Latest Articles
-
Section: Mathematical & Computational Biology ; Topics: Biophysics and computational biology, Genetics/genomics, Immunology and inflammation
Alignment-free detection and seed-based identification of multi-loci V(D)J recombinations in Vidjil-algo
10.24072/pcjournal.547 - Peer Community Journal, Volume 5 (2025), article no. e44.
Get full text PDFThe diversity of the immune repertoire is grounded on V(D)J recombinations in several loci. Many algorithms and software detect and designate these recombinations in high-throughput sequencing data. To improve their efficiency, we propose a multi-loci seed identification through an Aho-Corasick like automaton as well as a seed-based gene filtration. These algorithms were implemented into Vidjil-algo, used routinely by several labs for the analysis of hematologic malignancies. We benchmark the results of Vidjil-algo and of MiXCR on five datasets, evaluating the specificity and sensitivity of the detection, as well as the adequation of the designation to manually curated sequences. Compared to the previous algorithms, the new algorithms implemented in Vidjil-algo bring speedups between 3× and 30×, with a smaller memory footprint and without quality loss in results. They enable to precisely annotate in a few minutes millions of sequences coming from V(D)J recombinations, including incomplete V(D)J-like recombinations, improving our knowledge on immune repertoires.
-
Section: Genomics ; Topics: Genetics/genomics
Sequencing, de novo assembly of Ludwigia plastomes, and comparative analysis within the Onagraceae family
10.24072/pcjournal.536 - Peer Community Journal, Volume 5 (2025), article no. e43.
Get full text PDFThe Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera. This family includes the genus Ludwigia L., which is comprised of 82 species. In this study, we focused on the two aquatic invasive species Ludwigia grandiflora subsp. hexapetala (Lgh) and Ludwigia peploides subsp. montevidensis (Lpm) largely distributed in aquatic environments in North America and in Europe. Both species have been found to degrade major watersheds leading ecological and economical damages. Genomic resources for Onagraceae are limited, with only Ludwigia octovalvis (Lo) plastid genome available for the genus Ludwigia L. at the time of our study. This scarcity constrains phylogenetic, population genetics, and genomic studies. To brush up genomic ressources, new complete plastid genomes of Ludwigia grandiflora subps. hexapetala (Lgh) and Ludwigia peploides subsp. montevidensis (Lpm) were generated using a combination of MiSeq (Illumina) and GridION (Oxford Nanopore) sequencing technologies. These plastomes were then compared to the published Ludwigia octovalvis (Lo) plastid genome, which was re-annotated by the authors. We initially sequenced and assembled the chloroplast (cp) genomes of Lpm and Lgh using a hybrid strategy combining short and long reads sequences. We observed the existence of two Lgh haplotypes and two potential Lpm haplotypes. Lgh, Lpm, and Lo plastomes were similar in terms of genome size (around 159 Kb), gene number, structure, and inverted repeat (IR) boundaries, comparable to other species in the Myrtales order. A total of 45 to 65 SSRs (simple sequence repeats), were detected, depending on the species, with the majority consisting solely of A and T, which is common among angiosperms. Four chloroplast genes (matK, accD, ycf2 and ccsA) were found under positive selection pressure, which is commonly associated with plant development, and especially in aquatic plants such as Lgh, and Lpm. Our hybrid sequencing approach revealed the presence of two Lgh plastome haplotypes which will help to advance phylogenetic and evolutionary studies, not only specifically for Ludwigia, but also the Onagraceae family and Myrtales order. To enhance the robustness of our findings, a larger dataset of chloroplast genomes would be beneficial.
-
Section: Archaeology ; Topics: Archaeology, History
First evidence of a Palaeolithic occupation of the Po plain in Piedmont: the case of Trino (north-western Italy)
10.24072/pcjournal.551 - Peer Community Journal, Volume 5 (2025), article no. e42.
Get full text PDFThe Trino hill is an isolated relief located in north-western Italy, close to Trino municipality. The hill was subject of multidisciplinary studies during the 1970s, when, because of quarrying and agricultural activities, five concentrations of lithic artefacts were recognized and referred to a Palaeolithic occupation of the area. During the 1980s and the 1990s, surface collections continued, but the lithic finds have never been subject of specific studies. Even if most of the lithic assemblages count a few lithic implements, four collection areas (3, 13 E, 13 W and 14) have significative lithic assemblages, representing the most important evidence of a Palaeolithic frequentation of the Po plain in north-western Italy. The present work, in the limits imposed by a surface and not systematic collection, propose a technological study of the lithic artefacts from the Trino hill, with the aim to define the main features of the technological behaviour of the human groups that occupied the area. The results obtained allow to clearly identify a Middle Palaeolithic occupation of the Trino hill, characterized by the exploitation of vein quartz and other local raw materials; allochthonous varieties of chert were used in the next frequentation phases to produce blades and bladelets. Even if part of the laminar production can be referred to Neolithic, most of that remains of indeterminate chronology and could be the result of both an Upper Palaeolithic and Neolithic human presence. The systematic and inclusive approach to the study of the Paleolithic of the Piedmont region proposed here has made it possible to obtain a first and realistic overview of the Paleolithic of the region. The methods used for the technological study are similar to those used for other sites in the region and have made it possible to link Trino's surface collections with data from sites systematically investigated in recent years.
-
Section: Animal Science ; Topics: Agricultural sciences, Computer sciences
A pipeline with pre-processing options to detect behaviour from accelerometer data using Machine Learning tested on dairy goats
10.24072/pcjournal.545 - Peer Community Journal, Volume 5 (2025), article no. e41.
Get full text PDFAnimal behaviour is a significant component in the evaluation of animal welfare. Conducting continuous observations of animal behaviour is a time-consuming task and may not be feasible over extended periods for all animals. Thus, new technologies like sensors and cameras can be used to assess individual behaviour continuously. Combined with Artificial Intelligence (AI), accelerometers are promising to continuously and individually detect animal behaviour from the acceleration signals and characteristics of the behaviour. Such devices are commercialised for cattle but they have not been widely developed for small ruminants. Being able to automatically monitor behaviour at an individual scale represents a crucial step towards an objective assessment of animal welfare. This paper aims to present the use of a pipeline called ACT4Behav (Accelerometer-based Classification Tool for identifying Behaviours) involving a supervised classification algorithm for automatically characterising specific animal behaviours using accelerometer data, and to explore the best pre-processing steps for each behaviour. This algorithm is designed to be general-purpose and applicable with different species, behaviours and accelerometers. This paper presents the use of this pipeline with eight indoor-housed goats equipped with ear-mounted accelerometers. Rumination, head in the feeder, standing and lying behaviours were continuously sampled from camera recordings for 11 consecutive hours for each goat using The Observer software. The developed pipeline was used to identify optimal descriptive features and data preparation steps for each prediction model, one for each behaviour. A sensitivity analysis was conducted to assess the impact of the processing techniques and parameter value on the resulting AUC (Area Under the Curve) score, used as the performance score of the models. This analysis allowed the identification of the adequate filtering techniques, time-window segmentations, application of various transformations to raw data, and feature selections for each behaviour. Tuning the data pre-processing for each behaviour enhanced the ability to predict rumination (AUC score=0.800), head in the feeder (AUC score=0.819), lying (AUC score=0.829) and standing (AUC score=0.823) behaviours. When the application of the models on goats that did not participate in the training was tested by training the models on six goats and testing it on the two other goats, the AUC score for the four behaviours decreased (0.644, 0.733, 0.741 and 0.749 respectively for rumination, head in the feeder, lying and standing).
Follow us
People
Sections
- Animal Science 25
- Archaeology 22
- Ecology 108
- Ecotoxicology & Environmental Chemistry 11
- Evolutionary Biology 95
- Forest & Wood Sciences 7
- Genomics 43
- Health & Movement Sciences 6
- Infections 29
- Mathematical & Computational Biology 24
- Microbiology 16
- Network Science 6
- Nutrition 0
- Neuroscience 7
- Organization Studies 2
- Paleontology 11
- Psychology 0
- Registered Reports 1
- Zoology 24
Conferences
Indexed by
Supporters
Membership
Image Credits
The network image was drawn by Martin Grandjean: A force-based network visualization CC BY-SA