cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4535618
title: Supplementary Material for: Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges

description: Technological advances have led to an explosive growth of high-throughput functional genomic data. Exploiting the correlation among different data types, it is possible to predict one functional genomic data type from other data types. Prediction tools are valuable in understanding the relationship among different functional genomic signals. They also provide a cost-efficient solution to inferring the unknown functional genomic profiles when experimental data are unavailable due to resource or technological constraints. The predicted data may be used for generating hypotheses, prioritizing targets, interpreting disease variants, facilitating data integration, quality control, and many other purposes. This article reviews various applications of prediction methods in functional genomics, discusses analytical challenges, and highlights some common and effective strategies used to develop prediction methods for functional genomic data.
DOI: 10.6084/m9.figshare.4535621
title: Supplementary Material for: Neuromagnetic Cortical Activation during Initiation of Optokinetic Nystagmus: An MEG Pilot Study

description: <b><i>Purpose:</i></b> To investigate the spatiotemporal evolution of cortical activation during the initiation of optokinetic nystagmus using magnetoencephalography. <b><i>Background:</i></b> Previous imaging studies of optokinetic nystagmus in humans using positron emission tomography and functional magnetic resonance imaging discovered activation of a large set of cortical and subcortical structures during steady-state optokinetic stimulation, but did not provide information on the temporal dynamics of the initial response. Imaging studies have shown that cortical areas responsible for vision in occipital and temporo-occipital areas are involved, i.e. cortical areas control optokinetic stimulation in humans. Magnetoencephalography provides measures that reflect neural ensemble activity in the millisecond time scale, allowing the identification of early cortical components of visuomotor integration. <b><i>Design/Methods:</i></b> We studied neuromagnetic cortical responses during the initiation of optokinetic nystagmus in 6 right-handed healthy subjects. Neuromagnetic activity was recorded with a whole-head magnetoencephalograph, consisting of 143 planar gradiometers. <b><i>Results:</i></b> The mean (±SD) latency between stimulus onset and initiation of optokinetic nystagmus was 177.7 ± 59 ms. Initiation of optokinetic nystagmus evoked an early component in the primary visual cortex starting at 40-90 ms prior to the onset of the slow phase of nystagmus. Almost simultaneously an overlapping second component occurred bilaterally in the temporo-occipital area (visual motion areas), pronounced in the right hemisphere, starting at 10-60 ms prior to the slow-phase onset. Both components showed long-duration activity lasting for up to 100 ms after slow-phase onset. <b><i>Conclusions:</i></b> Our findings suggest that the initiation of optokinetic nystagmus induces early cortical activation in the occipital cortex and almost simultaneously bilaterally in the temporo-occipital cortex. These cortical regions might represent essential areas for the monitoring of retinal slip.
DOI: 10.6084/m9.figshare.4535603.v1
title: 6_4_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4535621.v1
title: Supplementary Material for: Neuromagnetic Cortical Activation during Initiation of Optokinetic Nystagmus: An MEG Pilot Study

description: <b><i>Purpose:</i></b> To investigate the spatiotemporal evolution of cortical activation during the initiation of optokinetic nystagmus using magnetoencephalography. <b><i>Background:</i></b> Previous imaging studies of optokinetic nystagmus in humans using positron emission tomography and functional magnetic resonance imaging discovered activation of a large set of cortical and subcortical structures during steady-state optokinetic stimulation, but did not provide information on the temporal dynamics of the initial response. Imaging studies have shown that cortical areas responsible for vision in occipital and temporo-occipital areas are involved, i.e. cortical areas control optokinetic stimulation in humans. Magnetoencephalography provides measures that reflect neural ensemble activity in the millisecond time scale, allowing the identification of early cortical components of visuomotor integration. <b><i>Design/Methods:</i></b> We studied neuromagnetic cortical responses during the initiation of optokinetic nystagmus in 6 right-handed healthy subjects. Neuromagnetic activity was recorded with a whole-head magnetoencephalograph, consisting of 143 planar gradiometers. <b><i>Results:</i></b> The mean (±SD) latency between stimulus onset and initiation of optokinetic nystagmus was 177.7 ± 59 ms. Initiation of optokinetic nystagmus evoked an early component in the primary visual cortex starting at 40-90 ms prior to the onset of the slow phase of nystagmus. Almost simultaneously an overlapping second component occurred bilaterally in the temporo-occipital area (visual motion areas), pronounced in the right hemisphere, starting at 10-60 ms prior to the slow-phase onset. Both components showed long-duration activity lasting for up to 100 ms after slow-phase onset. <b><i>Conclusions:</i></b> Our findings suggest that the initiation of optokinetic nystagmus induces early cortical activation in the occipital cortex and almost simultaneously bilaterally in the temporo-occipital cortex. These cortical regions might represent essential areas for the monitoring of retinal slip.
DOI: 10.6084/m9.figshare.4535597
title: Supplementary Material for: Does BDNF Val66Met Polymorphism Confer Risk for Posttraumatic Stress Disorder?

description: <b><i>Background:</i></b> Evidence has indicated that <i>BDNF</i> (brain-derived neurotrophic factor) Val66Met genetic variant could be linked to the development of posttraumatic stress disorder (PTSD). However, clinical observations studying the <i>BDNF</i> polymorphism and the risk of PTSD yielded contradictory results. In this meta-analysis we evaluated the association between <i>BDNF</i> Val66Met and PTSD risk. <b><i>Method:</i></b> Systematic searches in online databases retrieved 6 relevant publications. Different inherited models were utilized to perform the pooled analysis. Subgroup analyses and sensitive analyses based on Hardy-Weinberg equilibrium (HWE) test results were also carried out. <b><i>Results:</i></b> Our study did not found a significant overall effect of <i>BDNF</i> Val66Met on the susceptibility to PTSD under various genetic models. In contrast, subgroup analyses suggested that the stress status of the control group, but not ethnicity, may influence the relationship of <i>BDNF</i> Val66Met with PTSD risk. After the exclusion of a study that was not in HWE, our conclusions remained unchanged during the influence analyses. <b><i>Conclusions:</i></b> This meta-analysis suggested no genetic association of <i>BDNF</i> Val66Met with vulnerability to PTSD. Further research studies are warranted to clarify the impact of <i>BDNF </i>variants on the occurrence of PTSD.
DOI: 10.6084/m9.figshare.4535600
title: Supplementary Material for: Comprehensive Analyses of White-Handed Gibbon Chromosomes Enables Access to 92 Evolutionary Conserved Breakpoints Compared to the Human Genome

description: Gibbon species (Hylobatidae) impress with an unusually high number of numerical and structural chromosomal changes within the family itself as well as compared to other Hominoidea including humans. In former studies applying molecular cytogenetic methods, 86 evolutionary conserved breakpoints (ECBs) were reported in the white-handed gibbon (<i>Hylobates lar</i>, HLA) with respect to the human genome. To analyze those ECBs in more detail and also to achieve a better understanding of the fast karyotype evolution in Hylobatidae, molecular data for these regions are indispensably necessary. In the present study, we obtained whole chromosome-specific probes by microdissection of all 21 HLA autosomes and prepared them for aCGH. Locus-specific DNA probes were also used for further molecular cytogenetic characterization of selected regions. Thus, we could map 6 yet unreported ECBs in HLA with respect to the human genome. Additionally, in 26 of the 86 previously reported ECBs, the present approach enabled a more precise breakpoint mapping. Interestingly, a preferred localization of ECBs within segmental duplications, copy number variant regions, and fragile sites was observed.
DOI: 10.6084/m9.figshare.4535582
title: Supplementary Material for: Hearing Aid or Tinnitus Masker: Which One Is the Best Treatment for Blast-Induced Tinnitus? The Results of a Long-Term Study on 974 Patients

description: The aim of this longitudinal study was to explore whether a hearing aid or noise generator would be an effective audiological treatment for blast-induced chronic tinnitus. The amount of satisfaction from different hearing devices (hearing aid, noise generator, or both) during different time periods (1, 6, 12 and 24 months after fitting) was assessed. The 974 subjects enrolled in this study were Iran-Iraq war veterans, suffering from tinnitus for at least 2 years. About 84% of the subjects preferred just a hearing aid. Only 2.7% chose the noise generator, and the others preferred to use both devices. There were no significant differences between the hearing thresholds of the 3 groups. The satisfaction score for the hearing aid and combined devices increased by time but decreased for the noise generator. There was no correlation between the satisfaction score and parameters such as hearing thresholds, audiogram configuration and tinnitus pitch. We concluded that, compared with a noise generator, the most long-lasting treatment for blast-induced tinnitus is a hearing aid. The possible cause for such a performance is probably the recovery of the auditory function and neuroplasticity through the hearing aid.
DOI: 10.6084/m9.figshare.4535597.v1
title: Supplementary Material for: Does BDNF Val66Met Polymorphism Confer Risk for Posttraumatic Stress Disorder?

description: <b><i>Background:</i></b> Evidence has indicated that <i>BDNF</i> (brain-derived neurotrophic factor) Val66Met genetic variant could be linked to the development of posttraumatic stress disorder (PTSD). However, clinical observations studying the <i>BDNF</i> polymorphism and the risk of PTSD yielded contradictory results. In this meta-analysis we evaluated the association between <i>BDNF</i> Val66Met and PTSD risk. <b><i>Method:</i></b> Systematic searches in online databases retrieved 6 relevant publications. Different inherited models were utilized to perform the pooled analysis. Subgroup analyses and sensitive analyses based on Hardy-Weinberg equilibrium (HWE) test results were also carried out. <b><i>Results:</i></b> Our study did not found a significant overall effect of <i>BDNF</i> Val66Met on the susceptibility to PTSD under various genetic models. In contrast, subgroup analyses suggested that the stress status of the control group, but not ethnicity, may influence the relationship of <i>BDNF</i> Val66Met with PTSD risk. After the exclusion of a study that was not in HWE, our conclusions remained unchanged during the influence analyses. <b><i>Conclusions:</i></b> This meta-analysis suggested no genetic association of <i>BDNF</i> Val66Met with vulnerability to PTSD. Further research studies are warranted to clarify the impact of <i>BDNF </i>variants on the occurrence of PTSD.
DOI: 10.6084/m9.figshare.4535600.v1
title: Supplementary Material for: Comprehensive Analyses of White-Handed Gibbon Chromosomes Enables Access to 92 Evolutionary Conserved Breakpoints Compared to the Human Genome

description: Gibbon species (Hylobatidae) impress with an unusually high number of numerical and structural chromosomal changes within the family itself as well as compared to other Hominoidea including humans. In former studies applying molecular cytogenetic methods, 86 evolutionary conserved breakpoints (ECBs) were reported in the white-handed gibbon (<i>Hylobates lar</i>, HLA) with respect to the human genome. To analyze those ECBs in more detail and also to achieve a better understanding of the fast karyotype evolution in Hylobatidae, molecular data for these regions are indispensably necessary. In the present study, we obtained whole chromosome-specific probes by microdissection of all 21 HLA autosomes and prepared them for aCGH. Locus-specific DNA probes were also used for further molecular cytogenetic characterization of selected regions. Thus, we could map 6 yet unreported ECBs in HLA with respect to the human genome. Additionally, in 26 of the 86 previously reported ECBs, the present approach enabled a more precise breakpoint mapping. Interestingly, a preferred localization of ECBs within segmental duplications, copy number variant regions, and fragile sites was observed.
DOI: 10.6084/m9.figshare.4535567
title: Supplementary Material for: Differential Gene Expression in Gonadotropin-Releasing Hormone Neurons of Male and Metestrous Female Mice

description: <b><i>Background:</i></b> Gonadotropin-releasing hormone (GnRH) neurons play a pivotal role in the regulation of the hypothalamic-pituitary gonadal axis in a sex-specific manner. We hypothesized that the differences seen in reproductive functions of males and females are associated with a sexually dimorphic gene expression profile of GnRH neurons. <b><i>Methods and Results:</i></b> We compared the transcriptome of GnRH neurons obtained from intact metestrous female and male GnRH-green fluorescent protein transgenic mice. About 1,500 individual GnRH neurons from each sex were sampled with laser capture microdissection followed by whole-transcriptome amplification for gene expression profiling. Under stringent selection criteria (fold change &gt;1.6, adjusted p value 0.01), Affymetrix Mouse Genome 430 PM array analysis identified 543 differentially expressed genes. Sexual dimorphism was most apparent in gene clusters associated with synaptic communication, signal transduction, cell adhesion, vesicular transport and cell metabolism. To validate microarray results, 57 genes were selected, and 91% of their differential expression was confirmed by real-time PCR. Similarly, 88% of microarray results were confirmed with PCR from independent samples obtained by patch pipette harvesting and pooling of 30 GnRH neurons from each sex. We found significant differences in the expression of genes involved in vesicle priming and docking <i>(Syt1, Cplx1)</i>, GABAergic <i>(Gabra3, Gabrb3, Gabrg2)</i> and glutamatergic <i>(Gria1, Grin1, Slc17a6)</i> neurotransmission, peptide signaling <i>(Sstr3, Npr2, Cxcr4)</i> and the regulation of intracellular ion homeostasis <i>(Cacna1, Cacnb1, Cacng5, Kcnq2, Kcnc1)</i>. <b><i>Conclusion: </i></b>The striking sexual dimorphism of the GnRH neuron transcriptome we report here contributes to a better understanding of the differences in cellular mechanisms of GnRH neurons in the two sexes.
DOI: 10.6084/m9.figshare.4535582.v1
title: Supplementary Material for: Hearing Aid or Tinnitus Masker: Which One Is the Best Treatment for Blast-Induced Tinnitus? The Results of a Long-Term Study on 974 Patients

description: The aim of this longitudinal study was to explore whether a hearing aid or noise generator would be an effective audiological treatment for blast-induced chronic tinnitus. The amount of satisfaction from different hearing devices (hearing aid, noise generator, or both) during different time periods (1, 6, 12 and 24 months after fitting) was assessed. The 974 subjects enrolled in this study were Iran-Iraq war veterans, suffering from tinnitus for at least 2 years. About 84% of the subjects preferred just a hearing aid. Only 2.7% chose the noise generator, and the others preferred to use both devices. There were no significant differences between the hearing thresholds of the 3 groups. The satisfaction score for the hearing aid and combined devices increased by time but decreased for the noise generator. There was no correlation between the satisfaction score and parameters such as hearing thresholds, audiogram configuration and tinnitus pitch. We concluded that, compared with a noise generator, the most long-lasting treatment for blast-induced tinnitus is a hearing aid. The possible cause for such a performance is probably the recovery of the auditory function and neuroplasticity through the hearing aid.
DOI: 10.6084/m9.figshare.4535543
title: Supplementary Material for: The Evolution of Relative Brain Size in Marsupials Is Energetically Constrained but Not Driven by Behavioral Complexity

description: Evolutionary increases in mammalian brain size relative to body size are energetically costly but are also thought to confer selective advantages by permitting the evolution of cognitively complex behaviors. However, many suggested associations between brain size and specific behaviors - particularly related to social complexity - are possibly confounded by the reproductive diversity of placental mammals, whose brain size evolution is the most frequently studied. Based on a phylogenetic generalized least squares analysis of a data set on the reproductively homogenous clade of marsupials, we provide the first quantitative comparison of two hypotheses based on energetic constraints (maternal investment and seasonality) with two hypotheses that posit behavioral selection on relative brain size (social complexity and environmental interactions). We show that the two behavioral hypotheses have far less support than the constraint hypotheses. The only unambiguous associates of brain size are the constraint variables of litter size and seasonality. We also found no association between brain size and specific behavioral complexity categories within kangaroos, dasyurids, and possums. The largest-brained marsupials after phylogenetic correction are from low-seasonality New Guinea, supporting the notion that low seasonality represents greater nutrition safety for brain maintenance. Alternatively, low seasonality might improve the maternal support of offspring brain growth. The lack of behavioral brain size associates, found here and elsewhere, supports the general ‘cognitive buffer hypothesis' as the best explanatory framework of mammalian brain size evolution. However, it is possible that brain size alone simply does not provide sufficient resolution on the question of how brain morphology and cognitive capacities coevolve.
DOI: 10.6084/m9.figshare.4535564
title: Supplementary Material for: A RIG-I 2CARD-MAVS200 Chimeric Protein Reconstitutes IFN-β Induction and Antiviral Response in Models Deficient in Type I IFN Response

description: RIG-I-like receptors (RLRs) are cellular sensor proteins that detect certain RNA species produced during viral infections. RLRs activate a signaling cascade that results in the production of IFN-β as well as several other cytokines with antiviral and proinflammatory activities. We explored the potential of different constructs based on RLRs to induce the IFN-β pathway and create an antiviral state in type I IFN-unresponsive models. A chimeric construct composed of RIG-I 2CARD and the first 200 amino acids of MAVS (2CARD-MAVS200) showed an enhanced ability to induce IFN-β when compared to other stimulatory constructs. Furthermore, this human chimeric construct showed a superior ability to activate IFN-β expression in cells from various species. This construct was found to overcome the restrictions of blocking IFN-β induction or signaling by a number of viral IFN-antagonist proteins. Additionally, the antiviral activity of this chimera was demonstrated in influenza virus and HBV infection mouse models using adeno-associated virus (AAV) vectors as a delivery vehicle. We propose that AAV vectors expressing 2CARD-MAVS200 chimeric protein can reconstitute IFN-β induction and recover a partial antiviral state in different models that do not respond to recombinant IFN-β treatment.
DOI: 10.6084/m9.figshare.4535540
title: Supplementary Material for: A High-Resolution Comparative Chromosome Map of Cricetus cricetus and Peromyscus eremicus Reveals the Involvement of Constitutive Heterochromatin in Breakpoint Regions

description: Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, <i>Cricetus cricetus</i> and <i>Peromyscus eremicus</i>, and the index species <i>Mus musculus</i> and <i>Rattus norvegicus</i>. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in <i>C. cricetus</i> and <i>P. eremicus</i> since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the <i>C. cricetus</i> (derivative) and <i>P. eremicus</i> (conserved) genomes.
DOI: 10.6084/m9.figshare.4535513
title: Supplementary Material for: The Co-Expression of Kallikrein 5 and Kallikrein 7 Associates with Poor Survival in Non-HPV Oral Squamous-Cell Carcinoma

description: <b><i>Objective:</i></b> Oral squamous-cell carcinoma (OSCC) still has a poor prognosis. Lymph node metastasis (LNM) is a major determinant of treatment decisions and prognosis. Serine protease inhibitor Kazal-type 5 (SPINK5) is the inhibitor of kallikrein 5 (KLK5) and KLK7. SPINK5, KLK5 and KLK7 are three of the genes of a recently validated LNM-predicting gene expression profile in OSCC. This study evaluates their clinicopathological role and value as biomarkers in OSCC. <b><i>Methods:</i></b> Eighty-three patients with primary OSCC, treated surgically between 1996 and 2000, were included. Gene expression data were acquired from a previously reported study. Human papillomavirus (HPV) status was determined by an algorithm for HPV-16. Protein expression for KLK5, KLK7 and SPINK5 was semi-quantitatively determined in all 83 tumours by immunohistochemistry. All expression data were correlated with clinicopathological parameters. <b><i>Results:</i></b> Concurrent loss of KLK5 and KLK7 correlates with worse disease-specific and overall survival (DSS and OS). Multivariate analysis proved that co-expression is an independent prognostic factor for DSS (p = 0.029) and OS (p = 0.001). <b><i>Conclusion:</i></b> This report demonstrates that concurrent loss of KLK5 and KLK7 associates with a poor clinical outcome in OSCC and could therefore serve as prognostic marker in this disease.