Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals.

Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathogenic. To determine the genetic basis of its duality, we conducted a comparative genomic analysis of 813 B. fragilis strains, representing both commensal and pathogenic origins. Our findings reveal that pathogenic strains emerge across diverse phylogenetic lineages, due in part to rapid gene exchange and the adaptability of the accessory genome. We identified 16 phylogenetic groups, differentiated by genes associated with capsule composition, interspecies competition, and host interactions. A microbial genome-wide association study identified 44 genes linked to extra-intestinal survival and pathogenicity. These findings reveal how genomic diversity within commensal species can lead to the emergence of pathogenic traits, broadening our understanding of microbial evolution in the gut.

Antennal transcriptome analysis reveals sensory receptors potentially associated with host detection in the livestock pest Lucilia cuprina.

BACKGROUND: Lucilia cuprina (Wiedemann, 1830) (Diptera: Calliphoridae) is the main causative agent of flystrike of sheep in Australia and New Zealand. Female flies lay eggs in an open wound or natural orifice, and the developing larvae eat the host's tissues, a condition called myiasis. To improve our understanding of host-seeking behavior, we quantified gene expression in male and female antennae based on their behavior. METHODS: A spatial olfactometer was used to evaluate the olfactory response of L. cuprina mated males and gravid females to fresh or rotting beef. Antennal RNA-Seq analysis was used to identify sensory receptors differentially expressed between groups. RESULTS: Lucilia cuprina females were more attracted to rotten compared to fresh beef (> fivefold increase). However, males and some females did not respond to either type of beef. RNA-Seq analysis was performed on antennae dissected from attracted females, non-attracted females and males. Transcripts encoding sensory receptors from 11 gene families were identified above a threshold (≥ 5 transcript per million) including 49 ATP-binding cassette transporters (ABCs), two ammonium transporters (AMTs), 37 odorant receptors (ORs), 16 ionotropic receptors (IRs), 5 gustatory receptors (GRs), 22 odorant-binding proteins (OBPs), 9 CD36-sensory neuron membrane proteins (CD36/SNMPs), 4 chemosensory proteins (CSPs), 4 myeloid lipid-recognition (ML) and Niemann-Pick C2 disease proteins (ML/NPC2), 2 pickpocket receptors (PPKs) and 3 transient receptor potential channels (TRPs). Differential expression analyses identified sex-biased sensory receptors. CONCLUSIONS: We identified sensory receptors that were differentially expressed between the antennae of both sexes and hence may be associated with host detection by female flies. The most promising for future investigations were as follows: an odorant receptor (LcupOR46) which is female-biased in L. cuprina and Cochliomyia hominivorax Coquerel, 1858; an ABC transporter (ABC G23.1) that was the sole sensory receptor upregulated in the antennae of females attracted to rotting beef compared to non-attracted females; a female-biased ammonia transporter (AMT_Rh50), which was previously associated with ammonium detection in Drosophila melanogaster Meigen, 1830. This is the first report suggesting a possible role for ABC transporters in L. cuprina olfaction and potentially in other insects.

The changing landscape of text mining: a review of approaches for ecology and evolution.

In ecology and evolutionary biology, the synthesis and modelling of data from published literature are commonly used to generate insights and test theories across systems. However, the tasks of searching, screening, and extracting data from literature are often arduous. Researchers may manually process hundreds to thousands of articles for systematic reviews, meta-analyses, and compiling synthetic datasets. As relevant articles expand to tens or hundreds of thousands, computer-based approaches can increase the efficiency, transparency and reproducibility of literature-based research. Methods available for text mining are rapidly changing owing to developments in machine learning-based language models. We review the growing landscape of approaches, mapping them onto three broad paradigms (frequency-based approaches, traditional Natural Language Processing and deep learning-based language models). This serves as an entry point to learn foundational and cutting-edge concepts, vocabularies, and methods to foster integration of these tools into ecological and evolutionary research. We cover approaches for modelling ecological texts, generating training data, developing custom models and interacting with large language models and discuss challenges and possible solutions to implementing these methods in ecology and evolution.

Parauchenoglanis stiassnyae (Siluriformes: Auchenoglanididae): A new species of giraffe catfish from Mfimi-Lukenie basin, central Africa, Democratic Republic of Congo.

A new, distinctively short-bodied giraffe catfish of Parauchenoglanis is described from the Ndzaa River, a small left-bank tributary of the Mfimi-Lukenie basin in the Central basin of the Congo River in the Democratic Republic of the Congo. The new species can be distinguished from all congeners by having 29 or fewer (vs. 33 or more) total vertebrae. It can further be distinguished from all congeners, except Parauchenoglanis zebratus Sithole et al., 2023 and Parauchenoglanis ngamensis (Boulenger 1911), by having 13 or 14 (vs. 16 or more) pre-anal vertebrae. The species is endemic to the Mfimi River basin, where it has been collected mainly in blackwater tributaries.

Mechanically Triggered Bright Chemiluminescence from Polymers by Exploiting a Synergy between Masked 2-Furylcarbinol Mechanophores and 1,2-Dioxetane Chemiluminophores.

Mechanoluminescence, or the generation of light from materials under external force, is a powerful tool for biology and materials science. However, direct mechanoluminescence from polymers remains limited. Here, we report a novel design strategy for mechanoluminescent polymers that leverages the synergy between a masked 2-furylcarbinol mechanophore for mechanically triggered release and an adamantylidene-phenoxy-1,2-dioxetane chemiluminophore payload. Ultrasound-induced mechanochemical activation of polymers, in both organic and aqueous solutions, triggers a cascade reaction that ultimately results in bright green light emission. This novel strategy capitalizes on the modularity of the masked 2-furylcarbinol mechanophore system in combination with advances in the design of exceptionally bright and highly tunable adamantylidene-1,2-dioxetane chemiluminophores. We anticipate that this chemistry will enable diverse applications in optoelectronics, sensing, bioimaging, optogenetics, and many other areas.

Identification of a gene promoter active in Lucilia sericata larval salivary glands using a rapid transient expression assay.

Tissue-specific gene promoters are desired as they provide the specificity needed for control of gene expression in transgenic animals. Here we describe a relatively rapid two-component transient expression assay that was used to identify a gene promoter active in the larval salivary glands of the green blow fly, Lucilia sericata. Sterile L. sericata maggots are widely used for wound debridement. A larval salivary gland gene promoter could be used to make maggots that secrete factors for enhanced wound therapy. Embryos from a line that carry a tetracycline transactivator (tTA)-activated red fluorescent protein gene were injected with plasmid DNA with the tTA gene driven by a constitutive or tissue-specific gene promoter. The hatched larvae were reared on diet and then examined for red fluorescence. A promoter from the LsCG30371 gene was active in the larval salivary glands. The tissue-specificity of the promoter was subsequently confirmed with stable transgenic lines that carried the LsCG30371-tTA gene. The relatively rapid transient expression assay could potentially be used to determine the tissue-specificity of other gene promoters. Further, the stable LsCG30371-tTA lines could be used to make sterile maggots that secrete factors from the salivary glands for enhanced wound healing.

Chemical cyclization of tyrosine-containing peptides via in situ generated triazolinedione peptides.

Tyr-derived cyclic peptide natural products are formed by enzymatic manifolds that oxidatively cross-link embedded phenolic side chains of tyrosine (Tyr) and 4-hydroxyphenylglycine residues during their controlled production. Bioactive Tyr-derived cyclic peptides, such as the arylomycins and vancomycins, continue to motivate the development of enzymatic and chemical strategies for their de novo assembly and modification. However, chemical access to these structurally diverse natural cycles can be challenging and step intensive. Therefore, we developed an oxidative procedure to selectively convert Tyr-containing N4-substituted 1,2,4-triazolidine-3,5-dione peptides (urazole peptides) into stable Tyr-linked cyclic peptides. We show that Tyr-containing urazole peptides are simple to prepare and convert into reactive N4-substituted 1,2,4-triazoline-3,5-dione peptides by oxidation, which then undergo spontaneous cyclization under mildly basic aqueous conditions to form a cross-linkage with the phenol side chain of embedded Tyr residues. Using this approach, we have demonstrated access to over 25 Tyr-linked cyclic peptides (3- to 11-residue cycles) with good tolerance of native residue side chain functionalities. Importantly, this method is simple to perform, and product formation can be quickly confirmed by mass spectrometric and 1H NMR spectroscopic analyses.

Narrative as active inference: an integrative account of cognitive and social functions in adaptation.

While the ubiquity and importance of narratives for human adaptation is widely recognized, there is no integrative framework for understanding the roles of narrative in human adaptation. Research has identified several cognitive and social functions of narratives that are conducive to well-being and adaptation as well as to coordinated social practices and enculturation. In this paper, we characterize the cognitive and social functions of narratives in terms of active inference, to support the claim that one of the main adaptive functions of narrative is to generate more useful (i.e., accurate, parsimonious) predictions for the individual, as well as to coordinate group action (over multiple timescales) through shared predictions about collective behavior. Active inference is a theory that depicts the fundamental tendency of living organisms to adapt by proactively inferring the causes of their sensations (including their own actions). We review narrative research on identity, event segmentation, episodic memory, future projections, storytelling practices, enculturation, and master narratives. We show how this research dovetails with the active inference framework and propose an account of the cognitive and social functions of narrative that emphasizes that narratives are for the future-even when they are focused on recollecting or recounting the past. Understanding narratives as cognitive and cultural tools for mutual prediction in social contexts can guide research on narrative in adaptive behavior and psychopathology, based on a parsimonious mechanistic model of some of the basic adaptive functions of narrative.

Unique yellow shifts for small and brief stimuli in the central retina.

The spectral locus of unique yellow was determined for flashes of different sizes (<11 arcmin) and durations (<500 ms) presented in and near the fovea. An adaptive optics scanning laser ophthalmoscope was used to minimize the effects of higher-order aberrations during simultaneous stimulus delivery and retinal imaging. In certain subjects, parafoveal cones were classified as L, M, or S, which permitted the comparison of unique yellow measurements with variations in local L/M ratios within and between observers. Unique yellow shifted to longer wavelengths as stimulus size or duration was reduced. This effect is most pronounced for changes in size and more apparent in the fovea than in the parafovea. The observed variations in unique yellow are not entirely predicted from variations in L/M ratio and therefore implicate neural processes beyond photoreception.

The Wisconsin silicone oil study (report #1): anatomical and functional outcomes of repair of retinal detachment with proliferative vitreoretinopathy.

BACKGROUND: Silicone oil (SO) is a long-term tamponade for repair of complex retinal pathology but has limitations including late redetachment. This study describes our experience with SO tamponade for repair of retinal detachment with proliferative vitreoretinopathy (PVR), with attention to anatomic and functional outcomes. METHODS: Retrospective consecutive case series of eyes with retinal detachment (RD) complicated by proliferative vitreoretinopathy (PVR) receiving SO tamponade at the University of Wisconsin between 2013 and 2019. Group 1 defined as primary SO placement; Group 2 had SO placed after failing prior retinal detachment repair. RESULTS: Inclusion criteria of SO placement for repair of RD with PVR was met for 117 eyes. The final reattachment rate was 84% for all eyes, with no difference between Groups 1 and 2. Vision improvement was 2.1 lines for Group 1 (p = 0.06 from baseline) and 4.6 lines for Group 2 (p < 0.0001). The mean number of silicone oil placements was 1.4. Less improvement in vision was noted with repeat SO placement, though overall functional vision of 5/200 or better was achieved in 63.2% of patients. CONCLUSIONS: SO tamponade allows long-term anatomical stabilisation and substantial vision recovery in eyes with retinal detachment complicated by PVR. Rates of anatomic and functional success have improved significantly when compared to prior studies using oil tamponade for repair of PVR.

Cost analysis of one-time intravenous antibiotic doses in the emergency department.

BACKGROUND: Research shows that one-time doses of intravenous (IV) antibiotics do not improve resolution of infection. Providers, however, continue to use them - especially in the emergency department. Very few studies have aimed to quantify the cost of this practice. OBJECTIVES: The primary objective was to evaluate the difference in average total cost of emergency department (ED) stay between patients who received a one-time dose of intravenous antibiotics in the ED before discharging on oral antibiotics and patients who were just discharged on oral antibiotics. Secondary objectives were to evaluate the differences in durations of stay between the two groups, as well as the differences in adverse drug effects and need for healthcare contact after discharge. METHODS: Chart review was conducted to identify patients who received and did not receive a one-time dose of IV antibiotics in the ED between April 30, 2020, and April 30, 2022. A micro-costing approach was used to determine ED-associated costs per patient. Comparisons in primary and secondary outcomes were performed using statistical inferential tests. RESULTS: A total of 102 patients were analyzed in each group. Patients who received a one-time dose of intravenous antibiotics in the emergency department before being discharged on oral antibiotics had an average length of stay of 4.55 hours, as opposed to patients who did not receive a one-time dose of intravenous antibiotics before being discharged on oral antibiotics who had an average length of stay of 2.82 hours (absolute difference: 1.73 hours, p < 0.001). One-time dosing of intravenous antibiotics in the emergency department incurred an additional cost of approximately $556 per patient, totaling to over $56,000 in our study cohort. CONCLUSION: The use of one-time intravenous antibiotics in the emergency department did not confer any additional benefits to patients. Use of one-time doses resulted in significantly reduced throughput in the emergency department and significantly increased healthcare costs.

Short- and Long-Term Predicted and Witnessed Consequences of Digital Surveillance During the COVID-19 Pandemic: Scoping Review.

BACKGROUND: The COVID-19 pandemic has prompted the deployment of digital technologies for public health surveillance globally. The rapid development and use of these technologies have curtailed opportunities to fully consider their potential impacts (eg, for human rights, civil liberties, privacy, and marginalization of vulnerable groups). OBJECTIVE: We conducted a scoping review of peer-reviewed and gray literature to identify the types and applications of digital technologies used for surveillance during the COVID-19 pandemic and the predicted and witnessed consequences of digital surveillance. METHODS: Our methodology was informed by the 5-stage methodological framework to guide scoping reviews: identifying the research question; identifying relevant studies; study selection; charting the data; and collating, summarizing, and reporting the findings. We conducted a search of peer-reviewed and gray literature published between December 1, 2019, and December 31, 2020. We focused on the first year of the pandemic to provide a snapshot of the questions, concerns, findings, and discussions emerging from peer-reviewed and gray literature during this pivotal first year of the pandemic. Our review followed the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) reporting guidelines. RESULTS: We reviewed a total of 147 peer-reviewed and 79 gray literature publications. Based on our analysis of these publications, we identified a total of 90 countries and regions where digital technologies were used for public health surveillance during the COVID-19 pandemic. Some of the most frequently used technologies included mobile phone apps, location-tracking technologies, drones, temperature-scanning technologies, and wearable devices. We also found that the literature raised concerns regarding the implications of digital surveillance in relation to data security and privacy, function creep and mission creep, private sector involvement in surveillance, human rights, civil liberties, and impacts on marginalized groups. Finally, we identified recommendations for ethical digital technology design and use, including proportionality, transparency, purpose limitation, protecting privacy and security, and accountability. CONCLUSIONS: A wide range of digital technologies was used worldwide to support public health surveillance during the COVID-19 pandemic. The findings of our analysis highlight the importance of considering short- and long-term consequences of digital surveillance not only during the COVID-19 pandemic but also for future public health crises. These findings also demonstrate the ways in which digital surveillance has rendered visible the shifting and blurred boundaries between public health surveillance and other forms of surveillance, particularly given the ubiquitous nature of digital surveillance. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-https://doi.org/10.1136/bmjopen-2021-053962.

Interconnecting global threats: climate change, biodiversity loss, and infectious diseases.

The concurrent pressures of rising global temperatures, rates and incidence of species decline, and emergence of infectious diseases represent an unprecedented planetary crisis. Intergovernmental reports have drawn focus to the escalating climate and biodiversity crises and the connections between them, but interactions among all three pressures have been largely overlooked. Non-linearities and dampening and reinforcing interactions among pressures make considering interconnections essential to anticipating planetary challenges. In this Review, we define and exemplify the causal pathways that link the three global pressures of climate change, biodiversity loss, and infectious disease. A literature assessment and case studies show that the mechanisms between certain pairs of pressures are better understood than others and that the full triad of interactions is rarely considered. Although challenges to evaluating these interactions-including a mismatch in scales, data availability, and methods-are substantial, current approaches would benefit from expanding scientific cultures to embrace interdisciplinarity and from integrating animal, human, and environmental perspectives. Considering the full suite of connections would be transformative for planetary health by identifying potential for co-benefits and mutually beneficial scenarios, and highlighting where a narrow focus on solutions to one pressure might aggravate another.

Research ethics review during the COVID-19 pandemic: An international study.

Research ethics review committees (ERCs) worldwide faced daunting challenges during the COVID-19 pandemic. There was a need to balance rapid turnaround with rigorous evaluation of high-risk research protocols in the context of considerable uncertainty. This study explored the experiences and performance of ERCs during the pandemic. We conducted an anonymous, cross-sectional, global online survey of chairs (or their delegates) of ERCs who were involved in the review of COVID-19-related research protocols after March 2020. The survey ran from October 2022 to February 2023 and consisted of 50 items, with opportunities for descriptive responses to open-ended questions. Two hundred and three participants [130 from high-income countries (HICs) and 73 from low- and middle-income countries (LMICs)] completed our survey. Respondents came from diverse entities and organizations from 48 countries (19 HICs and 29 LMICs) in all World Health Organization regions. Responses show little of the increased global funding for COVID-19 research was allotted to the operation of ERCs. Few ERCs had pre-existing internal policies to address operation during public health emergencies, but almost half used existing guidelines. Most ERCs modified existing procedures or designed and implemented new ones but had not evaluated the success of these changes. Participants overwhelmingly endorsed permanently implementing several of them. Few ERCs added new members but non-member experts were consulted; quorum was generally achieved. Collaboration among ERCs was infrequent, but reviews conducted by external ERCs were recognized and validated. Review volume increased during the pandemic, with COVID-19-related studies being prioritized. Most protocol reviews were reported as taking less than three weeks. One-third of respondents reported external pressure on their ERCs from different stakeholders to approve or reject specific COVID-19-related protocols. ERC members faced significant challenges to keep their committees functioning during the pandemic. Our findings can inform ERC approaches towards future public health emergencies. To our knowledge, this is the first international, COVID-19-related study of its kind.

Shared Protentions in Multi-Agent Active Inference.

In this paper, we unite concepts from Husserlian phenomenology, the active inference framework in theoretical biology, and category theory in mathematics to develop a comprehensive framework for understanding social action premised on shared goals. We begin with an overview of Husserlian phenomenology, focusing on aspects of inner time-consciousness, namely, retention, primal impression, and protention. We then review active inference as a formal approach to modeling agent behavior based on variational (approximate Bayesian) inference. Expanding upon Husserl's model of time consciousness, we consider collective goal-directed behavior, emphasizing shared protentions among agents and their connection to the shared generative models of active inference. This integrated framework aims to formalize shared goals in terms of shared protentions, and thereby shed light on the emergence of group intentionality. Building on this foundation, we incorporate mathematical tools from category theory, in particular, sheaf and topos theory, to furnish a mathematical image of individual and group interactions within a stochastic environment. Specifically, we employ morphisms between polynomial representations of individual agent models, allowing predictions not only of their own behaviors but also those of other agents and environmental responses. Sheaf and topos theory facilitates the construction of coherent agent worldviews and provides a way of representing consensus or shared understanding. We explore the emergence of shared protentions, bridging the phenomenology of temporal structure, multi-agent active inference systems, and category theory. Shared protentions are highlighted as pivotal for coordination and achieving common objectives. We conclude by acknowledging the intricacies stemming from stochastic systems and uncertainties in realizing shared goals.

"She was finally mine": the moral experience of families in the context of trisomy 13 and 18- a scoping review with thematic analysis.

INTRODUCTION: The value of a short life characterized by disability has been hotly debated in the literature on fetal and neonatal outcomes. METHODS: We conducted a scoping review to summarize the available empirical literature on the experiences of families in the context of trisomy 13 and 18 (T13/18) with subsequent thematic analysis of the 17 included articles. FINDINGS: Themes constructed include (1) Pride as Resistance, (2) Negotiating Normalcy and (3) The Significance of Time. INTERPRETATION: Our thematic analysis was guided by the moral experience framework conceived by Hunt and Carnevale (2011) in association with the VOICE (Views On Interdisciplinary Childhood Ethics) collaborative research group. RELEVANCE: This article will be of interest and value to healthcare professionals and bioethicists who support families navigating the medically and ethically complex landscape of T13/18.

Doxycycline is a viable alternative to tetracycline for use in insect Tet-Off transgenic sexing systems, as assessed in the blowflies Cochliomyia hominivorax and Lucilia cuprina (Diptera: Calliphoridae).

Transgenic insect strains with tetracycline repressible (Tet-Off) female-lethal genes provide significant advantages over traditional sterile insect techniques for insect population control, such as reduced diet and labor costs and more efficient population suppression. Tet-Off systems are suppressed by tetracycline-class antibiotics, most commonly tetracycline (Tc) or doxycycline (Dox), allowing for equal sex ratio colonies of transgenic insects when reared with Tc or Dox and male-only generations in their absence. Dox is a more stable molecule and has increased uptake than Tc, which could be advantageous in some insect mass-rearing systems. Here, we evaluated the suitability of Dox for rearing Tet-Off female-lethal strains of Australian sheep blowfly, Lucilia cuprina (Wiedemann, 1830) (Diptera: Calliphoridae), and New World screwworm, Cochliomyia hominivorax (Coquerel, 1858) (Diptera: Calliphoridae), and the effects of dosage on strain performance. For both species, colonies were able to be maintained with mixed-sex ratios at much lower dosages of Dox than Tc. Biological yields of C. hominivorax on either antibiotic were not significantly different. Reduction of Dox dosages in C. hominivorax diet did not affect biological performance, though rearing with 10 or 25 µg/mL was more productive than 50 µg/mL. Additionally, C. hominivorax mating performance and longevity were equal on all Dox dosages. Overall, Dox was a suitable antibiotic for mass-rearing Tet-Off female-lethal L. cuprina and C. hominivorax and was functional at much lower dosages than Tc.