Complete Catalogue Research Articles

Young Star Clusters Dominate the Production of Detached Black Hole–Star Binaries

The recent discovery of two detached black hole–star (BH–star) binaries from Gaia’s third data release has sparked interest in understanding the formation mechanisms of these systems. We investigate the formation of these systems by dynamical processes in young star clusters (SCs) and via isolated binary (IB) evolution, using a combination of direct N-body and population synthesis simulations. We find that dynamical formation in SCs is nearly 50 times more efficient per unit of star formation at producing BH–star binaries than IB evolution. We expand this analysis to the full Milky Way (MW) using a FIRE-2 hydrodynamical simulation of an MW-mass galaxy. Even assuming that only 10% of star formation goes into SCs, we find that approximately four out of every five BH–star systems are formed dynamically, and that the MW contains a total of ∼2 × 105 BH–star systems. Many of these dynamically formed systems have longer orbital periods, greater eccentricities, and greater black hole masses than their isolated counterparts. For binaries older than 100 Myr, we show that any detectable system with e ≳ 0.5 or M BH ≳ 10 M ⊙ can only be formed through dynamical processes. Our MW model predicts between 64 and 215 such detections from the complete DR4 Gaia catalog, with the majority of systems being dynamically formed in massive and metal-rich SCs. Finally, we compare our populations to the recently discovered Gaia BH1 and Gaia BH2, and conclude that the dynamical scenario is the most favorable formation pathway for both systems.

AGNs in massive galaxy clusters: Role of galaxy merging, infalling groups, cluster mass, and dynamical state

Context. There is compelling evidence that active galactic nuclei (AGNs) in high-density regions have undergone a different evolution than their counterparts in the field, indicating that they are strongly affected by their environment. However, we still lack a comprehensive understanding of the dominant mechanisms that trigger the nucleus and the processes that drive the evolution of AGNs in clusters. Aims. To investigate (and possibly disentangle) the various factors that may affect the prevalence of AGNs in cluster galaxies, we selected a sample of 19 thoroughly studied X-ray-selected galaxy clusters from the LoCuSS survey. All these clusters are considered massive, with M500 ≳ 2 × 1014 M⊙, and span a narrow redshift range between z ∼ 0.16 and 0.28. Methods. We divided the cluster surroundings into two concentric annuli with a width of R500 radius. We considered the first annulus as the central cluster region and the second as the outskirts. We further divided the cluster sample based on the presence of infalling X-ray-detected groups, cluster mass, or dynamical state. We determined the AGN fraction in cluster galaxies of the various sub-samples by correlating the X-ray point-like sources selected from the 4XMM DR10 catalogue with the highly complete spectroscopic catalogue of cluster members obtained with Hectospec. We subsequently used the optical spectra to determine the type of nuclear activity and we visually inspected the host morphology for indications of galaxy mergers or other interactions. Results. We found that the X-ray AGN fraction in the outskirts is consistent with the field, but it is significantly lower in cluster centres, in agreement with previous results for massive clusters. We show that these results do not depend on cluster mass, at least within our cluster mass range, nor on the presence of X-ray-detected infalling groups. Furthermore, we did not find any evidence of a spatial correlation between infalling groups and AGNs. Nevertheless, a significant excess of X-ray AGNs is found in the outskirts of relaxed clusters at the 2σ confidence level, compared both to non-relaxed clusters and to the field. Finally, according to the literature, the fraction of broad- to narrow-line AGNs in clusters is roughly consistent with the field. However, broad-line AGNs may be preferably located in cluster centres. In the outskirts, the optical spectra of X-ray AGNs present narrow emission lines or they are dominated by stellar emission. Conclusions. Our results suggest that the mechanisms that trigger AGN activity may vary between cluster centres and the outskirts. Ram pressure can efficiently remove the gas from infalling galaxies, thereby triggering AGN activity in some cases. However, the reduced availability of gas globally diminishes the fraction of AGNs in cluster centers. The surplus of X-ray AGNs identified in the outskirts of relaxed clusters may be attributed to an increased frequency of galaxy mergers, a notion that is further supported by the disturbed morphology observed in several galaxies.

Analyzing 50 years of the Lacq induced seismicity (SouthWestern, France) highlights the role of fluid injection

Summary The Lacq area in southwest France has been associated with continuous moderate induced seismic activity since 1969. However, the mechanisms driving this induced seismicity are not fully understood: reservoir depletion has been proposed as the main factor, and more recently wastewater injection has been suggested to play a more important role (Grasso et al., 2021). The interpretation of these mechanisms relies heavily on the quality of earthquake locations, which we prove to be weak due to a lack of local instrumentation for several years. In order to provide the most complete and reliable induced event catalog for the studies of the Lacq induced seismicity mechanisms & seismic hazard, we made an exhaustive compilation, analysis and improvement of all available catalogs. We also provided new earthquake detections & relocations in a 3D velocity model from past and present temporary deployments never used for studying the Lacq area. Important remaining location uncertainties lead us to also carefully sort the events according to their location confidence, defining 3 classes of events (unconstrained location, location constrained within 2-3 km and 1-2 km respectively). This new harmonized catalog and the identification of well-constrained events, covering 50 years of induced seismicity, allow us to propose that wastewater injection is almost certainly the main mechanism driving the seismicity, with (i) most of the constrained events located within the reservoir boundaries and (ii) the released seismic energy variations following variations in injection operations at different scales. In particular, we have also highlighted a change in the injection-seismicity relationship around 2010–2013. From 2013, despite lower injection volumes, seismicity remained persistent and some clusters of earthquakes were detected predominantly in spring, summer, and early autumn, except in winter periods. From 2016, we observed a strong temporal relationship between days with higher rate/volume injections (approximately above 400m3/day) and both clustered events and higher magnitude earthquakes (greater than 2.4).

Cosmology and Astrophysics with Standard Sirens and Galaxy Catalogs in View of Future Gravitational Wave Observations

With the growing number of gravitational wave (GW) detections and the advent of large galaxy redshift surveys, a new era in cosmology is emerging. This study explores the synergies between GWs and galaxy surveys to jointly constrain cosmological and GW population parameters. We introduce CHIMERA, a novel code for GW cosmology combining information from the population properties of compact binary mergers and galaxy catalogs. We study constraints for scenarios representative of the LIGO-Virgo-KAGRA O4 and O5 observing runs, assuming to have a complete catalog of potential host galaxies with either spectroscopic or photometric redshift measurements. We find that a percent-level measurement of H 0 could be achieved with the best 100 binary black holes (BBHs) in O5 using a spectroscopic galaxy catalog. In this case, the intrinsic correlation that exists between H 0 and the BBH population mass scales is broken. Instead, by using a photometric catalog the accuracy is degraded up to a factor of ∼9, leaving a significant correlation between H 0 and the mass scales that must be carefully modeled to avoid bias. Interestingly, we find that using spectroscopic redshift measurements in the O4 configuration yields a better constraint on H 0 compared to the O5 configuration with photometric measurements. In view of the wealth of GW data that will be available in the future, we argue the importance of obtaining spectroscopic galaxy catalogs to maximize the scientific return of GW cosmology.

A first complete catalog of highly expressed genes in eight chicken tissues reveals uncharacterized gene families specific for the chicken testis.

Based on next-generation sequencing, we established a repertoire of differentially overexpressed genes (DoEGs) in eight adult chicken tissues: the testis, brain, lung, liver, kidney, muscle, heart, and intestine. With 4,499 DoEGs, the testis had the highest number and proportion of DoEGs compared with the seven somatic tissues. The testis DoEG set included the highest proportion of long noncoding RNAs (lncRNAs; 1,851, representing 32% of the lncRNA genes in the whole genome) and the highest proportion of protein-coding genes (2,648, representing 14.7% of the protein-coding genes in the whole genome). The main significantly enriched Gene Ontology terms related to the protein-coding genes were "reproductive process," "tubulin binding," and "microtubule cytoskeleton." Using real-time quantitative reverse transcription-polymerase chain reaction, we confirmed the overexpression of genes that encode proteins already described in chicken sperm [such as calcium binding tyrosine phosphorylation regulated (CABYR), spermatogenesis associated 18 (SPATA18), and CDK5 regulatory subunit associated protein (CDK5RAP2)] but whose testis origin had not been previously confirmed. Moreover, we demonstrated the overexpression of vertebrate orthologs of testis genes not yet described in the adult chicken testis [such as NIMA related kinase 2 (NEK2), adenylate kinase 7 (AK7), and CCNE2]. Using clustering according to primary sequence homology, we found that 1,737 of the 2,648 (67%) testis protein-coding genes were unique genes. This proportion was significantly higher than the somatic tissues except muscle. We clustered the other 911 testis protein-coding genes into 495 families, from which 47 had all paralogs overexpressed in the testis. Among these 47 testis-specific families, eight contained uncharacterized duplicated paralogs without orthologs in other metazoans except birds: these families are thus specific for chickens/birds.NEW & NOTEWORTHY Comparative next-generation sequencing analysis of eight chicken tissues showed that the testis has highest proportion of long noncoding RNA and protein-coding genes of the whole genome. We identified new genes in the chicken testis, including orthologs of known mammalian testicular genes. We also identified 47 gene families in which all the members were overexpressed, if not exclusive, in the testis. Eight families, organized in duplication clusters, were unknown, without orthologs in metazoans except birds, and are thus specific for chickens/birds.

The PAU Survey: a new constraint on galaxy formation models using the observed colour redshift relation

Abstract We use the GALFORM semi-analytical galaxy formation model implemented in the Planck Millennium N-body simulation to build a mock galaxy catalogue on an observer’s past lightcone. The mass resolution of this N-body simulation is almost an order of magnitude better than in previous simulations used for this purpose, allowing us to probe fainter galaxies and hence build a more complete mock catalogue at low redshifts. The high time cadence of the simulation outputs allows us to make improved calculations of galaxy properties and positions in the mock. We test the predictions of the mock against the Physics of the Accelerating Universe Survey, a narrow band imaging survey with highly accurate and precise photometric redshifts, which probes the galaxy population over a lookback time of 8 billion years. We compare the model against the observed number counts, redshift distribution and evolution of the observed colours and find good agreement; these statistics avoid the need for model-dependent processing of the observations. The model produces red and blue populations that have similar median colours to the observations. However, the bimodality of galaxy colours in the model is stronger than in the observations. This bimodality is reduced on including a simple model for errors in the GALFORM photometry. We examine how the model predictions for the observed galaxy colours change when perturbing key model parameters. This exercise shows that the median colours and relative abundance of red and blue galaxies provide constraints on the strength of the feedback driven by supernovae used in the model.

Мировые сейсмические сети и каталоги землетрясений

This paper is devoted to the review of currently functioning seismological agencies, seismic monitoring networks created, developed and supported by them, as well as earthquake catalogs produced. Particular attention is focused on international and national seismological centers and seismic networks. A historical insight about the first observations made by seismic networks completes the picture. The basic parameters of the main seismic networks and the principles of functioning for seismological centers are considered. The key characteristics of seismic catalogs that determine the criteria for their quality are discussed. The system-analytical approach to solving the urgent problem of creating the most complete and representative earthquake catalogs with a unified magnitude scale by integrating data from international, national and regional catalogs in the studied region is presented.

A Practical Approach to Automatic Earthquake Catalog Compilation in Local OBS Networks Using Deep-Learning and Network-Based Algorithms

Abstract In land-based seismology, modern automatic earthquake detection and phase picking algorithms have already proven to outperform classic approaches, resulting in more complete catalogs when only taking a fraction of the time needed for classic methods. For marine-based seismology, similar advances have not been made yet. For ocean-bottom seismometer (OBS) data, additional challenges arise, such as a lower signal-to-noise ratio and fewer labeled data sets available for training deep-learning models. However, the performance of available deep-learning models has not yet been extensively tested on marine-based data sets. Here, we apply three different modern event detection and phase picking approaches to an ∼12 month local OBS data set and compare the resulting earthquake catalogs and location results. In addition, we evaluate their performance by comparing different subcatalogs of manually detected events and visually revised picks to their automatic counterparts. The results show that seismicity patterns from automatically compiled catalogs are comparable to a manually revised catalog after applying strict location quality control criteria. However, the number of such well-constrained events varies between the approaches and catalog completeness cannot be reliably determined. We find that PhaseNet is more suitable for local OBS networks compared with EQTransformer and propose a pick-independent event detection approach, such as Lassie, as the preferred choice for an initial event catalog compilation. Depending on the aim of the study, different schemes of manual repicking should be applied because the automatic picks are not yet reliable enough for developing a velocity model or interpreting small-scale seismicity patterns.

Applying the Akaike Information Criterion (AIC) in earthquake spatial forecasting: a case study on probabilistic seismic hazard function (PSHF) estimation in the Sumatra subduction zone

This study uses complete earthquake catalog data and spatio-temporal analysis to construct a reliable model to forecast the potential seismogenic earthquake or earthquake fault zones. It integrates models developed based on different researchers’ methods and earthquake catalogs from different periods. It constructs and compares models - Model-1, Model-2, and Model-3 - from the complete shallow earthquake catalog between 1963-1999 and 1963-2006. The δAIC is used to evaluate the reliability of the models, with Model-3 emerging as the most reliable in all tests in this study. The model is constructed based on the product of the normalized model of the combined smooth seismicity model of a relatively small to moderate complete earthquake catalog data with a relatively uniform background model and weighted by the normalized seismic moment rate derived from the surface strain rate. It is suggested that a more extended observation period and using a complete, albeit relatively small-to-moderate, earthquake catalog leads to a more reliable and accurate model. Implementation of the Probabilistic Seismic Hazard Function (PSHF) window using the b-value of a 5-year window length with a 1-year sliding window prior to a significant seismic event proved successful, and the methodology demonstrates the importance of the temporal "b-value" in conjunction with the reliable seismicity rate and spatial probabilistic earthquake forecasting models in earthquake forecasting. The results showed large changes in the PSHF prior to giant and large earthquakes and the finding of a correlation between decreased b-value time window length and earthquake magnitude. The results have implications for the implementation of seismic mitigation measures.

The clustering of dark sirens' invisible host galaxies

Dark sirens are a powerful way to infer cosmological and astrophysical parameters from the combination of gravitational wave sirens and galaxy catalogues. Importantly, the method relies on the completeness of the galaxy catalogues being well modelled. A magnitude-limited catalogue will always be incomplete to some extent, requiring a completion scheme to avoid biasing the parameter inference. Standard methods include homogeneous and multiplicative completion, which have the advantage of simplicity but underestimate or overestimate the amplitude of structure at low completeness, respectively. In this work, we propose a new method to complete galaxy catalogues which uses clustering information to incorporate knowledge of the large scale structure into the dark sirens method. We find that if the structure of the true number of galaxies is sufficiently well preserved in the catalogue, our estimator can perform drastically better than both homogeneous and multiplicative completion. We lay the foundations for a maximally informative dark sirens analysis and discuss its limitations.

Perancangan Aplikasi Pemesanan Bahan Makanan Frozen Toko Makmur Jaya

In this digital era, online buying and selling transactions are increasingly popular with the public. This is also driven by increasing public awareness of the importance of convenience and efficiency in shopping. Toko Makmur Jaya, as a seller of frozen foodstuffs, has a great opportunity to develop in this digital era. By designing a special ordering application, Toko Makmur Jaya can reach customers more easily, increase sales and build customer loyalty. This research aims to design a frozen food ordering application for Toko Makmur Jaya that suits customer needs and desires. This research uses a qualitative research method with a case study approach. Research data was obtained through interviews with the owner of Toko Makmur Jaya and a survey of Toko Makmur Jaya customers. Based on the research results, the Toko Makmur Jaya frozen food ordering application needs to be equipped with features and functions which include: Complete and attractive product catalog, Easy to use and order, Various payments, Fast and reliable delivery, Attractive promotions and discounts Apart from these features and functions, the Toko Makmur Jaya frozen food ordering application also needs to be supported by an efficient and reliable logistics system to maintain the quality of frozen products. The success of the Toko Makmur Jaya application is not only determined by features and functions, but also several other important factors, such as branding and marketing, customer service, and continuous analysis and development..

A Systematic Review of Stemmers of Indian and Non-Indian Vernacular Languages

The stemming process is crucial and significant in the pre-processing step of natural language processing. The stemmer oversees the stemming process. It facilitates the extraction of morphological variants of a root or base word from the provided word. Over the period, several stemmers for various vernacular languages have been proposed. However, very few research studies have comprehensively investigated these available stemmers. This article makes multifold contributions. First, we discuss the various stemmers of 15 Indian and 17 non-Indian languages describing their key points, benefits, and drawbacks. All the Indian languages for which stemmers have been built are covered in this study. For the non-Indian languages, stemmers of commonly spoken languages have been covered. Second, we present a language-wise comparative analysis of stemmers based on our identified parameters. Third, we discuss the wordnets and dictionaries available for different languages. Fourth, we provide details of the datasets available for various languages. Fifth, we also provide challenges in existing stemmers and future directions for future researchers. The study presented in this article reveals that significant research has been carried out for the stemmers of influential languages such as English, Arabic, and Urdu. On the other hand, languages with d resources, such as Farsi, Polish, Odia, Amharic, and others, have received the least attention for research. Moreover, rigorous analysis reveals that most of the stemmers suffer from over-stemming errors. With a complete catalogue of available stemmers, this study aims at assisting the researchers and professionals working in the areas such as information retrieval, semantic annotation, word meaning disambiguation, and ontology learning.

LQAC-6: Sixth Release of the Large Quasar Astrometric Catalogue

Context. In addition to being objects of intense interest for cosmology and studies of the evolution of the universe, quasars are used to define quasi-inertial positions on the celestial sphere. Since its first publication in 2009, the purpose of the Large Quasar Astrometric Catalogue (LQAC) has been to provide the largest catalogue of bona fide quasars suitable for astrometry, with the high-precision positions from Gaia becoming available in the fourth release (LQAC-4). Aims Following the same kind of procedure as in the previous releases of the LQAC, our aim is to compile the maximum number of recorded quasars, with optimised equatorial coordinates and fundamental information about their physical properties such as the redshift, the photometry, radio fluxes, morphological index. Methods New quasars from the SDSS DR16Q release were cross-matched with the precedent LQAC-5 compilation with a 1" radius, which leads to 225 082 objects not present in the previous LQAC-5 release. Another cross-match was done with the Gaia Celestial Reference Frame 3 (GCRF3) catalogue, which is itself a compilation of a large number of quasars catalogues, accompanied with very accurate Gaia DR3 positions. Moreover, AGN's coming from 19 individual extragalactic surveys not considered in the previous LQAC compilations are added Results This new LQAC-6 release contains 2 073 099 objects, which is 3.5 times the number of objects recorded in the previous LQAC-5 release. Among them, 1 739 187 objects were found in common with the Gaia DR3, within a 1" search radius. A large part of new objects belong to the GCRF3 catalogue, which gathers a total number of 1 614 218 objects Conclusion The LQAC-6 delivers a nearly complete catalogue of quasars and AGN's to the astronomical community, with the aim of giving their best equatorial coordinates with respect to the recent ICRF3 and with exhaustive additional information. For as much as $83.9 <!PCT!>$ of the sample, these coordinates are extracted from the very recent Gaia DR3.

Compilation of a Comprehensive Earthquake Catalog and Relocations in the Caucasus Region

Abstract Instrumental seismic monitoring has a long history in the Caucasus and started in 1899 when the first seismograph was installed in Tbilisi, Georgia. Much of the analog paper records from this time period are preserved in the Tbilisi archives because Georgia served as the regional data center. In the 1990s, due to the collapse of the Soviet Union and the political turmoil in the region, the analog networks and the communication between the newly formed national networks deteriorated. In Georgia, for the next 13 yr, the seismic network coverage was poor until the 2002 Tbilisi earthquake. Following this earthquake, the first permanent digital seismic station in Georgia was established in Tbilisi in 2003. The digital era progressively improved the ability to collect and archive data and today more than a hundred broadband seismic stations (including temporary arrays) are operating in the southern Caucasus. Until recently, the region lacked a coordinated effort to catalog all analog and digital era data collected by different countries into a single repository. As a result of collaboration between Lawrence Livermore National Laboratory, the Ilia State University, and the Republican Seismic Survey Center of Azerbaijan, a comprehensive earthquake catalog was compiled for the Caucasus and neighboring areas as part of a broader probabilistic seismic hazard assessment project. This project digitized Soviet-era paper bulletins, compiled a unified earthquake catalog from regional bulletins, developed 1D reference velocity model, and used it to relocate the events. The final catalog contains 16,963 events with magnitudes 3.7 and above, bringing together all the available data sets in the Caucasus region from 1900 to 2015, significantly improving locations, and generating the most complete earthquake catalog in the region, temporally and geographically.

Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology.

The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues. A total of 160,820 unique transcripts (50% protein coding) representing 34,882 unique genes (60% protein coding) were identified across tissues. Among them, 118,563 transcripts (73% of the total) were structurally validated by independent datasets (PacBio isoform sequencing data, Oxford Nanopore Technologies sequencing data, de novo assembled transcripts from RNA sequencing data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as whole transcriptome termini site sequencing, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing. A large proportion of identified transcripts (69%) were unannotated, of which 86% were produced by annotated genes and 14% by unannotated genes. A median of two 5' untranslated regions were expressed per gene. Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as noncoding genes in fetal tissues but as protein-coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 annotated gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available quantitative trait loci data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network. These validated results show significant improvement over current bovine genome annotations.

Detection of microseismic events in continuous DAS data using convolutional neural networks

Detection and localization of microseismicity is an inevitable task in monitoring fluid injections into subsurface rocks during hydraulic stimulations. Traditionally, downhole geophones placed into boreholes or large surface geophone networks have been used for this, but in recent years, the use of distributed acoustic sensing (DAS) via fiber-optic cables placed into boreholes has become a common technique. However, DAS registrations still have lower signal-to-noise ratios than geophones; i.e., they cannot detect small-magnitude events. In this work, we develop and train a convolutional neural network capable of detecting microseismic events in continuous DAS recordings incorporating arrival-time information from geophones. The network is trained on DAS and geophone data from the Utah FORGE enhanced geothermal system project for which we are able to significantly shift the detection threshold toward smaller magnitude events. Although the number of microseismic events (approximately 150) used for training is small, the tested network performance is high and provides a complete event catalog down to magnitude MW = −1.6, a notable improvement over previous studies. Using a short recording period of several hours for training, such a network might be used for long-term, real-time monitoring of geothermal sites. Although the network is explicitly trained for the geometry of the data set used, the philosophy and network architecture can be adapted for similar case studies where long-term seismic monitoring is required (e.g., CO2 sequestration).

Integrated Earthquake Catalog of the Ossetian Sector of the Greater Caucasus

This article is the continuation of a study by authors to create the most complete and representative earthquake catalogs with a unified magnitude scale. The catalog created of the Ossetian sector of the Greater Caucasus (the territory of the Republic of North Ossetia–Alania and adjacent areas) was formed by the aggregation of all available data from Soviet, modern Russian, and Georgian catalogs, as well as the data from the International Seismological Centre. The integration was carried out using the author’s approach based on the modified nearest neighbor method. The integrated catalog of the Ossetian sector of the Greater Caucasus contains 16,285 events for the period 1962–2022. For all events, magnitude estimates are reduced to a unified “proxy-MW” scale. The integration of data from various sources made it possible to significantly replenish the beginning of the aftershock sequence of the Racha earthquake with MW = 7.0, which occurred on 29 April 1991. There has been a change in the level of registration over time. Thus, there is a significant lack of events for the periods 1967–1970 and 1988–1991; starting from 1995, the catalog is complete for magnitude 3.2, and since 2005 for magnitude 2.2. The integration of Soviet and modern Russian and Georgian catalogs made it possible to significantly increase the completeness and representativeness of seismic events in the studied Ossetian sector of the Greater Caucasus. This once again demonstrates both the fundamental importance of merging seismic data from global, national, and regional catalogs and the effectiveness of the author’s developed method.

Role of the first WHO mutation catalogue in the diagnosis of antibiotic resistance in Mycobacterium tuberculosis in the Valencia Region, Spain: a retrospective genomic analysis

In June, 2021, WHO published the most complete catalogue to date of resistance-conferring mutations in Mycobacterium tuberculosis. Here, we aimed to assess the performance of genome-based antimicrobial resistance prediction using the catalogue and its potential for improving diagnostics in a real low-burden setting. In this retrospective population-based genomic study M tuberculosis isolates were collected from 25 clinical laboratories in the low-burden setting of the Valencia Region, Spain. Culture-positive tuberculosis cases reported by regional public health authorities between Jan 1, 2014, and Dec 31, 2016, were included. The drug resistance profiles of these isolates were predicted by the genomic identification, via whole-genome sequencing (WGS), of the high-confidence resistance-causing variants included in the catalogue and compared with the phenotype. We determined the minimum inhibitory concentration (MIC) of the isolates with discordant resistance profiles using the resazurin microtitre assay. WGS was performed on 785 M tuberculosis complex culture-positive isolates, and the WGS resistance prediction sensitivities were: 85·4% (95% CI 70·8-94·4) for isoniazid, 73·3% (44·9-92·2) for rifampicin, 50·0% (21·1-78·9) for ethambutol, and 57·1% (34·0-78·2) for pyrazinamide; all specificities were more than 99·6%. Sensitivity values were lower than previously reported, but the overall pan-susceptibility accuracy was 96·4%. Genotypic analysis revealed that four phenotypically susceptible isolates carried mutations (rpoB Leu430Pro and rpoB Ile491Phe for rifampicin and fabG1 Leu203Leu for isoniazid) known to give borderline resistance in standard phenotypic tests. Additionally, we identified three putative resistance-associated mutations (inhA Ser94Ala, katG Leu48Pro, and katG Gly273Arg for isoniazid) in samples with substantially higher MICs than those of susceptible isolates. Combining both genomic and phenotypic data, in accordance with the WHO diagnostic guidelines, we could detect two new multidrug-resistant cases. Additionally, we detected 11 (1·6%) of 706 isolates to be monoresistant to fluoroquinolone, which had been previously undetected. We showed that the WHO catalogue enables the detection of resistant cases missed in phenotypic testing in a low-burden region, thus allowing for better patient-tailored treatment. We also identified mutations not included in the catalogue, relevant at the local level. Evidence from this study, together with future updates of the catalogue, will probably lead in the future to the partial replacement of culture testing with WGS-based drug susceptibility testing in our setting. European Research Council and the Spanish Ministerio de Ciencia.

Unsupervised Machine Learning Identify Cis‐Regulatory Network Involved in Neurodegeneration

AbstractBackgroundCis‐Regulatory Modules (CRMs) are crucial to ensure the precise spatiotemporal gene expression, but we still lack a complete catalog of mammalian CRMs.MethodsWe developed the Mammalian Regulatory Module Detector (MrMOD), that accurately predicts a comprehensive set of high‐resolution CRMs in mouse and human genomes including enhancers, promoters, silencers, locus control regions, and microRNA regulatory modules not limited to any tissue, cell type, developmental stage, or stimuli. We validated our predictions using 19 orthogonal experimental data sets, including thousands of experimental defined CRMs and millions of putative regulatory elements from multiple databases. Next, we used an unsupervised machine learning method to annotate CRM functions. We scanned the mouse genome for transcription factor binding sites (TFBS) using position weight matrices of known transcription factors (TF) from the CIS‐BP database and obtained TFBS abundance in each CRM for every TF. Unsupervised clustering was performed using Seurat on CRMs from chromosome 17. Each CRM cluster represents a set of CRMs with similar TFBS compositions. Cluster marker genes represent TFs whose binding sites are enriched in the CRM cluster. Genes associated with the CRMs in the cluster represent the putative target genes. Functional enrichment analyses of the TFs and CRM associated genes were performed using ClusterProfiler and disgenet2r.ResultsSeurat identified a total of 43 clusters. In particular, CRM cluster #17 is linked to neurodegeneration based on five supporting evidence: 1) TF marker genes of cluster #17 include TFs known to be involved in neurodegeneration such as Spi1, Yy1, Nr4a2, Nr4a3, and Tfeb. 2) TF marker genes of cluster #17 were significantly enriched for Alzheimer’s Disease, Parkinson’s Disease, Multiple Sclerosis, among others. 3) Genes associated with cluster #17 CRMs were significantly enriched for neurodegeneration: Multiple Sclerosis and neurodegenerative disorders. Gene Ontology Cellular Components terms significantly enriched for synapse, presynapse, axon, and synaptic membrane. 4) Genes associated with cluster #17 CRMs significantly overlap the known TF target genes in the ChIP‐Atlas database defined by human ChIP‐seq experiments. 5) Top TF marker genes of cluster #17 known to activate transcription in neurons cooperatively.ConclusionsWe developed a novel approach to elucidate mechanisms involved in neurodegeneration.

Assessment of the large-scale extraction of photovoltaic (PV) panels with a workflow based on artificial neural networks and algorithmic postprocessing of vectorization results

Having a complete and high-quality geospatial catalogue of existing large-scale photovoltaic (PV) panels is very important nowadays, due to the rapid increase in the use of this type of installations. This catalogue could be used to estimate, with a higher level of granularity, the energy that can be produced from solar radiation forecasts, to operate the electricity system efficiently by adjusting supply to demand, as well as for fiscal reasons. However, most existing works in the specialized literature focus on the extraction of PV panels in reduced, favourable scenes. In this study, a processing strategy to obtain PV panel arrays geometries from aerial orthoimages at a very large scale, is proposed. The processing strategy includes operations for PV panel array classification and semantic extraction, and algorithmic improvement and simplification of the vectorization results. The processing workflow was trained and tested on two datasets containing aerial images of 256 × 256 pixels with the studied polygonal feature at two different spatial resolutions (with more than 185,000 and 690,000 images for spatial resolutions of 0.5 m and 0.25 m, respectively). The image tiles were labelled at pixel level with PV panel information for both spatial resolutions and cover representative, extended urban and rural regions of Spain. The accuracies achieved in the PV panel arrays classification are superior to 0.999, while the semantic segmentation performance is superior to 0.90 in the Intersection over Union score. The assessment of the proposed procedure of fifteen new, unseen areas distributed over the Spanish territory (covering approximately 8125 km2) demonstrated its suitability (in the analysis, percentage of incompletely detected installations of only 11 % were achieved) and indicated that future works focused on the improvement of the initial predictions are should be carried out.