cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5120878
title: Supplementary Material for: Cytogenetic and Array-CGH Characterization of a Complex de novo Rearrangement Involving Duplication and Deletion of 9p and Clinical Findings in a 4-Month-Old Female

description: Approximately 15 patients with partial trisomy 9p involving de novo duplications have been previously described. Here, we present clinical, cytogenetic, FISH and aCGH findings in a patient with a de novo complex rearrangement in the short arm of chromosome 9 involving an inverted duplication at 9p24→p21.3 and a deletion at 9pter→p24.2. FISH probes generated from BACs selected from the UCSC genome browser were utilized to verify this rearrangement. It is likely that some previously described duplications of 9p may also be products of complex chromosomal aberrations. This report in which FISH and aCGH were used to more comprehensively characterize the genomic rearrangement in a patient with clinical manifestations of 9p duplication syndrome underscores the importance of further characterizing cytogenetically detected rearrangements.
DOI: 10.6084/m9.figshare.5120872
title: Supplementary Material for: Effects of Neurotrophic Factors on Growth and Glial Cell Alignment of Cultured Adult Spiral Ganglion Cells

description: Adult spiral ganglion cells were cultured in chorus to assess the influence of the neurotrophins brain-derived neurotrophic factor, neurotrophin 3 and glial cell line-derived neurotrophic factor (GDNF) on neurite growth and Schwann cell alignment. Over 1500 measurements were collected using each factor at 10 ng/ml and all three in combination. Evaluation was made with GDNF at concentrations of up to 100 ng/ml. Neurite dimensions were assessed at days 5, 7, 9 and 11 using a computer-based program (Axon Analyzer). GDNF had a strong effect on spiral ganglion cell growth almost attaining the level of all three factors in combination. GDNF increased glial cell alignment and nerve bundle formation. Results show the potential of GDNF to maintain and possibly restore auditory nerve integrity.
DOI: 10.6084/m9.figshare.5120875
title: Supplementary Material for: <i>Ccdc33, </i>a Predominantly Testis-Expressed Gene, Encodes a Putative Peroxisomal Protein

description: Many genes crucial for male fertility are often predominantly or exclusively expressed in male germ cells. The analysis of mouse models has demonstrated the functional importance of peroxisomes in spermatogenesis. The CCDC33 protein has been reported to be a cancer/testis (CT) antigen. We found that mouse <i>Ccdc33</i> is predominantly expressed in the testis and undergoes alternative splicing to produce at least 4 different transcripts. The protein encoded by <i>Ccdc33</i> contains 3 coiled-coil domains, a C2-domain, 2 ER membrane retention signal-like motifs and 2 putative peroxisomal targeting signals type 2 (PTS2). We could demonstrate that the second PTS2 sequence is functional and responsible for the targeting of CCDC33 to peroxisomes. Moreover, in HeLa cells CCDC33-dsRED fusion protein co-localized with a known peroxisomal protein, namely PXT1, and showed punctuate intracellular distribution. Taken together, the mouse <i>Ccdc33</i> encodes a putative peroxisomal protein and is predominantly expressed in male germ cells. The expression starts at the primary spermatocyte stage, suggesting an important role of this protein during spermatogenesis.
DOI: 10.6084/m9.figshare.5120869
title: Supplementary Material for: A Large-Scale RNAi Screen Identifies <i>Deaf1 </i>as a Regulator of Innate Immune Responses in <i>Drosophila</i>

description: Innate immune signalling pathways are evolutionarily conserved between invertebrates and vertebrates. The analysis of NF-ĸB signalling in <i>Drosophila</i> has contributed important insights into how organisms respond to infection. Nevertheless, significant gaps remain in our understanding of how the activation of intracellular signalling elicits specific transcriptional programs. Here we report a genome-wide RNA interference survey for transcription factors that are required for Toll-dependent immune responses. In addition to the NF-ĸB homologs Dif, Dorsal and factors of the general transcription machinery, we identified Deformed Epidermal Autoregulatory Factor 1 (Deaf1) to be required for the expression of the Toll target gene <i>Drosomycin</i> in cultured cells and in <i>Drosophila </i>in vivo. We show that Deaf1 is required for the survival of flies after fungal, but not <i>E. coli</i>, infection. We determine that Deaf1 acts downstream of the NF-ĸB factors Dorsal and Dif. These results indicate that Deaf1 is an important contributor to innate immune responses in vivo.
DOI: 10.6084/m9.figshare.5120878.v1
title: Supplementary Material for: Cytogenetic and Array-CGH Characterization of a Complex de novo Rearrangement Involving Duplication and Deletion of 9p and Clinical Findings in a 4-Month-Old Female

description: Approximately 15 patients with partial trisomy 9p involving de novo duplications have been previously described. Here, we present clinical, cytogenetic, FISH and aCGH findings in a patient with a de novo complex rearrangement in the short arm of chromosome 9 involving an inverted duplication at 9p24→p21.3 and a deletion at 9pter→p24.2. FISH probes generated from BACs selected from the UCSC genome browser were utilized to verify this rearrangement. It is likely that some previously described duplications of 9p may also be products of complex chromosomal aberrations. This report in which FISH and aCGH were used to more comprehensively characterize the genomic rearrangement in a patient with clinical manifestations of 9p duplication syndrome underscores the importance of further characterizing cytogenetically detected rearrangements.
DOI: 10.6084/m9.figshare.5120866
title: Supplementary Material for: Simultaneous Ring Voice-over-Internet Phone System Enables Rapid Physician Elicitation of Explicit Informed Consent in Prehospital Stroke Treatment Trials

description: <i>Background:</i> Cellular phone conversations between on-scene patients or their legally authorized representatives (LARs) and off-scene enrolling physician-investigators require immediate and reliable connection systems to obtain explicit informed research consent in prehospital treatment trials. <i>Methods:</i> The NIH Field Administration of Stroke Therapy – Magnesium (FAST-MAG) Trial implemented a voice-over-internet protocol (VOIP) simultaneous ring system (multiple investigator cell phones called simultaneously and first responder connected to call) to enable physician-investigators to elicit consent immediately from competent patients or LARs encountered by 228 ambulances enrolling patients in a multicenter prehospital stroke trial. For 1 month, the number, origin, duration, and yield of enrolling line calls were monitored prospectively. <i>Results:</i> Six investigators were connected to 106 enrolling line calls, with no identified unanswered calls. Thirty-five percent of new patient calls yielded an enrollment. The most common reasons for non-enrollment were last known well &gt;2 h (n = 7) and uncon sentable patient without LAR available (n = 7). No non-enrollments were directly attributable to the VOIP system. In enrollments, consent was provided by the patient in 67% and a LAR in 33%. The duration of enrollment calls (mean ± SD: 8.4 ± 2.5 min, range 6–14) was longer than non-enrollment calls (5.5 ± 3.5, range 2–13; p &lt; 0.001). The median interval from last known well to study agent start was 46 min, and 70% were enrolled within 60 min of onset. <i>Conclusions:</i> The simultaneous ring system was reliable and effective, permitting enrollment of a substantial number of patients within the first hour after stroke onset. VOIP cellular networks with simultaneous ring are a preferred means of facilitating consent in prehospital treatment trials.
DOI: 10.6084/m9.figshare.5120875.v1
title: Supplementary Material for: <i>Ccdc33, </i>a Predominantly Testis-Expressed Gene, Encodes a Putative Peroxisomal Protein

description: Many genes crucial for male fertility are often predominantly or exclusively expressed in male germ cells. The analysis of mouse models has demonstrated the functional importance of peroxisomes in spermatogenesis. The CCDC33 protein has been reported to be a cancer/testis (CT) antigen. We found that mouse <i>Ccdc33</i> is predominantly expressed in the testis and undergoes alternative splicing to produce at least 4 different transcripts. The protein encoded by <i>Ccdc33</i> contains 3 coiled-coil domains, a C2-domain, 2 ER membrane retention signal-like motifs and 2 putative peroxisomal targeting signals type 2 (PTS2). We could demonstrate that the second PTS2 sequence is functional and responsible for the targeting of CCDC33 to peroxisomes. Moreover, in HeLa cells CCDC33-dsRED fusion protein co-localized with a known peroxisomal protein, namely PXT1, and showed punctuate intracellular distribution. Taken together, the mouse <i>Ccdc33</i> encodes a putative peroxisomal protein and is predominantly expressed in male germ cells. The expression starts at the primary spermatocyte stage, suggesting an important role of this protein during spermatogenesis.
DOI: 10.6084/m9.figshare.5120863
title: Supplementary Material for: Protective Role of Complement C5a in an Experimental Model of <i>Staphylococcus aureus</i> Bacteremia

description: The complement system is a key component of the innate immune response. Here, we have examined the role of complement anaphylatoxin C5a in an experimental model of <i>Staphylococcus aureus</i> bacteremia. Our data provide compelling evidence for a protective role of C5a during staphylococcal bloodstream infection.
DOI: 10.6084/m9.figshare.5120872.v1
title: Supplementary Material for: Effects of Neurotrophic Factors on Growth and Glial Cell Alignment of Cultured Adult Spiral Ganglion Cells

description: Adult spiral ganglion cells were cultured in chorus to assess the influence of the neurotrophins brain-derived neurotrophic factor, neurotrophin 3 and glial cell line-derived neurotrophic factor (GDNF) on neurite growth and Schwann cell alignment. Over 1500 measurements were collected using each factor at 10 ng/ml and all three in combination. Evaluation was made with GDNF at concentrations of up to 100 ng/ml. Neurite dimensions were assessed at days 5, 7, 9 and 11 using a computer-based program (Axon Analyzer). GDNF had a strong effect on spiral ganglion cell growth almost attaining the level of all three factors in combination. GDNF increased glial cell alignment and nerve bundle formation. Results show the potential of GDNF to maintain and possibly restore auditory nerve integrity.
DOI: 10.6084/m9.figshare.5120857
title: Supplementary Material for: Characterization of the Bovine Pseudoautosomal Region and Comparison with Sheep, Goat, and Other Mammalian Pseudoautosomal Regions

description: The pseudoautosomal region (PAR) is a small region of sequence homology between mammalian X and Y chromosomes and is needed for sex chromosome segregation in male meiosis. The region, though studied as yet in only a few species, shows considerable variation in size and gene content. We have constructed a medium-density gene map for the cattle PAR and the adjacent X-specific region by isolating and mapping 18 BAC clones which contain 20 PAR- and 5 X-specific genes. One BAC clone containing <i>TBL1XY</i> and <i>GPR143</i> spanned the recently demarcated bovine pseudoautosomal boundary (PAB). Comparing the gene map of cattle PAR with the high-resolution maps of human, horse, and dog PAR allowed to estimate that the size of cattle PAR is approximately 5–9 Mb. BAC end sequence analysis showed that there is a gradient of decreasing GC content from PARter towards the PAB which is consistent with findings in human, mouse, and horse. The 20 PAR- and 5 X-specific cattle genes were mapped also in goat and sheep, showing that PAR in the 3 species is similar in size, gene content, and gene order. For the first time the PAB was determined in goat sex chromosomes. Comparison of cattle, goat, and sheep PAR with homologous regions on human and horse X chromosomes showed a high degree of linkage conservation between all species. However, the most terminal human, horse, and dog PAR gene, <i>PLCXD1</i>, is X-specific in ruminants. Since the human/horse linkage group containing <i>PLCXD1</i> is of ancestral origin, the location of <i>PLCXD1</i> can be considered as a de novo event in ruminant sex chromosome evolution. The gene map of the cattle PAR adds to our knowledge about the comparative organization and evolution of the eutherian PAR and aids the sequencing, sequence assembly, and annotation of the terminal region of BTAXq.
DOI: 10.6084/m9.figshare.5120860
title: Supplementary Material for: Cytokines Involved in Interferon-γ Production by Human Macrophages

description: Interferon (IFN)-γ is important to the immune defense against intracellular pathogens and specifically the ability of macrophages to control <i>Mycobacterium tuberculosis</i> (MTB). Increasing evidence has accumulated to support the idea that macrophages produce IFN-γ. We describe here the cytokine interactions that determine IFN-γ expression and secretion during MTB infection of human macrophages. Detection of biologically important IFN-γ levels in culture supernatants of MTB-infected human macrophages requires the addition of interleukin (IL)-12. IL-18 augmented IFN-γ production from human macrophages in response to the combination of MTB and supplemental IL-12. Although IL-18 gene expression was generally unchanged, IL-18 protein secretion was enhanced by the combination of MTB and IL-12, and functioned primarily to stimulate IFN-γ release. Importantly, IL-27 induced by MTB infection opposed IFN-γ production by antagonizing IL-18 activity in human macrophages. Neutralization of IL-27 increased the expression of the IL-18 receptor β-chain. Additionally, IL-27 blocked NF-ĸB activation in response to IL-18. These results define the signals required for IFN-γ production by human macrophages and highlight the interactions between cytokines produced during MTB infection. Together, they identify a novel role for IL-27 in regulating macrophage function by disrupting IL-18 activity.
DOI: 10.6084/m9.figshare.5120866.v1
title: Supplementary Material for: Simultaneous Ring Voice-over-Internet Phone System Enables Rapid Physician Elicitation of Explicit Informed Consent in Prehospital Stroke Treatment Trials

description: <i>Background:</i> Cellular phone conversations between on-scene patients or their legally authorized representatives (LARs) and off-scene enrolling physician-investigators require immediate and reliable connection systems to obtain explicit informed research consent in prehospital treatment trials. <i>Methods:</i> The NIH Field Administration of Stroke Therapy – Magnesium (FAST-MAG) Trial implemented a voice-over-internet protocol (VOIP) simultaneous ring system (multiple investigator cell phones called simultaneously and first responder connected to call) to enable physician-investigators to elicit consent immediately from competent patients or LARs encountered by 228 ambulances enrolling patients in a multicenter prehospital stroke trial. For 1 month, the number, origin, duration, and yield of enrolling line calls were monitored prospectively. <i>Results:</i> Six investigators were connected to 106 enrolling line calls, with no identified unanswered calls. Thirty-five percent of new patient calls yielded an enrollment. The most common reasons for non-enrollment were last known well &gt;2 h (n = 7) and uncon sentable patient without LAR available (n = 7). No non-enrollments were directly attributable to the VOIP system. In enrollments, consent was provided by the patient in 67% and a LAR in 33%. The duration of enrollment calls (mean ± SD: 8.4 ± 2.5 min, range 6–14) was longer than non-enrollment calls (5.5 ± 3.5, range 2–13; p &lt; 0.001). The median interval from last known well to study agent start was 46 min, and 70% were enrolled within 60 min of onset. <i>Conclusions:</i> The simultaneous ring system was reliable and effective, permitting enrollment of a substantial number of patients within the first hour after stroke onset. VOIP cellular networks with simultaneous ring are a preferred means of facilitating consent in prehospital treatment trials.
DOI: 10.6084/m9.figshare.5120854
title: Supplementary Material for: Molecular Cytogenetics and Comparative Mapping in Goats (<i>Capra hircus</i>, 2n = 60)

description: Few goat genome analysis projects have been developed in the last 10 years. The aim of this review was to compile and update all available cytogenetic mapping data, according to the last goat chromosome nomenclature, as well as human and cattle whole genome sequences. In particular, human regions homologous to most of the FISH-mapped microsatellites were identified in silico. This new goat cytogenetic map made it possible to refine delineation of conserved segments relative to the human and cattle genomic sequence. These improvements did not lead to detection of major new rearrangements within ruminants but confirmed the good conservation of synteny and the numerous intrachromosomal rearrangements observed between goats and humans.
DOI: 10.6084/m9.figshare.5120857.v1
title: Supplementary Material for: Characterization of the Bovine Pseudoautosomal Region and Comparison with Sheep, Goat, and Other Mammalian Pseudoautosomal Regions

description: The pseudoautosomal region (PAR) is a small region of sequence homology between mammalian X and Y chromosomes and is needed for sex chromosome segregation in male meiosis. The region, though studied as yet in only a few species, shows considerable variation in size and gene content. We have constructed a medium-density gene map for the cattle PAR and the adjacent X-specific region by isolating and mapping 18 BAC clones which contain 20 PAR- and 5 X-specific genes. One BAC clone containing <i>TBL1XY</i> and <i>GPR143</i> spanned the recently demarcated bovine pseudoautosomal boundary (PAB). Comparing the gene map of cattle PAR with the high-resolution maps of human, horse, and dog PAR allowed to estimate that the size of cattle PAR is approximately 5–9 Mb. BAC end sequence analysis showed that there is a gradient of decreasing GC content from PARter towards the PAB which is consistent with findings in human, mouse, and horse. The 20 PAR- and 5 X-specific cattle genes were mapped also in goat and sheep, showing that PAR in the 3 species is similar in size, gene content, and gene order. For the first time the PAB was determined in goat sex chromosomes. Comparison of cattle, goat, and sheep PAR with homologous regions on human and horse X chromosomes showed a high degree of linkage conservation between all species. However, the most terminal human, horse, and dog PAR gene, <i>PLCXD1</i>, is X-specific in ruminants. Since the human/horse linkage group containing <i>PLCXD1</i> is of ancestral origin, the location of <i>PLCXD1</i> can be considered as a de novo event in ruminant sex chromosome evolution. The gene map of the cattle PAR adds to our knowledge about the comparative organization and evolution of the eutherian PAR and aids the sequencing, sequence assembly, and annotation of the terminal region of BTAXq.
DOI: 10.6084/m9.figshare.5120845
title: Supplementary Material for: Detailed Expression Pattern of Foxp1 and Its Possible Roles in Neurons of the Spinal Cord during Embryogenesis

description: A member of winged-helix/forkhead transcription factors, Foxp1, is expressed in the developing spinal cord during mouse embryogenesis. To shed light on the potential role of Foxp1 in neurons of the developing spinal cord, we investigated the detailed expression pattern of Foxp1 between embryonic day (E) 9.5 and E17.5. At E10.25, some postmitotic neurons with strong expression of Foxp1 (Foxp1<sup>high</sup>) were first detected in the ventral half of the brachial spinal cord. By E11.5, Foxp1<sup>high</sup> neurons increased in the ventral spinal cord at the limb levels. All of Foxp1<sup>high</sup> neurons at the limb levels were Islet2<sup>+</sup>/Lhx3<sup>–</sup> motor neurons (MNs) of the lateral motor column and some neurons that expressed Foxp1 weakly (Foxp1<sup>low</sup>) at the thoracic level were MNs of the preganglionic motor column. Between E12.5 and E17.5, Foxp1<sup>low</sup> neurons were also observed in the intermediate zone throughout the ventral spinal cord, all of which were Pax2<sup>+</sup>, En1<sup>+</sup>, Evx1<sup>–</sup>, Chx10<sup>–</sup>, Gata3<sup>–</sup>, and Lhx3<sup>–</sup> V1 interneurons. Interestingly, no colocalization of Foxp1 with Lhx3 was observed in the developing spinal cord. In addition, overexpression of Foxp1 markedly attenuated the endogenous expression of Lhx3 in a neuroendocrine cell line. Chromatin immunoprecipitation assays in a neuronal cell line and E13.5 spinal cords revealed an interaction between Foxp1 and the consensus motif in the Lhx3 promoter. These results suggest that Foxp1 may play some important roles in the determination of neuronal fates of the ventral spinal cord, possibly through the suppression of Lhx3 expression.
DOI: 10.6084/m9.figshare.5120848
title: Supplementary Material for: Gonadectomy Influences Blood Pressure through the Kallikrein-Kinin System

description: The kallikrein-kinin system (KKS) appears to be involved in blood pressure regulation. We showed that ovariectomy (oVx) stimulates urinary kallikrein activity (UKa). So, we test whether gonadectomy (Gx) would affect blood pressure through an increase in KKS activity and which mechanism(s) were involved. We studied adult Wistar rats of either sex, with and without Gx. At baseline all groups were normotensive although the oVx mean arterial pressure (MAP) was lower than female MAP (p &lt; 0.05). KKS blockade by aprotinin increased MAP (p &lt; 0.05) exclusively in the oVx group. The probably mechanism(s) involved in KKS regulation (synthesis, renal content and UKa) were also studied. Previous Gx, kallikrein content (nkat/g kidney weight) and UKa (nkat/g kidney weight/day) were higher in female than in male rats: 12 ± 1.1 versus 6 ± 0.7 and 40 ± 6.8 versus 26 ± 3.4, respectively. After Gx, kallikrein content increased significantly in both orchiectomized (oRx) and oVx rats, and UKa showed a similar tendency (NS). Kallikrein synthesis did not show gender difference in non-Gx rats, but an increase after oVx was observed. KKS was found to be involved in blood pressure regulation in oVx animals. oVx may trigger the increase in kallikrein synthesis and content and UKa to act upon blood pressure.
DOI: 10.6084/m9.figshare.5120854.v1
title: Supplementary Material for: Molecular Cytogenetics and Comparative Mapping in Goats (<i>Capra hircus</i>, 2n = 60)

description: Few goat genome analysis projects have been developed in the last 10 years. The aim of this review was to compile and update all available cytogenetic mapping data, according to the last goat chromosome nomenclature, as well as human and cattle whole genome sequences. In particular, human regions homologous to most of the FISH-mapped microsatellites were identified in silico. This new goat cytogenetic map made it possible to refine delineation of conserved segments relative to the human and cattle genomic sequence. These improvements did not lead to detection of major new rearrangements within ruminants but confirmed the good conservation of synteny and the numerous intrachromosomal rearrangements observed between goats and humans.