Full Diversity Research Articles

Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses.

Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the USA. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the USA clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

Using Paleoclimate Analogues to Inform Climate Projections

Abstract Philosophers of science have paid close attention to climate simulations as means of projecting the severity and effects of climate change, but have neglected the full diversity of methods in climate science. This paper shows the philosophical richness of another method in climate science: the practice of using paleoclimate analogues to inform our climate projections. First, I argue that the use of paleoclimate analogues can offer important insights to philosophers of the historical sciences. Rather than using the present as a guide to the past, as is common in the historical sciences, paleoclimate analogues involve using the past as a guide to the future. I thereby distinguish different methods in the historical sciences and argue that these distinctions bear on debates over whether the historical sciences can produce generalizations or predictions. Second, I suggest that paleoclimate analogues might actually be considered a type of climate model, and, as such, their use expands on common characterizations of models to include those that are full-scale, naturally occurring, and non-manipulable.

Numerical simulation investigating the impact of regulated underflow rate on the performance of a cyclone with split flow

A novel cyclone design called enhanced cyclone with split flow (ECSF) incorporates bypass flow and underflow to eliminate or suppress localized secondary flow observed in conventional cyclones. The present study aims to investigate the mechanism of ECSF in suppressing localized secondary flow and explore methods for regulating the bottom flow rate. The turbulent characteristics within the ECSF are obtained using Reynolds stress model, while the trajectory of particles is predicted using discrete phase model to derive the separation performance. The accuracy of the simulation model has been validated through experimental verification. The results demonstrated that the full separation efficiency of ECSF for PM10 and PM2.5 remained above 90 % and 70 %, respectively. Moreover, it exhibited an increasing trend with the rise in the full split ratio, eventually stabilizing at approximately 95 % and 77 %, correspondingly, when the full split ratio reached 20 %. The bypass flow and underflow effectively eliminated or suppressed the upper ash ring and processing vortex core (PVC) phenomenon, respectively. However, the exacerbation of the short-circuit flow phenomenon hindered further improvement in separation efficiency beyond a full diversion ratio of 20 %. When the full split ratio is relatively small, particles may accumulate in the discharge pipe, which can be resolved by introducing auxiliary airflow; however, it is crucial to ensure that the flow rate of auxiliary flow does not exceed 14.29 % of that of feed flow to avoid compromising the separation efficiency. Furthermore, the split flow induces an additional reversed vortex within the ECSF, which extends from the overflow pipe to conical section. Its structural characteristics are influenced by both back pressure of discharge outlet and diameter of underflow pipe. To ensure optimal performance of the ECSF, it is recommended that the underflow pipe diameter should not be smaller than that of the outlet in conical section.

Brexit: Trade Diversion due to Trade Policy Uncertainty

AbstractThe paper quantifies how much of the reduction in Spanish trade flows with the UK after the 2016 Brexit referendum was diverted to other markets. To obtain reliable estimates of trade diversion we regress firm‐level changes in flows with all markets except the UK on changes in flows with the UK. In order to solve the positive correlation of trade flows between different markets we use the Brexit referendum as part of our instrumental variable. We then treat firms as units subjected to differential uncertainty shocks according to their initial patterns of sector and trade specialization. In particular, the referendum date is interacted with potential sectoral tariffs and pre‐referendum firm‐level exposure to the UK. The paper shows a close to full trade diversion for exports, mostly to other European countries, for those firms more exposed to that particular market (above 10%) and a heterogeneous response on the part of Spanish firms with low exposure (below 10%). Trade diversion for imports is weaker but the results are less robust. Given a particular share of exposure to the UK market, trade diversion appears to be more limited for big companies in comparison to small companies.

Molecular Evidence for Relaxed Selection on the Enamel Genes of Toothed Whales (Odontoceti) with Degenerative Enamel Phenotypes.

Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., Hyperoodon, Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman's rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development.

A novel iterative detection method based on a lattice reduction-aided algorithm for MIMO OFDM systems

The lattice reduction-aided algorithm has received broad attention from researchers since it operates as a maximum likelihood receiver with better system performance for multiple-input multiple-output orthogonal frequency division multiplexing systems and contains a full diversity. A novel iterative detection algorithm canceling parallel iterations that employ the lattice reduction-aided approach is proposed. Soft information is exchanged through the detector itself. Its iteration occurs inside the detector, which reduces much of the exchange cost between the multiple-input multiple-output orthogonal frequency division multiplexing detector and the turbo decoder. Since the parallel interference cancellation algorithm is constrained by the accuracy of the initial value of the detection, it is easy to form error propagation after several iterations. Due to the lattice reduction-aided algorithm, its performance is approximated with the maximum likelihood algorithm. Therefore, the lattice reduction-aided algorithm is introduced into the parallel interference cancellation algorithm to make its detection algorithm more accurate and overcome the effect of error propagation in the manuscript. Simulation results indicate that the proposed algorithm leads to an improvement of 0.8–2 dB when the bit error rate is set to 10–4 when compared to other algorithms.

Transcription-replication interactions reveal bacterial genome regulation.

Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome1. In bacteria, the relationship between the regulatory architecture of a gene and its expression is well understood for individual model gene circuits2,3. However, a broader perspective of these dynamics at the genome scale is lacking, in part because bacterial transcriptomics has hitherto captured only a static snapshot of expression averaged across millions of cells4. As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on the transcriptional response of each gene to its own replication, which we term the transcription-replication interaction profile (TRIP). Analysing single-bacterium RNA-sequencing data, we found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal the local regulatory contextof a gene. Whereas the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, and this is shaped by factors such as intra-operon position and repression state. By revealing the underlying mechanistic drivers of gene expression heterogeneity, this work provides a quantitative, biophysical framework for modelling replication-dependent expression dynamics.

Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers

DNA metabarcoding has been performed on a large number of river phytobenthos samples collected from the UK, using rbcL primers optimised for diatoms. Within this dataset the composition of non-diatom sequence reads was studied and the effect of including these in models for evaluating the nutrient gradient was assessed. Whilst many non-diatom taxonomic groups were detected, few contained the full diversity expected in riverine environments. This may be due to the performance of the current primers in characterising the wider phytobenthic community and influenced by the sampling method employed, as both were developed specifically for diatoms. Nevertheless, the study identified considerable diversity in some groups, e.g. Eustigmatophyceae and a wider distribution than previously thought for freshwater Phaeophyceae. These results offer a strong case for the benefits of metabarcoding for expanding knowledge of aquatic biodiversity in the UK and elsewhere.Many of the ASVs associated with non-diatoms showed significant pressure responses; however, models that included non-diatoms had similar predictive strength to those based on diatoms alone. Whilst limitations of the primers for assessing non-diatoms may play a role in explaining these results, the diatoms provide a strong signal along the nutrient gradient and other algae, therefore, add little unique information.We recommend that future developments should use ASVs to calculate metrics, with links to reference databases made as a final step to generate lists of taxa to support interpretation. Any further exploration of the potential of non-diatoms would benefit from access to a well-curated reference database, similar to diat.barcode. Such a database does not yet exist, and we caution against the indiscriminate use of NCBI GenBank as a taxonomic resource as many rbcL sequences deposited have not been curated.

UNRAVELLING THE EVOLUTIONARY TRAJECTORY OF EPIC HEROES: A THEORETICAL EXPLORATION

The scholarly investigation of epic heroes encompasses a complex and multifaceted realm, engaging researchers in grappling with the intricate task of defining and categorising these figures, while also endeavouring to comprehend their evolutionary trajectory. Academic discourse on epic heroes has yielded two distinctive approaches. The first group, denoted as the “ubiquitous fallacy group” within this article, employs anthropological, psychoanalytical, historical, and literary perspectives to argue for the temporal and spatial ubiquity of epic heroes at their core, accentuating shared patterns and recurring themes. This article provides a thorough critique of the first group, highlighting the inherent methodological and contextual problems in their analytical frameworks, and revealing their limitations, particularly in terms of selective data and potential oversimplification of complex phenomena. The second group, while acknowledging some generic influences over time, emphasises the impossibility of ascribing a single, stable, or universal form to the concept of epic hero. Although leaning towards favouring the latter approach, this article aims to identify the problems inherent in this group as well. This approach’s categorisation of epic heroes, creating heroic models or types to differentiate heroes, is also problematic, given the fluid boundaries between these categories and the potential inadequacy of models in capturing the full complexity and diversity of epic heroism they represent. This article further delves into two distinct analytical frameworks in this group, Doris Cecilia Werner’s socio-political reading and John Steadman’s “image and ideal” hypothesis, offering potential solutions to address gaps in their theoretical approaches. Accordingly, this article, while presenting fresh criticism on the theories of the evolution of epic heroes, argues that the ever-changing nature of epic heroes defies a uniform ubiquitous definition or categorizations, and offers solutions to fill the gaps in the latest scholarly analytical frameworks.

“Excluded from Memory”: The Question of Passing Down National History

This article considers the (partial) “exclusion” or “self-exclusion” of the “complex heritage” descendants from the “inheritance” of the official narratives of national history. As a rule, such discourses rely on antagonistic logic. In the article, the idea of “complex heritage” descendants denotes people whose family history includes both representatives of mutually exclusive groups (from the point of view of different public discourses of memory). When any single discourse is dominant in the public space or in a competition between antagonistic discourses of national history, descendants of “complex heritage” must independently cope with the emerging internal tension and discomfort (if they arise). In this article, in the context of common European trends, the author shows and analyses different options for such reactions with reference to competing discourses of national history in Russia, i. e., “Triumph” (Victory in the Great Patriotic War) and “Tragedy” (the era of political repression), as well as the most massive public practice of memory dedicated to the Great Patriotic War heroes: the civil event known as the “Immortal Regiment”. The analysis refers to forty indepth interviews conducted by the author in 2021–2023 with descendants of the repressed from the third, fourth, and further generations (as well as those who fought and showed themselves differently in the past). The author relies on the concept of antagonistic memory, supplemented by the ideas of Ts. Todorov on the principles of working with the “difficult past”, the theory of post-memory by M. Hirsch and others. As a result of the research, the author draws the following conclusions: first, the experience of “exclusion” from national history due to the lack of blood ancestors that give the right for “inclusion” into the “fundamental myth of the nation” really exists; second, in the conditions of (even unequal) competition of antagonistic discourses, the descendants of the “complex heritage” find themselves constrained between the narrow limits of each of them. At the same time, the need to meet externally set criteria and the impossibility of doing this lead to resistance to the imposed public antagonistic models of understanding the past; finally, those “excluded” from national history in one or different interpretations thereof, the descendants collect, preserve, and transmit their family histories as “heritage” in the full diversity and inconsistency, as life itself, and the circumstances in which their ancestors were placed.

Automatic annotation of the bHLH gene family in plants

BackgroundThe bHLH transcription factor family is named after the basic helix-loop-helix (bHLH) domain that is a characteristic element of their members. Understanding the function and characteristics of this family is important for the examination of a wide range of functions. As the availability of genome sequences and transcriptome assemblies has increased significantly, the need for automated solutions that provide reliable functional annotations is emphasised.ResultsA phylogenetic approach was adapted for the automatic identification and functional annotation of the bHLH transcription factor family. The bHLH_annotator, designed for the automated functional annotation of bHLHs, was implemented in Python3. Sequences of bHLHs described in literature were collected to represent the full diversity of bHLH sequences. Previously described orthologs form the basis for the functional annotation assignment to candidates which are also screened for bHLH-specific motifs. The pipeline was successfully deployed on the two Arabidopsis thaliana accessions Col-0 and Nd-1, the monocot species Dioscorea dumetorum, and a transcriptome assembly of Croton tiglium. Depending on the applied search parameters for the initial candidates in the pipeline, species-specific candidates or members of the bHLH family which experienced domain loss can be identified.ConclusionsThe bHLH_annotator allows a detailed and systematic investigation of the bHLH family in land plant species and classifies candidates based on bHLH-specific characteristics, which distinguishes the pipeline from other established functional annotation tools. This provides the basis for the functional annotation of the bHLH family in land plants and the systematic examination of a wide range of functions regulated by this transcription factor family.

Translating single-neuron axonal reconstructions into meso-scale connectivity statistics in the mouse somatosensory thalamus.

Characterizing the connectomic and morphological diversity of thalamic neurons is key for better understanding how the thalamus relays sensory inputs to the cortex. The recent public release of complete single-neuron morphological reconstructions enables the analysis of previously inaccessible connectivity patterns from individual neurons. Here we focus on the Ventral Posteromedial (VPM) nucleus and characterize the full diversity of 257 VPM neurons, obtained by combining data from the MouseLight and Braintell projects. Neurons were clustered according to their most dominantly targeted cortical area and further subdivided by their jointly targeted areas. We obtained a 2D embedding of morphological diversity using the dissimilarity between all pairs of axonal trees. The curved shape of the embedding allowed us to characterize neurons by a 1-dimensional coordinate. The coordinate values were aligned both with the progression of soma position along the dorsal-ventral and lateral-medial axes and with that of axonal terminals along the posterior-anterior and medial-lateral axes, as well as with an increase in the number of branching points, distance from soma and branching width. Taken together, we have developed a novel workflow for linking three challenging aspects of connectomics, namely the topography, higher order connectivity patterns and morphological diversity, with VPM as a test-case. The workflow is linked to a unified access portal that contains the morphologies and integrated with 2D cortical flatmap and subcortical visualization tools. The workflow and resulting processed data have been made available in Python, and can thus be used for modeling and experimentally validating new hypotheses on thalamocortical connectivity.

Islamic ADR in Britain: Diversity, Hybridity, and Women’s Experiences of Community Justice

Abstract Key developments in recent decades have contributed to Islamic community justice mechanisms in Britain becoming highly politicized, with a disproportionate focus on Sharia councils. The Sharia council phenomenon, however, does not encompass the full diversity of Islamic Alternative Dispute Resolution (ADR) in Britain. This article starts by providing a more comprehensive outlook on Sharia-based ADR mechanisms in Britain by exploring a variety of forums and actors involved in this line of work, including individual imams and Sheikhs, established and lesser-known Sharia councils, and other forums engaged in religious mediation and arbitration. Based on new empirical research conducted with women users and service providers, the article goes on to reflect on ADR processes of mediation and arbitration and reveals that religious actors frequently move back and forth between counselling, negotiating, mediating, and arbitrating within one case and one setting. Finally, the article explores women’s experiences and narratives about faith-based community justice, reflecting particularly on divorce cases which involve domestic violence. Insights into how such cases have been handled by community mechanisms are provided, highlighting where the latter are falling short and identifying avenues for going forward with setting appropriate procedures and responses to protect the welfare of Muslim women.

A generalized semi-analytic model for magnetar-driven supernovae

ABSTRACT Several types of energetic supernovae, such as superluminous supernovae (SLSNe) and broad-line Ic supernovae (Ic-BL SNe), could be powered by the spin-down of a rapidly rotating magnetar. Currently, most models used to infer the parameters for potential magnetar-driven supernovae make several unsuitable assumptions that likely bias the estimated parameters. In this work, we present a new model for magnetar-driven supernovae that relaxes several of these assumptions and an inference workflow that enables accurate estimation of parameters from light curves of magnetar-driven supernovae. In particular, in this model, we include the dynamical evolution of the ejecta, coupling it to the energy injected by the magnetar itself while also allowing for non-dipole spin down. We show that the model can reproduce SLSN and Ic-BL SN light curves consistent with the parameter space from computationally expensive numerical simulations. We also show the results of parameter inference on four well-known example supernovae, demonstrating the model’s effectiveness at capturing the considerable diversity in magnetar-driven supernova light curves. The model fits each light curve well and recovers parameters broadly consistent with previous works. This model will allow us to explore the full diversity of magnetar-driven supernovae under one theoretical framework, more accurately characterize these supernovae from only photometric data, and make more accurate predictions of future multiwavelength emission to test the magnetar-driven scenario better.

Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States.

Multivalent binding of CTCF to variable DNA sequences is thought to underlie its ability to mediate diverse cellular functions. CTCF typically binds a 20 base-pair consensus DNA sequence, but the full diversity of CTCF binding sites (CBS) within the genome has not been interrogated. We assessed CTCF occupancy in cultured cortical neurons and observed surprisingly that ~ 22% of CBS lack the consensus CTCF motif. We report here that sequence diversity at most of these atypical CBS involves degeneracy at specific nucleotide positions within the consensus CTCF motif, which likely affect the binding of CTCF zinc fingers 6 and 7. This mode of atypical CTCF binding defines most CBS at gene promoters, as well as CBS that are dynamically altered during neural differentiation and following neuronal stimulation, revealing how atypical CTCF binding could influence gene activity. Dynamic CBS are distributed both within and outside loop anchors and TAD boundaries, suggesting both looping-dependent and independent roles for CTCF. Finally, we describe a second mode of atypical CTCF binding to DNA sequences that are completely unrelated to the consensus CTCF motif, which are enriched within the bodies of tissue-specific genes. These tissue-specific atypical CBS are also enriched in H3K27ac, which marks cis-regulatory elements within chromatin, including enhancers. Overall, these results indicate how atypical CBS could dynamically regulate gene activity patterns during differentiation, development, and in response to environmental cues.

Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages.

The repeated emergence of multi-drug-resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug-resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. Given the rapid colonization observed in travel studies, it is possible that the presence of a type VI secretion system (T6SS) may be responsible for the rapid competitive advantage of drug-resistant E. coli clones. We employed large-scale genomic approaches to investigate this hypothesis. First, we searched for T6SS genes across a curated dataset of over 20 000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene carriage and MDR lineages. However, multiple clades containing MDR clones have lost essential structural T6SS genes. We characterized the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones.

A Path Forward: Creating an Academic Culture of Justice, Equity, Diversity, and Inclusion

AbstractInstitutions of higher education (IHE) throughout the United States have a long history of acting out various levels of commitment to diversity advancement, equity, and inclusion (DEI). Despite decades of DEI “efforts,” the academy is fraught with legacies of racism that uphold white supremacy and prevent marginalized populations from full participation. Furthermore, politicians have not only weaponized education but passed legislation to actively ban DEI programs and censor general education curricula (https://tinyurl.com/antiDEI). Ironically, systems of oppression are particularly apparent in the fields of Ecology, Evolution, and Conservation Biology (EECB), which recognize biological diversity as essential for ecological integrity and resilience. Yet, among EECB faculty, people who do not identify as cis‐heterosexual, nondisabled, affluent white males are poorly represented. Furthermore, IHE lacks metrics to quantify DEI as a priority. Here we show that only 30.3% of United States faculty positions advertised in EECB from Jan 2019 to May 2020 required a diversity statement; diversity statement requirements did not correspond with state‐level diversity metrics. Though many announcements “encourage women and minorities to apply,” empirical evidence demonstrates that hiring committees at most institutions did not prioritize an applicant's DEI advancement potential. We suggest a model for change and call on administrators and faculty to implement SMART (i.e., Specific, Measurable, Achievable, Realistic, and Timely) strategies for DEI advancement across IHE throughout the United States. We anticipate our quantification of diversity statement requirements relative to other application materials will motivate institutional change in both policy and practice when evaluating a candidate's potential “fit.” IHE must embrace a leadership role to not only shift the academic culture to one that upholds DEI but to educate and include people who represent the full diversity of our society. In the current context of political censure of education including book banning and backlash aimed at Critical Race Theory, which further reinforce systemic white supremacy, academic integrity and justice are more critical than ever.

Quasar Factor Analysis—An Unsupervised and Probabilistic Quasar Continuum Prediction Algorithm with Latent Factor Analysis

Since their first discovery, quasars have been essential probes of the distant Universe. However, due to our limited knowledge of its nature, predicting the intrinsic quasar continua has bottlenecked their usage. Existing methods of quasar continuum recovery often rely on a limited number of high-quality quasar spectra, which might not capture the full diversity of the quasar population. In this study, we propose an unsupervised probabilistic model, quasar factor analysis (QFA), which combines factor analysis with physical priors of the intergalactic medium to overcome these limitations. QFA captures the posterior distribution of quasar continua through generatively modeling quasar spectra. We demonstrate that QFA can achieve the state-of-the-art performance, ∼2% relative error, for continuum prediction in the Lyα forest region compared to previous methods. We further fit 90,678 2 < z < 3.5, signal-to-noise ratio >2 quasar spectra from Sloan Digital Sky Survey Data Release 16 and found that for ∼30% quasar spectra where the continua were ill-determined with previous methods, QFA yields visually more plausible continua. QFA also attains ≲1% error in the 1D Lyα power spectrum measurements at z ∼ 3 and ∼4% in z ∼ 2.4. In addition, QFA determines latent factors representing more physical motivation than principal component analysis. We investigate the evolution of the latent factors and report no significant redshift or luminosity dependency except for the Baldwin effect. The generative nature of QFA also enables outlier detection robustly; we showed that QFA is effective in selecting outlying quasar spectra, including damped Lyα systems and potential Type II quasar spectra.

Exploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution

Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, had its genome sequenced to study the biosynthetic potential to produce novel natural products within the Brevibacterium genus. The genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. Evaluating the antibacterial activity of strain H-BE7, it exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7’s genome.

Differential beamforming using Rotman lens for wireless sensor networks

In this article, an optimal beamforming technique using a low cost intelligent Rotman lens antenna is proposed. The proposed technique enjoys full diversity with high coding gain, has a very low encoding and decoding complexity, and does not require channel knowledge at any transmitting or receiving antenna. From our simulation results, the proposed technique outperforms the best known non-coherent multi-antenna techniques. Furthermore, we prove that the BER expressions obtained from the theoretical analysis enjoy full diversity gain and match our conducted simulations.