cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24222626
title: Plan robustness evaluation strategies in whole-pelvic proton therapy for high-risk prostate cancer patients within a randomised clinical trial

description: Inter-fractional anatomical changes challenge robust delivery of whole-pelvic proton therapy for high-risk prostate cancer. Pre-treatment robust evaluation (PRE) takes uncertainties in isocenter shifts and distal beam edge in treatment plans into account. Using weekly control computed tomography scans (cCTs), the aim of this study was to evaluate the PRE strategy by comparing to an off-line during-treatment robust evaluation (DRE) while also assessing plan robustness with respect to protocol planning constraints. Treatment plans and cCTs from ten patients included in the pilot phase of the PROstate PROTON Trial 1 were analysed. Treatment planning followed protocol guidelines with 78 Gy to the primary clinical target volume (CTVp) and 56 Gy to the elective target (CTVe) in 39 fractions. Recalculations of the treatment plans were performed for a total of 64 cCTs and dose/volume measures corresponding to clinical constraints were evaluated for this DRE against the simulated scenario interval from the PRE. Of the 64 cCTs, 59 showed DRE CTVp measures within the robustness range from the PRE; this was also the case for 39 of the cCTs for the CTVe measures. However, DRE CTVe coverage was still within constraints for 57 of the 64 cCTs. DRE dose/volume measures for CTVp fulfilled target coverage constraints in 59 of 64 cCTs. All DRE measures for the rectum, bladder, and bowel were inside the PRE range in 63, 39, and 31 cCTs, respectively. The PRE strategy predicted the DRE scenarios for CTVp and rectum. CTVe, bladder, and bowel showed more complex anatomical variations than simulated by the PRE isocenter shift. Both original and recalculated nominal treatment plans showed robust treatment delivery in terms of target coverage.
DOI: 10.6084/m9.figshare.24222626.v1
title: Plan robustness evaluation strategies in whole-pelvic proton therapy for high-risk prostate cancer patients within a randomised clinical trial

description: Inter-fractional anatomical changes challenge robust delivery of whole-pelvic proton therapy for high-risk prostate cancer. Pre-treatment robust evaluation (PRE) takes uncertainties in isocenter shifts and distal beam edge in treatment plans into account. Using weekly control computed tomography scans (cCTs), the aim of this study was to evaluate the PRE strategy by comparing to an off-line during-treatment robust evaluation (DRE) while also assessing plan robustness with respect to protocol planning constraints. Treatment plans and cCTs from ten patients included in the pilot phase of the PROstate PROTON Trial 1 were analysed. Treatment planning followed protocol guidelines with 78 Gy to the primary clinical target volume (CTVp) and 56 Gy to the elective target (CTVe) in 39 fractions. Recalculations of the treatment plans were performed for a total of 64 cCTs and dose/volume measures corresponding to clinical constraints were evaluated for this DRE against the simulated scenario interval from the PRE. Of the 64 cCTs, 59 showed DRE CTVp measures within the robustness range from the PRE; this was also the case for 39 of the cCTs for the CTVe measures. However, DRE CTVe coverage was still within constraints for 57 of the 64 cCTs. DRE dose/volume measures for CTVp fulfilled target coverage constraints in 59 of 64 cCTs. All DRE measures for the rectum, bladder, and bowel were inside the PRE range in 63, 39, and 31 cCTs, respectively. The PRE strategy predicted the DRE scenarios for CTVp and rectum. CTVe, bladder, and bowel showed more complex anatomical variations than simulated by the PRE isocenter shift. Both original and recalculated nominal treatment plans showed robust treatment delivery in terms of target coverage.
DOI: 10.6084/m9.figshare.23999909
title: An experimental setup for proton irradiation of a murine leg model for radiobiological studies

description: The purpose of this study was to introduce an experimental radiobiological setup used for <i>in vivo</i> irradiation of a mouse leg target in multiple positions along a proton beam path to investigate normal tissue- and tumor models with varying linear energy transfer (LET). We describe the dosimetric characterizations and an acute- and late-effect assay for normal tissue damage. The experimental setup consists of a water phantom that allows the right hind leg of three to five mice to be irradiated at the same time. Absolute dosimetry using a thimble (Semiflex) and a plane parallel (Advanced Markus) ionization chamber and Monte Carlo simulations using Geant4 and SHIELD-HIT12A were applied for dosimetric validation of positioning along the spread-out Bragg peak (SOBP) and at the distal edge and dose fall-off. The mice were irradiated in the center of the SOBP delivered by a pencil beam scanning system. The SOBP was 2.8 cm wide, centered at 6.9 cm depth, with planned physical single doses from 22 to 46 Gy. The biological endpoint was acute skin damage and radiation-induced late damage (RILD) assessed in the mouse leg. The dose–response curves illustrate the percentage of mice exhibiting acute skin damage, and at a later point, RILD as a function of physical doses (Gy). Each dose–response curve represents a specific severity score of each assay, demonstrating a higher ED50 (50% responders) as the score increases. Moreover, the results reveal the reversible nature of acute skin damage as a function of time and the irreversible nature of RILD as time progresses. We want to encourage researchers to report all experimental details of their radiobiological setups, including experimental protocols and model descriptions, to facilitate transparency and reproducibility. Based on this study, more experiments are being performed to explore all possibilities this radiobiological experimental setup permits.
DOI: 10.6084/m9.figshare.23999909.v1
title: An experimental setup for proton irradiation of a murine leg model for radiobiological studies

description: The purpose of this study was to introduce an experimental radiobiological setup used for <i>in vivo</i> irradiation of a mouse leg target in multiple positions along a proton beam path to investigate normal tissue- and tumor models with varying linear energy transfer (LET). We describe the dosimetric characterizations and an acute- and late-effect assay for normal tissue damage. The experimental setup consists of a water phantom that allows the right hind leg of three to five mice to be irradiated at the same time. Absolute dosimetry using a thimble (Semiflex) and a plane parallel (Advanced Markus) ionization chamber and Monte Carlo simulations using Geant4 and SHIELD-HIT12A were applied for dosimetric validation of positioning along the spread-out Bragg peak (SOBP) and at the distal edge and dose fall-off. The mice were irradiated in the center of the SOBP delivered by a pencil beam scanning system. The SOBP was 2.8 cm wide, centered at 6.9 cm depth, with planned physical single doses from 22 to 46 Gy. The biological endpoint was acute skin damage and radiation-induced late damage (RILD) assessed in the mouse leg. The dose–response curves illustrate the percentage of mice exhibiting acute skin damage, and at a later point, RILD as a function of physical doses (Gy). Each dose–response curve represents a specific severity score of each assay, demonstrating a higher ED50 (50% responders) as the score increases. Moreover, the results reveal the reversible nature of acute skin damage as a function of time and the irreversible nature of RILD as time progresses. We want to encourage researchers to report all experimental details of their radiobiological setups, including experimental protocols and model descriptions, to facilitate transparency and reproducibility. Based on this study, more experiments are being performed to explore all possibilities this radiobiological experimental setup permits.
DOI: 10.6084/m9.figshare.24280032
title: Dose planning study of proton versus photon radiotherapy for head and neck squamous cell carcinoma of unknown primary in the primary and recurrent setting

description: Patients with head and neck squamous cell carcinoma of unknown primary (HNCUP) are often treated with extensive radiotherapy (RT). Frequently, the bilateral nodal clinical target volume (nCTV) and the volumes of suspected mucosal primary sites (mCTV) of the pharynx and larynx is irradiated. This treatment is effective but toxic. New data suggest that omission of the contralateral nCTV and mCTV, results in few recurrences. The present study explores photon versus proton therapy, in the primary and recurrent setting. An analysis of twelve patients previously treated for HNCUP was performed. A fictitious recurrence was defined in patients treated for unilateral disease. Independently a volumetric arc photon plan and an intensity-modulated proton plan was made for all cases and scenarios. Compared to the standard bilateral treatment this study shows that limiting the target to unilateral nCTV leads to a significant decrease in dysphagia of 18% and 17% and xerostomia of 4.0% and 5% for photon and protons, respectively. Comparing photon RT directly to proton RT shows a small and often insignificant gain, using protons for both bilateral and unilateral targets. Focusing on re-irradiation, benefits from using protons in both the primary setting and at re-irradiation were limited. However, using protons for re-irradiation only leads to a decrease in the tissue volume receiving a specific dose outside the target overlapping region, e.g., V90Gy<sub>mean</sub> was 31, 25, and 22 cm<sup>3</sup> for photons-photons, photons-protons, and protons-protons, respectively. For V100Gy of the ipsilateral carotid artery, no differences were observed. Omitting contralateral nCTV irradiation and mCTV irradiation will significantly reduce toxicity. The accumulated high dose volumes can be minimised using protons for re-irradiation. However, the use of protons for primary treatment provides limited benefit in most patients.
DOI: 10.6084/m9.figshare.24280032.v1
title: Dose planning study of proton versus photon radiotherapy for head and neck squamous cell carcinoma of unknown primary in the primary and recurrent setting

description: Patients with head and neck squamous cell carcinoma of unknown primary (HNCUP) are often treated with extensive radiotherapy (RT). Frequently, the bilateral nodal clinical target volume (nCTV) and the volumes of suspected mucosal primary sites (mCTV) of the pharynx and larynx is irradiated. This treatment is effective but toxic. New data suggest that omission of the contralateral nCTV and mCTV, results in few recurrences. The present study explores photon versus proton therapy, in the primary and recurrent setting. An analysis of twelve patients previously treated for HNCUP was performed. A fictitious recurrence was defined in patients treated for unilateral disease. Independently a volumetric arc photon plan and an intensity-modulated proton plan was made for all cases and scenarios. Compared to the standard bilateral treatment this study shows that limiting the target to unilateral nCTV leads to a significant decrease in dysphagia of 18% and 17% and xerostomia of 4.0% and 5% for photon and protons, respectively. Comparing photon RT directly to proton RT shows a small and often insignificant gain, using protons for both bilateral and unilateral targets. Focusing on re-irradiation, benefits from using protons in both the primary setting and at re-irradiation were limited. However, using protons for re-irradiation only leads to a decrease in the tissue volume receiving a specific dose outside the target overlapping region, e.g., V90Gy<sub>mean</sub> was 31, 25, and 22 cm<sup>3</sup> for photons-photons, photons-protons, and protons-protons, respectively. For V100Gy of the ipsilateral carotid artery, no differences were observed. Omitting contralateral nCTV irradiation and mCTV irradiation will significantly reduce toxicity. The accumulated high dose volumes can be minimised using protons for re-irradiation. However, the use of protons for primary treatment provides limited benefit in most patients.
DOI: 10.6084/m9.figshare.25451788
title: High-density spike recordings from motor cortex in awake head-fixed mice [Shew Lab]

description: High-density spike recordings using a single Neuropixels probe. The probe spans all layers of mouse motor cortex. Mice were awake head-fixed and free to run on a wheel. Recordings were 45 - 60 min in duration and typically included about 100 to 200 units. Data includes spike times, unit IDs, and wheel speed. These data were analyzed and first published in the paper: Fontenele, A. J., Sooter, J. S., Norman, V. K., Gautam, S. H. & Shew, W. L. Low dimensional criticality embedded in high dimensional awake brain dynamics. Science Advances (2024). (Also on bioRxiv at doi:10.1101/2023.01.05.522896)Conditions for use of data: Please cite Fontenele et al Science Advances 2024.
DOI: 10.5281/zenodo.10850170
title: [IO Islamic 486] مُرَقّع

description: Râzî-Muraḳḳa

This manuscript is now IO Islamic 1638 in the India Office collections.

[metadata: Hermann Ethé, Catalogue of Persian Manuscripts in the Library of the India Office, 2 vols. (Oxford: India Office, 1903): volume 1, number 486 here with notations and hyperlinks].


1638

Muraḳḳa’ (مُرَقّع ).

Patchwork or scrap-book, a mystical mathnawî on the chief points of Ṣûfism, illustrated by short tales, somewhat in the style of Jalâl-aldîn Rûmi’s mathnawî, by the same ‘Âḳilkhân Râzî, beginning:

(Pertsch Sprenger فى العمام ;) ايّها السّاقى اغثنى فى الغمام المنام 

الكرام (Pertsch and Sprenger الكاس) من جرعة كاس (read اسقنى) اشقنى  

Sarkhwush in his tadhkirah كلمات الشّعرا (see A. Sprenger, Catal., p. 111) says: ‘it may be considered as a poetical version of the امواج خوبى,’ but to what book does that title apply ?

No date. The transcriber was Mîr Ibrâhîm Ḥusain alḥusainî.

No. 486, ff. 156, 2 coll. each ll. 13; slightly injured and worm-eaten here and there; size, 87/8 in. by 5 in.
DOI: 10.5281/zenodo.10850171
title: [IO Islamic 486] مُرَقّع

description: Râzî-Muraḳḳa

This manuscript is now IO Islamic 1638 in the India Office collections.

[metadata: Hermann Ethé, Catalogue of Persian Manuscripts in the Library of the India Office, 2 vols. (Oxford: India Office, 1903): volume 1, number 486 here with notations and hyperlinks].


1638

Muraḳḳa’ (مُرَقّع ).

Patchwork or scrap-book, a mystical mathnawî on the chief points of Ṣûfism, illustrated by short tales, somewhat in the style of Jalâl-aldîn Rûmi’s mathnawî, by the same ‘Âḳilkhân Râzî, beginning:

(Pertsch Sprenger فى العمام ;) ايّها السّاقى اغثنى فى الغمام المنام 

الكرام (Pertsch and Sprenger الكاس) من جرعة كاس (read اسقنى) اشقنى  

Sarkhwush in his tadhkirah كلمات الشّعرا (see A. Sprenger, Catal., p. 111) says: ‘it may be considered as a poetical version of the امواج خوبى,’ but to what book does that title apply ?

No date. The transcriber was Mîr Ibrâhîm Ḥusain alḥusainî.

No. 486, ff. 156, 2 coll. each ll. 13; slightly injured and worm-eaten here and there; size, 87/8 in. by 5 in.
DOI: 10.17909/qz7b-bf83
title: Data from paper "No H I or Metal Escape Detected off of the Young Sub-Neptune AU Mic c"

description: This dataset consists of five HST/STIS exposures completed in May 2023 surrounding a transit of AU Mic c. The spectra extracted from these observations were used to create light curves to search for escaping material around the planet.
DOI: 10.5517/cc115n40
title: CCDC 958741: Experimental Crystal Structure Determination

description: Related Article: Haiyan Li,Yong Zhang,Yuanchen Ding,Lixin Dai,Jianping Lang|2010|Suzhou Daxue Xuebao, Ziran Kexueban|26|91-3|
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc115wsw
title: CCDC 958978: Experimental Crystal Structure Determination

description: Related Article: Sanjib Ganguly|2012|J.Indian Chem.Soc.|89|107|
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc13b73s
title: CCDC 1022724: Experimental Crystal Structure Determination

description: Related Article: Yawei Lin|2014|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25345/c5z892s0h
title: MassIVE MSV000094375 - Single-cell m6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation
title: Ten micrograms of each sample were reduced and alkylated followed by trypsin digestion using a suspension trap (S-trap). An SPQC was made by combining equal volumes of each sample. After lyophilization and reconstitution of the sample in 20 uL, 1-2 uL of each was analyzed by LC-MS/MS using a 30 min gradient on a Thermo Vanquish Neo coupled to a Thermo Orbitrap Astral via a Nanospray Flex ionization source. Briefly, the sample was first trapped on a PepMap C18 0.3 mm x 5 mm trapping column (50 ul/min at 99.9/0.1 v/v water/acetonitrile), followed by analytical separation using a 1.5 um 150um ID x 8cm (PepSep) column with a 20 min gradient of 5 to 30% acetonitrile with 0.1% formic acid at a flow rate of 500 nanoliters/minute (nL/min) with a column temperature of 55C. Data collection on the Orbitrap Astral mass spectrometer was performed in a data-independent acquisition (DIA) mode of acquisition with a r=240,000 (@ m/z 200) full MS scan every 0.6s from m/z 380-980 with an AGC target of 500%. DIA MS/MS scans were acquired in the Astral analyzer using fixed windows of 4 m/z from m/z 380, target AGC of 500% and max fill time of 6 ms. HCD collision energy setting of 27% was used for all MS2 scans. Raw MS data was demultiplexed and converted to *.htrms format using HTRMS converter and processed in Spectronaut 18 (Biognosys). A spectral library was built using direct-DIA searches which used a Mus muculus database, downloaded from Uniprot on 4/08/23, and appended the transgene APOBEC1-YTH as well as contaminant sequences using FragPipe. Search settings included N-terminal trypsin/P specificity up to 2 missed cleavages; peptide length from 7-52 amino acids with the following modifications: acetyl (N-term), carbamidomethyl(Cys) and oxidation (M). For DIA analysis, default extraction, calibration, identification and protein inference settings were used. Normalization, imputation and protein quantification was performed using an in-house script.
DOI: 10.17909/5hz4-vx12
title: Data from paper "The Variable Detection of Atmospheric Escape around the Young, Hot Neptune AU Mic b"

description: This dataset consists of twelve HST/STIS exposures completed in July 2020 and October 2021 surrounding the transit of AU Mic b. The spectra extracted from these observations were used to create light curves to search for escaping material around the planet.
DOI: 10.17909/ekgk-8d20
title: Data from paper "No H I or Metal Escape Detected off of the Young Sub-Neptune AU Mic c"

description: This dataset consists of four HST/STIS exposures completed in September 1998 of AU Mic. The spectra extracted from these observations were used as a baseline to understand the emission and variability of the star in the far ultraviolet.
DOI: 10.6084/m9.figshare.19780558
title: Table 1. Genome sequence context for JMJD1C SNPs associated with bovine congestive heart failure (BCHF)

description:   
<strong>Background:</strong>  The power and resolution of genome-wide association studies (GWAS) may be enhanced with increased DNA marker density and reduced ascertainment bias of whole genome sequence (WGS) technology compared to that of bead-based microarrays.  However, validation of WGS marker associations may be challenging since preexisting assays for these variants will not always be available.  Here, our aim was to provide preliminary molecular, genetic, and statistical information for JMJD1C variants associated with bovine congestive heart failure (BCHF) for the purpose of assay development.
<strong>Methods: </strong> A WGS data set with greater than 10-fold genome coverage per animal was generated from 102 BCHF matched case-control pairs.  Paired nominal data from 11 million single nucleotide polymorphisms (SNPs), filtered for frequency and quality, were analyzed with McNemar’s test and sorted genome-wide by false discovery rate (FDR).
<strong>Results:</strong>   A 45 kb region spanning introns 2 and 3 of JMJD1C on chromosome 28 was identified as being significantly associated with BCHF with a FDR q-value less than 0.05.  This association was in addition to those in ARRDC3 and NFIA previously reported (Heaton et al. F1000Research 2022, 11:385).  Nine linked SNPs in JMJD1C comprised exactly two haplotypes with an average minor allele frequency (MAF) of 0.005 and 0.132 in the cases and controls, respectively.  Two copies of the major SNP alleles were associated with disease development, while one or two copies of the minor SNP alleles were not.   There were 25 informative pairs for each of the nine linked SNPs, and the “protective” allele was absent from all 25 diseased animals in these informative pairs (McNemar’s b/c = 0/25, OR = 0, mid p-value = 3.0 x 10E-8, FDR = 9.8 x 10E-3).
 <strong>Conclusion:</strong> These preliminary results indicate that selection for the protective JMJD1C  alleles may be useful in reducing BCHF in severely affected herds, however genotype assay development will be needed for further validation.   The marker details are publicly available for use without restriction (https://doi.org/10.6084/m9.figshare.19780558.v1).