cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10147
title: Dataset For Cushing'S And Acromegaly Studies

description: This is the code for the second submission. The major changes from the first submission include

Switch from DESeq to DESeq2

DESeq2 controls for the false positive rate differently, allowing for a more powerful statistical analysis. We switched all the analyses over to DESeq2. This dramatically changed the number of statistically significant genes. This was done in issue #9 for the code and issue #14 for the manuscript. We also upgraded to GRCh37.74 version of the human genome in issue #13.

Counts Mapping Algoritm

Based on utility, and avoiding the need to filter out extra transcripts that we are not analysing we mapped genes using HTSseq rather than Genomic Ranges. This was done in issue #1.

Clinical Measurements

We noted that some of the clinical measurements seemed to be non-normally distributed. We adjusted the clinical analysis script to first test for normality, then test for equal variance. The resulting p-values are now based on either a Wilcoxon, Welch or Student's T-Test. This was done in issue #16 (commit 6143ff1).

Gene Set Enrichment

Added analysis using GSEA to replace/complement the GOseq analysis. GSEA (http://www.broadinstitute.org/gsea/index.jsp) incorporates the rank of genes in the entire data set, rather than just the top significant hits. This allowed us to analyse more data sets including miRNA, TRANSFAC, Reactome. This was done in issue #12 and largely in commit 1e25f3b054631e549495c482eb5cbc655910c865. These data are presented in Supplementary Tables 2,3 and 4 as done in issue #20
DOI: 10.1594/wdcrsat.6umv2upy
title: Nocturnal means of OH(3-1) airglow rotational temperatures from the mesopause region obtained with GRIPS 6 located at the German Remote Sensing Data Center, Oberpfaffenhofen

description: The temperatures are derived from the rotational vibrational transition of the OH molecule originating from a thin layer in approximately 87 km centroid height. The spectra have been obtained with the Ground-based Infrared P-branch Spectrometer (GRIPS 6) located at the German Remote Sensing Data Center (DFD) of the German Aerospace Center (DLR) in Oberpfaffenhofen (11.271E, 48.081N), Germany - a measurement station of the international Network for the Detection of Mesospheric Change (NDMC). During routine operation one spectrum is obtained every 15 s, originating from a field of view of approximately 15.5° x 15.5° corresponding to ca. 24 x 24 km2 in 87 km height, the peak height of the OH emission layer. The covered wavelength range allows the observation of the OH(3-1) Q- and P-branches as well as of the OH(4-2) R- and Q-branches. Rotational temperatures are calculated using OH(3-1) P-branch emissions between 1520 nm and 1550 nm. For the estimation of a nocturnal mean value all samples of the nightly temperature time series are weighted according to their individual precision. Thus, mean temperatures between 1 and 2 K are lower compared to the unweighted arithmetic mean. A mean is only calculated, when at least two hours of observation time are available.
description: GRIPS 6 is equipped with a Czerny-Turner spectrograph and a thermoelectrically cooled InGaAs array. Only the P1(2), P1(3) and P1(4) rotational lines of the (3-1) vibrational transition are used for the derivation of temperatures. Intensities are only read out at the line centers of the smoothed spectra due to residual overlapping of the lines at their wings. Important physical constants applied during the processing are taken from Mies (1974) (Einstein coefficients) and Krassovsky et al. (1962) (rotational term values).
Further details concerning the derivation of rotational temperatures are presented in Schmidt, C., Höppner, K. and Bittner, M. (2013): A ground-based spectrometer equipped with an InGaAs array for routine observations of OH(3-1) rotational temperatures in the mesopause region. Journal of Atmospheric and Solar-Terrestrial Physics 102 (2013) 125–139. http://dx.doi.org/10.1016/j.jastp.2013.05.001
DOI: 10.1594/wdcrsat.6vmdmvph
title: Nocturnal means of OH(3-1) airglow rotational temperatures from the mesopause region obtained with GRIPS 6 located at the German Remote Sensing Data Center, Oberpfaffenhofen

description: The temperatures are derived from the rotational vibrational transition of the OH molecule originating from a thin layer in approximately 87 km centroid height. The spectra have been obtained with the Ground-based Infrared P-branch Spectrometer (GRIPS 6) located at the German Remote Sensing Data Center (DFD) of the German Aerospace Center (DLR) in Oberpfaffenhofen (11.271E, 48.081N), Germany - a measurement station of the international Network for the Detection of Mesospheric Change (NDMC). During routine operation one spectrum is obtained every 15 s, originating from a field of view of approximately 15.5° x 15.5° corresponding to ca. 24 x 24 km2 in 87 km height, the peak height of the OH emission layer. The covered wavelength range allows the observation of the OH(3-1) Q- and P-branches as well as of the OH(4-2) R- and Q-branches. Rotational temperatures are calculated using OH(3-1) P-branch emissions between 1520 nm and 1550 nm. For the estimation of a nocturnal mean value all samples of the nightly temperature time series are weighted according to their individual precision. Thus, mean temperatures between 1 and 2 K are lower compared to the unweighted arithmetic mean. A mean is only calculated, when at least two hours of observation time are available.
description: GRIPS 6 is equipped with a Czerny-Turner spectrograph and a thermoelectrically cooled InGaAs array. Only the P1(2), P1(3) and P1(4) rotational lines of the (3-1) vibrational transition are used for the derivation of temperatures. Intensities are only read out at the line centers of the smoothed spectra due to residual overlapping of the lines at their wings. Important physical constants applied during the processing are taken from Mies (1974) (Einstein coefficients) and Krassovsky et al. (1962) (rotational term values).
Further details concerning the derivation of rotational temperatures are presented in Schmidt, C., Höppner, K. and Bittner, M. (2013): A ground-based spectrometer equipped with an InGaAs array for routine observations of OH(3-1) rotational temperatures in the mesopause region. Journal of Atmospheric and Solar-Terrestrial Physics 102 (2013) 125–139. http://dx.doi.org/10.1016/j.jastp.2013.05.001
DOI: 10.1594/wdcrsat.6wlw6wp0
title: Nocturnal means of OH(3-1) airglow rotational temperatures from the mesopause region obtained with GRIPS 5 located at Abastumani Astrophysical Observatory, Georgia

description: The temperatures are derived from the rotational vibrational transition of the OH molecule originating from a thin layer in approximately 87 km centroid height. The spectra have been obtained with the Ground-based Infrared P-branch Spectrometer (GRIPS 5) located at Evgeni Kharadze Abastumani Astrophysical Observatory (ABA: 41.75°N, 42.82°E) - a measurement station of the international Network for the Detection of Mesospheric Change (NDMC). It is jointly operated by the German Remote Sensing Data Center (DFD) of the German Aerospace Center (DLR) and the Section Atmosphere and Ionosphere Physics of Ilia State University (Iliauni). During routine operation one spectrum is obtained every 15 s, originating from a field of view of approximately 4.5° x 4.5° which corresponds to ca. 660 km2 in 87 km height, as the instruments points northwards with a zenith angle of 45°. The covered wavelength range allows the observation of the OH(3-1) Q- and P-branches as well as of the OH(4-2) R- and Q-branches. Rotational temperatures are calculated using OH(3-1) P-branch emissions between 1520 nm and 1550 nm. For the estimation of a nocturnal mean value all samples of the nightly temperature time series are weighted according to their individual precision. Thus, mean temperatures between 1 and 2 K are lower compared to the unweighted arithmetic mean. A mean is only calculated, when at least two hours of observation time are available.
description: GRIPS 5 is equipped with a Czerny-Turner spectrograph, with an off-axis parabolic mirror in front of the entrance slit and a thermoelectrically cooled InGaAs array. Only the P1(2), P1(3) and P1(4) rotational lines of the (3-1) vibrational transition are used for the derivation of temperatures. Intensities are only read out at the line centers of the smoothed spectra due to residual overlapping of the lines at their wings. Important physical constants applied during the processing are taken from Mies (1974) (Einstein coefficients) and Krassovsky et al. (1962) (rotational term values).
Further details concerning the derivation of rotational temperatures are presented in Schmidt, C., Höppner, K. and Bittner, M. (2013): A ground-based spectrometer equipped with an InGaAs array for routine observations of OH(3-1) rotational temperatures in the mesopause region. Journal of Atmospheric and
Solar-Terrestrial Physics 102 (2013) 125–139. http://dx.doi.org/10.1016/j.jastp.2013.05.001
DOI: 10.1594/wdcrsat.6xleqxoj
title: Nocturnal means of OH(3-1) airglow rotational temperatures from the mesopause region obtained with GRIPS 5 located at Abastumani Astrophysical Observatory, Georgia

description: The temperatures are derived from the rotational vibrational transition of the OH molecule originating from a thin layer in approximately 87 km centroid height. The spectra have been obtained with the Ground-based Infrared P-branch Spectrometer (GRIPS 5) located at Evgeni Kharadze Abastumani Astrophysical Observatory (ABA: 41.75°N, 42.82°E) - a measurement station of the international Network for the Detection of Mesospheric Change (NDMC). It is jointly operated by the German Remote Sensing Data Center (DFD) of the German Aerospace Center (DLR) and the Section Atmosphere and Ionosphere Physics of Ilia State University (Iliauni). During routine operation one spectrum is obtained every 15 s, originating from a field of view of approximately 4.5° x 4.5° which corresponds to ca. 660 km2 in 87 km height, as the instruments points northwards with a zenith angle of 45°. The covered wavelength range allows the observation of the OH(3-1) Q- and P-branches as well as of the OH(4-2) R- and Q-branches. Rotational temperatures are calculated using OH(3-1) P-branch emissions between 1520 nm and 1550 nm. For the estimation of a nocturnal mean value all samples of the nightly temperature time series are weighted according to their individual precision. Thus, mean temperatures between 1 and 2 K are lower compared to the unweighted arithmetic mean. A mean is only calculated, when at least two hours of observation time are available.
description: GRIPS 5 is equipped with a Czerny-Turner spectrograph, with an off-axis parabolic mirror in front of the entrance slit and a thermoelectrically cooled InGaAs array. Only the P1(2), P1(3) and P1(4) rotational lines of the (3-1) vibrational transition are used for the derivation of temperatures. Intensities are only read out at the line centers of the smoothed spectra due to residual overlapping of the lines at their wings. Important physical constants applied during the processing are taken from Mies (1974) (Einstein coefficients) and Krassovsky et al. (1962) (rotational term values).
Further details concerning the derivation of rotational temperatures are presented in Schmidt, C., Höppner, K. and Bittner, M. (2013): A ground-based spectrometer equipped with an InGaAs array for routine observations of OH(3-1) rotational temperatures in the mesopause region. Journal of Atmospheric and
Solar-Terrestrial Physics 102 (2013) 125–139. http://dx.doi.org/10.1016/j.jastp.2013.05.001
DOI: 10.1594/wdcrsat.6ykxayo2
title: Nocturnal means of OH(3-1) airglow rotational temperatures from the mesopause region obtained with GRIPS 8 located at the Environmental Research Station “Schneefernerhaus”

description: The temperatures are derived from the rotational vibrational transition of the OH molecule originating from a thin layer in approximately 87 km centroid height. The spectra have been obtained with the Ground-based Infrared P-branch Spectrometer (GRIPS 8) located at the Environmental Research Station “Schneefernerhaus” (UFS: 10.98°E, 47.42°N) - a measurement station of the international Network for the Detection of Mesospheric Change (NDMC). It is operated by the German Remote Sensing Data Center (DFD) of the German Aerospace Center (DLR). During routine operation one spectrum is obtained every 15 s, originating from a field of view of approximately 15.5° x 15.5° which corresponds to ca. 1600 km2 in 87 km height, because the instruments points southwards with a zenith angle of 45°. The covered wavelength range allows the observation of the OH(3-1) Q- and P-branches as well as of the OH(4-2) R- and Q-branches. Rotational temperatures are calculated using OH(3-1) P-branch emissions between 1520 nm and 1550 nm. For the estimation of a nocturnal mean value all samples of the nightly temperature time series are weighted according to their individual precision. Thus, mean temperatures between 1 and 2 K are lower compared to the unweighted arithmetic mean. A mean is only calculated, when at least two hours of observation time are available.
description: GRIPS 8 is equipped with a Czerny-Turner spectrograph and a thermoelectrically cooled InGaAs array. Only the P1(2), P1(3) and P1(4) rotational lines of the (3-1) vibrational transition are used for the derivation of temperatures. Intensities are only read out at the line centers of the smoothed spectra due to residual overlapping of the lines at their wings. Important physical constants applied during the processing are taken from Mies (1974) (Einstein coefficients) and Krassovsky et al. (1962) (rotational term values).
Further details concerning the derivation of rotational temperatures are presented in Schmidt, C., Höppner, K. and Bittner, M. (2013): A ground-based spectrometer equipped with an InGaAs array for routine observations of OH(3-1) rotational temperatures in the mesopause region. Journal of Atmospheric and
Solar-Terrestrial Physics 102 (2013) 125–139. http://dx.doi.org/10.1016/j.jastp.2013.05.001
DOI: 10.1594/wdcrsat.6zkfuznl
title: Nocturnal means of OH(3-1) airglow rotational temperatures from the mesopause region obtained with GRIPS 8 located at the Environmental Research Station “Schneefernerhaus”

description: The temperatures are derived from the rotational vibrational transition of the OH molecule originating from a thin layer in approximately 87 km centroid height. The spectra have been obtained with the Ground-based Infrared P-branch Spectrometer (GRIPS 8) located at the Environmental Research Station “Schneefernerhaus” (UFS: 10.98°E, 47.42°N) - a measurement station of the international Network for the Detection of Mesospheric Change (NDMC). It is operated by the German Remote Sensing Data Center (DFD) of the German Aerospace Center (DLR). During routine operation one spectrum is obtained every 15 s, originating from a field of view of approximately 15.5° x 15.5° which corresponds to ca. 1600 km2 in 87 km height, because the instruments points southwards with a zenith angle of 45°. The covered wavelength range allows the observation of the OH(3-1) Q- and P-branches as well as of the OH(4-2) R- and Q-branches. Rotational temperatures are calculated using OH(3-1) P-branch emissions between 1520 nm and 1550 nm. For the estimation of a nocturnal mean value all samples of the nightly temperature time series are weighted according to their individual precision. Thus, mean temperatures between 1 and 2 K are lower compared to the unweighted arithmetic mean. A mean is only calculated, when at least two hours of observation time are available.
description: GRIPS 8 is equipped with a Czerny-Turner spectrograph and a thermoelectrically cooled InGaAs array. Only the P1(2), P1(3) and P1(4) rotational lines of the (3-1) vibrational transition are used for the derivation of temperatures. Intensities are only read out at the line centers of the smoothed spectra due to residual overlapping of the lines at their wings. Important physical constants applied during the processing are taken from Mies (1974) (Einstein coefficients) and Krassovsky et al. (1962) (rotational term values).
Further details concerning the derivation of rotational temperatures are presented in Schmidt, C., Höppner, K. and Bittner, M. (2013): A ground-based spectrometer equipped with an InGaAs array for routine observations of OH(3-1) rotational temperatures in the mesopause region. Journal of Atmospheric and
Solar-Terrestrial Physics 102 (2013) 125–139. http://dx.doi.org/10.1016/j.jastp.2013.05.001
DOI: 10.1594/wdcrsat.70jyf0n4
title: Nocturnal means of OH(3-1) airglow rotational temperatures from the mesopause region obtained with GRIPS 8 located at the Environmental Research Station “Schneefernerhaus”

description: The temperatures are derived from the rotational vibrational transition of the OH molecule originating from a thin layer in approximately 87 km centroid height. The spectra have been obtained with the Ground-based Infrared P-branch Spectrometer (GRIPS 8) located at the Environmental Research Station “Schneefernerhaus” (UFS: 10.98°E, 47.42°N) - a measurement station of the international Network for the Detection of Mesospheric Change (NDMC). It is operated by the German Remote Sensing Data Center (DFD) of the German Aerospace Center (DLR). During routine operation one spectrum is obtained every 15 s, originating from a field of view of approximately 15.5° x 15.5° which corresponds to ca. 1600 km2 in 87 km height, because the instruments points southwards with a zenith angle of 45°. The covered wavelength range allows the observation of the OH(3-1) Q- and P-branches as well as of the OH(4-2) R- and Q-branches. Rotational temperatures are calculated using OH(3-1) P-branch emissions between 1520 nm and 1550 nm. For the estimation of a nocturnal mean value all samples of the nightly temperature time series are weighted according to their individual precision. Thus, mean temperatures between 1 and 2 K are lower compared to the unweighted arithmetic mean. A mean is only calculated, when at least two hours of observation time are available.
description: GRIPS 8 is equipped with a Czerny-Turner spectrograph and a thermoelectrically cooled InGaAs array. Only the P1(2), P1(3) and P1(4) rotational lines of the (3-1) vibrational transition are used for the derivation of temperatures. Intensities are only read out at the line centers of the smoothed spectra due to residual overlapping of the lines at their wings. Important physical constants applied during the processing are taken from Mies (1974) (Einstein coefficients) and Krassovsky et al. (1962) (rotational term values).
Further details concerning the derivation of rotational temperatures are presented in Schmidt, C., Höppner, K. and Bittner, M. (2013): A ground-based spectrometer equipped with an InGaAs array for routine observations of OH(3-1) rotational temperatures in the mesopause region. Journal of Atmospheric and
Solar-Terrestrial Physics 102 (2013) 125–139. http://dx.doi.org/10.1016/j.jastp.2013.05.001
DOI: 10.1594/wdcrsat.71jgz1mn
title: Nocturnal means of OH(3-1) airglow rotational temperatures from the mesopause region obtained with GRIPS 9 located at ALOMAR, Norway

description: The temperatures are derived from the rotational vibrational transition of the OH molecule originating from a thin layer in approximately 87 km centroid height. The spectra have been obtained with the Ground-based Infrared P-branch Spectrometer (GRIPS 9) located at the Arctic Lidar Observatory for Middle Atmosphere Research (ALOMAR: 16.01°E, 69.28°N) - a measurement station of the international Network for the Detection of Mesospheric Change (NDMC). It is operated by the German Remote Sensing Data Center (DFD) of the German Aerospace Center (DLR). During routine operation one spectrum is obtained every 15 s, originating from a field of view of approximately 15.5° x 15.5° which corresponds to ca. 24 x 24 km2 in zenith direction at 87 km height. The covered wavelength range allows the observation of the OH(3-1) Q- and P-branches as well as of the OH(4-2) R- and Q-branches. Rotational temperatures are calculated using OH(3-1) P-branch emissions between 1520 nm and 1550 nm. For the estimation of a nocturnal mean value all samples of the nightly temperature time series are weighted according to their individual precision. Thus, mean temperatures between 1 and 2 K are lower compared to the unweighted arithmetic mean. A mean is only calculated, when at least two hours of observation time are available.
description: GRIPS 9 is equipped with a Czerny-Turner spectrograph and a thermoelectrically cooled InGaAs array. Only the P1(2), P1(3) and P1(4) rotational lines of the (3-1) vibrational transition are used for the derivation of temperatures. Intensities are only read out at the line centers of the smoothed spectra due to residual overlapping of the lines at their wings. Important physical constants applied during the processing are taken from Mies (1974) (Einstein coefficients) and Krassovsky et al. (1962) (rotational term values).
Further details concerning the derivation of rotational temperatures are presented in Schmidt, C., Höppner, K. and Bittner, M. (2013): A ground-based spectrometer equipped with an InGaAs array for routine observations of OH(3-1) rotational temperatures in the mesopause region. Journal of Atmospheric and Solar-Terrestrial Physics 102 (2013) 125–139. http://dx.doi.org/10.1016/j.jastp.2013.05.001
DOI: 10.1594/wdcrsat.72izj2m6
title: Nocturnal means of OH(3-1) airglow rotational temperatures from the mesopause region obtained with GRIPS 9 located at ALOMAR, Norway

description: The temperatures are derived from the rotational vibrational transition of the OH molecule originating from a thin layer in approximately 87 km centroid height. The spectra have been obtained with the Ground-based Infrared P-branch Spectrometer (GRIPS 9) located at the Arctic Lidar Observatory for Middle Atmosphere Research (ALOMAR: 16.01°E, 69.28°N) - a measurement station of the international Network for the Detection of Mesospheric Change (NDMC). It is operated by the German Remote Sensing Data Center (DFD) of the German Aerospace Center (DLR). During routine operation one spectrum is obtained every 15 s, originating from a field of view of approximately 15.5° x 15.5° which corresponds to ca. 24 x 24 km2 in zenith direction at 87 km height. The covered wavelength range allows the observation of the OH(3-1) Q- and P-branches as well as of the OH(4-2) R- and Q-branches. Rotational temperatures are calculated using OH(3-1) P-branch emissions between 1520 nm and 1550 nm. For the estimation of a nocturnal mean value all samples of the nightly temperature time series are weighted according to their individual precision. Thus, mean temperatures between 1 and 2 K are lower compared to the unweighted arithmetic mean. A mean is only calculated, when at least two hours of observation time are available.
description: GRIPS 9 is equipped with a Czerny-Turner spectrograph and a thermoelectrically cooled InGaAs array. Only the P1(2), P1(3) and P1(4) rotational lines of the (3-1) vibrational transition are used for the derivation of temperatures. Intensities are only read out at the line centers of the smoothed spectra due to residual overlapping of the lines at their wings. Important physical constants applied during the processing are taken from Mies (1974) (Einstein coefficients) and Krassovsky et al. (1962) (rotational term values).
Further details concerning the derivation of rotational temperatures are presented in Schmidt, C., Höppner, K. and Bittner, M. (2013): A ground-based spectrometer equipped with an InGaAs array for routine observations of OH(3-1) rotational temperatures in the mesopause region. Journal of Atmospheric and Solar-Terrestrial Physics 102 (2013) 125–139. http://dx.doi.org/10.1016/j.jastp.2013.05.001