AndreaBozzo/ceres-open-data-index huggingface dataset:
Identification of single nucleotide polymorphisms in sheep Mx genes: a premature stop codon abolishes Mx2 protein expression but did not affect fertility and early animal development.

Whole genome sequence data of 68 sheep representing 43 breeds from 19 countries was generated by the International Sheep Genomics Consortium, a partnership of researchers and funding agencies (http://www.sheephapmap.org/). The SAMtools suite (http://samtools. sourceforge.net) was used to extract reads aligned to genome regions (O. aries genome sequence NC_019458.2) that correspond to ovine MX1 (Gene ID: 443146) and MX2 (Gene ID: 780441) sequences. The reads obtained were re-aligned to MX1 or MX2 sequences using Geneious v. 10.1.3 (Biomatters, Auckland, New Zealand; 69Kearse et al. 2012) and variant calling was undertaken. Potential variants were further analysed to produce lists of variant sequences that fulfil the following criteria: (i) the nucleotide variation was observed in regions of 10-fold or higher read coverage in each individual dataset; (ii) the observed nucleotide variation with a minor allele read frequency was greater than 0.45 for at least one individual; (iii) homozygotes all had one of the two possible nucleotides (or gaps) observed in the heterozygotes, or were all homozygous for the non-reference allele; and (iv) the observed nucleotide variation was of the same type in at least two heterozygous individuals and was the same type in all heterozygous individuals considered. To ensure that the frequency of variants was not overly affected by sample size, a “suitable coverage region” criterion was added. Suitable coverage regions were defined as the part of the alignment where the total number of reads across all individuals with a minimum read coverage of 10 exceeded 99 reads. 

Organization: CSIRO Data Access Portal
Parkes observations for project P1365 semester 2025OCTS_05

Following the successful demonstration of a pilot first-pass (shallow) search of a small fraction of the sky, the second-pass processing has commenced for the SMART pulsar survey, which involves deep searches of 80-minute observations. The processing over the past year has led to the discovery of 11 new pulsars (including two millisecond ones), thus tripling the initial count from the first pass, and hinting at the exciting promise of this first southern-sky pulsar survey in the frequency band of SKA-Low.  All new pulsars need to be timed in order to determine their spin and astrometric parameters and to select specialised targets for detailed follow-ups. With the MWA no longer supporting routine pulsar observations for the coming year, timing follow-ups rely on other telescopes. The Parkes \emph{Murriyang} telescope, with an identical sky coverage, sensitivity and the wide frequency coverage, offers the best option to time SMART discoveries. We have demonstrated \emph{Murriyang's} suitability for this through a pilot project last semester and are now extending the project to a larger sample of 10 pulsars including two from the pilot project. The data will also allow us to study pulse profiles, polarisation, and flux densities from $\sim$100 MHz to 4 GHz. The analysis/results will be included in a publication in preparation that will detail the deep-search pipeline and report on initial pulsar discoveries.

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Long-term project observations for project P456 semester 2025OCTS_01

The Parkes Pulsar Timing Array (PPTA) project has three primary goals: (a) detection of gravitational waves from astronomical sources, (b) establishment of a pulsar timescale, and (c) improvement of our understanding of Solar-system dynamics. We are now in an exciting regime where a signal detected in our (and other data sets) has the form expected for a gravitational wave background. We, along with the international community, are now working hard to either confirm or deny this result, and to determine the astrophysical origin of this signal. With this proposal, we aim to maintain our pre-eminent position in the field. This is a continuing proposal for which observations of millisecond pulsars (MSPs) will continue to improve bounds on ultra-low-frequency gravitational waves until they are detected with confidence. Continued Parkes observations will remain valuable at least until the first stage of the SKA is able to improve on our sensitivity and observing cadence. Even after the gravitational wave background is detected, continued observations will resolve the background origin and individual sources will be identified; advancing the nascent field of gravitational wave astronomy.

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Long-term project observations for project P574 semester 2025OCTS_02

We request time to observe 270 pulsars on a regular basis in order to achieve three main science goals. The first is to understand pulsars: how do they spin down and what disrupts this process, how and why their profiles vary with time, whether they precess or have planetary mass companions, in short all the things that make pulsar timing noisier than the perfect clock. Secondly we want to understand the interstellar medium of our Galaxy through repeated monitoring of dispersion measure, rotation measure and flux density variations in conjunction with scintillation parameters. Finally, we provide these data as a community service both to the high-energy community where we have strong collaborative links (particularly to Fermi) and to the radio pulsar astronomers generally through the CSIRO archive. The project is on-going since 2007, we are (co-)authors on 107 papers arising from the P574 data. The data have contributed to the PhD theses of students from Bordeaux, Manchester, Oxford, Stanford, and Swinburne. We are seeking long-term project status with a view to continuing the project into the SKA era.

Organization: CSIRO Data Access Portal
Parkes observations for project P1380 semester 2025OCTS_02

The association of FRB 200428 with the Galactic magnetar SGR 1935+2154 confirms that magnetars can power fast radio bursts (FRBs). However, FRB 200428 is 4 to 8 orders of magnitude less energetic than the typical population of cosmological FRBs. This discrepancy is likely due to the moderate magnetic field strength and evolved age of SGR 1935+2154. In contrast, newborn extragalactic magnetars, such as those formed in gamma-ray burst (GRB) central engines, are expected to have much stronger magnetic fields, more rapid spin-down, and highly dynamic magnetospheres, all of which favor the production of brighter and more frequent FRBs.

We propose a targeted search for FRBs from the recently localized GRB 230307A, a long-duration GRB with evidence suggesting the formation of a young magnetar. Given the source's relatively close distance (291 Mpc) and possible youth (less than 3 years), it offers a compelling opportunity to test FRB generation mechanisms during the early evolution of a magnetar.

We request 30 hours of observing time with the Parkes 64-m Murriyang telescope using the ultra-wideband low-frequency (UWL) receiver. Our plan includes one 10-hour long-duration session to detect rare or clustered bursts, and ten 2-hour sessions spread over 2-3 months to sample temporal variability. Data will be processed with state-of-the-art pipelines for single-pulse searches and coherent dedispersion.

A detection would strongly support magnetar-origin FRB models and provide key constraints on the early-time activity of GRB-formed neutron stars.

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Long-term project observations for project P1321 semester 2025OCTS_02

The atomic interstellar medium shows tiny-scale optical depth fluctuations on the scale of 0.1~10,000 AU, whose origin and nature are poorly understood. The existence of this Tiny-Scale Atomic Structure (TSAS) has significant implications, potentially calling into question our fundamental understanding of heating, cooling and dynamical processes in the interstellar medium. Yet observations remain sparse. This long-term project plans to search for temporal variations in HI absorption spectra seen against background pulsars to characterise TSAS in the Milky Way interstellar medium (ISM). These observations constitute the largest number of sightlines and densest temporal sampling ever performed in a single experiment, and will test predictions that TSAS is the tail end of a turbulent cascade, constrain its minimum size scale (down to resolutions of ~0.05 AU) and potentially provide the first direct measurements of pressures in "large" TSAS features of &gt; 1000 AU. We make use of the phase-resolved spectral line mode that we have recently implemented on Parkes, which has cut data rates and processing times by factors of ~1000 compared to past studies. This is an expansion of our pilot P1321 to a long term study.

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Parkes observations for project P1375 semester 2025OCTS_03

Open clusters have historically shown a striking absence of neutron stars due to their shallow gravitational potential wells that cannot retain these compact objects after supernova explosions with large natal kicks. However, our recent archival search of Parkes observations has discovered three promising Rotating Radio Transient (RRAT) candidates, RRAT J1749-25, RRAT J1702-44, and RRAT J1237-60, in the direction of old open clusters. The dispersion measure (DM) analysis provides compelling evidence for cluster membership, with RRAT J1749-25 showing DM consistent with Theia 1661's predicted values, and RRAT J1237-60 exhibiting DM comparable to Trumpler 20's expectations. These detections are based on limited single-pulse observations with signal-to-noise ratios of ~7-8, requiring confirmation through extended observations. We propose follow-up observations using the Parkes Ultra-Wideband Low receiver with doubled integration times (2 hours per source, repeated twice) to confirm the astrophysical nature of these candidates and characterise their emission properties. Confirmation of neutron stars in open clusters would have profound implications for stellar evolution models, neutron star retention mechanisms, and our understanding of binary evolution in different stellar environments.

Organization: CSIRO Data Access Portal
Long-term project observations for project P885 semester 2025OCTS_02

We propose a modest program to continue monitoring 4 of the 6 known radio magnetars in order to achieve three primary science goals. The first is to characterise magnetar outbursts over long timescales, for which tracking their rotational, flux density, and polarisation properties provide a clear view of the impulse response of their magnetic fields. Second, understanding the links between magnetars the mysterious fast radio burst phenomenon through the discovery of rare emission and propagation effects, shared spectro-temporal phenomenology, and connections to high-energy (X-ray/gamma-ray) phenomena. Lastly, our continued monitoring has enormous benefit to the wider magnetar community, providing rapid alerts to changes in activity, adding context to unusual behaviour detected by high-energy observations, and a host of supplementary science through the teams extensive collaborative networks. The project and its precursors have been running since 2007 and have contributed to 21 publications since then. We are seeking to convert the project to long-term status, thereby also carrying these investigations into the SKA era.

Organization: CSIRO Data Access Portal
Parkes observations for project P1382 semester 2025OCTS_05

The prevalence of millisecond pulsars (MSPs) in and around the Galactic center and the bulge has been one of the key questions in pulsar astronomy. In addition to finding more exotic and interesting binary systems at and around the Galactic center and bulge due to the enhanced density of stars/stellar remnants, MSPs are also proposed to be one of the candidates to explain the observed Fermi gamma-ray excess. However, most of the MSPs discovered so far are field (disk) MSPs or those in globular clusters. Initial steps towards addressing the question of Galactic center/bulge MSPs were made with the discovery of the first MSPs in a Galactic filament, but more progress comes from the discovery of a sample of MSPs around the Galactic center. Blind surveys targeting MSPs can suffer from many observational biases that smear the pulses due to binary acceleration, scattering from the enhanced density, and so on, which increases the parameter space for discovery and can sometimes make the problem intractable. However, if pulsar candidates can be identified reliably from imaging surveys, then targeted observations can make the problem tractable in identifying the pulsations. We followed up a sample of polarized sources identified in the MeerKAT bulge imaging survey and discovered a sample of 16 new MSPs. Here we request the timing observations of 8 interesting MSPs (a subset of our discovery sample), to study the binary nature of these sources and their potential inclusion in pulsar timing array efforts.

Organization: CSIRO Data Access Portal
Parkes observations for project P1382 semester 2025OCTS_04

The prevalence of millisecond pulsars (MSPs) in and around the Galactic center and the bulge has been one of the key questions in pulsar astronomy. In addition to finding more exotic and interesting binary systems at and around the Galactic center and bulge due to the enhanced density of stars/stellar remnants, MSPs are also proposed to be one of the candidates to explain the observed Fermi gamma-ray excess. However, most of the MSPs discovered so far are field (disk) MSPs or those in globular clusters. Initial steps towards addressing the question of Galactic center/bulge MSPs were made with the discovery of the first MSPs in a Galactic filament, but more progress comes from the discovery of a sample of MSPs around the Galactic center. Blind surveys targeting MSPs can suffer from many observational biases that smear the pulses due to binary acceleration, scattering from the enhanced density, and so on, which increases the parameter space for discovery and can sometimes make the problem intractable. However, if pulsar candidates can be identified reliably from imaging surveys, then targeted observations can make the problem tractable in identifying the pulsations. We followed up a sample of polarized sources identified in the MeerKAT bulge imaging survey and discovered a sample of 16 new MSPs. Here we request the timing observations of 8 interesting MSPs (a subset of our discovery sample), to study the binary nature of these sources and their potential inclusion in pulsar timing array efforts.

Organization: CSIRO Data Access Portal
2024 Yanco Durum Wheat Long Coleoptile Trial: Multi-Factor Evaluation of Genotype, Sowing Depth, Sowing Time, and Fusarium Crown Rot Inoculation Effects on Crop Performance

This dataset captures detailed agronomic and phenological data from a 2024 field trial conducted at Yanco, New South Wales, to evaluate the performance of durum wheat genotypes with long coleoptiles under varying sowing depths, sowing times, and Fusarium crown rot (FCR) inoculation treatments. The trial includes three durum wheat varieties—Scepter, Vittaroi, and V190245-6—each subjected to two sowing depths (shallow and deep), two sowing times (early and late), and two FCR treatments (plus and minus inoculation), resulting in a factorial design. The dataset is structured in a single sheet containing 93 entries, each representing a unique plot. Variables include identifiers such as entry number, genotype, treatment combinations, sowing and emergence dates, and positional data (replicate, range, row). Agronomic measurements include plant density (plants/m²), biomass at GS30 (g/m²), plot height (cm), head count per m², and key growth stages (GS51, GS65, GS92) with corresponding calendar and time since sowing. Yield-related metrics include hand and header grain yield (t/ha), total biomass yield (t/ha), harvest index, 1000 grain weight, screenings percentage, test weight (kg/hL), and grain protein content (%). The dataset enables analysis of genotype by environment by management interactions, particularly focusing on the influence of deep sowing and FCR pressure on crop establishment, development, and yield. All variables are consistently labelled, and treatments are encoded using descriptive names (e.g., “Deep Early Scepter”, “Shallow Late Vittaroi”) to facilitate filtering and analysis. The dataset supports statistical modelling and agronomic decision-making for optimizing durum wheat production under variable sowing conditions and disease pressures.

Organization: CSIRO Data Access Portal
2024 Breeza Long Coleoptile Wheat Trials: Multi-Environment Evaluation of Genotypic and Agronomic Interactions Across Depth, Seed Size, and Water Regimes

This dataset comprises comprehensive agronomic and phenotypic data from the 2024 long coleoptile wheat trials conducted at Breeza, New South Wales, Australia. The trials include four major experiments: N_MET_24 (multi-environment trial), N_Durum_24 (durum wheat trial), Seed_size (seed size and depth interaction), and Victrado (water regime and depth interaction). The trials were established on 36 ranges with 5 rows per bed, 2-meter bed centres, and 11-meter ranges (10.8 meters planted). Fertilisation included 238 kg/ha of urea and 70 kg/ha of Granulock Z Extra Treated starter. Herbicide applications included Axil Xtra, Starane, MCPA, and Metsulfuron. Sowing occurred in two time-of-sowing (TOS) windows: TOS1 on 28 May and TOS2 on 4 July 2024. The trials evaluated multiple genotypes including Mace, Mace18, Scepter, Magenta, Magenta13, Calibre, Westcourt, V190245-6, and Sunchaser, under varying treatments such as sowing depth (4 cm and 12 cm), seed size (small and large), FCR resistance (plus/minus), and water regimes (well-watered and dryland). The dataset includes over 450 unique plots across the trials. Variables recorded include emergence and plant counts (outside and inside row counts, plants per square meter), seedling traits (depth and length), Zadok growth stage scores, dry biomass at GS32, and final harvest metrics such as yield (T/ha), protein content, test weight, grain weight, and grain size. Temperature logger data and phenological observations are also included. Data is structured across multiple sheets, each corresponding to a specific trial or measurement type, with consistent identifiers for site, trial, TOS, genotype, depth, and treatment. The dataset enables analysis of genotype-by-environment interactions, agronomic performance under deep sowing, and the influence of seed size and water availability on wheat establishment, growth, and yield.

Organization: CSIRO Data Access Portal
Waikerie 2024 Long Coleoptile Wheat Trial: Genotype, Sowing Depth and Presswheel Pressure Effects on Early Establishment and Yield

This dataset originates from a 2024 field experiment conducted at Waikerie, South Australia, designed to investigate the interaction between wheat genotype, sowing depth, and presswheel pressure on crop establishment and performance. The trial included six wheat genotypes (e.g., Mace18, Scepter, Calibre, Magenta, Magenta13, Mace) sown at two depths (shallow: 30–40 mm and deep: 80–100 mm) under three presswheel pressure treatments (light, standard, heavy). The experiment was laid out in a randomized block design with four replicates, using 12 m × 2.2 m plots and 28 cm row spacing. Fertiliser treatments varied by placement (above, with, or below seed) and rate (standard, high), and seed size (standard or small) was recorded for each plot.

The Excel file (.xlsx) contains seven sheets. The “Trial details” sheet outlines the experimental design, site conditions, soil test results, and assessment schedule. The “Trial plan” sheet maps plot layout and treatment combinations. The “Metafile” provides metadata including sowing date, genotype list, and measured variables. The “Exp_data” sheet is the core dataset, containing 56 plots with variables such as plant density at three time points, sowing depth, coleoptile length, root and shoot biomass, NDVI at two dates, dry biomass at GS31 and GS65, grain yield, protein content, 1000-grain weight, and harvest index. The “Exp_soildata” sheet includes gravimetric soil water content at three depths (0–5, 5–10, 10–15 cm) for selected plots. The “predicta B” sheet reports soil-borne pathogen DNA levels and nematode counts across depths and blocks. The “soil fertility” sheet provides detailed chemical and physical soil properties (e.g., pH, organic carbon, macro- and micronutrients, salinity, texture) across five depth intervals (0–100 cm).

The dataset includes over 40 variables. Codes such as “deep_Small_fert with_High rate” describe treatment combinations. Depths are in mm, biomass in t/ha, and nutrient concentrations in standard agronomic units. The dataset supports analysis of genotype performance under varying mechanical and environmental constraints, with implications for optimizing deep sowing strategies in low rainfall environments.

Organization: CSIRO Data Access Portal
Parkes observations for project P1054 semester 2025OCTS_04

With this proposal we ask time to continue our timing follow-up campaign of pulsars discovered with the MeerKAT telescope. Fourtyfour sources have been discovered in targeted observations of Fermi unidentified point sources, two towards Supernova Remnants, 26 in the Magellanic Clouds, 106 in Globular Clusters and 87 in a survey of the Galactic plane. A large fraction of the new discoveries are recycled pulsars (including a few relativistic systems, a pulsar with a planetary companion and  several 'spider' binaries), or young pulsars. Timing observations have an essential role in exploiting the full potential of any pulsar discovery, allowing for the precise measurement of rotational, astrometric and orbital parameters which, in turn, give us powerful tools to improve our understanding of the physics in extreme environments as well as of the population of neutron stars as a whole. The UWL receiver of the Parkes telescope is a sensitive, versatile instrument that is allowing us to successfully time these new sources, in the bright-end of TRAPUM discoveries.

Organization: CSIRO Data Access Portal
Parkes observations for project P1382 semester 2025OCTS_06

The prevalence of millisecond pulsars (MSPs) in and around the Galactic center and the bulge has been one of the key questions in pulsar astronomy. In addition to finding more exotic and interesting binary systems at and around the Galactic center and bulge due to the enhanced density of stars/stellar remnants, MSPs are also proposed to be one of the candidates to explain the observed Fermi gamma-ray excess. However, most of the MSPs discovered so far are field (disk) MSPs or those in globular clusters. Initial steps towards addressing the question of Galactic center/bulge MSPs were made with the discovery of the first MSPs in a Galactic filament, but more progress comes from the discovery of a sample of MSPs around the Galactic center. Blind surveys targeting MSPs can suffer from many observational biases that smear the pulses due to binary acceleration, scattering from the enhanced density, and so on, which increases the parameter space for discovery and can sometimes make the problem intractable. However, if pulsar candidates can be identified reliably from imaging surveys, then targeted observations can make the problem tractable in identifying the pulsations. We followed up a sample of polarized sources identified in the MeerKAT bulge imaging survey and discovered a sample of 16 new MSPs. Here we request the timing observations of 8 interesting MSPs (a subset of our discovery sample), to study the binary nature of these sources and their potential inclusion in pulsar timing array efforts.

Organization: CSIRO Data Access Portal