Evolution of Alternative Adaptive Immune Systems in Vertebrates.

Adaptive immunity in jawless fishes is based on antigen recognition by three types of variable lymphocyte receptors (VLRs) composed of variable leucine-rich repeats, which are differentially expressed by two T-like lymphocyte lineages and one B-like lymphocyte lineage. The T-like cells express either VLRAs or VLRCs of yet undefined antigen specificity, whereas the VLRB antibodies secreted by B-like cells bind proteinaceous and carbohydrate antigens. The incomplete VLR germline genes are assembled into functional units by a gene conversion-like mechanism that employs flanking variable leucine-rich repeat sequences as templates in association with lineage-specific expression of cytidine deaminases. B-like cells develop in the hematopoietic typhlosole and kidneys, whereas T-like cells develop in the thymoid, a thymus-equivalent region at the gill fold tips. Thus, the dichotomy between T-like and B-like cells and the presence of dedicated lymphopoietic tissues emerge as ancestral vertebrate features, whereas the somatic diversification of structurally distinct antigen receptor genes evolved independently in jawless and jawed vertebrates.

Why marginal CO2 emissions are not decreasing for US electricity: Estimates and implications for climate policy.

Marginal emissions of CO2 from the electricity sector are critical for evaluating climate policies that rely on shifts in electricity demand or supply. This paper provides estimates of marginal CO2 emissions from US electricity generation using the most recently available and comprehensive data. The estimates vary by region, hour of the day, and year to year over the last decade. We identify an important and somewhat counterintuitive finding: While average emissions have decreased substantially over the last decade (28% nationally), marginal emissions have increased (7% nationally). We show that underlying these trends is primarily a shift toward greater reliance on coal to satisfy marginal electricity use. We apply our estimates to an analysis of the Biden administration's target of having electric vehicles (EVs) make up 50% of new vehicle purchases by 2030. We find that, without significant and concurrent changes to the electricity sector, the increase in electricity emissions is likely to offset more than half of the emission reductions from having fewer gasoline-powered vehicles on the road. Moreover, using average rather than marginal emissions to predict the impacts significantly overestimates the emission benefits. Overall, we find that the promise of EVs for reducing emissions depends, to a large degree, on complementary policies that decarbonize both average and marginal emissions in the electricity sector.

Analysis of financial challenges faced by graduate students in Canada.

Graduate students are vital to the creation of research and innovation in Canada. The National Graduate Student Finance Survey was launched in 2021 by the Ottawa Science Policy Network to investigate the financial realities of Canadian graduate students. Closing in April 2022, the survey received 1305 responses from graduate students representing various geographical locations, years of study, fields of education, and demographic backgrounds. The results capture a snapshot into graduate student finances, including an in-depth analysis of stipends, scholarships, debt, tuition, and living expenses. In its entirety, we found that the majority of graduate students are facing serious financial concerns. This is largely due to stagnant funding for students both from federal and provincial granting agencies and from within their institutions. This reality is even worse for international students, members of historically underrepresented communities, and those with dependents, all of whom experience additional challenges that impact their financial security. Based on our findings, we propose several recommendations to the Tri-Council agencies (Natural Sciences and Engineering Research Council, Social Science and Humanities Research Council, and Canadian Institute for Health Research) and academic institutions to strengthen graduate student finances and help sustain the future of research in Canada.

Trust and The Acquisition and Use of Public Health Information.

Information is clearly vital to public health, but the acquisition and use of public health data elicit serious privacy concerns. One strategy for navigating this dilemma is to build 'trust' in institutions responsible for health information, thereby reducing privacy concerns and increasing willingness to contribute personal data. This strategy, as currently presented in public health literature, has serious shortcomings. But it can be augmented by appealing to the philosophical analysis of the concept of trust. Philosophers distinguish trust and trustworthiness from cognate attitudes, such as confident reliance. Central to this is value congruence: trust is grounded in the perception of shared values. So, the way to build trust in institutions responsible for health data is for those institutions to develop and display values shared by the public. We defend this approach from objections, such as that trust is an interpersonal attitude inappropriate to the way people relate to organisations. The paper then moves on to the practical application of our strategy. Trust and trustworthiness can reduce privacy concerns and increase willingness to share health data, notably, in the context of internal and external threats to data privacy. We end by appealing for the sort of empirical work our proposal requires.

Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae. Most vertebrate AADs, including AID and APOBECs1-3, diversified in the vertebrates, whereas the APOBEC4-like clade has a deeper origin in metazoa. Positional entropy analysis suggests that several AAD clades are diversifying rapidly, especially in the positions predicted to interact with the nucleic acid target motif, and with potential viral inhibitors. Further, several AADs have evolved neomorphic metal-binding inserts, especially within loops predicted to interact with the target nucleic acid. We also observe polymorphisms, driven by alternative splicing, gene loss, and possibly intergenic recombination between paralogs. We propose that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems. Deaminases like AID represent versions "institutionalized" from the broader array of AADs pitted in such arms races for mutagenesis of self-DNA, and similar recruitment might have independently occurred elsewhere in metazoa.

Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys.

Cytidine deaminases of the AID/APOBEC family catalyze C-to-U nucleotide transitions in mRNA or DNA. Members of the APOBEC3 branch are involved in antiviral defense, whereas AID contributes to diversification of antibody repertoires in jawed vertebrates via somatic hypermutation, gene conversion, and class switch recombination. In the extant jawless vertebrate, the lamprey, two members of the AID/APOBEC family are implicated in the generation of somatic diversity of the variable lymphocyte receptors (VLRs). Expression studies linked CDA1 and CDA2 genes to the assembly of VLRA/C genes in T-like cells and the VLRB genes in B-like cells, respectively. Here, we identify and characterize several CDA1-like genes in the larvae of different lamprey species and demonstrate that these encode active cytidine deaminases. Structural comparisons of the CDA1 variants highlighted substantial differences in surface charge; this observation is supported by our finding that the enzymes require different conditions and substrates for optimal activity in vitro. Strikingly, we also found that the number of CDA-like genes present in individuals of the same species is variable. Nevertheless, irrespective of the number of different CDA1-like genes present, all lamprey larvae have at least one functional CDA1-related gene encoding an enzyme with predicted structural and chemical features generally comparable to jawed vertebrate AID. Our findings suggest that, similar to APOBEC3 branch expansion in jawed vertebrates, the AID/APOBEC family has undergone substantial diversification in lamprey, possibly indicative of multiple distinct biological roles.

Stages of life: A new metaphysics of conceptionism.

When a human being comes into existence is crucial in bioethics. Conceptionism is the view that a human being comes into existence at conception. The twinning argument is an influential objection to this view. All versions of the twinning argument rely on a metaphysics of material objects, namely, endurantism. Given this, a strategy for defending conceptionism against the twinning argument is to deny endurantism and adopt an alternative metaphysics of material objects. A version of this strategy which has been debated in this journal is to adopt perdurantism, or the 'multiple occupancy view', on which monozygotic twins share the zygote region as a temporal part. We present a novel version of this strategy: conceptionists can evade the twinning argument by adopting an exdurantist metaphysics of material objects. We suggest reasons for thinking that this is a plausible and, indeed, preferable way for conceptionists to avoid the twinning argument.

Direct detection of neural activity in vitro using magnetic resonance electrical impedance tomography (MREIT).

We describe a sequence of experiments performed in vitro to verify the existence of a new magnetic resonance imaging contrast - Magnetic Resonance Electrical Impedance Tomography (MREIT) -sensitive to changes in active membrane conductivity. We compared standard deviations in MREIT phase data from spontaneously active Aplysia abdominal ganglia in an artificial seawater background solution (ASW) with those found after treatment with an excitotoxic solution (KCl). We found significant increases in MREIT treatment cases, compared to control ganglia subject to extra ASW. This distinction was not found in phase images from the same ganglia using no imaging current. Further, significance and effect size depended on the amplitude of MREIT imaging current used. We conclude that our observations were linked to changes in cell conductivity caused by activity. Functional MREIT may have promise as a more direct method of functional neuroimaging than existing methods that image correlates of blood flow such as BOLD fMRI.

Characterization of Lamprey IL-17 Family Members and Their Receptors.

IL-17 is an ancient cytokine implicated in a variety of immune defense reactions. We identified five members of the sea lamprey IL-17 family (IL-17D.1, IL-17D.2, IL-17E, IL-17B, and IL-17C) and six IL-17R genes (IL-17RA.1, IL-17RA.2, IL-17RA.3, IL-17RF, IL-17RE/RC, and IL-17RD), determined their relationship with mammalian orthologs, and examined their expression patterns and potential interactions to explore their roles in innate and adaptive immunity. The most highly expressed IL-17 family member is IL-17D.1 (mammalian IL-17D like), which was found to be preferentially expressed by epithelial cells of skin, intestine, and gills and by the two types of lamprey T-like cells. IL-17D.1 binding to rIL-17RA.1 and to the surface of IL-17RA.1-expressing B-like cells and monocytes of lamprey larvae was demonstrated, and treatment of lamprey blood cells with rIL-17D.1 protein enhanced transcription of genes expressed by the B-like cells. These findings suggest a potential role for IL-17 in coordinating the interactions between T-like cells and other cells of the adaptive and innate immune systems in jawless vertebrates.

Genomic donor cassette sharing during VLRA and VLRC assembly in jawless vertebrates.

Lampreys possess two T-like lymphocyte lineages that express either variable lymphocyte receptor (VLR) A or VLRC antigen receptors. VLRA(+) and VLRC(+) lymphocytes share many similarities with the two principal T-cell lineages of jawed vertebrates expressing the αß and γδ T-cell receptors (TCRs). During the assembly of VLR genes, several types of genomic cassettes are inserted, in step-wise fashion, into incomplete germ-line genes to generate the mature forms of antigen receptor genes. Unexpectedly, the structurally variable components of VLRA and VLRC receptors often possess partially identical sequences; this phenomenon of module sharing between these two VLR isotypes occurs in both lampreys and hagfishes. By contrast, VLRA and VLRC molecules typically do not share their building blocks with the structurally analogous VLRB receptors that are expressed by B-like lymphocytes. Our studies reveal that VLRA and VLRC germ-line genes are situated in close proximity to each other in the lamprey genome and indicate the interspersed arrangement of isotype-specific and shared genomic donor cassettes; these features may facilitate the shared cassette use. The genomic structure of the VLRA/VLRC locus in lampreys is reminiscent of the interspersed nature of the TCRA/TCRD locus in jawed vertebrates that also allows the sharing of some variable gene segments during the recombinatorial assembly of TCR genes.

Selection of the lamprey VLRC antigen receptor repertoire.

The alternative adaptive immune system of jawless vertebrates is based on different isotypes of variable lymphocyte receptors (VLRs) that are composed of leucine-rich repeats (LRRs) and expressed by distinct B- and T-like lymphocyte lineages. VLRB is expressed by B-like cells, whereas VLRA and VLRC are expressed by two T-like lineages that develop in the thymoid, a thymus-like structure in lamprey larvae. In each case, stepwise combinatorial insertions of different types of short donor LRR cassettes into incomplete germ-line genes are required to generate functional VLR gene assemblies. It is unknown, however, whether the diverse repertoires of VLRs that are expressed by peripheral blood lymphocytes are shaped by selection after their assembly. Here, we identify signatures of selection in the peripheral repertoire of VLRC antigen receptors that are clonally expressed by one of the T-like cell types in lampreys. Selection strongly favors VLRC molecules containing four internal variable leucine-rich repeat (LRRV) modules, although VLRC assemblies encoding five internal modules are initially equally frequent. In addition to the length selection, VLRC molecules in VLRC(+) peripheral lymphocytes exhibit a distinct pattern of high entropy sites in the N-terminal LRR1 module, which is inserted next to the germ-line-encoded LRRNT module. This is evident in comparisons to VLRC gene assemblies found in the thymoid and to VLRC gene assemblies found in some VLRA(+) cells. Our findings are the first indication to our knowledge that selection operates on a VLR repertoire and provide a framework to establish the mechanism by which this selection occurs during development of the VLRC(+) lymphocyte lineage.

Trust and Its Role in the Medical Encounter.

This paper addresses two research questions. The first is theoretical: What is trust? In the first half of this paper we present a distinctive tripartite analysis. We describe three attitudes, here called reliance, specific trust and general trust, each of which is characterised and illustrated. We argue that these attitudes are related, but not reducible, to one another. We suggest that the current impasse in the analysis of trust is in part due to the fact that some writers allude to these distinctions, but unclearly so, whilst others elide them altogether. The second research question focuses on doctor-patient interaction. Trust is often said to be central in medical encounters but this strikes us as too vague. The success of doctor-patient relations in part depends on adopting the most appropriate of the three attitudes we delineate. We argue that reliance is the appropriate attitude for most medical encounters. When circumstances do require trust, the distinction between specific trust and general trust is crucial. We describe medical encounters requiring specific trust. General trust is less often required in medicine; but it is appropriate in some cases and, when called for, it is called for strongly.

Immune response to enzyme replacement therapies in lysosomal storage diseases and the role of immune tolerance induction.

The US Food and Drug Administration (FDA) and National Organization for Rare Disease (NORD) convened a public workshop titled "Immune Responses to Enzyme Replacement Therapies: Role of Immune Tolerance Induction" to discuss the impact of anti-drug antibodies (ADAs) on efficacy and safety of enzyme replacement therapies (ERTs) intended to treat patients with lysosomal storage diseases (LSDs). Participants in the workshop included FDA staff, clinicians, scientists, patients, industry, and advocacy group representatives. The risks and benefits of implementing prophylactic immune tolerance induction (ITI) to reduce the potential clinical impact of antibody development were considered. Complications due to immune responses to ERT are being recognized with increasing experience and lengths of exposure to ERTs to treat several LSDs. Strategies to mitigate immune responses and to optimize therapies are needed. Discussions during the workshop resulted in the identification of knowledge gaps and future areas of research, as well as the following proposals from the participants: (1) systematic collection of longitudinal data on immunogenicity to better understand the impact of ADAs on long-term clinical outcomes; (2) development of disease-specific biomarkers and outcome measures to assess the effect of ADAs and ITI on efficacy and safety; (3) development of consistent approaches to ADA assays to allow comparisons of immunogenicity data across different products and disease groups, and to expedite reporting of results; (4) establishment of a system to widely share data on antibody titers following treatment with ERTs; (5) identification of components of the protein that are immunogenic so that triggers and components of the immune responses can be targeted in ITI; and (6) consideration of early ITI in patients who are at risk of developing clinically relevant ADA that have been demonstrated to worsen treatment outcomes.

Damages and Expected Deaths Due to Excess NOx Emissions from 2009 to 2015 Volkswagen Diesel Vehicles.

We estimate the damages and expected deaths in the United States due to excess emissions of NOx from 2009 to 2015 Volkswagen diesel vehicles. Using data on vehicle registrations and a model of pollution transport and valuation, we estimate excess damages of $430 million and 46 excess expected deaths. Accounting for uncertainty about emissions gives a range for damages from $350 million to $500 million, and a range for excess expected deaths from 40 to 52. Our estimates incorporate significant local heterogeneity: for example, Minneapolis has the highest damages despite having fewer noncompliant vehicles than 13 other cities. Our estimated damages greatly exceed possible benefits from reduced CO2 emissions due to increased fuel economy.

Retrospective analyses of optical coherence tomography in recurrent macular edema following intravitreal therapy in patients with retinal vein occlusion.

BACKGROUND: Optical coherence tomography has focused mainly on central subfield thickness to quantify macular edema in central and branch retinal vein occlusion. We examined macular fields other than the central subfield to determine if they are possibly independent indicators of recurrent macular edema. METHODS: Single center, retrospective, consecutive case study of patients with recurrent macular edema secondary to either central or branch retinal vein occlusion. Thickness estimates of serial domain optical coherence tomography macular fields were obtained at the time of recurrent macular edema and analyzed retrospectively. Changes were expressed as a percentage of previous baseline levels. Change in thickness at each retreatment episode as well as average changes in thickness were calculated for each macular field for each eye. Data were analyzed via analysis of variance and Fisher's post hoc analyses. The macular field which most frequently had the largest percent increase at the time of recurrence was also assessed using averages for each subject as well as for each retreatment episode. Individual episodes of recurrent macular edema were also examined to ascertain the frequency in which there was minimal foveal edema (<15 µm increase), but non-foveal edema was considered severe enough to warrant retreatment. RESULTS: 429 episodes of recurrent macular edema in 80 eyes were examined. In addition to the central subfield, the average mean change in thickness of the most affected quadrant (central vein occlusion) or hemisphere (branch vein occlusion) of the extrafoveal 3 mm band had the largest mean changes and also most frequently had the largest increases at the time of recurrent macular edema. In approximately 20 % of both central and branch occlusions, recurrent macular edema was detected in non-central macular fields in the absence of significant edema in the central subfield. CONCLUSIONS: Analyses of non-central macular fields as well as the central subfield may be useful in the early detection and treatment of recurrent macular edema in retinal vein occlusion.

The T-cell receptor is not hardwired to engage MHC ligands.

The bias of αß T cells for MHC ligands has been proposed to be intrinsic to the T-cell receptor (TCR). Equally, the CD4 and CD8 coreceptors contribute to ligand restriction by colocalizing Lck with the TCR when MHC ligands are engaged. To determine the importance of intrinsic ligand bias, the germ-line TCR complementarity determining regions were extensively diversified in vivo. We show that engagement with MHC ligands during thymocyte selection and peripheral T-cell activation imposes remarkably little constraint over TCR structure. Such versatility is more consistent with an opportunist, rather than a predetermined, mode of interface formation. This hypothesis was experimentally confirmed by expressing a hybrid TCR containing TCR-γ chain germ-line complementarity determining regions, which engaged efficiently with MHC ligands.

Experiential benefits, place meanings, and environmental setting preferences between proximate and distant visitors to a national scenic trail.

Effective management of conserved natural areas often requires a good understanding of recreation visitors who possess various values for those areas. This study examined differences in experiential benefits sought, place meanings, and environmental setting preferences between proximate and distant visitors to a publicly managed national scenic trail, which transects a variety of conserved public lands. Data were collected using on-site post-hike interviews with visitors at low, moderate, and high use trailheads. Proximate visitors sought mental and physical health more strongly than distant visitors, while distant visitors sought environmental exploration more strongly than proximate visitors. No significant difference in family bonding and achievement benefits existed between the two groups. Meanings related to place dependence, family identity, community identity, and place identity were more strongly ascribed by proximate visitors, and both groups rated ecological integrity meanings highly. Distant visitors showed stronger tendencies toward preferring a lesser level of trail development, lower level of encounters with other groups, and higher level of natural landscapes, which indicated an inclination toward natural settings. These findings indicate a managerially relevant role of the degree of proximity to environmental resources on individuals' recreation behaviors, meanings ascribed to the resources and setting conditions. Understanding differences and similarities between groups dichotomized by proximity to natural resources should advance more effective management of recreation and benefit opportunities for diverse visitor groups.

Reflection and transmission of guided ultrasonic plate waves by vertical stiffeners.

Ultrasonic guided waves are very useful for structural health monitoring. They have the potential to interrogate and detect damage in a structure over a large area with few transducers. Guided plate modes (Lamb waves) are used and proposed for damage detection at a distance in semi-monococque structures such as airplane fuselages and spacecraft structures. The interaction of guided plate waves with stiffening members such as ribs, stringers, or the integral stiffeners used in spacecraft structures limits the distance over which structural health monitoring non-destructive evaluation systems can detect damage. This paper develops a simple explanatory model for the scattering of low-order ultrasonic Lamb waves crossing a stiffening device. The model illuminates the underlying mechanics of waves crossing a stiffener. The model shows that stop-bands for transmission of S(0) (longitudinal pressure) waves across a stiffener line up with flexural resonances of the stiffener. It also demonstrates why transmission of A(0) (flexural) waves is more complicated and harder to predict. The model is shown to agree well with both boundary element method calculations and experimental measurements.

Death, treatment decisions and the permanent vegetative state: evidence from families and experts.

Some brain injured patients are left in a permanent vegetative state, i.e., they have irreversibly lost their capacity for consciousness but retained some autonomic physiological functions, such as breathing unaided. Having discussed the controversial nature of the permanent vegetative state as a diagnostic category, we turn to the question of the patients' ontological status. Are the permanently vegetative alive, dead, or in some other state? We present empirical data from interviews with relatives of patients, and with experts, to support the view that the ontological state of permanently vegetative patients is unclear: such patients are neither straightforwardly alive nor simply dead. Having defended this view from counter-arguments we turn to the practical question as to how these patients ought to be treated. Some relatives and experts believe it is right for patients to be shifted from their currently unclear ontological state to that of being straightforwardly dead, but many are concerned or even horrified by the only legally sanctioned method guaranteed to achieve this, namely withdrawal of clinically assisted nutrition and hydration. A way of addressing this distress would be to allow active euthanasia for these patients. This is highly controversial; but we argue that standard objections to allowing active euthanasia for this particular class of permanently vegetative patients are weakened by these patients' distinctive ontological status.