cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5122561
title: Supplementary Material for: Abnormal T<sub>2</sub>-Weighted MRI Signal Surrounding Leads in a Subset of Deep Brain Stimulation Patients

description: <i>Background:</i> Deep brain stimulation (DBS) surgery is a common treatment option for numerous neurological disorders. However, it is not without potential complications, such as hemorrhage and infection. Interestingly, we have observed several instances of abnormal T<sub>2</sub>-weighted signal hyperintensity surrounding DBS leads on postoperative MRI that are not associated with hemorrhage or infection. <i>Methods:</i> To better characterize the incidence and timing associated with this finding, we retrospectively reviewed postoperative imaging for all DBS implants performed over 9 years at one institution. <i>Results and Conclusions:</i> Fifteen instances of T<sub>2</sub> signal hyperintensity surrounding DBS leads on postoperative MRI scans were observed across 239 implants (6.3% incidence) in 133 patients. The signal characteristics were most consistent with vasogenic edema, possibly representing an inflammatory response. The finding was typically unilateral, even in patients with simultaneous bilateral lead implants. Most affected patients were asymptomatic, although 3 were symptomatic and 1 experienced marked gait instability that was treated with steroids. T<sub>2</sub> signal abnormality was seen more commonly in scans obtained 3 or more days after surgery than in those collected immediately postoperatively. No differences in age, anatomical target, diagnosis, or number of microelectrode passes were noted between patients with or without T<sub>2</sub> signal. Further research will be needed to explain this curious neuroimaging finding, and to rule out cause for clinical concern.
DOI: 10.6084/m9.figshare.5122570.v1
title: Supplementary Material for: Overexpression of <i>Lis1</i> in Different Stages of Spermatogenesis Does Not Result in an Aberrant Phenotype

description: Previous studies showed that in the mouse mutant <i>Lis1</i><sup>GT/GT</sup> gene trap integration in intron 2 of <i>Lis1</i> gene leads to male infertility in homozygous <i>Lis1</i><sup>GT/GT</sup> mice. We further analyzed this line and could confirm the suggested downregulation of a testis-specific <i>Lis1</i> transcript in mutant animals in a quantitative manner. Moreover, we analyzed the gene trap mutation on different genetic backgrounds in incipient congenic animals and could exclude a genetic background effect. To gain further insights into the role and requirement of LIS1 in spermatogenesis, 3 transgenic lines were generated, that overexpress <i>Lis1</i> under control of the testis-specific promoters <i>hEF-1</i>α, which is exclusively active in spermatogonial cells, <i>PGK2</i>, which is active in pachytene spermatocytes and following stages of spermatogenesis, and <i>Tnp2</i> which is active in round spermatids and following stages of spermatogenesis, respectively. All 3 transgenic lines remained fertile and testis sections displayed no abnormalities. To overcome the infertility of <i>Lis1</i><sup>GT/GT</sup> males, these transgenic <i>Lis1</i>-overexpressing animals were mated with <i>Lis1</i><sup>GT/GT</sup> mice to generate ‘rescued’ <i>Lis1</i><sup>GT/GT</sup><i>/Lis1</i><sup>Tpos</sup> males. ‘Rescued’ animals from all transgenic lines remained infertile, thus overexpression of <i>Lis1</i> in different stages of spermatogenesis could not rescue the infertility phenotype of homozygous gene trap males.
DOI: 10.6084/m9.figshare.5122552
title: Supplementary Material for: Reduction of Oxidative Damage Reflects a Better Kidney Transplantation Outcome

description: <i>Background/Aims:</i> DNA fragmentation is one of the typical features of apoptosis, frequently induced by oxidative stress. Increased oxidative stress is known to be related to several pathological processes. In this study, we assessed oxidative damage in the early follow-up period after kidney transplantation measuring DNA oxidation and fragmentation of mononuclear cells and the circulating levels of inflammatory cytokines. <i>Methods:</i> Blood samples from 30 kidney transplant recipients were collected before transplantation and after 2 days, 1 month and 6 months. Oxidative DNA fragmentation was measured by Comet Assay, whereas DNA oxidation was evaluated measuring 8-OHdG leukocyte levels. Serum IL-1β, IL-4, IL-6, IL-8, IL-10, IFN-γ and TNF-α were assayed using a multiplex ELISA analysis. <i>Results:</i> At 6 months after transplantation, a significant reduction in DNA fragmentation and IL-6 plasma levels was observed; DNA oxidation was higher in patients with a worse outcome, with delayed graft function and low nutritional status. We also found a correlation of IL-6 and IL-10 levels with DNA fragmentation and of IL-10 levels with DNA oxidation. <i>Conclusion:</i> Low levels of oxidation and apoptosis at 6 months after transplantation correlate with a better recovery of renal function in kidney allografts. The measurement of cytokine levels confirmed a reduction of inflammatory parameters within 6 months of follow-up.
DOI: 10.6084/m9.figshare.5122555
title: Supplementary Material for: Chemo- and Thermosensory Responsiveness of Grueneberg Ganglion Neurons Relies on Cyclic Guanosine Monophosphate Signaling Elements

description: Neurons of the Grueneberg ganglion (GG) in the anterior nasal region of mouse pups respond to cool temperatures and to a small set of odorants. While the thermosensory reactivity appears to be mediated by elements of a cyclic guanosine monophosphate (cGMP) cascade, the molecular mechanisms underlying the odor-induced responses are unclear. Since odor-responsive GG cells are endowed with elements of a cGMP pathway, specifically the transmembrane guanylyl cyclase subtype GC-G and the cyclic nucleotide-gated ion channel CNGA3, the possibility was explored whether these cGMP signaling elements may also be involved in chemosensory GG responses. Experiments with transgenic mice deficient for GC-G or CNGA3 revealed that GG responsiveness to given odorants was significantly diminished in these knockout animals. These findings suggest that a cGMP cascade may be important for both olfactory and thermosensory signaling in the GG. However, in contrast to the thermosensory reactivity, which did not decline over time, the chemosensory response underwent adaptation upon extended stimulation, suggesting that the two transduction processes only partially overlap.
DOI: 10.6084/m9.figshare.5122561.v1
title: Supplementary Material for: Abnormal T<sub>2</sub>-Weighted MRI Signal Surrounding Leads in a Subset of Deep Brain Stimulation Patients

description: <i>Background:</i> Deep brain stimulation (DBS) surgery is a common treatment option for numerous neurological disorders. However, it is not without potential complications, such as hemorrhage and infection. Interestingly, we have observed several instances of abnormal T<sub>2</sub>-weighted signal hyperintensity surrounding DBS leads on postoperative MRI that are not associated with hemorrhage or infection. <i>Methods:</i> To better characterize the incidence and timing associated with this finding, we retrospectively reviewed postoperative imaging for all DBS implants performed over 9 years at one institution. <i>Results and Conclusions:</i> Fifteen instances of T<sub>2</sub> signal hyperintensity surrounding DBS leads on postoperative MRI scans were observed across 239 implants (6.3% incidence) in 133 patients. The signal characteristics were most consistent with vasogenic edema, possibly representing an inflammatory response. The finding was typically unilateral, even in patients with simultaneous bilateral lead implants. Most affected patients were asymptomatic, although 3 were symptomatic and 1 experienced marked gait instability that was treated with steroids. T<sub>2</sub> signal abnormality was seen more commonly in scans obtained 3 or more days after surgery than in those collected immediately postoperatively. No differences in age, anatomical target, diagnosis, or number of microelectrode passes were noted between patients with or without T<sub>2</sub> signal. Further research will be needed to explain this curious neuroimaging finding, and to rule out cause for clinical concern.
DOI: 10.6084/m9.figshare.5122573.v1
title: Supplementary Material for: The Evolutionary History of TLR4 Polymorphisms in Europe

description: Infections exert important evolutionary pressures shaping the human genome, especially on genes involved in host defense. A crucial step for host defense is recognition of pathogens by pattern recognition receptors on innate immune cells, among which Toll-like receptor 4 (<i>TLR4)</i> is one of the best known. Genetic variation in <i>TLR4</i> (Asp299Gly, Thr399Ile) has been recently described. Haplotype frequencies of these polymorphisms differ among African, Asian and European populations, suggesting evolutionary pressures exerted by local infections. The <i>TLR4</i> 299Gly/399Ile haplotype, characteristic mainly of European populations, has relatively high frequency in the Iberian peninsula. This region is also described as refuge area during the last glacial maximum 20,000 years ago, from which repopulation of Europe took place. We speculate that a genetic bottleneck in the Iberian peninsula could have promoted the increased frequency of this haplotype by genetic drift. This hypothesis is supported by three arguments: (1) the West-East gradient of prevalence in the haplotype among European populations; (2) ancient DNA from Neolithic burials in the Iberian peninsula, dated 6,600–4,500 years before present, confirmed the relatively high frequency of this haplotype in the region, and (3) no functional differences between this haplotype and wild-type <i>TLR4</i> have been found. In contrast, the disappearance of the 299Gly/399Thr haplotype in Europe is most likely due to negative selection due to sepsis. In conclusion, differences in distribution of <i>TLR4</i> polymorphisms Asp299Gly and Thr399Ile in European populations are most likely due to a combination of population migration events combined with selection due to sepsis.
DOI: 10.6084/m9.figshare.5122549
title: Supplementary Material for: Does Perfusion Computed Tomography Facilitate Clinical Decision Making for Thrombolysis in Unselected Acute Patients with Suspected Ischaemic Stroke?

description: <i>Background:</i> Despite use in clinical practice and major positive trials of thrombolysis, non-contrast computed tomography (NCCT) is not sensitive for identifying penumbral tissue in acute stroke. This study evaluated how physiological imaging using CT perfusion (CTP) could add to the diagnostic utility of an NCCT and inform clinical decisions regarding thrombolysis. <i>Methods:</i> Forty imaging datasets containing NCCT and CTP were retrospectively identified from a cohort of consecutive acute stroke patients. Two sets of observers (n = 6) and a neuroradiologist evaluated the images without knowledge of clinical symptoms. Inter-observer agreement was calculated using the ĸ statistic for identifying acute ischaemic change on NCCT: perfusion abnormalities (namely cerebral blood volume, cerebral blood flow and time to peak), and penumbral tissue on perfusion maps obtained by two image processing algorithms. <i>Results:</i> Inter-rater agreement was moderate (ĸ = 0.54) for early ischaemic change on NCCT. Perfusion maps improved this to substantial for cerebral blood volume (ĸ = 0.67) and to almost perfect for time to peak (ĸ = 0.87) and cerebral blood flow (ĸ = 0.87). The agreement for qualitative assessment of penumbral tissue was substantial to perfect for images obtained using the two different perfusion algorithms. Overall, there was a high rate of decision to thrombolyse based on NCCT (81.25%). CTP strengthened the decision to thrombolyse based on NCCT in 38.3% of cases. It negatively influenced the decision in 14.6% of cases, this being significantly more common in experienced observers (p = 0.02). <i>Conclusions:</i> We demonstrate that the qualitative evaluation of CTP produces near perfect inter-observer agreement, regardless of the post-processing method used. CTP is a reliable, accessible and practical imaging modality that improves confidence in reaching the appropriate diagnosis. It is particularly useful for less experienced clinicians, to arrive at a physiologically informed treatment decision.
DOI: 10.5281/zenodo.3726907
title: EMUE-D1-2-BayesianMassCalibration

description: This example describes the calibration of a conventional mass of a weight W against a reference weight R with a nominal mass of 100 g. The example builds on that given in JCGM 101:2008. This time a Bayesian evaluation of the measurement is performed. A Bayesian approach differs from the Monte Carlo method (MCM) of JCGM 101:2008 and the law of propagation of uncertainty (LPU) in JCGM 100:2008 in that it combines prior knowledge about the measurand with the data obtained during calibration. From the joint posterior probability density function which is obtained from this combination, a value and a coverage interval for the measurand are obtained. Files contained in the dataset are: - EMUEActivity113_MassCalibration.pdf: report “Bayesian approach applied to the mass calibration example in JCGM 101:2008”; - EMUEActivity113_MassCalibration.tex: LaTeX source file to be compiled in order to produce EMUEActivity113_MassCalibration.pdf; - Compendium.bib: bibliography file; - conjugateBayesKnownV.pdf: image contained in the report; - MCMvsBayesNI.pdf: image contained in the report; - JCGM101_Mass_calibration_code.R : R code to run the example from the report.
description: The report relies on the following publications: - BIPM, IEC, IFCC, ILAC, ISO, IUPAC, IUPAP, and OIML. Supplement 1 to the 'Guide to the Expression of Uncertainty in Measurement' – Propagation of distributions using a Monte Carlo method, JCGM 101:2008. BIPM, 2008. - A. Gelman, J. B. Carlin, H. S. Stern, D. B. Dunson, A. Vehtari, and D. B. Rubin. Bayesian Data Analysis, 3rd edition. Chapman and Hall/CRC, 2013. - G.E.P. Box and G.C. Tiao. Bayesian Inference in Statistical Analysis. Wiley, 1992. - C. Elster. Bayesian uncertainty analysis compared with the application of the GUM and its supplements. Metrologia, 51:S159–S166, 2014. - BIPM, IEC, IFCC, ILAC, ISO, IUPAC, IUPAP, and OIML. Guide to the Expression of Uncertainty in Measurement, JCGM 100:2008, GUM 1995 with minor corrections. BIPM, 2008. - J. A. Sousa, A. B. Forbes, A. S. Ribeiro, P. M. Harris, F. Carvalho, and L. Bacelar. The evaluation of uncertainty in mass calibration: possible approaches in a comparison study. Journal of Physics: Conference Series, 459:012033, sep 2013. - S. Chib and E. Greenberg. Understanding the metropolis-hastings algorithm. The American Statistician, 49(4):327–335, 1995.
DOI: 10.5281/zenodo.3726908
title: EMUE-D1-2-BayesianMassCalibration

description: This example describes the calibration of a conventional mass of a weight W against a reference weight R with a nominal mass of 100 g. The example builds on that given in JCGM 101:2008. This time a Bayesian evaluation of the measurement is performed. A Bayesian approach differs from the Monte Carlo method (MCM) of JCGM 101:2008 and the law of propagation of uncertainty (LPU) in JCGM 100:2008 in that it combines prior knowledge about the measurand with the data obtained during calibration. From the joint posterior probability density function which is obtained from this combination, a value and a coverage interval for the measurand are obtained. Files contained in the dataset are: - EMUEActivity113_MassCalibration.pdf: report “Bayesian approach applied to the mass calibration example in JCGM 101:2008”; - EMUEActivity113_MassCalibration.tex: LaTeX source file to be compiled in order to produce EMUEActivity113_MassCalibration.pdf; - Compendium.bib: bibliography file; - conjugateBayesKnownV.pdf: image contained in the report; - MCMvsBayesNI.pdf: image contained in the report; - JCGM101_Mass_calibration_code.R : R code to run the example from the report.
description: The report relies on the following publications: - BIPM, IEC, IFCC, ILAC, ISO, IUPAC, IUPAP, and OIML. Supplement 1 to the 'Guide to the Expression of Uncertainty in Measurement' – Propagation of distributions using a Monte Carlo method, JCGM 101:2008. BIPM, 2008. - A. Gelman, J. B. Carlin, H. S. Stern, D. B. Dunson, A. Vehtari, and D. B. Rubin. Bayesian Data Analysis, 3rd edition. Chapman and Hall/CRC, 2013. - G.E.P. Box and G.C. Tiao. Bayesian Inference in Statistical Analysis. Wiley, 1992. - C. Elster. Bayesian uncertainty analysis compared with the application of the GUM and its supplements. Metrologia, 51:S159–S166, 2014. - BIPM, IEC, IFCC, ILAC, ISO, IUPAC, IUPAP, and OIML. Guide to the Expression of Uncertainty in Measurement, JCGM 100:2008, GUM 1995 with minor corrections. BIPM, 2008. - J. A. Sousa, A. B. Forbes, A. S. Ribeiro, P. M. Harris, F. Carvalho, and L. Bacelar. The evaluation of uncertainty in mass calibration: possible approaches in a comparison study. Journal of Physics: Conference Series, 459:012033, sep 2013. - S. Chib and E. Greenberg. Understanding the metropolis-hastings algorithm. The American Statistician, 49(4):327–335, 1995.
DOI: 10.25549/one-c4-15250
title: ONE, Inc. meeting minutes (1964)

description: Minutes for the annual, corporate, board of directors meetings (1964)
DOI: 10.15156/bio/sh1249151.08fu
title: SH1249151.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1249152.08fu
title: SH1249152.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1249153.08fu
title: SH1249153.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1249154.08fu
title: SH1249154.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1249155.08fu
title: SH1249155.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1249156.08fu
title: SH1249156.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.