0.0015), with rs3213207 being the most frequently reported associated marker in previous studies. A non-conservative missense variant (Pro272Ser) in the 3′ region of <i>DTNBP1</i> that may impair <i>DTNBP1</i> function was more common in SZ probands (8.2%) than in founders (5%) and in dbSNP (2.1%), but did not reach statistical significance. <i>Conclusion: </i>Our results provide evidence for an association of SZ with SNPs at the 3′ end of <i>DTNBP1</i> in the samples studied.
DOI: 10.6084/m9.figshare.5104570
title: Supplementary Material for: A model for genetic complementation controlling the chromosomal abnormalities and loss of heterozygosity formation in cancer

description: The relationship between the apparently random chromosomal changes found in aneuploidy and the genetic instability driving the progression of cancer is not clear. We report a test of the hypothesis that aneuploid chromosomal abnormalities might be selected to preserve cell-survival genes during loss of heterozygosity (LOH) formations which eliminate tumor suppressor genes. The LOHs and structurally abnormal chromosomes present in the aneuploid LoVo (colon), A549 (lung), SUIT-2 (pancreas), and LN-18 (glioma) cancer cell lines were identified by single nucleotide polymorphisms (SNPs) and Spectral Karyotyping (SKY). The Mann-Whitney U and chi square tests were used to evaluate possible differences in chromosome numbers and abnormalities between the cell lines, with two-tailed <i>P</i> values of &lt;0.01 being considered significant. The cell lines differed significantly in chromosome numbers and frequency of structurally abnormal chromosomes. The SNP analysis revealed that each cell line contained at least a haploid set of somatic chromosomes, consistent with our hypothesis that cell-survival genes are widely scattered throughout the genome. Further, over 90% of the chromosomal abnormalities seemed to be selected, often after LOH formation, for gene-dosage compensation or to provide heterozygosity for specific chromosomal regions. These results suggest that the chromosomal changes of aneuploidy are not random, but may be selected to provide gene-dosage compensation and/or retain functional alleles of cell-survival genes during LOH formation.
DOI: 10.6084/m9.figshare.5104576
title: Supplementary Material for: De novo Subtelomeric Deletion Additional to an Inherited Apparently Balanced Reciprocal Translocation

description: <i>Objective:</i> We describe the analysis of an apparently balanced inherited reciprocal translocation in a fetus presenting with multiple congenital abnormalities, characterize the structural chromosome rearrangement, and report an unexpected additional imbalance to the inherited rearrangement. <i>Methods:</i> DNA microarray was used to screen for genomic imbalance in subtelomeric and interstitial critical regions. High-resolution comparative genomic hybridization was used to screen for genomic imbalance at a genome-wide level. Fluorescence in situ hybridization using whole-chromosome painting and specific probes was used to characterize the inherited translocation, and the size of the de novoadditional deletion. <i>Results:</i> An unexpected additional deletion was found in 7qter on derivative 10 of the inherited maternal reciprocal translocation t(7;10)(q11.23; p14). <i>Conclusions:</i> We show the usefulness of genome-wide and specific molecular cytogenetic techniques to explore apparently balanced rearrangements.