Miracle-dz/UniFAR-FTUs huggingface dataset:
Computing Linkage Disequilibrium Aware Genome Embeddings using Autoencoders

Motivation The completion of the human genome has paved the way for genome-wide association studies (GWAS), which have already succeeded in explaining certain proportions of heritability. GWAS are not optimally suited to detect potential non-linear effects in disease risk, possibly hidden in non-additive interactions (epistasis). Alternative methods for epistasis detection using e.g. deep neural networks are currently under active development. Despite their promise to scale to high-dimensional data, deep neural networks (DNNs) are constrained by finite computational resources, which can be rapidly depleted due to increasing complexity with the sheer size of the genome. Besides, the curse of dimensionality complicates the task of capturing meaningful genetic patterns for DNNs; therefore calls for precaution in the form of dimensionality reduction. Results We propose a method to compress genotyping data, involving single nucleotide polymorphisms (SNPs), while leveraging the LD structure in the genome and preserving non-linear relations among variants. This method involves clustering correlated SNPs into haplotype blocks and training per-block autoencoders that are able to learn a compressed representation of the block’s relevant genetic content. We provide an adjustable autoencoder design to accommodate diverse blocks and to bypass extensive hyperparameter tuning. We applied this method to genotyping data from Project MinE which involves a total of 23,209 ALS cases and 90,249 healthy controls. We compressed the haplotype blocks of an entire chromosome using our autoencoder-based approach, and show that this leads to more than 99% average test reconstruction accuracy - i.e. minimal information loss - while compressing the input to nearly 10% of the original size. We demonstrate that haplotype-block based autoencoders outperform their linear alternative Principal Component Analysis (PCA) by approximately 3% chromosome-wide accuracy of reconstructed variants. To the extent of our knowledge, our approach is the first to simultaneously leverage genome haplotype structure and deep neural networks for dimensionality reduction of genetic data. Availability and Implementation Data used in this study are available for academic use through the Project MinE Consortium at https://www.projectmine. com/research/data-sharing/. Data accessibility is contingent upon any terms or requirements specified by the source studies. Codes for data compression are available at https://github.com/gizem-tas/haploblock-autoencoders.
Dynamic Regulation of Innate Lymphoid Cell Development During Ontogeny

Innate lymphoid cells (ILCs) are crucial for maintaining tissue homeostasis. The dynamic composition of ILC subsets during ontogeny has been observed for over a decade, yet the underlying mechanisms remain incompletely understood. Here, we combined differentiation assay and scRNA-seq analysis to compare the fetal and adult ILC development, and assessed their contribution to the dynamic change of ILC subsets. We revealed the preference for LTi cell differentiation in fetal hematopoietic progenitors, contrasted with a non-LTi differentiation bias in adult stages. Our analyses elucidated that the two stages shared a conserved differentiation trajectory and regulatory programs but used different controlling logic. Through computational prediction and dose-response experiments, we proposed a model where a transition from fetal RORγt-dominant states to adult Notch-GATA3-dominant states orchestrates these changes. This study suggests that ILC development can be modulated to accommodate the varying demands for specific ILC subsets within the body at different developmental stages. Highlight The ratio of LTi cells to non-LTi ILCs decreases from fetal to adult stage Modified fate determination of ILC progenitors contributes to this decrease of LTi cell ratio during ontogeny A conserved trajectory exists from early αLPs to Innate Lymphoid Cell Precursors (ILCPs) during both fetal and adult ILC development Enhanced activity of Notch-GATA3 signaling in ILC precursors accounts for the transition of their differentiation from LTi cells in the fetal to non-LTi ILCs in adults. Graphical abstract
Unraveling the Genomic and Environmental Diversity of the Ubiquitous Solirubrobacter

Solirubrobacter, a genus within the Actinobacteriota phylum, is commonly found in soils and rhizospheres yet remains unexplored despite its widespread presence and diversity, as revealed through metagenomic studies. Previously recognized as a prevalent soil bacterium, our study delved into phylogenomics, pangenomics, environmental diversity, and bacterial interactions of Solirubrobacter. Analyzing the limited genomic sequences available for this genus, we uncovered a pangenome consisting of 19,645 protein families, with 2,644 constituting a strict core genome. While reported isolates do not exhibit motility, we intriguingly discovered the presence of flagellin genes, albeit with an incomplete flagellum assembly pathway. Our examination of 16S ribosomal genes unveiled a considerable diversity (3,166 operational taxonomic units OTUs) of Solirubrobacter in Mexican soils, and co-occurrence network analysis indicated its extensive connectivity with other bacterial taxa. Through phylogenomic analysis, we delved into the relatedness of sequenced strains and notably dismissed ASM999324v1 as a member of this genus. Our investigation extended to the metagenomic diversity of Solirubrobacter across various environments, affirming its pervasive presence in rhizospheres and certain soils. This broader pangenomic view revealed genes linked to transcription, signal transduction, defense mechanisms, and carbohydrate metabolism, highlighting Solirubrobacter’s adaptability. We observed that Solirubrobacter’s prevalence in rhizospheres is geographically indiscriminate, prompting intriguing questions about its potential interactions with plants and the biotic and abiotic determinants of its soil occurrence. Given its richness and diversity, Solirubrobacter might be a versatile yet overlooked keystone species in its environments, meriting further recognition and study. 3. Impact statement This study explored the enigmatic world of Solirubrobacter, a widespread microbe commonly found in soils and plants across various regions. Despite its prevalence, little is known about its genetic diversity and functionality and how it thrives in diverse environments. Our research unveils the genetic secrets of Solirubrobacter, shedding light on its adaptability and ecological interactors and roles. We showed that Solirubrobacter environmental prevalence makes it a good candidate for studying the genetic basis of being a successful microbe associated with soil and plants. 4. Data summary Data, scripts and statistical analysis available in GitHub: https://github.com/genomica-fciencias-unam/Solirubrobacter Sequences, phylogenetic analysis, raw data structures: https://doi.org/10.6084/m9.figshare. 24446521 16S rRNA gene raw data: https://www.ncbi. nlm.nih. gov/sra/PRJNA603586 https://www.ncbi. nlm.nih. gov/sra/PRJNA603590 Shotgun metagenomes: https://www.ncbi. nlm.nih. gov/bioproject/603603 All supporting data, code, and protocols are within the article, supplementary files, and described repositories.
Model-based testing with chi and TorX : a case study of the ASML laser subsystem

Within the TANGRAM project, a case study on model-based testing of the ASML laser subsystem has been performed. The approach used in the case study is based on the proposed model-based testing framework, instantiated with state-of-the-art tooling from the TANGRAM project partners: chi as specification language and TorX as test tool. A chi specification model of the laser state behavior and communication interface has been developed. After verification and validation, the model has been used for automatic model-based testing with TorX. Using this approach, discrepancies between the implementation and specification of the laser subsystem have been found.
New isotopic age determinations for the Torridonian, NW Scotland

Isotopic data are used to determine a new chronology for the Torridonian of NW Scotland. The calcite fraction of the Stoer Group Limestone Member yields a Pb–Pb age of 1199 ± 70 (2σ) Ma (MSWD = 1.1). Rb–Sr whole-rock regressions from siltstones of the Diabaig and Applecross Formations (both Torridon Group) produce ages of 994 ± 48 (2σ) Ma (MSWD = 17) and 977 ± 39 (2σ) Ma (MSWD = 10) respectively. These dates, which agree well with palaeomagnetic estimates, are interpreted as the time of early diagenesis which is probably within error of the time of deposition. Previous isotopic age determinations are shown to be in error. Size fractionsfrom shales of the Stoer Group and Applecross Formation have been analysed for Rb–Sr and produce ages of 689 ± 87 (2 σ) Ma (MSWD = 14) and 667 ± 66 (2 σ) Ma (MSWD = 55) respectively. They are used, together with Sm-Nd isotopic data, to suggest a thermal event affecting the entire Torridonian at this time. Our new chronology for the Torridonian is consistent with the Proterozoic geology of Scotland and Laurentia. It suggests that deposition of the Stoer Group is contemporaneous with uplift of the Lewisian and the Torridon Group may be associated with the extensional collapse of the Grenville orogen. The c. 700Ma diagenetic event is possibly related to Neoproterozoic rifting of the Laurentian margin.
Evaluation of Speaker Veriﬁcation Security and Detection of Synthetic Speech

—In this paper, we evaluate the vulnerability of speaker veriﬁcation (SV) systems to synthetic speech. The SV systems are based on either the Gaussian Mixture Model-Universal Background Model (GMM-UBM) or Support Vector Machine (SVM) using Gaussian supervectors. We use a Hidden Markov Model (HMM)-based text-to-speech (TTS) synthesizer, which can synthesize speech for a target speaker using small amounts of training data through model adaptation of an average voice or background model. Although the SV systems have a very low equal error rate (EER), when tested with synthetic speech generated from speaker models derived from the Wall-Street Journal (WSJ) speech corpus, over 91% of the matched claims are accepted. This result suggests a vulnerability in SV systems and thus a need to accurately detect synthetic speech. We propose a new feature based on relative phase shift (RPS), demonstrate reliable detection of synthetic speech, and show how this classiﬁer can be used to improve security of SV systems.
Water column conditions in a coastal lagoon near Jeddah, Red Sea

Abstract Water column conditions in a lagoon near Jeddah are investigated on the basis of changes in potential energy. Three major factors including balance of surface heat at the air-sea interface, wind and tidal mixing are considered. A negative potential energy change dv dt will develop stratification, whereas positive dv dt will tend to mix the water column. The tidal effect is greater in summer with wind mixing showing no great variations. The buoyancy effect of the heat balance at the surface is negative from April to October. This negative buoyancy effect will tend to develop stratification but the positive contributions of wind and tide counteract this and the water column remains mixed except in September and October, when a weak stratification may develop. Generally, the water column remains practically mixed throughout the year. The change in heat content of the water column from mid-April to mid-September is about 3.3 × 10 8 J. During this period the net heat input at the air interface is about 2.0 × 10 8 J, which is about 40% less than the heat content of the water column, showing that the heat is advected towards the central area from the shallower periphery of the lagoon.
University of Birmingham Food choices in the presence of 'healthy' and 'unhealthy' eating partners

Eating with others has been shown to inﬂuence the amount of food eaten in a meal or snack. We examined whether choosing food in the presence of another person who is choosing either predominantly low-energy-dense or high-energy-dense foods affects food choices. A between-subjects laboratory-based study was used. A group of 100 young females selected a lunch-time meal from a buffet consisting of a range of high-energy-dense and low-energy-dense foods, in the presence of an ‘unhealthy’ eating partner (who chose predominantly high-energy-dense foods) or a ‘healthy’ eating partner (who chose predominantly low-energy-dense foods) or when alone. Participants in the ‘unhealthy’ eating partner condition were signiﬁcantly less likely to choose and consume a low-energy-dense food item (carrots), than when choosing alone or in the presence of a ‘healthy’ eater. Choice of high-energy-dense food did not differ across the conditions, nor did the total energy consumed. These data suggest that social inﬂuences on food choice are limited in this context but the presence of an ‘unhealthy’ eating partner may undermine intentions to consume low-energy-dense foods.
Effect of Public Sensitization and Awareness Campaigns on Adoption of e-government Services at Local Government level in Uganda

The successful adoption of e-government systems leads to efficient delivery of government services. Despite several e-government initiatives by the Uganda government, there has been limited success, with the levels of adoption and use remaining generally low. Countries like Uganda are facing challenges like lack of up-to-date technology, but the biggest challenges raise from non-technical issues to include lack of public awareness and sensitization in regards to the benefits of e-government, availability of different e-government services and systems together with a low e-readiness index. Therefore, for a developing country like Uganda much energy and efforts by government should mainly focus on more sensitization and mobilization of the citizens to embrace e-government and its challenges. Different customized e-government models have been developed for Uganda but there is more need to sell them out to citizens through mobilization and sensitization as this increases awareness amongst the community. This study therefore justified the need for sensitization and awareness creation in order to increase participation and implementation of e-government at local level, because different models and designs are in place, different eservices available but still low usage by citizens which is a bigger challenge that needs government to focus resources at sensitization and awareness campaigns. Sensitization campaigns can be conducted through radio and television programmes and adverts, face to face group trainings, schools and institutions trainings, social media, conferences and workshops.
Charge transfer evaluation in solid insulating materials encapsulating the gaseous voids of submillimeter dimensions using transmission line method

: In this work, using a lumped RC circuit model which is based on transmission line modeling (TLM) method, the charge transfer in a solid insulating system encapsulating a gaseous void of submillimeter dimensions is evaluated. Here, both the dielectric material and gaseous void are considered simultaneously as a transmission line. The transmission line includes the capacitive and resistance elements and, the obtained circuit equations were coupled with the continuity and kinetic energy equations for charged species along with Poisson’s equation. These equations are solved via 4th order Runge-Kutta method and, the electric field and potential, density of all the charged species, discharge current and electron temperature are calculated in the gaseous media. Hence, the discharge propagation in the gaseous void and its mutual influences on dielectric medium are described. The partially penetration of electrons in the avalanche head into the anode dielectric bulk is shown, and it is observed that their movements towards the electrodes are much faster than ions. Besides, the total transferred charge particles at both the avalanche and streamer phases in the void is calculated. Besides, it was found that, the electrons temperature distribution completely influenced by electric field in the gaseous void. In addition, the effects of voids thickness and their location on the discharge current are examined. It is shown that, at the higher void thicknesses and for the cavities locating in the electrodes adjacent, the magnitude of discharge current increases
Damage on Slope due to the Near Izu-Oshima Earthquake 1978

The main shock (M=7.0), occurred in near Izu-Oshima Island on January 14, 1978, caused the violent disaster in central part of Izu peninsula.Disasters were found out in roads, railways and buildings. Slope failures occurred remarkably in the area.A total number of slope failure was awfully counted as about six hundred and twenty, and the greater part of slope failure occurred on near mountain ridge, that is, near slope changing line. Half number of failures was 20-40 meter in height and 10-20 meter in width as shown in Fig. 1 and 2. Geology of failure site was mainly tertiary and andesitic lava, and a few failure occurred in scoria and volcanic mud flow as shown in Fig. 10.Failures taked place along the earthquake fault by the shock and coincided with after shocks as shown in Fig. 12.The ratio of failure area is about 6% near the earthquake fault and about 0.1% farther than 5 kilometer away from the fault.
Sexual Dimorphism in the Adult South African (Cape) Fur Seal 'Arctocephalus pusillus pusillus' (Pinnipedia: Otariidae): Standard Body Length and Skull Morphology

We examine differences in standard body length and skull morphology of male (n = 65) and female (n = 18) South African (Cape) fur seals, 'Arctocephalus pusillus pusillus', from the coast of southern Africa with the aim to develop an objective method for determining the sex of fur seal skulls. Males were found to be significantly larger than females in standard body length, with K-means cluster analysis successfully identifying 2 relatively homogeneous groups. Principal component analysis (covariance matrix) showed that the underlying data structure for male and female skull variables was different, and that most of this variation was expressed in overall skull size rather than shape. Males were significantly larger than females in 30 of the 31 skull variables. Breadth of brain case was significantly different for the genders. Relative to condylobasal length, males were significantly larger than females in 13 of the 31 skull variables used in the present study. These were gnathion to posterior end of nasals, breadth at preorbital processes, least interorbital constriction, breadth at supraorbital processes, greatest bicanine breadth, breadth of palate at postcanine 1 and 3, calvarial breadth, mastoid breadth, gnathion to anterior of foramen infraorbital, gnathion to posterior border of preorbital process, height of skull at base of mastoid and height of mandible at meatus. In males, these variables were associated with the acquisition and defense of territory (e.g., large head size and mass; increased structural strength of the skull; increased bite capacity). Two skull ratio parameters, breadth of braincase/condylobasal length and length of upper postcanine row/condylobasal length were significantly higher in females compared to males. Based solely on the skull data, mature males can be reliably distinguished from immature males and females using both (a) Classification and Regression Tree (CART) and (b) Hierarchical Cluster Analysis. Both approaches had difficulty in reliably distinguishing immature males from females. The Classification and Regression Tree method was the more successful in correctly distinguishing immature males from females.
Earthquake source‐parameter estimation using regional waveforms: Implications for tsunami alerting in the Caribbean

Three‐component seismic waveforms recorded at the single broadband station SJG have been examined for four MW ≥ 6 Caribbean earthquakes using a regional moment‐tensor (RMT) inversion procedure that uses a general crustal velocity model to generate synthetic Green's functions at a fixed depth. Comparisons of the computed source parameters with solutions reported by international agencies indicate that the RMT procedure provides a rapid estimate of the earthquake magnitude using a single station. Focal mechanisms are not as well resolved and may require a more complete azimuthal coverage. The inversion procedure thus provides a timely estimate of the earthquake magnitude that would be useful for tsunami alerting. Warning intervals for the Caribbean region would vary from about 12 minutes for a tsunami generated at a distance of 200 km to more than 60 minutes for a tsunami originating at a distance of 800 km from the recording site.
Using Deep Learning to Track Stray Animals with Mobile Device

The purpose of this paper is to protect stray animals and reduce the social problems they cause through mobile devices. We wrote an app on the mobile device to explicitly identify the dog or cat. The system combined with the backend repository and placed the Open Street Map (OSM) to show the geographic location of the animal. Through this app, users can know where the stray animals are, which type, and what kind of assistance is needed. At the same time, if the user finds that there are stray animals in his location, but the APP does not display. The user can identify the animals through the system upload the location, type, and other issues to the database. In the part of the observation, we used You Look Only Once (Yolo) to train and put the training module into the system for the identification of stray animals with a precision of 95%. The system can reduce the problems caused by stray animals to increase the willingness of people to adopt stray animals and let shelter reduce the cost of dealing with stray animals.