Comparison of simulated longitudinal profiles of hadronic air showers with MASS2 balloon data

The KASKADE and CORSIKA air shower generators are compared to the data collected by MASS2 balloon experiment in 1991. The test of longitudinal profile for proton, helium and muon flux production provide good constraints on these air shower generators. KASKADE and CORSIKA especially with the new simulator UrQMD for low energies are found to fit these data well. This study is limited to a comparison of longitudinal profiles and therefore does not provide constraints on the overall shower development.Comment: to be published in Astroparticle Physic

Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer

IntroductionWe present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer.MethodWe mined the sequence reads of breast tumor tissue that are usually discarded as discordant paired-end reads and discovered cancer specific fusion transcripts using tissue from cancer free controls as reference. Binding affinity predictions of novel peptide sequences crossing the fusion junction were analyzed by the MHC Class I binding predictor, MHCnuggets. CD8+ T cell responses against the 15 peptides were assessed through in vitro Enzyme Linked Immunospot (ELISpot).ResultsWe uncovered 20 novel fusion transcripts from 75 breast tumors of 3 subtypes: TNBC, HER2+, and HR+. Of these, the NSFP1-LRRC37A2 fusion transcript was selected for further study. The 3833 bp chimeric RNA predicted by the consensus fusion junction sequence is consistent with a read-through transcription of the 5’-gene NSFP1-Pseudo gene NSFP1 (NSFtruncation at exon 12/13) followed by trans-splicing to connect withLRRC37A2 located immediately 3’ through exon 1/2. A total of 15 different 8-mer neoantigen peptides discovered from the NSFP1 and LRRC37A2 truncations were predicted to bind to a total of 35 unique MHC class I alleles with a binding affinity of IC50<500nM.); 1 of which elicited a robust immune response.ConclusionOur data provides a framework to identify immunogenic neoantigen candidates from fusion transcripts and suggests a potential vaccine strategy to target the immunogenic neopeptides in patients with tumors carrying the NSFP1-LRRC37A2 fusion

Lung Sound Classification With Multi-Feature Integration Utilizing Lightweight CNN Model

Detecting respiratory diseases is of utmost importance, considering that respiratory ailments represent one of the most prevalent categories of diseases globally. The initial stage of lung disease detection involves auscultation conducted by specialists, relying significantly on their expertise. Therefore, automating the auscultation process for the detection of lung diseases can yield enhanced efficiency. Artificial intelligence (AI) has shown promise in improving the accuracy of lung sound classification by extracting features from lung sounds that are relevant to the classification task and learning the relationships between these features and the different pulmonary diseases. This paper utilizes two publicly available respiratory sound recordings namely, ICBHI 2017 challenge dataset and another lung sound dataset available at Mendeley Data. Foremost in this paper, we provide a detailed exposition about employing a Convolutional Neural Network (CNN) that utilizes feature extraction from Mel spectrograms, Mel frequency cepstral coefficients (MFCCs), and Chromagram. The highest accuracy achieved in the developed classification is 91.04% for 10 classes. Extending the contribution, this paper elaborates on the explanation of the classification model prediction by employing Explainable Artificial Intelligence (XAI). The novel contribution of this study is a CNN model that classifies lung sounds into 10 classes by combining audio-specific features to enhance the classification process

Masking Ability of Various Metal Complexing Ligands at 1.0 mM Concentrations on the Potentiometric Determination of Fluoride in Aqueous Samples

Fluoride is a common anion present in natural waters. Among many analytical methods used for the quantification of fluoride in natural waters, potentiometric analysis is one of the most widely used methods because of minimum interferences from other ions commonly present in natural waters. The potentiometric analysis requires the use of ionic strength adjusting buffer abbreviated as TISAB to obtain accurate and reproducible data. In most of the reported literature, higher concentrations of strong metal chelating ligands are used as masking agents generally in the concentration range of 1.0 to 0.01 M. In the present study, effectiveness of the masking agents, phosphate, citrate, CDTA ((1,2-cyclohexylenedinitrilo)tetraacetic acid), EDTA (ethylenediaminetetraacetic acid) HE-EDTA ((hydroxyethyl)ethylenediaminetriacetic acid)), triethanolamine, and tartaric acid at 1.0 mM in TISAB solutions was investigated. The experimental data were compared with a commercially available WTW 140100 TISAB solution as the reference buffer. According to the experimental data, the reference buffer always produced the highest fluoride concentrations and the measured fluoride concentrations were in the range of 0.611 to 1.956 mg/L. Out of all the masking agents investigated, only CDTA performed marginally well and approximately a quarter of the samples produced statistically comparable data to the reference buffer. All the other masking agents produced significantly low concentrations compared to the reference buffer. The most probable reasons for the underestimation of fluoride concentrations could be shorter decomplexing time and lower masking agent concentrations

Sequential Anaerobic/Aerobic Methods in Dye Elimination

Almost all the modern dyes widely used in industrial processes like textile, leather, paint, food, cosmetic, and pharmaceutical manufacturing are synthetic organic compounds. Dyes are responsible for the dyeing phase of the product of interest, and it has been estimated that the annual synthetic organic dye production exceeds 700,000 tons globally. Dyes can be categorized based on their structure and application: reactive, acid, disperse, vat, and azo dyes are some of those classes. The discharge of these dyes into the environment is a major threat due to the adverse effects such as carcinogenicity, toxicity, and mutagenicity of themselves and their biological transformation products. Therefore, the elimination of dyes from wastewater is a major requirement today, and various types of treatments are available in the world. Some of those methods are physical processes like adsorption and membrane filtration, and chemical processes like coagulation–flocculation and ozonation. The application of these methods has some restrictions such as effectiveness of the dye removal process, need for expensive chemicals/reagents, etc. Yet, the biological processes may exhibit better effectiveness and only require relatively cheaper, environmentally friendly reagents. Azo dyes can be considered as a representative class of dyes for the treatment with biological processes under aerobic and anaerobic conditions. The biodegradation of azo dyes is occurring via two steps; first, the reduction of the azo linkage (favorable under anaerobic conditions) to produce colorless amines and subsequently, further degradation of aromatic amines (favorable in aerobic conditions). The fate of the dyes upon treating with biological processes may vary based on the structure of the organic moiety and the conditions used. Such cases are discussed in this chapter in great detail

Efficacy and safety of deferoxamine, deferasirox and deferiprone triple iron chelator combination therapy for transfusion-dependent β-thalassaemia with very high iron overload: a protocol for randomised controlled clinical trial

Introduction Despite the improvement in medical management, many patients with transfusion-dependent β-thalassaemia die prematurely due to transfusion-related iron overload. As per the current guidelines, the optimal chelation of iron cannot be achieved in many patients, even with two iron chelators at their maximum therapeutic doses. Here, we evaluate the efficacy and safety of triple combination treatment with deferoxamine, deferasirox and deferiprone over dual combination of deferoxamine and deferasirox on iron chelation in patients with transfusion-dependent β-thalassaemia with very high iron overload.Methods and analysis This is a single-centre, open-label, randomised, controlled clinical trial conducted at the Adult and Adolescent Thalassaemia Centre of Colombo North Teaching Hospital, Ragama, Sri Lanka. Patients with haematologically and genetically confirmed transfusion-dependent β-thalassaemia are enrolled and randomised into intervention or control groups. The intervention arm will receive a combination of oral deferasirox, oral deferiprone and subcutaneous deferoxamine for 6 months. The control arm will receive the combination of oral deferasirox and subcutaneous deferoxamine for 6 months. Reduction in iron overload, as measured by a reduction in the serum ferritin after completion of the treatment, will be the primary outcome measure. Reduction in liver and cardiac iron content as measured by T2* MRI and the side effect profile of trial medications are the secondary outcome measures.Ethics and dissemination Ethical approval for the study has been obtained from the Ethics Committee of the Faculty of Medicine, University of Kelaniya (Ref. P/06/02/2023). The trial results will be disseminated in scientific publications in reputed journals.Trial registration number The trial is registered in the Sri Lanka Clinical Trials Registry (Ref: SLCTR/2023/010)