cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23652282
title: ConflictBench: A Benchmark to Evaluate Software Merge Tools

description: Related sheets for paper "ConflictBench: A Benchmark to Evaluate Software Merge Tools"
DOI: 10.58032/agh/rrjhyu
title: Replication Data for the manuscript "Direct imaging of surface melting on a single Sn nanoparticle"

description: The document contains a set of unprocessed high-resolution scanning transmission electron microscopy images (HAADF-STEM) of a tin (Sn) nanoparticle at different temperatures for the abovementioned article. The file name includes the magnification (x1400k) and the temperature of the specimen in degrees Celsius.
DOI: 10.6084/m9.figshare.22294056
title: Hyperosmolar therapies for neurological deterioration in mild and moderate traumatic brain injury: A scoping review

description: To explore the available evidence on hyperosmolar therapies(HT) in mild and moderate traumatic brain injury(TBI) and to evaluate the effects on outcomes. A scoping review was conducted according to the Joanna Briggs Institute methodology. Inclusion criteria: (a)randomized controlled trials(RCTs), prospective and retrospective cohort studies and case-control studies; (b)all-ages mild and moderate TBIs; (c)HT administration; (d)functional outcomes recorded; (e)comparator group. From 4424 records, only 3 respected the inclusion criteria. In a retrospective cohort study of adult moderate TBIs, the Glasgow Coma Scale(GCS) remained the same at 48 hours in those treated with hypertonic saline(HTS) while it worsened in the non-treated. A trend toward increased pulmonary infections and length of stay was found. In an RCT of adult severe and moderate TBIs, moderate TBIs treated with HTS showed a trend toward better secondary outcomes than standard care alone, with similar odds of adverse effects. An RCT enrolling children with mild TBI found a significant improvement in concussive pain immediately after HTS administration and after 2–3 days. No adverse events occurred. A gap in the literature about HTs’ role in mild and moderate TBI was found. Some benefits may exist with limited side effects and further studies are desirable.
DOI: 10.6084/m9.figshare.22294056.v1
title: Hyperosmolar therapies for neurological deterioration in mild and moderate traumatic brain injury: A scoping review

description: To explore the available evidence on hyperosmolar therapies(HT) in mild and moderate traumatic brain injury(TBI) and to evaluate the effects on outcomes. A scoping review was conducted according to the Joanna Briggs Institute methodology. Inclusion criteria: (a)randomized controlled trials(RCTs), prospective and retrospective cohort studies and case-control studies; (b)all-ages mild and moderate TBIs; (c)HT administration; (d)functional outcomes recorded; (e)comparator group. From 4424 records, only 3 respected the inclusion criteria. In a retrospective cohort study of adult moderate TBIs, the Glasgow Coma Scale(GCS) remained the same at 48 hours in those treated with hypertonic saline(HTS) while it worsened in the non-treated. A trend toward increased pulmonary infections and length of stay was found. In an RCT of adult severe and moderate TBIs, moderate TBIs treated with HTS showed a trend toward better secondary outcomes than standard care alone, with similar odds of adverse effects. An RCT enrolling children with mild TBI found a significant improvement in concussive pain immediately after HTS administration and after 2–3 days. No adverse events occurred. A gap in the literature about HTs’ role in mild and moderate TBI was found. Some benefits may exist with limited side effects and further studies are desirable.
DOI: 10.6084/m9.figshare.23551536
title: Supplementary Table 3. Orthology information of zebrafish protein corresponding to 99 up-regulated factors

description: This data sheet describes the orthology information of zebrafish protein corresponding to 99 up-regulated factors. NA in the "Drer.Ensembl-pid" column indicates that orthologue was not found in zebrafish. Zebrafish information follows Ensembl release 108.
DOI: 10.6084/m9.figshare.23551536.v1
title: Supplementary Table 3. Orthology information of zebrafish protein corresponding to 99 up-regulated factors

description: This data sheet describes the orthology information of zebrafish protein corresponding to 99 up-regulated factors. NA in the "Drer.Ensembl-pid" column indicates that orthologue was not found in zebrafish. Zebrafish information follows Ensembl release 108.
DOI: 10.25919/5p4z-aj23
title: Parkes observations for project P1050 semester 2023APRS_07

description: This is a request for the observation time for the timing campaign of new pulsars discovered in the reprocessing of the low-latitude Galactic plane section of the HTRU-S survey (HTRU-S LowLat) and the Parkes Multibeam Pulsar Survey (PMPS). We have completed 90 % of the HTRU-S LowLat survey and completed zero acceleration PMPS search with GPU-based coherent acceleration search, template bank, and fast folding algorithm pipelines and now have discovered 112 previously unknown pulsars among which 18 were found in the PMPS. Interesting science can usually only be derived from a new pulsar after confirmation, and a follow-up timing campaign is carried out. At least one year of initial timing is the minimum timespan required to fully characterise any newly-discovered pulsars, essential for deriving pulsar parameters such as the characteristic age, magnetic field strength, and spin-down rate, as well as for detecting any unexpected behaviour of the pulsar which might result from emission instabilities. This project is necessary for the timing of several interesting pulsars, including binary pulsars, high DM pulsars, scattered profile pulsars, and bright ones that show emissions in larger bandwidths in the UWL band. Apart from this, finding the nature of a unique binary pulsar system via a dedicated observing campaign is also another goal. The follow-up timing in semester 2023APRS will assist in completing many exciting large-term science goals.
DOI: 10.6084/m9.figshare.23551818
title: Supplementary Table 4. Orthology information of zebrafish protein corresponding to 69 down-regulated factors.

description: This data sheet describes the orthology information of zebrafish protein corresponding to 69 down-regulated factors. Zebrafish information follows Ensembl release 108.
DOI: 10.6084/m9.figshare.23551818.v1
title: Supplementary Table 4. Orthology information of zebrafish protein corresponding to 69 down-regulated factors.

description: This data sheet describes the orthology information of zebrafish protein corresponding to 69 down-regulated factors. Zebrafish information follows Ensembl release 108.
DOI: 10.5281/zenodo.7783847
title: A Framework for Individualized Splice-Switching Oligonucleotide Therapy

description: This RNA-seq dataset was generated and analyzed as described in Kim, Woo, de Gusmao, Zhao et al, "A Framework for Individualized Splice-Switching Oligonucleotide Therapy" Nature 2023. The RNA-seq dataset was obtained from cells derived from ataxia-telangiectasia (A-T) patients or their parents, and it comprises four groups: (1) RNA-seq of fibroblasts from an A-T patient with c.7865C&gt;T (proband) and her mother and father. (2) RNA-seq of fibroblasts from an A-T patient with c.7865C&gt;T (proband), transfected with ASOs (mock, NT-22, AT008, AT026). (3) RNA-seq of whole blood from an A-T patient with c.5763-1050A&gt;G (DDP_ATCP_42) and three other A-T patients without the variant (DDP_ATCP_96, DDP_ATCP_103, DDP_ATCP_151). (4) RNA-seq of fibroblasts from an A-T patient with c.5763-1050A&gt;G (DDP_ATCP_42), transfected with ASOs (naive, NT-22, AT043, AT056, AT057).
DOI: 10.5281/zenodo.7783848
title: A Framework for Individualized Splice-Switching Oligonucleotide Therapy

description: This RNA-seq dataset was generated and analyzed as described in Kim, Woo, de Gusmao, Zhao et al, "A Framework for Individualized Splice-Switching Oligonucleotide Therapy" Nature 2023. The RNA-seq dataset was obtained from cells derived from ataxia-telangiectasia (A-T) patients or their parents, and it comprises four groups: (1) RNA-seq of fibroblasts from an A-T patient with c.7865C&gt;T (proband) and her mother and father. (2) RNA-seq of fibroblasts from an A-T patient with c.7865C&gt;T (proband), transfected with ASOs (mock, NT-22, AT008, AT026). (3) RNA-seq of whole blood from an A-T patient with c.5763-1050A&gt;G (DDP_ATCP_42) and three other A-T patients without the variant (DDP_ATCP_96, DDP_ATCP_103, DDP_ATCP_151). (4) RNA-seq of fibroblasts from an A-T patient with c.5763-1050A&gt;G (DDP_ATCP_42), transfected with ASOs (naive, NT-22, AT043, AT056, AT057).
DOI: 10.5281/zenodo.8128984
title: The Pollution from Obsolete Issue Report: An Empirical Study

description: The Pollution from Obsolete Issue Report: An Empirical Study Project summary In software development, programmers use issue trackers to manage their maintenance issues and record valuable maintenance details in issue reports. Based on these issue reports, programmers have enhanced code comprehension and researchers have mined knowledge from issue reports to assist various programming tasks. Although issue reports are useful, some of them can be obsolete, in that their corresponding commits are overwritten or rolled back, with the evolution of software. The obsolete issue reports can invalidate their references and descriptions, and can have far-reaching impacts on the approaches built on them. To deepen the understanding of obsolete issue reports, we conducted the first empirical study to analyze obsolete issue reports. We consider that an issue report is obsolete if its revisions are partially or totally removed in later commits. To measure how an issue report becomes obsolete, we define an obsolete ratio of an issue report as its deleted lines over all its modified lines. In this paper, we build a tool, ICLINKER, to inspect the obsolete issue reports and calculate the obsolete ratios. With ICLINKER, we analyze 70,180 commits and 46,257 issue reports that are collected from five Apache projects. Taking them as our inputs, we explore four research questions, which concern the distributions, the references, and the explanations of obsolete issue reports. Our findings on these research questions enrich the knowledge of obsolete issue reports, and some are even counterintuitive. For example, we find that obsolete issue reports are mixed with other issue reports. As another example, we find that only a small portion of issue reports are mentioned in code comments, but about half of them are obsolete. Based on our results, we analyze some directions that are worthy of exploration. Our identified obsolete ratios We identified the obsolete ratios of the issue reports from five projects. Their obsolete ratios are as follows: calcite.txt, cassandra.txt, derby.txt, hbase.txt, and hive.txt. Our Dataset Our dataset is stored in the data folder.
DOI: 10.5281/zenodo.8128983
title: The Pollution from Obsolete Issue Report: An Empirical Study

description: The Pollution from Obsolete Issue Report: An Empirical Study Project summary In software development, programmers use issue trackers to manage their maintenance issues and record valuable maintenance details in issue reports. Based on these issue reports, programmers have enhanced code comprehension and researchers have mined knowledge from issue reports to assist various programming tasks. Although issue reports are useful, some of them can be obsolete, in that their corresponding commits are overwritten or rolled back, with the evolution of software. The obsolete issue reports can invalidate their references and descriptions, and can have far-reaching impacts on the approaches built on them. To deepen the understanding of obsolete issue reports, we conducted the first empirical study to analyze obsolete issue reports. We consider that an issue report is obsolete if its revisions are partially or totally removed in later commits. To measure how an issue report becomes obsolete, we define an obsolete ratio of an issue report as its deleted lines over all its modified lines. In this paper, we build a tool, ICLINKER, to inspect the obsolete issue reports and calculate the obsolete ratios. With ICLINKER, we analyze 70,180 commits and 46,257 issue reports that are collected from five Apache projects. Taking them as our inputs, we explore four research questions, which concern the distributions, the references, and the explanations of obsolete issue reports. Our findings on these research questions enrich the knowledge of obsolete issue reports, and some are even counterintuitive. For example, we find that obsolete issue reports are mixed with other issue reports. As another example, we find that only a small portion of issue reports are mentioned in code comments, but about half of them are obsolete. Based on our results, we analyze some directions that are worthy of exploration. Our identified obsolete ratios We identified the obsolete ratios of the issue reports from five projects. Their obsolete ratios are as follows: calcite.txt, cassandra.txt, derby.txt, hbase.txt, and hive.txt. Our Dataset Our dataset is stored in the data folder.
DOI: 10.5281/zenodo.8128945
title: SPIT - Quantification files for tissue-dependent DTUs

description: Quantification and phenotype files for GTEx samples used in the detection of 4 tissue-dependent DTU events. These events are provided as positive controls for the evaluation of SPIT. Corresponding sashimi plots with all transcripts for the given genes are included.
DOI: 10.5281/zenodo.8128944
title: SPIT - Quantification files for tissue-dependent DTUs

description: Quantification and phenotype files for GTEx samples used in the detection of 4 tissue-dependent DTU events. These events are provided as positive controls for the evaluation of SPIT. Corresponding sashimi plots with all transcripts for the given genes are included.
DOI: 10.25919/mtg4-pw98
title: Parkes observations for project P1172 semester 2023APRS_05

description: PSR J1713+0747 is a very important millisecond pulsar for global pulsar timing array campaigns, due to its long-term observation history, very stable and narrow profile and strong S/N. In April 2021, the pulsar experienced a significant event related to a change in its magnetosphere, presented as an observable change in the pulsar profile. Since then, the pulsar has been slowly recovering and we wish to observe this recovery with high-cadence observations to allow us to create a detailed time-resolved series of variations in the MSPs profile, polarisation, and other properties. Under this proposal, we wish to probe the profile recovery on weekly timescales (once per week per month), revealing additional short timescale behaviours, indicative of changes in the magnetosphere which are not available to other telescopes in the world, thanks to the Parkes UWL. This will also allow us to determine if the magnetosphere has returned to its original configuration or is settling into a new one. Understanding the recovery of this event is key for demonstrating that such pulsars are still viable clocks for use in gravitational wave studies, and in turn, provide us with new data on how the normally stable magnetosphere of this millisecond pulsar responds to an impulsive change in state.
DOI: 10.25919/dw4q-ah98
title: Parkes pulsar observations with undefined project IDs for 2023APRS_05

description: Parkes pulsar observations with undefined project IDs for 2023APRS. This collection contains observations from project ID PX107.
DOI: 10.15151/esrf-es-1118675158
title: PROTEINS RELATED TO PATHOGENESIS OF DISEASES, VIRAL PROTEINS, CELL DIVISION, SIGNALLING AND CHROMATIN PROCESSES

description: Our BAG is composed of eight PIs at six different institutions in Italy and Austria. We focus on a large variety of human, bacterial, viral and synthetic protein targets and address diverse biological contexts by combining structural biology with biochemistry, biophysics, cellular and in vivo investigations.
DOI: 10.15151/esrf-es-1218279823
title: Serial data collection approaches for radiation sensitive reaction intermediates at ambient temperature

description: Serial synchrotron crystallography (SSX) is an emerging method that builds on serial femtosecond crystallography (SFX) at XFELs, which our group co-pioneered. In particular, for both SFX and SSX various approaches exist for crystal delivery into the X-ray beam that differ not only in technical complexity and sample consumption but also in the “cleanliness” of the experimental protocol and thus of the diffraction data. The latter is particularly important for SSX with respect to radiation damage. Thus, our BAG proposal has two aspects, a technical one, the implementation and comparison of various sample delivery approaches at ID29, using a highly radiation sensitive metalloprotein model system and a scientific one, the structure determination of a predicted but so far elusive flavin N5-oxide intermediate of the enzyme EncM. Obviously, the technical aspect not only affects the scientific aspect, but also has implications for the community at large using SSX.
DOI: 10.15151/esrf-es-1217484073
title: The origins and early diversity of social behaviour in mammalian ancestors

description: Reconstructing ancient behaviour is crucial to better grasping the evolutionary origins of mammals; however, fossilised evidence of behavioural complexity is elusive. Here we propose to use SRµCT to describe and compare the cranial bone histology, brain, nerves and inner ear of a carefully selected sample of mammalian ancestors (therapsids), which display a diversity of head ornamentations (horns, bosses, enlarged canines, etc.) that suggests male to male combat, face biting, and sexual display. Improved knowledge of the adaptations of the nervous system and cranial structure to withstand those fights will provide, for the first time, insight into the diversity of complex social behaviours in therapsids. This will be accompanied by a study of brain size to address whether sociality had an effect on encephalisation. This study has the potential to highlight the existence of complex social behaviours many millions of years before the origin of mammals.
DOI: 10.15151/esrf-es-1217487632
title: Structural and Kinetic investigation of PreQ1 riboswitch

description: Modulating the conformational dynamics of RNA riboswitches is a promising route toward understanding gene expression and the development of antibiotic alternatives. A prerequisite for this is detailed structural and kinetic information along the folding/unfolding pathway of the riboswitch’s aptamer domain. Therefore, we request time for microfluidic-based cSAXS measurement to investigate the aptamer conformation of three different 7-aminomethyl-7-deazaguanine (preQ1)-I riboswitches folding upon the addition of the ligand preQ1 and divalent ions (namely Mg2+ and Ca2+). These SAXS profiles will be visualized using our SAXS-driven molecular dynamics approach. In this way, we will obtain RNA conformation that will be the starting point for subsequent all-atom molecular dynamics simulation and utilized to interpret further biophysical investigation of preQ1-I riboswitches.
DOI: 10.15151/esrf-es-1217489142
title: Anomalous Differential Pair Distributon Function experiment to reveal nanosized compositional fluctuations in Sr1-xBaxTiO3 relaxor ferroelec

description: The aim of the experiment is to perform an Anomalous Differential Pair Distribution Function experiment at the Ba-K edge on Sr1-xBaxTiO3 (SBTO) solid solutions, Diffraction patterns at two slightly different E values in the proximity of Ba-K absorption edge will be collected at 90 K on 7 SBTO samples in the whole 0
DOI: 10.15151/esrf-es-1214163349
title: Insight into the local structural evolution and structural dynamics in Na-Y-Zr-Cl solid electrolytes for solid state battery applications

description: Ionic diffusion in a solid is affected by both local and long-range crystal order. Understanding the relationship between ionic diffusion and crystal structure in different length scales will help to design new and better high-performance solid electrolytes for solid-state battery. We want to perform a detailed local structure analysis of newly discovered Na3-xY1-xZrxCl6 (NYZCx) based Na ionic conductor. Various parameters of NYZCx at local length scale, including transition metal ordering, mixing, and intrinsic vacancy effect on Na ion dynamics. For example, NYZCx synthesized at different processes shows a drastic change in conductivities like other Na-based superionic conductors such as Na3PS4, and NaZrCl6. We believe that a detailed understanding of the local structure of this NYZCx synthesized at different routes explains more insights about Na ion dynamics and help to create the design principle of high superionic conductor for solid-state battery applications.
DOI: 10.15151/esrf-es-1216303207
title: Unravelling the size effect on vibration-induced self-assembly of crystal lattice using in situ micro-scale tomography

description: Cellular architected materials with unique combination of mechanical and functional properties have attracted significant attention from the scientific and industrial community. These materials possess complex microarchitectures, which require slow and expensive fabrication technique (i.e. 3D printing). The inverse opal approach is a brilliant solution, the key step of which is the self-assembly of metallic spherical particles into crystal lattice structure. The main driving force that settles the structure is considered as the gravity. However, when the spherical particle size is less than 30-50 microns, air friction starts to dominate the particles’ motion. The crucial question remains to be answered: what is the particle size effect on the self-assembly crystallization process? We seek to observe the self-assembly process of spherical particles of various sizes using in situ micro-tomography, therefore identifying the influence zone of this size effect.
DOI: 10.15151/esrf-es-1216307575
title: Evaluating the three-dimensional stress tensor fields in cyclically deformed EUROFER97

description: Clean, sustainable, and predictable energy may be produced via nuclear fusion in the not-too-distant future. However, given that fusion reactors operate at elevated temperatures under complex cyclic loading regimes, the fatigue behaviour of the structural steel, EUROFER97, and its relationship with the development and evolution of intragranular stress tensor fields must be evaluated. This is essential for the qualification of in-vessel components and will shed significant light on the microstructural aspects of the mechanisms permitting fatigue failure. Considering the above, we propose to measure both the intergranular (type II) and intragranular (type III) three-dimensional stress tensor fields before and after the fatigue testing of EUROFER97 using scanning 3DXRD and the ID11 beamline.
DOI: 10.15151/esrf-es-1216309048
title: Developing a model for nanoparticle-plant cell interactions: layered double hydroxide nanocarrier surface chemistry influence on mesophyll p

description: Nanocarriers (NC) can provide highly efficient agrochemical delivery, potentially transforming the way that we deliver nutrients to crops. However, relating NC design to the ability to target active agents to specific locations in the plants is needed to realize this goal. Plant protoplasts (plant cells without their cell walls) are the primary cell compartments in plant leaves where nutrients and active agents are needed. This study proposes to use synchrotron X-ray fluorescence imaging and spot XANES to determine how NC surface chemistry can influence their capacity to cross lipid membranes. We hypothesize that the surface chemistry of layered double hydroxide NCs (amine, arginine, histidine, PEG, OH) will enable NC targeting and delivery onto or into protoplasts. XRF imaging will be used to determine if NCs are outside, inside, and/or associated with specific organelles of the protoplast. µ-XANES are used to ensure that the NCs are being imaged rather than the metal tracer.