The classification and categorisation of Gamma-Ray Bursts with machine learning techniques for neutrino detection

While Gamma-Ray Burst (GRBs) are clear and distinct observed events, every individual GRB is unique. In fact, GRBs are known for their variable behaviour, and BATSE was already able to discover two categories of GRB from the T90 distribution; the short and long GRBs. These two categories match up with the expected two types of GRB progenitors. Nowadays, more features have been found to be able to further distinguish them, such as the hardness ratio or the presence of supernovae. However, that does not mean that it is by any means simple to categorise individual GRBs. Furthermore, more GRB categories have been theorised as well, such as low-luminosity or X-ray-rich GRBs. These different types of GRBs also could indicate a different neutrino spectrum, with different types of GRBs more likely to emit higher amounts of neutrinos. We present an ongoing effort to use machine learning to categorise and classify GRBs, searching for subpopulations that could yield a larger neutrino flux. We specifically use unsupervised learning, as it allows hidden patterns and correlations to come to light. With the help of features such as the T90, hardness, fluence, SNR, spectral index and even the full light curve and spectra, different structures and categories of Gamma-Ray bursts can be found.Comment: Presented at the 38th International Cosmic Ray Conference (ICRC2023

IceCube search for neutrinos from GRB 221009A

GRB 221009A is the brightest Gamma Ray Burst (GRB) ever observed. The observed extremely high flux of high and very-high-energy photons provide a unique opportunity to probe the predicted neutrino counterpart to the electromagnetic emission. We have used a variety of methods to search for neutrinos in coincidence with the GRB over several time windows during the precursor, prompt and afterglow phases of the GRB. MeV scale neutrinos are studied using photo-multiplier rate scalers which are normally used to search for galactic core-collapse supernovae neutrinos. GeV neutrinos are searched starting with DeepCore triggers. These events don't have directional localization, but instead can indicate an excess in the rate of events. 10 GeV - 1 TeV and >TeV neutrinos are searched using traditional neutrino point source methods which take into account the direction and time of events with DeepCore and the entire IceCube detector respectively. The >TeV results include both a fast-response analysis conducted by IceCube in real-time with time windows of T$_0 - 1$ to T$_0 + 2$ hours and T$_0 \pm 1$ day around the time of GRB 221009A, as well as an offline analysis with 3 new time windows up to a time window of T$_0 - 1$ to T$_0 + 14$ days, the longest time period we consider. The combination of observations by IceCube covers 9 orders of magnitude in neutrino energy, from MeV to PeV, placing upper limits across the range for predicted neutrino emission.Comment: Presented at the 38th International Cosmic Ray Conference (ICRC2023). See arXiv:2307.13047 for all IceCube contribution

Characterization of an Oct1 orthologue in the channel catfish, Ictalurus punctatus: A negative regulator of immunoglobulin gene transcription?

BACKGROUND: The enhancer (Eμ3') of the immunoglobulin heavy chain locus (IGH) of the channel catfish (Ictalurus punctatus) has been well characterized. The functional core region consists of two variant Oct transcription factor binding octamer motifs and one E-protein binding μE5 site. An orthologue to the Oct2 transcription factor has previously been cloned in catfish and is a functionally active transcription factor. This study was undertaken to clone and characterize the Oct1 transcription factor, which has also been shown to be important in driving immunoglobulin gene transcription in mammals. RESULTS: An orthologue of Oct1, a POU family transcription factor, was cloned from a catfish macrophage cDNA library. The inferred amino acid sequence of the catfish Oct1, when aligned with other vertebrate Oct1 sequences, revealed clear conservation of structure, with the POU specific subdomain of catfish Oct1 showing 96% identity to that of mouse Oct1. Expression of Oct1 was observed in clonal T and B cell lines and in all tissues examined. Catfish Oct1, when transfected into both mammalian (mouse) and catfish B cell lines, unexpectedly failed to drive transcription from three different octamer-containing reporter constructs. These contained a trimer of octamer motifs, a fish V(H )promoter, and the core region of the catfish Eμ3' IGH enhancer, respectively. This failure of catfish Oct1 to drive transcription was not rescued by human BOB.1, a co-activator of Oct transcription factors that stimulates transcription driven by catfish Oct2. When co-transfected with catfish Oct2, Oct1 reduced Oct2 driven transcriptional activation. Electrophoretic mobility shift assays showed that catfish Oct1 (native or expressed in vitro) bound both consensus and variant octamer motifs. Putative N- and C-terminal activation domains of Oct1, when fused to a Gal4 DNA binding domain and co-transfected with Gal4-dependent reporter constructs were transcriptionally inactive, which may be due in part to a lack of residues associated with activation domain function. CONCLUSION: An orthologue to mammalian Oct1 has been found in the catfish. It is similar to mammalian Oct1 in structure and expression. However, these results indicate that the physiological functions of catfish Oct1 differ from those of mammalian Oct1 and include negative regulation of transcription

Major histocompatibility genes in the Lake Tana African large barb species flock: evidence for complete partitioning of class II B, but nog class I, genes among different species

The 16 African large barb fish species of Lake Tana inhabit different ecological niches, exploit different food webs and have different temporal and spatial spawning patterns within the lake. This unique fish species flock is thought to be the result of adaptive radiation within the past 5 million years. Previous analyses of major histocompatibility class II B exon 2 sequences in four Lake Tana African large barb species revealed that these sequences are indeed under selection. No sharing of class II B alleles was observed among the four Lake Tana African large barb species. In this study we analysed the class II B exon 2 sequences of seven additional Lake Tana African large barb species and African large barbs from the Blue Nile and its tributaries. In addition, the presence and variability of major histocompatibility complex class I UA exon 3 sequences in six Lake Tana and Blue Nile African large barb species was analysed. Phylogenetic lineages are maintained by purifying or neutral selection on non-peptide binding regions. Class II B intron 1 and exon 2 sequences were not shared among the different Lake Tana African large barb species or with the riverine barb species. In contrast, identical class I UA exon 3 sequences were found both in the lacustrine and riverine barb species. Our analyses demonstrate complete partitioning of class II B alleles among Lake Tana African large barb species. In contrast, class I alleles remain for the large part shared among species. These different modes of evolution probably reflect the unlinked nature of major histocompatibility genes in teleost fishes

(Cost-)effectiveness of an individualised risk prediction tool (PERSARC) on patient’s knowledge and decisional conflict among soft-tissue sarcomas patients:protocol for a parallel cluster randomised trial (the VALUE-PERSARC study)

Introduction Current treatment decision-making in high-grade soft-tissue sarcoma (STS) care is not informed by individualised risks for different treatment options and patients’ preferences. Risk prediction tools may provide patients and professionals insight in personalised risks and benefits for different treatment options and thereby potentially increase patients’ knowledge and reduce decisional conflict. The VALUE-PERSARC study aims to assess the (cost-)effectiveness of a personalised risk assessment tool (PERSARC) to increase patients’ knowledge about risks and benefits of treatment options and to reduce decisional conflict in comparison with usual care in high-grade extremity STS patients. Methods The VALUE-PERSARC study is a parallel cluster randomised control trial that aims to include at least 120 primarily diagnosed high-grade extremity STS patients in 6 Dutch hospitals. Eligible patients (≥18 years) are those without a treatment plan and treated with curative intent. Patients with sarcoma subtypes or treatment options not mentioned in PERSARC are unable to participate. Hospitals will be randomised between usual care (control) or care with the use of PERSARC (intervention). In the intervention condition, PERSARC will be used by STS professionals in multidisciplinary tumour boards to guide treatment advice and in patient consultations, where the oncological/ orthopaedic surgeon informs the patient about his/her diagnosis and discusses benefits and harms of all relevant treatment options. The primary outcomes are patients’ knowledge about risks and benefits of treatment options and decisional conflict (Decisional Conflict Scale) 1 week after the treatment decision has been made. Secondary outcomes will be evaluated using questionnaires, 1 week and 3, 6 and 12 months after the treatment decision. Data will be analysed following an intention-to-treat approach using a linear mixed model and taking into account clustering of patients within hospitals. Ethics and dissemination The Medical Ethical Committee Leiden-Den Haag-Delft (METC-LDD) approved this protocol (NL76563.058.21). The results of this study will be reported in a peer-review journal.</p