Divergence Values Research Articles

Beyond Preferences in AI Alignment

AbstractThe dominant practice of AI alignment assumes (1) that preferences are an adequate representation of human values, (2) that human rationality can be understood in terms of maximizing the satisfaction of preferences, and (3) that AI systems should be aligned with the preferences of one or more humans to ensure that they behave safely and in accordance with our values. Whether implicitly followed or explicitly endorsed, these commitments constitute what we term a preferentist approach to AI alignment. In this paper, we characterize and challenge the preferentist approach, describing conceptual and technical alternatives that are ripe for further research. We first survey the limits of rational choice theory as a descriptive model, explaining how preferences fail to capture the thick semantic content of human values, and how utility representations neglect the possible incommensurability of those values. We then critique the normativity of expected utility theory (EUT) for humans and AI, drawing upon arguments showing how rational agents need not comply with EUT, while highlighting how EUT is silent on which preferences are normatively acceptable. Finally, we argue that these limitations motivate a reframing of the targets of AI alignment: Instead of alignment with the preferences of a human user, developer, or humanity-writ-large, AI systems should be aligned with normative standards appropriate to their social roles, such as the role of a general-purpose assistant. Furthermore, these standards should be negotiated and agreed upon by all relevant stakeholders. On this alternative conception of alignment, a multiplicity of AI systems will be able to serve diverse ends, aligned with normative standards that promote mutual benefit and limit harm despite our plural and divergent values.

Protein digestion and amino acid absorption mechanisms along the midgut of Musca domestica larvae

A model of protein digestion and peptide and amino acid absorption along the midgut of Musca domestica larvae was proposed and supported by RNA-Seq analyses, protein bioinformatics, microvillar-membrane-enriched midgut proteomics, and enzymatic activities. Peptidase genes are highly expressed in the posterior midgut (PM), whereas those for cathepsins have expression limited to the middle midgut (MM). MM has the lowest levels of gene expression of almost all peptidases but has high expression of genes for membrane-bound serine endopeptidases. The anterior midgut (AM) has intermediate expression values of serine endopeptidase and aminopeptidase (AP) genes and low expression of carboxypeptidases (CPs). Gene expression and peptidase activities were usually consistent for putative intracellular and membrane-bound enzymes. However, secreted peptidase gene expression and activities have divergent values, especially in the PM, which may be due to the countercurrent water flux causing enzyme recycling, thus decreasing their excretion. Data suggest that Trys and APs act in the AM. In the acidic MM, lysozymes kill microorganisms found in the diet, releasing proteins digested by cathepsins D, which may also digest Trys coming from the AM. Finally, highly active serine endopeptidases, CPs, dipeptidases, and APs complete protein digestion in PM. Absorption of peptides and amino acids coupled to protons may occur along the midgut, especially in PM, as occurs for facilitated amino acid transport. Absorption with sodium ions is probably restricted to AM and PM. Our findings provide valuable insights into the protein digestion and amino acid absorption mechanism in M. domestica larvae.

Phylogenetic analysis of selected species of Asteraceae on the basis of RPS 11 Gene

The Asteraceae family is a prominent group of flowering plants found across the globe, with the exception of Antarctica. The Asteraceae family is a largest flowering family pivotal group in plant evolution and diversification. Despite its importance, the genetic diversity within this family remains understudied. We focused on the rps-11 gene, a chloroplast marker previously utilized in phylogenetic studies, to investigate its potential in resolving Asteraceae relationships. The focus was on examining genetic diversity within sixteen specifically chosen species from the Asteraceae family. This assessment was based on an analysis of a chloroplast gene responsible for encoding the ribosomal protein of the smaller subunit 11 (rps 11). Nearly 417 bp of rps 11 gene was amplified, sequenced, computationally translated into amino acid sequence and the data was used for phylogenetic analysis as well as for rps 11 protein structure predictions. Based on nucleotide and amino acid sequences phylograms were drawn with the help of Molecular Evolutionary Genetic Analysis (MEGA 6), which exhibited clear genetic relationship among species under investigation. The observed genetic distance was 0.02 for Maximum likelihood tree based on nucleotide sequences whereas it was 0.05 for phylogram based on amino acid sequences. These values revealed that amino acid-based tree has demonstrated greater diversity among selected species in comparison to nucleotides-based tree. On the basis of pair wise distance calculations, genetic divergence values were found within the range of 0.015–0.309. Moreover, 3D protein modeling for rps 11 protein of sixteen selected species was also carried out by iterative threading assembly refinement (I-Tasser) software. The models exhibiting the highest C-score were picked with satisfactory plot statistics (> 90%) and structurally validated by PROCHECK. Furthermore, Ramachandran plots displayed that the rps 11 protein structures of Tagetes minuta, Xanthium strumarium, Lactuca sativa and Chrysanthemum indicum have best feature models with > 90% of residues in the allowed region and ≤ 2% in the disallowed region. The research is not enough to stand alone to validate the viability of the rps11 gene as a prospective contender for phylogenetic analysis. İn future we will focus on the maximum genetic diversity theory for phylogenetic analysis of this family.

Unique among high passes: Insights into the genetic uniqueness among butterflies of Ladakh Trans-Himalaya through DNA barcoding.

The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a COI barcode reference library of 60 specimens representing 23 species. Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani. Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species. Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.

Composition, divergence and variability: A comprehensive analysis of fish trait responses to connectivity

Connectivity, a fundamental concept in ecology, refers to the extent to which different habitats or ecosystems are interconnected through the movement of organisms, nutrients, and energy. Lateral hydrological connectivity (LHC) plays an especially critical role in shaping aquatic community organization in river-floodplain systems. However, a comprehensive understanding of various trait responses to LHC remains elusive. We characterized how attributes of fish community traits, specifically composition, divergence, and temporal variability respond to LHC in the Austrian-Hungarian floodplains of the Danube River using environmental DNA (eDNA) metabarcoding. Trait composition was quantified by community-level weighted means (CWM) as the degree of changes in trait responses along the LHC gradient from isolated oxbows to the main river. Divergence was measured using Rao’s quadratic functional diversity index and a null model approach to calculate standardized effect sizes (SES), with larger SES values indicating greater divergence and smaller values indicating convergence. Temporal variability, representing the degree of instability in community traits over time, was calculated using a functional beta diversity measure for multiple communities. Our findings revealed apparent compositional changes for many trait variables, highlighting the significance of LHC in shaping community functional diversity. Divergence patterns indicated that isolated habitats foster trait convergence presumably due to habitat filtering, whereas more connected areas promote trait divergence due to higher species richness and habitat availability. Temporal variability of traits associated with flow preference exhibited a hump-shaped relationship with LHC, suggesting intermediate connectivity zones are hotspots of ecological dynamism. The study suggests that examining composition, divergence, and temporal variability together provides a more complete understanding of trait responses to connectivity, stressing the importance of maintaining diverse connectivity levels in river-floodplain systems for effective conservation and ecosystem management.

Phylogeography and population genetics of the endemic Italian water voles, Arvicola italicus

The genus Arvicola has a wide palearctic distribution and present two ecological forms – terrestrial and aquatic – characterizing the genus. In Europe two species are present: the most widespread, A. amphibius and A. italicus, endemic to Italy. The aim of the study was to describe the genetic structure and variability in A. italicus and the genetic identity of populations in northeast Italy, an area of biogeographic importance as contact zone for small mammal species.Thirty-six Italian water voles, displaced in population from south to north of Italy, were analyzed by two mitochondrial markers and 8 autosomal microsatellite loci. The phylogenetic analysis on the genus confirmed the presence of major groups mostly corresponding to the species and clades already described. About the Italian specimens, the individuals from one population in northeastern Italy resulted included in A. amphibius revealing the presence of this species in Italy and, in consequence, the possible presence of a putative contact zone between A. italicus and A. amphibius in the northeast. The phylogeny includes a second population from northeast Italy within A. amphibius, but in basal position and with a low support. The values of divergence of this lineage from A. italicus and A. amphibius lie on the threshold between intraspecific and interspecific divergence. Conversely, microsatellite data support a clear distinction between A. amphibius and A. italicus and includes the ambiguous mitochondrial lineage in this latter species. Furthermore, this northeastern population shows evidence of admixture of nuclear loci with the southcentral A. italicus populations, supporting the attribution of these specimens to A. italicus. This pattern could suggest that A. italicus in northeast Italy retained an ancestral haplotype and undergone a long period of isolation respect to the southern populations, without genetic exchange until recent times. Within A. italicus, the admixture shows northern population as the most differentiated showing limited evidence of admixture with the most diverse southcentral. The intraspecific diversity decreases from south to north as expected for an endemic small mammal in Italy. Finally, the low genetic diversity observed in the northern population can be challenging for a species as Arvicola living in fragmented habitats and susceptible to habitat loss; consequently, became important identifying suitable conservation measures for this barely known endemic small mammal.

Phylogeographic structuring in a widespread southern African grass snake (Psammophiinae: Psammophylax rhombeatus)

ABSTRACT The structural and environmental heterogeneity within southern Africa has given rise to many morphological forms of Psammophylax rhombeatus distributed throughout the country, with previous studies neglecting the associated molecular significance of these forms. The species’ widespread, generalist ecology coupled with the substantial phylogenetic structuring previously acknowledged within the species, makes P. rhombeatus the ideal candidate for phylogeographic analyses. Using 103 samples, representing the full distribution of the species, phylogenetic analyses retrieved four well-supported clades: south-eastern South Africa, south-western South Africa, north-eastern South Africa and western South Africa. Although not variable enough to warrant taxonomic re-evaluation, the clades are phylogenetically distinguishable, with relatively high intraspecific genetic divergence values separating them, irrespective of the small geographic distances separating populations. This is likely a product of the taxon’s habitat-generalist lifestyle, enabling them to bypass vicariant barriers that might otherwise cause speciation in less versatile species. The clades are also geographically distinct, with little overlap, indicating previous vicariance, a finding that is supported by the split of P. rhombeatus from P. ocellatus in the mid-Pliocene, followed by the diversification of P. rhombeatus into four clades throughout the Pleistocene. The genetic structuring observed in P. rhombeatus may be a product of population expansion following ancient refugial isolation (potentially Last Glacial Maximum). The morphological groupings highlighted in previous studies are loosely attributable to the molecular clades identified in the phylogenetic reconstruction, highlighting the complex interplay of genetic and morphological characteristics in the process of speciation, and their representation in systematic accounts.

Assessing clustering methods using Shannon's entropy

Unsupervised clustering techniques are crucial for effectively partitioning datasets into meaningful subgroups. In this paper, we introduce a novel clustering fuzziness metric based on Shannon's entropy, which quantifies the level of uncertainty in clustering assignments. This metric is employed to develop a statistical test for evaluating clustering algorithms and to propose parametric corrections to enhance their performance. We provide empirical evidence showing that our approach significantly improves clustering quality compared to well-known algorithms such as Fuzzy K-Means (FKM) and Fanny. For instance, applying our correction method led to a notable decrease in Jensen-Shannon Divergence (JSD) values, indicating enhanced clustering accuracy. Our methodology is demonstrated through comprehensive experiments on both simulated and real-world datasets. Additionally, our approach proves effective in determining the optimal number of clusters, showing superiority over traditional methods. These results highlight the practical benefits of our metric and correction techniques for improving clustering performance.

Generative Adversarial Networks with Radiomics Supervision for Lung Lesion Generation.

Data-driven methods for lesion generation are quickly emerging due to the need for realistic imaging targets for image quality assessment and virtual clinical trials. We proposed a generative adversarial network (GAN) architecture for conditional generation of lung lesions based on user-specified classes of lesion size and solidity. The network consists of two discriminators, one for volumetric lesion data, and one for radiomics features derived from the lesion volume. A Wasserstein loss with gradient penalty was adopted for each discriminator. Training data were drawn from contoured and annotated lesions from a public lung CT database. Four quantitative evaluation methods were devised to assess the network performance: 1) overfitting (similarity between generated and real lesions), 2) diversity (similarity among generated lesions), 3) conditional consistency (capability of generating lesions according to user-specified classes), and 4) similarity in distributions of various lesion properties between the generated and real lesions. Ablation studies were also performed to investigate the importance of individual network component. The proposed network was found to generate lesions that resemble real lesions by visual inspection. Solid lesions are distinct from non-solid ones, and lesion sizes largely correspond to their specified classes. With a classifier trained on real lesions, the classification accuracies of generated and real lesions in both solid and non-solid classes are similar. Radiomics features of generated and real lesions were found to have similar distributions, indicated by the relatively low Kullback-Leibler (KL) divergence values. Furthermore, the correlations between pairwise radiomics features in generated lesions were comparable to those of real lesions. The proposed network presents a promising approach for generating realistic lesions with clinically relevant features crucial for the comprehensive assessment of medical imaging systems.

Innovative Integration of Dual Quantum Cascade Lasers on Silicon Photonics Platform.

For the first time, we demonstrate the hybrid integration of dual distributed feedback (DFB) quantum cascade lasers (QCLs) on a silicon photonics platform using an innovative 3D self-aligned flip-chip assembly process. The QCL waveguide geometry was predesigned with alignment fiducials, enabling a sub-micron accuracy during assembly. Laser oscillation was observed at the designed wavelength of 7.2 μm, with a threshold current of 170 mA at room temperature under pulsed mode operation. The optical output power after an on-chip beam combiner reached sub-milliwatt levels under stable continuous wave operation at 15 °C. The specific packaging design miniaturized the entire light source by a factor of 100 compared with traditional free-space dual lasers module. Divergence values of 2.88 mrad along the horizontal axis and 1.84 mrad along the vertical axis were measured after packaging. Promisingly, adhering to i-line lithography and reducing the reliance on high-end flip-chip tools significantly lowers the cost per chip. This approach opens new avenues for QCL integration on silicon photonic chips, with significant implications for portable mid-infrared spectroscopy devices.

Determination of Species Identity and Genetic Diversity of Aedes aegypti and Other Medically Important Mosquitoes of India Using DNA Barcoding.

Aedes aegypti-borne viruses (i.e., dengue, chikungunya, and Zika) have become endemic to India, posing a severe threat to public health. Vector control remains the mainstay of disease management due to nonavailability of licensed vaccines/therapeutics. Conventional morpho-taxonomical methods cannot differentiate between closely related sibling species or species complexes, and hence we evaluated two molecular markers, mitochondrial cytochrome c oxidase subunit 1 (Cox1) and nuclear DNA internal transcribed spacer 2 (-2) gene sequences, to characterize seven populations of Ae. aegypti and four medically important mosquito species (Aedes albopictus, Anopheles stephensi, Culex tritaeniorhyncus, and Culex murrelli). DNA extracted from the 11 mosquito populations (two mosquitoes per population) was polymerase chain reaction amplified, sequenced, and analyzed. Molecular characterization was found to be congruent with morphological identification, suggesting no variants or cryptic species exist in Ae. aegypti and the other mosquitoes studied. Phylogenetic analysis with sequences obtained with Cox1 gene of Ae. aegypti and other Aedes and non-Aedes mosquito species showed clustering of sequences from different species representing different clades, distinctly separating one taxon from the other, whereas ITS-2 sequences of Aedes aegypti from across the world clustered tightly. Nucleotide divergence values revealed a low percentage of intraspecies variation and a higher percentage of interspecies variation. The present study authenticates the applicability of Cox1 and ITS-2 in the precise identification of Ae. aegypti mosquitoes against cryptic or sibling species. Cox1 appeared to be a more reliable marker because it showed distinct clustering of mosquito species, and some sequence variations to represent genetic diversity.

Treading the Narrow Path – Rethinking Democratic Education in Times of Polarization

Abstract This essay examines the relationship between knowledge, politics, and education in the context of the global crisis of democracy and the growing prevalence of political polarization. Focusing on the issue of vaccine hesitancy, I explore how citizens’ reference to knowledge and values shapes their political judgements and argue for the importance of education in facilitating informed and reasoned decision-making. Drawing on Hannah Arendt’s dialectical account of politics and knowledge, I highlight the limitations of reducing political debates to a quest for ‘right knowledge’, arguing that it neglects the coordination of diverse values and interpretations that is essential to democratic processes. To do so, I discuss ‘educationalization’ of the political during the COVID-19 pandemic, wherein the dissemination of empirically grounded information became a strategy to generate public consent. However, my essay cautions against the hegemony of empirical knowledge, which can lead to despotic politics and the proliferation of misinformation. To ensure differentiated and reasonable judgements in uncertain situations and conflicts, I turn to Arendt’s concept of reflective and political judgement, emphasizing the ability to imagine others’ perspectives and construct general principles. The educational task, therefore, encompasses not only conveying factual knowledge but also nurturing reflective judgement that strikes a balance between factual truth and divergent interpretations, values, and interests.

Mechanisms of coexistence: Exploring species sorting and character displacement in woody plants to alleviate belowground competition.

Rarely do we observe competitive exclusion within plant communities, even though plants compete for a limited pool of resources. Thus, our understanding of the mechanisms sustaining plant biodiversity might be limited. In this study, we explore two common ecological strategies, species sorting and character displacement, that promote coexistence by reducing competition. We assess the degree to which woody plants may implement these two strategies to lower belowground competition for nutrients which occurs via nutritional (mostly mycorrhizal) mutualisms. First, we compile data on plant traits and the mycorrhizal association state of woody angiosperms using a global inventory of indigenous flora. Our analysis reveals that species in locations with high mycorrhizal diversity exhibit distinct mean values in leaf area and wood density based on their mycorrhizal type, indicating species sorting. Second, we reanalyse a large dataset on leaf area to demonstrate that in areas with high mycorrhizal diversity, trees maintain divergent leaf area values, showcasing character displacement. Character displacement among plants is considered rare, making our observation significant. In summary, our study uncovers a rare occurrence of character displacement and identifies a common mechanism employed by plants to alleviate competition, shedding light on the complexities of plant coexistence in diverse ecosystems.

Ultraviolet signaling in a butterfly is preferred by females and conveys male genetic quality.

Indicator models of sexual selection posit that females choose males on the basis of traits that reveal male genetic quality and thereby enjoy increased offspring production. Here, we report that females of the butterfly Eurema hecabe receive indirect benefits from choosing males based on their ultraviolet (UV) wing coloration, a heritable and condition-dependent trait in this species. We first used a large laboratory-bred pedigree to demonstrate a per-family association between inbreeding and male UV trait value. Females exerted choice for UV-bright males within this protocol, and the average male UV trait value increased over six consecutive generations, presumably due to such selection and despite an increasing rate of pedigree-wide inbreeding. We then experimentally imposed a standard strength of inbreeding upon lines of divergent male UV trait values. Inbreeding depressed the siring performance of low UV treatment males more severely and resulted in a marginal reduction of their UV brightness, which rebounded sharply following subsequent outcrossing. These findings are consistent with the ornament-based signaling of genetic quality as a function of underlying individual-level mutational load.

COAT Project: Intercomparison of Thermometer Radiation Shields in the Arctic

A metrological field intercomparison of thermometer radiation shields in the Arctic was conducted with the aim of obtaining information to increase the worldwide comparability of air temperature measurements. Air temperature measurements are performed by different combinations of thermometers and shields. The response of each system (thermometer + shield) to local meteorological conditions depends on the system itself, limiting the comparability of air temperature measurements. Ten different models of radiation shields were included in the intercomparison, involving two campaigns: (1) the laboratory campaign, where all the instrumentation was calibrated just before and just after the field campaign, and (2) the field campaign that lasted 14 months where 41 thermometers were sampled every 2 min. All the delivered data were subjected to quality control to assure the robustness of the conclusions. A reference shield was defined, and the other shields were compared to the reference one for the conditions where maximum divergences were expected, solar irradiance being the highest impact factor. A maximum divergence value of 1.29 °C was derived for one of the shields and, for all the shields, the difference from the reference one decreases with wind speed. Finally, the uncertainties associated with the shields intercomparison were calculated.

Ethnic cosmopolitanism, cultural identity and conflict dynamics in the Kusaug Traditional Area of Northern Ghana

ABSTRACT This study investigates the perceptions of ethnicity and their impact on conflict dynamics and cultural identity with the aim of proposing a pathway towards the building of an ethnic cosmopolitan worldview for peaceful coexistence. The research adopted a qualitative methodological approach with interviews and focus group discussions involving 50 purposively sampled participants from the Kusaasi, Mamprusi, Mossi, Busanga, and Hausa ethnic groups resident in the Kusaug Traditional Area of northern-eastern Ghana. Participants recognize the possibility of developing a cosmopolitan worldview that respects divergent identities and values but also acknowledge the challenges and complexities involved. The study argues that the development of ethnic cosmopolitanism that integrates all the core values of the differentiated ethnic groups in Kusaug holds the potential to de-escalate conflicts and to promote peaceful coexistence. Public sensitization, education, and awareness programmes are recommended to promote tolerance, respect, and appreciation of unity in diversity.

Variational Autoencoders for Generative Drug-Gene Interactions in Periodontal Bone Resorption.

Introduction Periodontal bone resorption is a significant dental problem causing tooth loss and impaired oral function. It is influenced by factors such as bacterial plaque, genetic predisposition, smoking, systemic diseases, medications, hormonal changes, and poor oral hygiene. This condition disrupts bone remodeling, favoring resorptive processes. Variational autoencoders (VAEs) can learn the distribution of drug-gene interactions from existing data, identify potential drug targets, and predict therapeutic effects. This study investigates the generation of drug-gene interactions in periodontal bone resorption using VAEs. Methods A bone resorptive drugs dataset was retrieved from Probes and Drugs and analyzed using Cytoscape (https://cytoscape.org/) and CytoHubba (https://apps.cytoscape.org/apps/cytohubba), powerful tools for studying drug-gene interactions in bone resorption. The dataset was then prepared for matrix representation, with normalized input data. It was subsequently divided into training, validation, and testing sets. We then built an encoder-decoder network, defined a loss function, optimized parameters, and fine-tuned hyperparameters. Using VAEs, we generated new drug-gene interactions, assessed model performance, and visualized the latent space with reconstructed drug-gene interactions for further insights. Results The analysis revealed the top hub genes in drug-gene interactions, including Matrix Metalloproteinase (MMP) 14, MMP 9, HIF1A, STAT1, MAPT, CAS9, MMP2, CASP3, MMP1, and MAK1. The VAE's reconstruction accuracy was measured using mean squared error (MSE), with an average squared difference of 0.077. Additionally, the KL divergence value was 2.349, and the average reconstruction log-likelihood was -246. Conclusion The generative variational encoder model for drug-gene interactions in bone resorption demonstrates high accuracy and reliability in representing complex drug-gene relationships within this context.

Photorhabdus africana sp. nov. isolated from Heterorhabditis entomopathogenic nematodes

One Gram-negative, rod-shaped bacterial strain, isolated from an undescribed Heterorhabditis entomopathogenic nematode species was characterized to determine its taxonomic position. The 16S rRNA gene sequences indicate that it belongs to the class Gammaproteobacteria, to the family Morganellaceae, to the genus Photorhabdus, and likely represents a novel bacterial species. This strain, designated here as CRI-LCT, was therefore molecularly, biochemically, and morphologically characterized to describe the novel bacterial species. Phylogenetic reconstructions using 16S rRNA gene sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. The 16rRNA gene sequences between CRI-LCT and P. laumondii subsp. laumondii TT01T are 99.1% identical, and between CRI-LCT and P. laumondii subsp. clarkei BOJ-47T are 99.2% identical. Phylogenetic reconstructions using whole genome sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. Moreover, digital DNA-DNA hybridization (dDDH) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 65% and 63%, respectively. In addition, we observed that average nucleotide identity (ANI) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 95.8% and 95.5%, respectively. These values are below the 70% dDDH and the 95–96% ANI divergence thresholds that delimits prokaryotic species. Based on these genomic divergence values, and the phylogenomic separation, we conclude that CRI-LCT represents a novel bacterial species, for which we propose the name Photorhabdus africana sp. nov. with CRI-LCT (= CCM 9390T = CCOS 2112T) as the type strain. The following biochemical tests allow to differentiate P. africana sp. nov. CRI-LCT from other species of the genus, including its more closely related taxa: β-Galactosidase, citrate utilization, urease and tryptophan deaminase activities, indole and acetoin production, and glucose and inositol oxidation. Our study contributes to a better understanding of the taxonomy and biodiversity of this important bacterial group with great biotechnological and agricultural potential.

Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode

Asgardarchaeota, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest archaeal relatives of eukaryotes. Despite their prevalence in the scientific literature, the name Asgardarchaeota lacks nomenclatural validation. Here, we describe a novel high-quality metagenome-assembled genome (MAG), AB3033_2TS, proposed to serve as the nomenclatural type for the species Asgardarchaeum abyssiTS according to the rules of the SeqCode. Based on protein content and compositional features, we infer that A. abyssi AB3033_2TS is an acetogenic chemoheterotroph, possibly a facultative lithoautotroph, and is adapted to a thermophilic lifestyle. Utilizing genomes from Asgard archaea, TACK, and Euryarchaea, we perform phylogenomic reconstructions using the GTDB archaeal marker genes, the current reference set for taxonomic classification. Calibrating relative evolutionary divergence (RED) values for Asgardarchaeota using established Thermoproteota lineages in the GTDB r207 reference tree, we establish a robust classification and propose Asgardarchaeum as the type genus for the family Asgardarchaeaceae (fam. nov)., the order Asgardarchaeales (ord. nov.), the class Asgardarchaeia (class. nov.), and the phylum Asgardarchaeota (phyl. nov.). This effort aims to preserve taxonomic congruence in the scientific literature.

Characterizing Multisystem Barriers to Women's Residential SUD Treatment: A Multisite Qualitative Analysis in Los Angeles.

Residential substance use disorder (SUD) treatment programs are challenged by the differing values of the problem-solving court (PSC) and child welfare (CW) systems, along with communication barriers between staff. This study aimed to understand, from the viewpoints of SUD treatment providers, how divergent values and communication barriers adversely affect women's residential SUD treatment. We conducted qualitative semistructured interviews with 18 SUD treatment clinicians and six directors from four women's residential SUD treatment programs. Using a thematic analysis framework, we identified salient themes across specified codes. Analysis revealed six main themes, suggesting differing values and communication barriers across the SUD, PSC, and CW systems adversely affect the provision of SUD treatment. For differing values, three main themes emerged: (a) unaddressed trauma and fear of mental health treatment seeking; (b) perceptions of mothers with a SUD; and (c) the Adoption and Safe Families Act (ASFA) timeline as a barrier to SUD treatment provision. For communication barriers, three themes emerged: (a) inadequate communication and responsiveness with PSC and CW systems adversely affect treatment coordination, induce patient stress, and treatment disengagement; (b) lack of PSC and CW communication regarding child visitation planning adversely affects treatment motivation and retention; and (c) competing ASFA, PSC, and CW priorities and inadequate cross-system communication adversely affect treatment planning. Treatment providers face significant barriers in providing effective treatment to women simultaneously involved in the CW and PSC systems. Aligning values and addressing communication barriers, changes in policy, and enhanced cross-system training are crucial. Additionally, it is essential to reevaluate the ASFA timeline to align with the long-term treatment needs of mothers with a SUD. Further research should explore the viewpoints of patients, CW, and PSC staff to gain deeper insights into these SUD treatment barriers.