Wolbachia. Regular releases of male Wolbachia-infected mosquitoes can lead to the suppression of mosquito populations, thereby reducing the risk of transmission of vector-borne diseases such as dengue. However, due to imperfect sex-sorting under IIT, fertile Wolbachia-infected female mosquitoes may potentially be unintentionally released into the environment, which may result in replacement and failure to suppress the mosquito populations. As such, mitigating Wolbachia establishment requires a combination of IIT with other strategies. We introduced a simple compartmental model to simulate ex-ante mosquito population dynamics subjected to a Wolbachia-IIT programme. In silico, we explored the risk of replacement, and strategies that could mitigate the establishment of the released Wolbachia strain in the mosquito population. Our results suggest that mitigation may be achieved through the application of a sterile insect technique. Our simulations indicate that these interventions do not override the intended wild type suppression of the IIT approach. These findings will inform policy makers of possible ways to mitigate the potential establishment of Wolbachia using the IIT population control strategy.The Incompatible Insect Technique (IIT) strategy involves the release of male mosquitoes infected with the bacterium  Aedes aegypti (Ae. aegypti) mosquito is an efficient vector of several arboviruses, such as dengue, Zika, chikungunya and yellow fever )  declined steadily during the intervention but did not reach elimination at the end of the intervention. Subsequently, the wAlbB female mosquito population rose again and stabilized at a non-zero levels at the simulation endpoint. At higher release numbers (S4 [II] and S4 [III]),  G, the wA [III]), H,I, the Wolbachia-IIT strategy has been shown to be a promising method for suppressing mosquito populations [The ulations ,45 and oulations . Howeverulations . FirstlyWolbachia-IIT with conventional vector control measures [Wolbachia strain due to lowered competition from wild type mosquitoes in the environment. This could result in Wolbachia mosquitoes replacing the wild type population, jeopardizing the suppression effort and rendering the strategy unsuccessful. Intervention measures are therefore required to prevent the establishment of Wolbachia in wild type mosquito populations. As such, we sought to implement possible strategies for mitigating the establishment of the formerly released Wolbachia strain (wAlbB) within an appropriate modelling framework.At baseline, we demonstrated a significant reduction in the wild type mosquito population C,D of upmeasures , with himeasures ,48,49,50Wolbachia strain. Namely, (i) the persistent use of irradiated male and female Wolbachia mosquitoes via SIT-IIT (S3B) and (ii) the release of a second Wolbachia strain  after establishment of the former Wolbachia wAlbB has occurred. Under S3B, even if imperfect sex sorting (FRER > 0) persists together with SIT-IIT, the established wAlbB female mosquito population can be successfully eliminated. Similarly, under S4, the established female wAlbB female mosquito population can be successfully eliminated, but under non-zero FRERs for the wMel releases, the establishment of wMel female mosquito populations will occur. In both cases, the wild type mosquito population remains suppressed compared to the baseline levels, demonstrating that these interventions do not undermine the accrued suppression benefits from the originally released Wolbachia strain. These findings support the use of a hybrid approach [Wolbachia male mosquitoes to significantly reduce high mosquito populations, followed by the use of irradiated male and female mosquitoes (S3B) to counter the potential issue of establishment.We presented several key strategies which may be used to mitigate the potential establishment of the released approach , where aWolbachia strain (See Wolbachia strain (See Wolbachia mosquito population’s niche—considering, for example, the intrinsic rate of population growth—the release of a minimum number of sterile or bi-directionally cytoplasmic incompatible mosquitoes may be required. The release numbers and intensity govern the probability of mating between the released sterile/bi-directionally cytoplasmic incompatible male mosquitoes with the established Wolbachia female mosquitoes. Consequently, whether the niche is taken over depends on the release numbers and intensity. Under fewer number of mosquitoes being released this threshold might not be achieved and the probability of mating between the released Wolbachia males and established Wolbachia females may be insufficient to take over this niche, preventing the successful elimination of the established Wolbachia-infected Ae. aegypti strain. While actual mosquito populations are difficult to ascertain in the real world, our results demonstrate the need to couple proposed interventions with entomological surveillance to assess the efficacy of interventions targeted at mitigating establishment and for the appropriate timing of intervention scale ups and/or rollbacks.Among the various release ratios and female release error rates explored under S3B and S4, we found that higher release ratios were more effective in driving down the female population of the released rain See . These irain See . To takeWolbachia-infected males were released at every release event under the constant release approach in S3B,4, negating the need for real-time and accurate population surveillance. Scaling up such a strategy in terms of release numbers and frequency would be far simpler, without additional resources required for operational purposes.In our study, we explored the possibility of establishment under a constant release strategy and several interventions to mitigate this. Pagendam et al. highlighted the possibility for adaptive and crude adaptive releases under IIT to mitigate establishment . HoweverWe followed Pagendam et al. , Jansen Wolbachia establishment, we required a simulation framework that could easily parameterize various facets about the mosquito populations. Existing stochastic models were difficult to adapt, with Jansen et al. [Wolbachia strain strategies are employed.In tackling the question about strategies to mitigate n et al.  assumingn et al.  requirinEmpirical evidence suggests that mosquito larval breeding sites are often fragmented , with thIn our study, an independent IIT programme had been initiated to suppress mosquito populations, resulting in the issue of establishment of the Wolbachia strain in the field ,41. We tWolbachia strain, our study suggests the irradiation of male and female Wolbachia mosquitoes under SIT-IIT with all FRERs can be effective. Our simulations indicate that this intervention does not override the intended effect of wild type suppression under the IIT approach.To mitigate establishment of the released


Apex and mesopredators such as elasmobranchs are important for maintaining ocean health and are the focus of conservation efforts to mitigate exposure to fishing and other anthropogenic hazards. Quantifying fishing mortality components such as at-vessel mortality (AVM) is necessary for effective bycatch management. We assembled a database for 61 elasmobranch species and conducted a global meta-synthesis to estimate pelagic longline AVM rates. Evolutionary history was a significant predictor of AVM, accounting for up to 13% of variance in Bayesian phylogenetic meta-regression models for Lamniformes and Carcharhiniformes clades. Phylogenetically related species may have a high degree of shared traits that explain AVM. Model-estimated posterior mean AVM rates ranged from 5% (95% HDI 0.1%–16%) for pelagic stingrays and 76% (95% HDI 49%–90%) for salmon sharks. Measures that reduce catch, and hence AVM levels, such as input controls, bycatch quotas and gear technology to increase selectivity are appropriate for species with higher AVM rates. In addition to reducing catchability, handling-and-release practices and interventions such as retention bans in shark sanctuaries and bans on shark finning and trade hold promise for species with lower AVM rates. Robust, and where applicable, phylogenetically-adjusted elasmobranch AVM rates are essential for evidence-informed bycatch policy. Overexploitation is the primary cause of declines of marine species. It can cause protracted or irreparable harm and permanent loss of populations, with changes and loss in marine biodiversity and ecosystem services5. Bycatch in pelagic longline fisheries is a global threat to the conservation of some elasmobranchs6. Pelagic sharks experienced a 71% decline in abundance over the past 50 years7. Depending on a fishery’s management framework and markets, catch composition and practices of individual vessels, sharks and rays may be discarded or retained as either incidental or target catch9. Retention may entail the entire fish or only shark fins or ray gill rakers.Elasmobranchs (sharks and rays) belong to one of the most diverse marine taxonomic groups and include apex and mesopredators essential for maintaining ecosystem structure, functions and stability12. There has also been increasing attention to the socioeconomic costs to fisheries from shark interactions such as from the depredation of catch and bait13 and risks to food, nutrition and livelihood security of coastal fishing communities from declining elasmobranch abundance15.There has been increasing concern in recent decades over the sustainability of elasmobranch mortality in pelagic fisheries given elasmobranchs’ vulnerability to exploitation, ecosystem-level cascading effects from declines in elasmobranch abundance, and fisheries-induced evolution and reduced population fitness that results from selective removals based on heritable traits17. For non-retained catch, a key component of total fishing morality is at-vessel mortality (AVM), also referred to as haulback or capture mortality, which is the proportion of the catch that is dead upon retrieval of the fishing gear before being handled by crew. Because small changes in mortality can result in large changes in mature biomass and therefore population growth, uncertainty in AVM rates is a major impediment to effective management and sustainable fisheries, in particular for elasmobranchs18. Robust estimates of species-specific AVM rates enable performance assessments of conservation and management measures, such as retention bans—including within Shark Sanctuaries, bans on international trade, bycatch quotas, shark finning bans, gear design requirements and handling-and-release practices. Identifying informative predictors of AVM risk, including phylogeny, physiological attributes, fishing methods and gear designs, facilitates estimation of AVM rates for data-limited species and identification of effective methods to mitigate AVM.Accurate estimates of all sources of mortality are needed for robust assessments of the ecological effects of fishing, including through quantitative stock assessments, population viability models and multispecies ecosystem models21. Independent and unbiased synthesis of all accumulated scientific information is a fundamental transparency principle for developing evidence-informed conservation management decisions23. Meta-analytic based synthesis approaches typically produce the strongest evidence with generalizable results that are optimal for global and regional decision-making25.There is limited information available on AVM rates for most elasmobranchs, and quantitative meta-analytic synthesis studies of AVM rates in longline fisheries have been conducted for few elasmobranch species30 through: (1) the inclusion of a much larger number of studies and species; (2) applying Bayesian multilevel or hierarchical meta-regression models to account for informative covariates; and (3) phylogenetically adjusting the AVM rate estimates for the evolutionary history for two major shark clades with either relatively high (Carcharhiniformes) or low (Lamniformes) extant species diversity31. The study objectives were to:Derive robust species-specific estimates and measures of uncertainty of AVM rates for elasmobranchs captured in pelagic longline fisheries;Determine if phylogeny, operational longline fishing methods and gear designs, ventilation mode, morphology and ocean region are informative predictors of AVM rates; andIdentify gaps in information on priority potentially informative predictors and in taxonomic groups and regions for which additional primary studies are required for robust meta-syntheses of AVM rates.This study fills this priority research gap on elasmobranch AVM rates. We assembled an extensive database and conducted a global meta-synthesis to aggregate, test and summarize species-specific AVM rates for elasmobranchs captured in pelagic longline fisheries. The study significantly extends previous meta-analysesThe AVM rates derived for 61 elasmobranch species, estimated using robust statistical procedures for synthesizing evidence from multiple studies, supports evidence-informed conservation and fisheries management for sharks and rays.The random forest derived variable importance plot identified several potentially informative predictors of elasmobranch AVM for the entire sample of 1,438 effect sizes summarized in Fig. Rhat < 1.0132, reflected convergence of the Bayesian GAMMs with binomial-Normal likelihood. The best-fit GAMMs identified by the LOOcv and Bayesian stacking metrics fitted the clade-specific AVM datasets well as shown for example by the graphical posterior predictive check tests summarized in Fig. Convergence diagnostics such as multiple chain rank plots, and the effective posterior sample size (ESS) metrics coupled with the rank-based diagnostic statistic The pooled mean AVM estimates for the Carcharhiniform species Fig. A and LamThe mean phylogenetic signal or constraint estimated for Carcharhiniform species was estimated to be 0.06 (95% HDI 0.01–0.23) and 0.13 (95% HDI 0.01–0.42) for Lamniform species. These are significant but moderate phylogenetic signals, implying that evolutionary history played an important but relatively minor role in explaining the AVM rate differences among the 26 Carcharhiniform species and the 13 Lamniform species.Carcharhiniform species had a > 0.95 probability of lower AVM rates in the Pacific Ocean than the Atlantic Ocean. Carcharhiniform species in the Atlantic were 2.9 times 95% HDI 1.6–4.8) more likely to be dead at haulback than in the Pacific. The ocean-specific effect was significant for sharks caught on either circle or J-shaped hooks . The overall AVM rate from a binomial-Normal GAMM was mean of 0.047 (95% HDI 0.001–0.157) (Table The pelagic stingray 7) Table . Ocean b7) Table A and hoo7) Table C were si7) Table B and num7) Table D were noMobula birostris, cookie cutter shark Isistius brasiliensis and velvet dogfish Zameus squamulosus, overall AVM rates from binomial-Normal GAMMs were a mean of 0.332 (95% HDI 0.015–0.707), 0.295 (95% HDI 0.055–0.564), and 0.226 (95% HDI 0.071–0.368), respectively  for the night shark Carcharhinus signatus. For rays, mean AVM rates ranged from a low for the pelagic stingray (“Glaucostegus cemiculus.AVM rates were estimated for 54 shark species (n = 1322 records), and for 7 ray species (n = 116 records) Table . Of thestingray “” sectionRhizoprionodon terraenovae, with separate forest plots from records using only squid bait shown in Panel A and records using only fish, a mix of fish and squid, or unknown bait type in Panel B. Weighted relative risk estimates are ordered by effect size, and an estimated overall Pooled Effect log relative risk ratio is shown at the bottom of the forest plot and by the dashed vertical line. The overall AVM rate with only squid bait of 0.878 (95% HDI 0.75–0.99) was significantly higher than a mix of bait types of 0.427 (95% HDI 0.26–0.61).Figure 34. Not accounting for phylogeny potentially risks estimating biased species-specific AVM rates, reduces the robustness of stock assessments, perhaps drawing incorrect conclusions and adopting misinformed policy. This finding is consistent with conclusions of previous studies that not accounting for phylogenetic non-independence of taxa in ecological meta-analyses produces biased results35.This is the first study to comprehensively assess the relationship between phylogeny and AVM risk for elasmobranch species exposed to pelagic longline fisheries. The finding of a moderate but significant relationship highlights the importance of accounting for phylogenetic dependence in elasmobranch multispecies meta-analytic syntheses on AVM rateMore accurate estimates of shark species-specific AVM rates are obtained when meta-analytic syntheses are designed to account for phylogeny—the degree of shared evolutionary histories between species. Accounting for phylogeny in meta-analytic syntheses produces more robust species-specific AVM estimates for Lamniform and Carcharhiniform clades. The significant phylogenetic signal does not mean that species within these two clades have similar AVM rates; conversely, there is a broad range in species-specific AVM within these clades Figs. . Instead36. They may have a high degree of shared non-heritable as well as heritable traits—if traits were conserved during evolution leading to descendent lineages, which occurs when traits are under strong selection (phylogenetic niche conservatism)38. For example, while there is some co-occurrence, most extant Lamniformes and Carcharhiniformes are ecologically differentiated by diet, morphology and in some cases habitat type39. Some shared physiological, morphological and behavioral traits may be informative predictors of AVM risk. For example, the lamnid sharks and common thresher shark (Alopias vulpinus) are the only elasmobranchs with regional red aerobic myotomal muscle endothermy41. They can occupy deeper and cooler habitats on an ephemeral basis. Not being dependent on ambient temperature for thermoregulation may contribute to their AVM rate being less affected by the duration hooked and ocean temperature relative to ectothermic elasmobranchs42. Endothermic sharks, which may have had a single origin in the Cretaceous, also tend to have larger body sizes than ectothermic sharks, which previous studies have found to be an informative predictor of AVM risk—larger fishes have larger energy stores relative to smaller individuals, making them more resilient to stressors, including a fight response to capture46. However, not all traits may be conserved during evolution. Trait divergence can occur during adaptive radiation, when species quickly diverge to avoid competition and fill different ecological niches37. Fisheries are also altering populations’ evolution through selective removals based on heritable traits12, possibly including through selective AVM within populations based on traits such as for fitness47.The phylogenetic signal estimated by the Bayesian multilevel meta-regression models accounted for the dependence among elasmobranch species due to shared evolutionary histories. Closely related taxa share a phylogenetic history and would be expected to be ecologically similar48. While conserved traits, such as thermal tolerance and niche tracking, will be expressed consistently by individuals of a population, flexible, labile traits such as stress response, shyness/boldness and timing of reproduction may have high variability in their expression both by an individual and between individuals of a population49. The strength of any phylogenetic signal may be decreased by this complex mixture of conserved and labile traits that affect AVM rates49.Furthermore, it is likely that vulnerability to AVM is a function of both evolutionarily conserved and labile traitsAlopias pelagicus), with a relatively high mean AVM rate of 58%, which is categorized as Endangered by IUCN50, with a relatively low phylogenetically adjusted rmax  of 0.1551 and low mean rmax of 0.0652. Based on phylogenetically adjusted estimates of rmax, Lamniformes have a high extinction risk and have moderate to high AVM rates. Carcarhiniformes had highest AVM rates but a lower extinction risk relative to Lamniformes51.Some sharks with high AVM rates have relatively high extinction risks due to pelagic longline fisheries. This includes the pelagic thresher shark  and environmental factors  may be more important predictors of AVM than manageable, operational fishing parameters. Similarly, there may be fisheries where a species tends to be retrieved alive but are subsequently discarded dead. For elasmobranch species with low AVM rates, in fisheries where these species have low retention, comparing at-vessel and release conditions would help determine if improved handling and release practices could increase the proportion of released catch that are alive, as well as reduce the post-release mortality rate. Furthermore, in fisheries where elasmobranch species with low AVM rates are retained, output controls that limit or ban their retention or trade have the potential to substantially reduce fishing mortality.For elasmobranchs with relatively high AVM rates, methods that avoid and reduce their catch risk hold promise to reduce total fishing mortality. For these species, retention bans, shark finning restrictions and other output controls may be inappropriate approaches, unless they indirectly lead to the use of methods that reduce catch rates. Instead, measures that avoid and minimize shark and ray catch in pelagic longline fisheries are needed, either by: (1) reducing effort; or reducing one or more capture susceptibility attributes of: (2) spatial and temporal overlap through static and dynamic area-based management tools; (3) vertical overlap by managing fishing depth and the time of day of fishing; and (4) selectivity such as by adjusting leader material, hook and bait type and restricting the use of light attractors Section . For spe54. Supplemental Information Section 56. We found little support for such predictors affecting estimated AVM rates for our two clades of 39 shark species. Species-specific interactions with all operational predictors could not be explored for most of these 39 species because the publications compiled to assemble our dataset provided insufficient coverage of all predictors included in the models. However, the sample forest plot presented for the Atlantic sharpnose shark , may also cause fishers to discontinue using fishing methods and gear designs used to target sharks, such as shark lines, wire leaders, and using pieces of incidental catch for bait. If both a bycatch quota and consequences of reaching the threshold are sufficient, then quotas may incentivize fishers to adjust fishing gear and methods to increase selectivity66. Furthermore, relative to species with low AVM rates, for shark species with high AVM rates, finning bans will be less effective at reducing fishing mortality.Bans on shark finning, where fins are retained and the remaining carcass is discarded, might reduce retention of sharks with little or no market value other than for the fins, and might discontinue fishing methods and gear designs used to target sharks. If shark carcasses have low market value, then shark finning bans will be a disincentive for targeting sharks, as fishers will want to use space in the fish hold for more valuable catch. However, for shark species that are retained for their meat and various other products, finning bans are unlikely to affect fishing mortality rates67. While most pelagic longline elasmobranch catch is from incidental capture by fisheries targeting tuna and tuna-like species (Scombroidei) and billfishes (Xiphioidei)11, these fisheries may also use gear designs to target sharks on shallower branchlines. This shark targeting would be discontinued if shark retention or trade were banned68 and subject to robust surveillance and enforcement. Several elasmobranch species are listed on Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which establishes close control of their international trade, but none are currently listed on Appendix I, which would ban their international trade69. Retention bans, such as through measures adopted by regional fisheries management organizations (RFMOs) and under national Shark Sanctuaries, have been documented to decrease shark fishing mortality rates in some fisheries68 but may be ineffective under certain management frameworks70.Banning elasmobranch retention and international trade might cause pelagic longline fisheries to change targeting practices, discontinue retention and prevent sharks from becoming targets72. While discard bans may incentivize fishers to implement more selective fishing gear designs and methods to reduce catch rates of unwanted species and sizes of catch subject to the policy, this may be counterproductive, in particular for species with low AVM and post-release mortality rates53.Reducing discards is prescribed in international guidelines and required by a growing number of fisheries management frameworks77. This leaves substantial opportunities to improve regional conservation and management measures for elasmobranch longline bycatch.The five tuna RFMOs tap a very small subset of elasmobranch bycatch mitigation methods. They all ban shark finning and have retention bans in place for certain elasmobranch species. One has catch limits for two shark stocks, some restrict the use of wire leaders and shark lines, and some have voluntary guidelines on handling and release practices78. We found a paucity of elasmobranch haulback condition records from the Indian Ocean and Mediterranean Sea, and no records from the Black Sea. Addressing these regional gaps is an additional priority.Completely resolving elasmobranch phylogeny may enable more robust accounting of phylogenetic dependence in multispecies meta-syntheses of AVM rates. Several species had insufficient sample sizes for robust meta-regression models. Additional haulback condition records are needed for these species, in particular for threatened, rare and phylogenetically distinct species which may play relatively large roles in shaping evolutionary processes and ecosystem resilience56. Unfortunately, most of these variables are rarely or never measured.Richer datasets would enable the inclusion of additional potentially informative predictors of AVM. Numerous predictors could not be explored here due to limitations of the assembled database. This includes, for example, duration spent hooked (fight time), dissolved oxygen, sea surface temperature, depth of the thermocline/mixed layer, salinity, body size and sex of the catch, hook number of the catch (which hook between two floats and hence relative fishing depth), whether the catch was on a shark line, anatomical hooking position, hook size, hook degree of offset, and time-of-day of the gear soak18. Compiling records from a broader range of pelagic longline fisheries employing diverse fishing methods and gear designs, including from artisanal, small-scale longline fisheries, would enable a more robust assessment of the significance of these variables.Furthermore, many of the potentially informative predictors that were extracted from the compiled publications had low variability, including soak duration, hooks between floats and branchline length, the latter being particularly important for obligate ram-ventilating elasmobranchs53, ventilation mode and body form (morphology) were not informative predictors of haulback condition for pelagic elasmobranchs in our study. Body form categories based on gill slit morphology and ventilation mode used here may be correlated with phylogeny80, so when models are phylogenetically adjusted, these variables become redundant.Phylogeny was a moderate but significant predictor of pelagic longline AVM rate. This was the first comprehensive study to assess the influence of elasmobranch phylogeny on AVM. Contrary to some hypothesesThe most promising approach to reduce total fishing mortality of species with high AVM rates is to employ methods that reduce catch risk. To reduce total fishing mortality of species with low AVM rates, in addition to reducing catchability, handling-and-release practices and policy interventions that, under certain enabling environments, reduce retention, including retention bans in blue water shark sanctuaries, and shark finning and trade bans, are appropriate. The elasmobranch AVM rates, estimated here through Bayesian meta-regression analysis, a robust statistical procedure for synthesizing evidence from multiple studies, support evidence-informed elasmobranch conservation and fisheries bycatch management. When combined with robust estimates of natural and other anthropogenic hazards, including other components of fishing mortality, these AVM rates can improve the reliability of models of elasmobranch population dynamics and support developing strategies to mitigate risks.81, Collaboration for Environmental Evidence83 and Preferred Reporting Items for Systematic reviews and Meta-Analyses84. An unstructured literature search was implemented by reviewing reference lists of the compiled publications from the systematic search. Supplemental Information Section A two-tiered literature search was employed to compile relevant peer-reviewed published and grey literature and assemble a dataset suitable for meta-analytic evaluation. A link to the assembled dataset, which includes references for retained publications, is provided in the Data Availability section. The methods for the systematic literature review were adapted from the Reporting Standards for Systematic Evidence Synthesesca. 70%). We excluded from meta-regression modelling the remaining 18 species with limited data records, including zero dead for 1 or more of the records but, nonetheless, derived AVM rates for further qualitative consideration in our meta-synthesis. The AVM rate for each of those 18 species  was estimated using a Bayesian binomial likelihood estimator that accounts for zero recorded mortalities85. The mean posterior rate and a 95% highest posterior density interval (HDI) was summarized by sampling from a binomial likelihood with a Bayes-Laplace prior85 using the binom package for R86—rather than just using the raw study-specific summaries.Our dataset comprised 1438 study-specific summary or aggregate AVM rates for 61 elasmobranch species from 33 genera, 22 families and 9 orders. Two shark clades or taxonomic orders  accounted for 39 of those species (ca 64%) and phylogenetic Bayesian meta-regression models were fitted to those data. Separate Bayesian meta-regression models without phylogenetic adjustment were fitted to the AVM data for 4 other species —far too few species to explicitly account for any phylogenetic resolution. Overall, we used some form of Bayesian meta-regression model to summarize the AVM rates for 43 of the 61 elasmobranch species  phylogeny remains unresolved94, so we derived the phylogenetic correlation matrix for all the 61 elasmobranch (shark and ray) species in our study by using the phylogenetic tree construction proposed by Stein et al.95 for 1192 Chondrichthyan species. Credible sets of the species-level phylogenetic history are available for subsetting and downloading at http://vertlife.org/phylosubsets. We recovered 100 random Chondrichthyan phylogenetic trees in NEXUS file format96 from a posterior of distribution of 10,000 phylogenetic trees using the “[fully resolved 1 fossil (set of 10 k trees)]” source—Upham et al.97 provide details on how these phylogenetic tree posterior distributions have been constructed using a Bayesian 2-level “backbone-and-patch” approach. We then randomly selected one tree from that 100-tree selection, which was used as the phylogenetic hypothesis or template for our meta-synthesis. Similar results were found using other randomly selected trees. With that phylogenetic tree we were then able to derive variance and correlation matrices using the ape package for R98 and tree visualisations using the ggtree package for R99—see Fig. The multilevel or hierarchical meta-regression modelling approach100. We fitted this model to each of the two clades: the Carcharhiniformes  and the Lamniformes . These data comprised 706 study-specific effect sizes for the Carcharhiniformes and 466 effect sizes for the Lamniformes, covering both the Atlantic and Pacific Oceans for both clades—records from the Mediterranean and Indian Ocean were excluded from this meta-analysis due to small sample sizes. We fitted these meta-analytic models to the study-specific proportion for each species recorded dead at haulback in pelagic longline gear. The multilevel structure for each model comprised the individual study identification, multiple records nested within some studies and the research group cluster for the various studies . We included the potentially informative covariates or predictors in the meta-regression structured models to evaluate whether AVM rate was a function of those predictors. We had previously screened a range of potential predictors to determine a minimal set of informative predictors using machine learning approaches discussed above.We modelled the effect of potentially informative predictors on elasmobranch species-specific AVM rates using a Bayesian multilevel or hierarchical regression modelling approach, which included a species-level phylogenetic structure as a group-level or random effect to adjust for any phylogenetic dependence101 using the Stan computation back-end102 via the brms interface for R103. This is also known as a binomial-Normal hierarchical meta-analytic model104 but was fit within a Bayesian inference framework105 using weakly informative priors106. It is a binomial-Normal GAMM regression model because: (1) the model likelihood is binomial to account for the proportion response data, (2) the group-level or random effects including the phylogenetic structure are sampled from a multivariate Gaussian distribution104, and (3) any nonlinear covariate functional form was accounted for using a thin plate regression spline basis commonly applied to fit generalized additive mixed models or GAMMs107. The fitted binomial-Normal model to the study-specific estimates for each species were then used to derive the overall or pooled mean AVM rate based on the posterior for each estimate comprising 10,000 samples or draws that were also used to derive the uncertainty estimates.We fitted these random-effects meta-regression models with binomial likelihood appropriate for proportion data108. The HDIs were summarized from the posterior samples for each species meta-analytic model fit using the tidybayes package for R109. A probability statement about the existence of a particular predictor-specific effect can also be determined with those 10,000 draws using the probability of direction metric proposed recently using the BayestestR package for R110.We used HDI as our measure of uncertainty, which is the shortest credible interval111 and implemented using the emmeans package for R112. We then summarized the marginal effect posterior densities to assess any apparent difference for instance between the estimated marginal AVM rates for the Atlantic and Pacific estimates. The posterior ratio summary was included in the summary plot for this effect.The estimated effect summaries based on the best-fit conditional regression GAMMs were then adjusted for variable sample size using the predicted estimated marginal means approach113. The phylogenetic signal or constraint is a simple metric that reflects the apparent effect of shared evolutionary history or ancestry on the specific trait or attribute state being evaluated114.We estimated the model-specific phylogenetic signal as the mean posterior proportion (with 95% HDI) of the summed group-level variances attributable to the phylogenetic group-level component—this approach assumes a Brownian diffusion or genetic drift process of character evolution for a continuous species-specific traitRhat statistic32. We also used leave-one-out cross-validation (LOOcv) metrics and Bayesian stacking116 to explore any comparative difference in expected predictive accuracy between models fitted with or without a specific predictor such as for instance body form, ventilation mode or phylogenetic correlation structure. Further evaluation of the best-fit-model was then assessed using graphical posterior predictive checks117. All inference was then made using the best-fit model and the posterior predictive samples118.All models were fit with 4 Markov chains with 10,000 iterations per chain after a warm-up of 2000 iterations. Model convergence was assessed using parameter-specific diagnostics such as multiple chain rank plots, bulk and tail effective sample size metrics and a rank-based Manta (Mobula) birostris, Pteroplatytrygon violacea) and two Squaliformes species .We modelled the effect of potential informative predictors on AVM rates for each of the following four species using a similar Bayesian GAMM modelling approach but without phylogenetic adjustment as no phylogenetic structure was relevant for this small subset of species—two Myliobatiformes species  effects used in the Bayesian GAMMs. Metafor cannot directly fit a binomial-Normal GAMM (or GLMM) with phylogenetic structure, so we used the multivariate parameterization form of a meta-regression model in metafor122 with logit transformed AVM response to mimic a GLMM and specifically accommodate in metafor the more complex forms of random-effect structures used here including the phylogenetic tree structure33.We explored potential publication biasSupplementary Information.


Low-dose computed tomography (CT) denoising algorithms aim to enable reduced patient dose in routine CT acquisitions while maintaining high image quality. Recently, deep learning (DL)-based methods were introduced, outperforming conventional denoising algorithms on this task due to their high model capacity. However, for the transition of DL-based denoising to clinical practice, these data-driven approaches must generalize robustly beyond the seen training data. We, therefore, propose a hybrid denoising approach consisting of a set of trainable joint bilateral filters (JBFs) combined with a convolutional DL-based denoising network to predict the guidance image. Our proposed denoising pipeline combines the high model capacity enabled by DL-based feature extraction with the reliability of the conventional JBF. The pipeline’s ability to generalize is demonstrated by training on abdomen CT scans without metal implants and testing on abdomen scans with metal implants as well as on head CT data. When embedding RED-CNN/QAE, two well-established DL-based denoisers in our pipeline, the denoising performance is improved by 10%/82% (RMSE) and 3%/81% (PSNR) in regions containing metal and by 6%/78% (RMSE) and 2%/4% (PSNR) on head CT data, compared to the respective vanilla model. Concluding, the proposed trainable JBFs limit the error bound of deep neural networks to facilitate the applicability of DL-based denoisers in low-dose CT pipelines. Low-dose CT acquisitions reduce patient dose4 but contain higher noise levels in the measured data6. To enhance the image quality of low-dose CT acquisitions, image-based denoising approaches have been proposed, which aim to preserve clinically relevant features compromised with noise. Classical approaches are based on physically motivated conventional filters, considering the inherent properties of the image features11. Although such filters produce reliable results through a clear algorithmic formulation, their performance is restricted by a limited capability to extract complex features. In addition, conventional filters often require hyperparameters that have to be tuned by hand. Therefore, deep learning (DL)-based denoising methods gained interest due to their flexibility, strong performance, and data-driven optimization17. However, deep neural networks usually do not robustly generalize beyond their finite training data distribution, which so far limits clinical applications of DL-based denoising for low-dose CT19.Minimizing patient dose in computed tomography (CT) is necessary to avoid radiation-related diseases22. Consequently, different image processing pipelines were proposed, employing physical assumptions about noise characteristics to leverage prediction reliability of DL-based methods in the context of image denoising24. The joint bilateral filter (JBF) is a conventional denoising filter that allows edge-preserving denoising while considering additional information in terms of a guidance image during its filter operation. Imitating the JBF with a shallow convolutional network led to a reduction of trainable parameters in the JBFnet23 and the MJBF architecture25. Although both network architectures are inspired by the JBF operation, they both learn filter operations through fully convolutional neural networks with a relatively large number of free parameters compared to the JBF. Therefore, both architectures can learn any possible filter kernels and are not enforced to perform the well-know JBF operation, which raises questions on data integrity and interpretability likewise to other DL methods24. A different approach employs a custom bilateral filter approximation built from neural network building blocks that can be optimized26, but it does not allow integration of additional learned information into the filter process. Other works presented methods to find optimal filter27 or training28 hyperparameters by predicting them through external neural networks. However, such approaches do not allow for direct integration into DL models as they can not compute gradients toward those hyperparameters.Previously, Maier et al. proved that including physical knowledge in terms of known operators in neural networks reduces the absolute error bound of the model29. However, the prediction of bilateral filter layers is solely dependent on three learned spatial parameters and one intensity parameter9. Therefore, the bilateral filter operation is conceptually different from the joint bilateral filter algorithm, as JBFs allow considering additional information in terms of a guidance image in their denoising algorithm30. In this work, we extend our research on bilateral filtering by proposing a fully differentiable, trainable joint bilateral filter that allows denoising using a learned guidance image which broadens its applicability. Our filter layer derives analytical gradients toward the filter input, the image guide, and all filter parameters to achieve differentiability and enable data-driven optimization. Guidance images are estimated using two well-established denoising algorithms: RED-CNN12, an encoder–decoder architecture achieving competitive performance in recent works32, and Quadratic Autoencoder (QAE)13, employing quadratic neurons. Our proposed hybrid filter model bridges the gap between deep neural networks’ high model capacities and the robustness of conventional denoising filters due to the well-defined, restricted influence of the learned guide.In our previous work, we presented a trainable bilateral filter with competitive denoising performance that can be included in a differentiable pipeline and optimized in a data-driven fashionOur contributions are threefold. First, we propose a GPU-based, trainable JBF based on an analytical gradient that can be included in any differentiable pipeline. To the best of our knowledge a directly trainable JBF was never presented before. Second, we introduce a hybrid denoising pipeline combining the flexibility of deep neural networks with the robustness of the trainable JBF. Third, we demonstrate the robustness of our model on abdomen CT scans containing metal, with metal not being present in the training data distribution and on out-of-domain head CT scans. Our hybrid JBF-based denoising setting improves the prediction reliability of existing DL-based models with limited computational overhead.L calculated from network predictions to fulfill a desired task33. This requires calculating the derivative of the loss L with respect to each trainable model parameter to iteratively update the network during training.Artificial neural networks are generally trained via gradient descent optimization by minimizing a loss metric In this section, the analytical gradient of the proposed trainable JBF layer with respect to filter input, guidance image, and filter parameters is derived as the algorithmic contribution of our work. Figure 30 the JBF operation is defined ask, and a guidance image L with respect to each trainable parameter to enable data-driven optimization. We can calculate the gradient for our joint bilateral filter layer by using the chain ruleL with respect to each voxel of the guidance image In the following, bold letters are used to indicate vectors. According to Petschnigg et al.PyTorch deep learning framework34 to leverage computational performance. The processing time of one torch.nn.Conv2d layers (PyTorch) approximately require NVIDIA Quadro RTX 4000 GPU. Please note that run times can strongly vary depending on the used hardware.The filter window size of the JBF is chosen dynamically dependent on the spatial kernel sizes as https://github.com/faebstn96/trainable-joint-bilateral-filter-source and can be installed via the well-known Python Package Index (PyPI) as plug-and-play PyTorch layer. In addition, our code repository contains example scripts and a test script that compares the implementation of the analytical gradients with numerical gradient approximations using the torch.autograd.gradcheck function to make sure the filter derivative is correctly implemented.Our filter layer is publicly available at 23 and our previous experimental findings on using multiple stacked bilateral filters29 which improved performance compared to employing only a single denoising step. The three trainable JBFs add in total twelve independently trainable parameters to the denoising model. The forward pass of each filter layer is calculated as written in Eq. 35, containing paired low-dose (25% dose) and high-dose CT volumes. The goal of our experiment is to quantitatively evaluate the robustness of the introduced denoising models and compare them with the vanilla DL-based denoising models RED-CNN and QAE. Therefore, we manually split the abdomen data into two domains. First, patients without metal pieces and second reconstructions containing pieces of metal like implants or catheters that appear as bright regions due to their strong x-ray absorption. Only data from the first domain not containing metal is used for training (21 scans) and validation (two scans). Subsequently, we test our models on the previously unseen metal domain scans (24 scans) to evaluate how the different architectures can handle examples that are insufficiently represented by the training data domain. As the metal pieces are usually located in small sub-volumes of the reconstructions, we additionally define 17 three-dimensional regions of interest (ROIs) that are evaluated separately to get more expressive results on the sensitivity to the out-of-domain features. The coordinates of all 17 ROIs are provided in the 35.All used abdomen and head CT scans are from the public 36 are calculated to compare model prediction with their respective high-dose target reconstruction. RMSE and PSNR particularly assess deviations from the target image intensities, whereas SSIM aims to imitate human perception to compare image content. We found that all performance differences between vanilla and respective JBF-based model in Table 37 on a p-value We present quantitative denoising results on the entire abdomen test data set and only on the abdomen ROIs containing metal pieces in Table Whereas the hybrid JBF layer-based pipelines perform comparably to the vanilla deep denoising models over the entire abdomen test data, an explicit performance improvement is recognized on the 17 abdomen ROIs as well as on the head CT scans on all three investigated image quality metrics. Both JBF-based pipelines decrease the RMSE by 10%/82% and improve the PSNR and SSIM by 3%/81% and 0.1%/30% around the out-of-training-domain metal features compared to the vanilla RED-CNN and QAE respectively. The denoising performance on the head CT data is improved by 6%/78% (RMSE), 2%/4% (PSNR), and 0.1%/0.1% (SSIM).Visual results on one ROI and a head CT slice are displayed in Fig. The QAE predicts strong artifacts that are visible in the abdomen intensity images and difference images surrounding metal implants. Using such predictions as an image guide in a JBF-based pipeline produces results that visually look much closer to the high-dose target where features like the shape of metal pieces or the adjacent anatomy are visible. Further, intensity distortions in QAE predictions on the head CT data set are removed using the combined QAE+JBFs filtering approach. Only regions around the dental crowns with heavy metal reconstruction artifacts remain disturbed.Although one could simply add abdomen scans containing metal pieces or head CT data to the training data set to improve denoising performance, our experiment is particularly designed to evaluate and quantify robustness to real CT data that is underrepresented in the training data. Our experiment, therefore, mimics the present clinical scenario where a model is only trained on a limited number of scans but must also handle differing anatomies or scanning parameters. The denoising performance of a JBF depends on an optimal intensity range kernel In our conducted experiments, pre-trained denoising networks predict the guidance images that are input to the JBF layers. We performed additional experiments, training the JBFs together with the denoising networks in a combined end-to-end setting. Although this setting enhanced performance within the training data domain, we did not recognize explicit performance improvements in terms of robustness on the investigated out-of-training-domain data sets. Eventually, we did not design our experiments to answer the question how a guidance image that is optimized for JBFs is handled in the training data domain but we particularly want to investigate how JBFs handle the displayed artifacts predicted by the denoising networks as the primary goal of our study.JBF-based pipelines almost entirely prevent the predictions from artifacts introduced by the DL-based models but the combined QAE+JBFs predictions still contain some slight distortions around the spine metal implant in Fig. PyTorch34 allow an automatic calculation of gradients in their operators. Therefore, one could think of implementing a JBF directly from PyTorch tensors instead of using analytical gradients to make its parameters trainable. Although this is possible, training such a filter would require expensive Python loops over the training batches and kernel windows which would accumulate huge computational graphs for the gradient calculation. In practice, training such a model with reasonable image and batch sizes, therefore, is infeasible in terms of computational time and GPU memory. The analytical filter derivative presented in this work greatly simplifies the required computations to enable data-driven optimization and limit the computational overhead through adding JBF layers as shown by comparing run times with convolutional layers. Eventually, we believe that our open-source filter layer can be useful in further hybrid applications as a known denoising operator that can be optimized in a data-driven manner.DL frameworks like In this work, we presented a trainable JBF layer that can be incorporated into any deep model. We propose a hybrid denosing pipeline using these JBF layers and pre-trained deep denoising neural networks. The latter can produce faulty predictions when tested on data that is insufficiently represented in the training domain. In our experiments, we show that JBFs prevent DL-based models from severe prediction failures although the JBFs make use of distorted guidance images predicted from the neural networks. These results are explained by the clear algorithmic design of the JBF that limits the influence of the guidance image to the contribution of the intensity range filter kernel. We think that JBF layers can combine the flexibility of deep neural networks with the prediction reliability of conventional methods to leverage the power of deep models in clinical low-dose CT applications.Supplementary Information.


The COVID-19 pandemic impacted daily life worldwide. It may also have had a psychological impact, especially on those with less resources already before the crisis and those who reported substantial changes to their work situation.To investigate whether socioeconomic status before the crisis and changes in work situation during the crisis  are associated with psychological impact in a cohort of young Swiss men.A total of 2345 young Swiss men (mean age = 29) completed assessments shortly before (April 2019 to February 2020) and early during the COVID-19 crisis (May to June 2020). Assessments covered psychological outcomes assessed before and during COVID-19 crisis , and assessed during the crisis , socioeconomic status  before the crisis and changes in work situation .About a fifth of the sample were in partial unemployment or lost their job during COVID-19 crisis. Those in partial or full unemployment, those mostly working from home and those with a lower socioeconomic status already prior to the crisis showed overall higher levels of depression, stress, psychological trauma, fear and isolation.Even in a country with high social security such as Switzerland, the COVID-19 crisis had a higher psychological impact on those who were already disadvantaged before the crisis or experienced deteriorations in their work situation. Supporting disadvantaged subpopulations during the crisis may help to prevent an amplification of pre-existing inequalities.No significant relationships.


Sintilimab is a fully human IgG4 monoclonal antibody against programmed death-1 (PD-1) used to treat classical Hodgkin’s lymphoma and various solid tumors. With increasing use of sintilimab, some rare adverse reactions have been reported. Here, we report a case of a 50-year-old woman with squamous non-small cell lung cancer (NSCLC) (metastasis to pericardium and pleura) who received two cycles of 200 mg sintilimab immunotherapy combined with albumin-bound paclitaxel and carboplatin chemotherapy and one cycle of sintilimab monotherapy. She was diagnosed with Sjogren’s syndrome  after three cycles’ treatment and received standard steroidal therapy. Prior to admission, the patient experienced severe stomach discomfort with vomiting and was hospitalized. Upper gastrointestinal iodine angiography showed significant gastric stenosis as well as lower esophageal stenosis. Subsequent ultrafine gastroscopy revealed ulceration at the stenotic site and an absence of normal peristalsis of the gastric wall. Pathological examination of the lesions showed reactive changes, including ulceration, fibrosis, and inflammatory cell infiltration. After multidisciplinary consultation, it was considered that the patient’s gastric stenosis with inflammatory fibrosis changes was due to a sintilimab-induced immune hyperinflammatory reaction. The patient had been treated with standard steroidal therapy since suffering from Sjogren’s syndrome, but the gastric stenotic changes were not relieved. The patient then received regular bouginage of esophago-cardiac stenosis under gastroscopy to physically reexpand the fibrous hyperplasia and stenotic site, enabling normal eating function. To our knowledge, this is the first case of gastric stenosis in a patient with squamous NSCLC after using sintilimab and may help clinicians better understand potential immune-related adverse events due to sintilimab and improve assessment and management. Cancer cells can take advantage of PD-1 signaling to escape immune surveillance . Clinica2A 50-year-old woman with a history of squamous NSCLC and metastasis to pericardium and pleura, who had pathological tissue samples that were ALK negative and PD-L1 positive with Tumor cell Proportion Score (TPS) of 80%, received two cycles of 200 mg sintilimab immunotherapy combined with chemotherapy of albumin-bound paclitaxel and carboplatin (from July to August 2020) and one cycle of sintilimab monotherapy (September 2020). The patient developed symptoms of fever, thirst, dysphagia, and difficulty eating, as well as severely damaged submandibular gland (no response to acid stimulation) and lacrimal gland (a tear flow rate of zero in both eyes) function after three cycles’ treatment. She was diagnosed with Sjogren’s syndrome through consultation with an immunologist in September 2020 and discontinued sintilimab immunotherapy. The patient was then treated with steroidal therapy (80 mg methylprednisolone). The symptoms of fever and thirst were relieved and food intake started to increase one week later. The steroid dose was gradually reduced . While treating Sjogren’s syndrome, four cycles of albumin-bound paclitaxel mono-chemotherapy were administered (from October 2020 to January 2021).12/L, hemoglobin of 106 g/L, D-D dimer of 1.1 μg/mL FEU, creatinine of 35 μmol/L . Fecal occult blood was weakly positive. Gastroscopy was performed under anesthesia by a gastroenterologist. Circumferential stenosis of the lower esophagus was observed approximately 34–37 cm from the esophageal incisors  and pathological manifestation of inflammatory hyperplasia with fibrosis, after multidisciplinary consultation, the patient’s gastric stenosis with inflammatory fibrosis changes was determined to be caused by a sintilimab-induced immune hyperinflammatory reaction.The patient had been treated with steroidal therapy since suffering from Sjogren’s syndrome. As the gastric stenotic changes were not relieved, this complication was not sensitive to steroidal therapy. To relieve vomiting and increase the patient’s energy level, gastroscopic nasointestinal tube placement was performed. Five months later (July 2021), when the patient’s nutritional status improved, laser incision of the stenosis site under gastroscopy was performed , and results in 18% of cancer-associated fatalities globally, making it the leading cause among all cancer types . More th%, and reAlthough immunotherapy has achieved great success, there are increasing reports of treatment-related adverse events (TRAE) induced by ICIs. Thus, this issue cannot be ignored . A meta-Follow-up of PD-1 monotherapy in patients with neoadjuvant resectable NSCLC showed that patients with high PD-L1 expression (TPS ≥ 50%) tended to have a higher two-year disease-free survival rate . PD-L1 iThe patient developed Sjogren’s syndrome after three cycles of sintilimab treatment, and obvious gastric stenosis was found five months later. Due to the long time since sintilimab was discontinued, gastroscope pathological examination and PET/CT examination was performed; tumor-associated lesions of the stenosis area were not considered.In addition to sintilimab, the patient had also received chemotherapy of albumin-bound paclitaxel and carboplatin. However, the main adverse reactions of albumin-bound paclitaxel are leukopenia, neutropenia, neuropathy, fatigue, and infection , and thaThis patient had suffered from dry mouth and swallowing and eating discomfort since Sjogren’s syndrome was diagnosed and these symptoms were relieved by steroidal therapy. Thus, the symptom of eating discomfort was always considered to be related to Sjogren’s syndrome. Gastroscope examination was not performed until 5 months later because of increasingly discomfort after eating accompanied by vomiting, which finally revealed obvious gastric stenosis with ulcer and fibrosis. Our experience suggests that if patients experience stomach discomfort or difficulty eating after using sintilimab, gastroscopy should be performed as soon as possible to detect any gastric lesions and allow adjustment of the dose or discontinuation.Glucocorticoids remain the first-line treatment for irAEs. Patients with severe reactions or reactions involving important organs might also require biological immunomodulators. Individualized treatment is recommended for irAEs of different organs caused by ICIs . Althoug4This is the first reported case of gastric stenosis caused by sintilimab. Since sintilimab monotherapy or combination therapy is widely used for various malignant tumors, it is essential to understand the potential irAEs and conduct adequate evaluation and management.The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.The studies involving human participants were reviewed and approved by Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology. The patients/participants provided their written informed consent to participate in this study. Written informed consent was obtained from the individual(s) for the publication of any potentially identifiable images or data included in this article.KS: Designed the case report and wrote the manuscript. HD: Collected the patient’s data. SJ: Edited the image. XX: Collated and verified the data. QW: Revised and reviewed the manuscript. CZ: Analyzed the pathological results. QC: Edited and Analyze the digestive endoscopy images. All authors contributed to the article and approved the submitted version.


Teaching Point: Intraspinal azygos vein is an extremely rare anatomical variant; knowledge is important for correct imaging interpretation. A 26-year-old man was referred to our radiology department with atypical complaints of muscle tension and upper back pain localized mainly midthoracic and radiating anteriorly. Given his young age, the patient initially underwent magnetic resonance imaging (MRI) of the thoracal and lumbar spine. No relevant abnormalities of the thoracic vertebra, intervertebral discs, facet joints or spinal cord were present. However, a nodular structure in the right neural foramen Th3-Th4 was detected. This structure was hypointense on T1-  imaging was performed with injection of intravenous contrast material . This demonstrated an azygos lobe in the right lung  and enters the chest through the aortic hiatus. Therefore, azygos vein ascends in the posterior mediastinum and arches over the right main bronchus to join the superior vena cava. Multiple anatomical variants exist, including azygos lobe, azygos continuation of the inferior vena cava or absence of the azygos vein. Intraspinal azygos vein is an extremely rare variant and according to our knowledge there is one other case reported in the literature [2-L2 and


We found that in a neural subspace predictive of hand forces, changes in preparatory activity tracked the learned behavioural modifications and reassociated4 existing activity patterns with updated movements. Along a neural population dimension orthogonal to the force-predictive subspace, we discovered that preparatory activity shifted uniformly for all movement directions, including those unaltered by learning. During a washout period when the curl field was removed, preparatory activity gradually reverted in the force-predictive subspace, but the uniform shift persisted. These persistent preparatory activity patterns may retain a motor memory of the learned field6 and support accelerated relearning of the same curl field. When a set of distinct curl fields was learned in sequence, we observed a corresponding set of field-specific uniform shifts which separated the associated motor memories in the neural state space9. The precise geometry of these uniform shifts in preparatory activity could serve to index motor memories, facilitating the acquisition, retention and retrieval of a broad motor repertoire.The brain’s remarkable ability to learn and execute various motor behaviours harnesses the capacity of neural populations to generate a variety of activity patterns. Here we explore systematic changes in preparatory activity in motor cortex that accompany motor learning. We trained rhesus monkeys to learn an arm-reaching task Motor adaptation is a form of motor learning by which motor commands are modified to achieve desired movements in a new environment. Decades of studies have explored the behavioural principles of motor adaptation, describing the process of error-driven movement calibration, the generalization of learned skills across contexts, memory retention and savings, and interference between multiple skills13. However, the neural mechanisms that support these diverse motor learning phenomena remain poorly understood.Motor learning encompasses a wide range of phenomena, from low-level calibration of movement parameters to high-level cognitive decisions in action selection16. Recently, this framework has begun to elucidate the neural foundation of motor learning at the population level20. Preparatory neural activity that precedes movement serves to initialize the pattern-generating neural population dynamics that control movement. To support motor learning, preparatory neural states and the subsequent neural population dynamics must adapt to modify outgoing motor commands. Consequently, we expect that some changes in preparatory activity that accompany motor learning would be tethered to changes in motor output20. Moreover, we propose that additional changes in neural preparatory activity, not directly coupled to movement output, might also emerge during learning. Such changes might facilitate learning and retention by organizing the population dynamics that implement new motor behaviours. We sought to test these hypotheses using a curl force field motor learning task.One emerging approach to understanding these neural computations is through the study of neural population dynamics, which has provided insight into complex activity patterns that defy understanding at the level of individual neuronsWe trained two rhesus monkeys (U and V) to perform an instructed-delay reaching task that elicited adaptation to counteract a curl force field . Before 11.Monkeys displayed gradual behavioural learning and washout, performing straighter reaches with reduced lateral deviation , c. The 19. To search for structured changes in preparatory neural population activity accompanying learning21, we applied targeted dimensionality reduction22 (TDR) on before-learning trials, which identified a neural subspace in which preparatory states were predictive of initial hand forces in the upcoming movement. In this force-predictive subspace, before-learning neural states were radially organized by reach directions23  and primary motor (M1) cortices using Neuropixels probes, Utah arrays and V-probe linear arrays. Single-neuron activity during learning and washout was heterogeneous and complex, consistent with previous reportsctions23 ; during ctions23 , b.24. These neural changes may reflect the state of an adapting internal model that maps between desired movements and neural commands. In this framework, generalization may result from a neural population code in which spatial basis functions are shared by reaches to nearby targets25. Adapting to a curl field at the trained target modifies this shared basis, thereby influencing untrained reaches in a spatially localized manner.Following learning, preparatory states for nearby, untrained targets also rotated towards the adjacent preparatory states . These r27. They are also consistent with a more general ‘reassociation’ strategy observed during short-term brain-computer interface (BCI) learning4. Within this neural subspace, the motor system may repurpose existing activity patterns, reflecting a common strategy across different motor learning contexts30.The learning-induced changes in preparatory states within this force-predictive subspace were closely coupled to changes in movement output. These changes are similar to the re-aiming strategy reported in visuomotor rotation (VMR) learning tasks, in which motor preparatory activity rotates in the opposite direction of the rotated visual feedback31  to preparatory activity to probe for additional changes during learning. The first two principal components largely overlapped with the force-predictive subspace ; however31 . The uni4 .Additionally, in both interference experiments, we observed a residual neural shift that accompanied interference during simultaneous learning, orthogonal to the field-specific uniform shifts during sequential learning , 8e. Not34. Over hundreds of washout trials without the field, monkeys gradually reverted to their before-learning reaching behaviour  owing to relatively stationary neural activity during the preparatory period . By cont30 (see Through the lens of curl field learning, we identified structured changes in cortical preparatory activity that reflected distinct components of motor learning. We found reassociation-like changes in preparatory activity in a movement-predictive neural subspace closely coupled to changes in movement parameters, similar to those reported in VMR and short-term BCI learning30 see . Notably37. Uniform shifts that separate these initial states may serve to isolate learning-induced modifications to the subsequent neural dynamics, thus separating motor memories to facilitate adaptive behavioural improvements in a specific context8. Conversely, when the motor system is unable to engage separate indices, such as when opposing curl fields are randomly interleaved13, opposing modifications to neural dynamics adjust the neural trajectory originating from the shared preparatory state, resulting in interference. Recent behavioural studies demonstrate that when certain contextual cues or movement components are added to differentiate movements, opposing fields can be learned without interference8. Our results suggest that the motor system leverages the shifts of preparatory states along orthogonal neural dimensions to index distinct motor memories, consistent with the central role of movement preparation reported in these studies.Cortical preparatory states provide the initial condition of the dynamical system whose evolution generates activity patterns that drive movementSupp MatsSupplementary Table 1Supplementary Table 2


The expansion of indications for neurointerventional procedures, combined with the need to treat a diverse patient population, has driven a need for broader access options. Concurrent arterial and venous access is often necessary for the diagnosis and treatment of various neurovascular diseases. Although complication rates are low, life-threatening severe complications have been reported with these access methods. Moreover, venous access through traditional routes can be challenging in patients with large body habitus. There is a growing trend of utilizing radial artery access for neuroendovascular procedures due to the increased ease of access and similar efficacy. Nevertheless, the use of upper limb veins in neurointerventional procedures is still rare. Upper extremity transvenous access (UETV) has recently emerged as an alternative strategy for neurointerventionalists, but data are limited. This study reports two cases of successful combined upper extremity transvenous access (TVA) and transradial access (TRA) in the treatment of carotid artery-cavernous fistulae. Combined TRA and UETV is a feasible, promising access strategy for patients and may also confer the same safety and patient satisfaction outcomes that have been seen with TRA. Further studies are needed to elucidate the exact impact this strategy has on patient outcomes and satisfaction. Radial artery access for transarterial procedures has gained recent traction among neurointerventionalists due to technical feasibility, decreased patient morbidity, and improved patient satisfaction. Upper extremity transvenous access (UETV) has also emerged as an alternative strategy for neurointerventionalists, but data are limited . The autCase 1An 82-year-old male underwent successful mechanical thrombectomy for large vessel occlusion of the right middle cerebral artery (MCA) M1 segment. During the procedure, he sustained perforation of the cavernous internal carotid artery (ICA) at the posterior genu due to severe tortuosity and underlying atherosclerosis, resulting in a direct CCF Figure . The nexCase 2A 71-year-old male presented to the clinic with a three-week history of decreased visual acuity in the left eye. Physical examination was significant for left-sided vision loss, lid lag, and chemosis without proptosis. Cerebral angiography revealed a CCF supplied by both indirect internal and external carotid feeding arteries, with drainage into the superior ophthalmic vein and ipsilateral inferior petrosal sinus Figure . The patProcedure descriptionTransradial AccessThe radial artery was cannulated using a single-wall technique with ultrasound guidance. A 6 French Merit Prelude Ideal radial vascular sheath  was placed approximately halfway into the artery. A radial artery angiogram was performed, and a standard radial cocktail was administered. Under roadmap guidance, the dilator and wire were reinserted to allow the 23-cm sheath to be inserted fully, placing the sheath tip in the brachial artery. IV heparin was administered. A Simmons 2 Catheter was used to selectively catheterize the carotid arteries of interest for cerebral angiography. At the end of the procedure, patent hemostasis of the radial artery was obtained in a standard fashion using a transradial band.Transvenous Access and Venogram With Coil Embolization of the Cavernous FistulaA sterile 18-gauge IV was placed in the preoperative area in the cephalic vein of the forearm (Case 1) Figure  or into The authors present the cases of two patients undergoing combined TRA and UETV for CCF embolization. UETV has been well-explored in interventional cardiology literature, but there are few studies in the neurointerventional literature, as UETV is still an emerging strategy in the field . CombineNo access site or procedural complications were noted in either of the authors’ cases. Obtaining venous access with an IV in the preoperative area likely decreased the time required to obtain venous access compared to standard TVA. Both patients were able to benefit from early mobility and ambulation compared to standard transfemoral approaches. Combined TRA and UETV is a feasible, promising access strategy for patients and may confer the same safety and patient satisfaction outcomes that have been seen with TRA in neurointerventional procedures ,8. FurthUpper extremity transvenous access (UETV) is a promising access site that may confer the same safety, cost, and preference benefits as its arterial counterpart, transradial access (TRA). Both presented patients were able to benefit from early mobility and ambulation compared to standard transfemoral venous approaches.


Pol epsilon is a tetrameric assembly that plays distinct roles during eukaryotic chromosome replication. It catalyses leading strand DNA synthesis; yet this function is dispensable for viability. Its non-catalytic domains instead play an essential role in the assembly of the active replicative helicase and origin activation, while non-essential histone-fold subunits serve a critical function in parental histone redeposition onto newly synthesised DNA. Furthermore, Pol epsilon plays a structural role in linking the RFC–Ctf18 clamp loader to the replisome, supporting processive DNA synthesis, DNA damage response signalling as well as sister chromatid cohesion. In this minireview, we discuss recent biochemical and structural work that begins to explain various aspects of eukaryotic chromosome replication, with a focus on the multiple roles of Pol epsilon in this process. In all replicating systems a hexameric, ring-shaped helicase is loaded around DNA and uses the energy derived from nucleotide hydrolysis to unwind the double helix, providing the single-stranded DNA template for the replicative polymerases . A direcIn bacteria, the initiator DnaA wraps around the double helix and promotes its melting . DnaA alIn this review article, we describe how recent structural work is shedding light on the disparate functions of Pol epsilon in origin activation, replication fork progression and epigenetic inheritance.in vitro studies. In fact, disassembly can be promoted upon high-salt treatment, which yields the loaded double hexamer scaffold. Tight association of a subset of factors can be achieved upon ATP binding by MCM, which leads to the retention of GINS and Cdc45 on the MCM, in turn causing disengagement of the double hexamer into two separate CMG particles and initial untwisting of duplex DNA. Mcm10 then promotes ejection of the lagging strand template from the MCM central channel, activation of ATP-hydrolysis dependent DNA unwinding and the recruitment of RPA that protects and stabilises the newly established replication fork  has become inactivated during evolution, however, it is the only Pol2 domain essential for viability . The seciability . Electroiability . Pol epsiability  via its iability . In partiability , explainiability . Altogetiability . It shouOnce activated, the CMG helicase must uncoil nucleosomes ahead of the replication fork to achieve the unwinding of parental DNA, and at the same time re-package duplicated DNA filaments into nucleosome arrays ,26. NuclIn vitro reconstitution work demonstrated that human Pole3–Pole4 function as histone chaperones that can engage H3–H4, promoting tetrasome formation and DNA supercoiling [Pole4−/− cells showed reduced origin activation and replicative damage. Structural flexibility in the Pol epsilon complex might be required for Dpb3–Dpb4 to engage parental histones. Indeed, several electron microscopy reports indicate that, in particular when engaged with the CMG, Pol epsilon exists primarily in a flexible state, with the catalytic domain of Pol2 free to move with respect to the rest of the complex [per se, but rather unstructured negatively charged tails of Dpb3 and Dpb4. In vitro interaction studies and hydrogen-deuterium exchange mass spectrometry analysis on human proteins support this notion [The mechanism of nucleosome uncoiling by the advancing replisome is not understood. Early work on CMG in the absence of DNA led to the suggestion that the helicase spools DNA through its central pore through a pumpjack-like movement of a set of C-terminal winged-helix domains appended to the MCM module . Later srcoiling   increases processivity of DNA synthesis both on the leading as well as on the lagging strand [Biochemical observations on leading and lagging strand synthesis established that the isolated Pol epsilon is a more processive polymerase compared with Pol delta . Crystalg strand ,94,96,97g strand ,99. In tg strand . How Polg strand . PCNA isg strand . Knowledg strand , it is lg strand , togetheg strand . Notablyg strand ,105. Ctfg strand , checkpog strand , Ctf18–Rg strand .Here we reviewed recent advances in biochemistry and structural biology that begin to explain the molecular mechanism of chromosome replication, with a focus on the multiple roles of Pol epsilon in different stages of origin activation and replication fork progression. To reach a complete understanding of the structural mechanism of DNA replication several questions need to be addressed. These include the mechanism of Pol epsilon incorporation into the pre-initiation complex, on the path to replication fork establishment; the mechanism whereby the Dpb3–Dpb4 subunits of Pol epsilon deposit parental histones H3–H4 onto leading strand DNA; a complete view of the leading-strand priming process and substrate handoff between Pol alpha, delta and epsilon, on route to processive and continuous leading strand synthesis; the mechanism whereby the clamp loader hands the clamp-engaged DNA substrate to Pol epsilon to achieve processive leading strand synthesis. Cryo-EM of reconstituted DNA replication reactions will play a major role in elucidating these processes.Biochemical reconstitution and single-particle cryo-EM are shaping our understanding of DNA replication mechanisms.DNA unwinding and nucleosome uncoiling, processive DNA synthesis and the redeposition of parental histones are tightly coupled processes.Future cryo-EM on entire DNA replication reactions will provide a complete understanding of chromosome replication.


Salivary gland tumor Sialadenoma papilliferum  clinically resembles papillary epithelial lesions, such as squamous papilloma (SqP) or verrucous leukoplakia. Pathological sampling including an adequate depth of both the mucosa and submucosa layer is required for discrimination between the diseases. Though ductal proliferation in the submucosa is characteristic in SialP, papillary lesions arising at the mouth floor, specifically near the ductal orifice, are more problematic. Salivary gland ductal ectasia, along with the overlying papillary hyperplasia, may mimic the biphasic tumorous growth pattern of SialP, making discrimination extremely difficult. Further cellular dysplasia in the papillary mucosal lesion raises the possibility of malignant transformation in a known benign lesion, SialP. Herein, we present a case of SqP at the mouth floor which mimicked both clinical and pathological features of SialP and compared it with a definite case of SialP. Moreover, we discuss major differential points that clinicians and pathologists should consider during diagnosis of oral papillary lesions arising near the salivary glands. The majority of oral solitary papillary lesions are derived from the surface squamous epithelium. Depending on the size, shape and amount of keratinization, the papillary lesions may be clinically assumed as squamous papilloma, verruca vulgaris, verruciform xanthoma, verrucous carcinoma or papillary squamous cell carcinoma. Among these, squamous papilloma (SqP) is a benign epithelial tumor prevalent in the oral cavity. The characteristic clinical features of a solitary exophytic lesion with pink to whitish multiple papillary projections, in many cases pedunculated , and limited growth within a diameter of 1 cm easily leads to the impression of SqP.However, in papillary lesions that occur over or near the minor salivary glands or major salivary gland ductal structures, a completely distinct entity called sialadenoma papilliferum  must be considered for differential diagnosis. SialP is a rare benign salivary gland tumor first reported in the literature in 1969 -6. It isCase #1  A 53-year-old Asian female visited the Department of Oral and Maxillofacial Surgery at Yonsei Dental Hospital, complaining of a whitish painless growing mass on the left retromolar trigone (RMT) which had started a month before. According to the patient, there had been no pain. She was on medication for rheumatoid arthritis that had been prescribed by a local clinic. There were no other specific past medical or dental histories associated with the lesion. The lesion was a whitish-to-yellowish verrucous mass on the left RMT area . There wCase #2  A 47-year-old Asian male visited the Department of Oral and Maxillofacial Surgery at the Yonsei Dental Hospital complaining of a papillary mass under the tongue that had occurred a month before without a specific event. There was no pain or other remarkable symptoms. He had a past medical history of treated tuberculosis. On clinical examination, an exophytic verrucous mass was observed from the floor of mouth to the lingual frenum . It had Although the overall lesion did not present definite cellular pleomorphism or loss of polarity, since the epithelial basal cells showed bulbous architecture, we evaluated the lesion for the possibility of early-stage malignant transformation. The IHC results showed that the Ki-67 proliferation index and p53 expression were minimal and localized at the basal layer in both the lesional epithelium and adjacent normal mucosa . This paDespite the similar clinical features of SialP and papillary lesions of the squamous mucosa such as SqP, histological discrimination is generally not a problem because of the submucosal glandular proliferation in addition to the common squamous papillary growth , 9-11. Tin situ. Papillary epithelial lesions may have a various spectrum of cellular atypia which may extend into the superficial salivary duct when arising at the orifice. Mild basal cell dysplasia is a common feature in benign SqP, not a sign of malignant transformation , S-100, and smooth muscle actin (SMA) made it possible to distinguish whether the ductal proliferation was true neoplastic growth as in SialP or dilation of the normal duct. In the case of SialP, ductal proliferation shows diffuse and strong positivity of CK7, while it is expressed only in the luminal columnar cells of the duct in the latter case -20. In aTP53 mutation profile which may present as a gain-of-function positive IHC pattern during and after malignant transformation (TP53 gene mutations in salivary gland tumors is less conspicuous than in oral squamous cell carcinomas (Importantly, the limited protein expression of p53 and Ki-67 in Case #1 and #2 suggested both lesions were benign tumors without direct evidence of malignant potential. Squamous cell carcinoma, the most prevalent type of oral cancer, and high grade precancerous lesions derived from oral mucosa frequently have an aberrant ormation -24. The rcinomas -27. Onlyrcinomas . In mostRecent studies have determined that SialP is a true neoplastic region with mutual genetic alterations , 28, 29.However, SialP is known as a benign lesion with excellent prognosis. In reports with sufficient follow-up data, only 2 cases of recurrence have been recorded, with 4 cases being reported to have malignant transformation  7, 12-1, 32, 33.


Correction: BMC Women’s Health (2022) 22:476 10.1186/s12905-022-02068-3Following publication of the original article , In thisIn our study, hormonal medication did not seem to interfere with the risk of recurrence in a statistical significance way, which deviates from the rudimentary results that GnRH-a correlated with reduced recurrence in prior observations. However, after the diagnosis of recurrence, the pain symptom of most recurrent cases were well relieved after timely hormone intervention. Likewise, it has been reported that PEM lesions could spontaneously regress after pregnancy, suggesting the hormone-responsive feature of the disease [30]. In agreement to our findings, Seong et al. found hormone therapy was associated with longer recurrence-free interval from the time of surgery to the onset of recurrence after primary surgery for ovarian endometrioma [31]. Hormonal therapy maintains the minimal disease state by slowing down the regrowth rather than eliminate residuals, as revealed by Sharpe et al. in a rat model that the implant lesion was significantly inhibited by GnRH-a while regrowth sustained spontaneously after the cessation of hormone suppressive treatment [32]. Taken together, these results suggest postoperative hormonal suppression has beneficial effects on extending disease-free interval but does not completely prevent recurrence of PEM.The original article has been corrected.


Hepatocellular carcinoma (HCC) is a global healthcare challenge, which affects more than 815,000 new cases every year. Activated hepatic stellate cells (aHSCs) remain the principal cells that drive HCC onset and growth. aHSCs suppress the anti-tumor immune response through interaction with different immune cells. They also increase the deposition of the extracellular matrix proteins, challenging the reversion of fibrosis and increasing HCC growth and metastasis. Therapy for HCC was reported to activate HSCs, which could explain the low efficacy of current treatments. Conversely, recent studies aimed at the deactivation of HSCs show that they have been able to inhibit HCC growth. In this review article, we discuss the role of aHSCs in HCC pathophysiology and therapy. Finally, we provide suggestions for the experimental implementation of HSCs in HCC therapies. Liver cancer is a global health problem, with an estimated increase of 32% by 2040 . RepreseAlthough HCC pathogenesis is complex and varies depending on underlying etiology, the usual background setting for HCC is liver injury, chronic inflammation, irreversible fibrosis, and cirrhosis . In factIn HCC, aHSCs receive signals from individual immune cells, and, in turn, they produce soluble mediators, acting on surrounding immune cells . HSC medThe antigen-directed cytotoxicity of T lymphocytes (TLs) boosts the immune response against cancer . ActivataHSCs also induce expansion of two suppressive immune cell populations; myeloid-derived suppressor cells (MDSCs)  and T heMacrophages polarize in the liver with strong plasticity into pro-inflammatory M1 or anti-inflammatory M2 in response to local signals from the tumor microenvironment ,31. M1 mNatural killer (NK) cells defend the body against tumors by engaging death-inducing receptors to stimulate cancer cell apoptosis. HCC patients with low intratumoral NK cells infiltration have shorter disease-free survival . In animAlthough the role of immune system in liver cancer is complex , the oveUnder normal conditions, the rate of ECM production in the liver equals that of its degradation, resulting in no net accumulation of the matrix. Fibrogenesis occurs when there is an imbalance between ECM production and degradation , resultiThe reversibility of fibrosis and cirrhosis is dependent on the activity of matrix metalloproteinases (MMPs) . MMPs arIncreased production of ECM proteins, such as collagen I and laminin-5 (Ln-5), is associated with the growth and metastasis of HCC. Collagen I promotes HCC cell proliferation by regulating the integrin β1/FAK signaling pathway . HSCs prUpregulation of Ln-5 in HCC patients promotes the migration of tumor cells, which is directly related to poor prognosis and tumor metastasis . HCC groNormalization of ECM may represent an important therapeutic strategy for HCC . AnalysiCurrent conventional therapy can activate HSCs, which could explain its limited success in curing HCC . ChemothSorafenib, as an anti-tumor molecular inhibitor, can impede HCC cell proliferation but can also activate HSCs through the mitogen-activated protein kinase (MAPK) signaling pathway . In miceThe main challenge to classic radiotherapy is its side effects on the surrounding tissues . Upon raAlthough radiofrequency ablation (RFA) is increasingly incorporated into HCC treatment, available data indicate its ability to stimulate residual tumor growth and cause tumor recurrence . It was Defining and analyzing the interconnected factors between HSC activation and conventional therapies could help to enhance the efficacy of current treatment modalities.Pharmacological trials that target activated HSCs suggest a new paradigm that “hitting one target leads to a domino effect”. This is easy to understand since targeting aHSCs will affect subsequently HSC-induced immunosuppression, drug resistance, and tumor metastasis .The trials are based mainly on targeting molecular pathways of HSCs activation. TGF-β signaling is considered the key pathway that drives HSC activation . TargetiAnother pathway for HSC activation implies the involvement of peripheral nerves. Peripheral nerves secret substance P (SP), which transmits the information via a neurokinin-1 receptor (NK-1R)—expressed on HSCs. SP activates HSCs through the SP/NK-1R signal pathway . In vivoPD-L1 is required for HSC activation by stabilizing TGF-β receptors . TargetiGrowing evidence of the role of HSCs in HCC suggests that HSC-related therapies might revolutionize the therapy for HCC. Yet, several gaps still limit the application of HSC deactivation in the treatment of HCC. The first obstacle is the obscure nature of molecular mechanisms of HSC activation and deactivation . In partThe second obstacle is that HSCs account only for 5% to 8% of total liver cells, and targeting HSCs may be blocked by the condensed nature of the perisinusoidal space . TargetiControlled studies to define the main factors of HSC activation and the proper delivery system to target it should promote the potential of HSCs in the context of HCC therapies. The final step is to define the inclusion and exclusion criteria for such therapies. The inclusion criteria need to consider HCC staging and hepatic microenvironment, including immune cells and ECM materials.HSCs play an exemplary role in the tumor regulating different cytokines and growth factors for the progress of HCC. They interact with different immune cells to suppress HCC immunosurveillance. Targeting HSC-related immune suppression would improve immune response to HCC. aHSCs disturb the balance of ECM proteins, which leads to the progression of fibrosis and HCC. Exploring how HSCs destabilize ECM could identify possible targets for HCC treatment. As current therapies activate HSCs, deactivation of HSCs has become a critical therapeutic strategy. Targeting aHSCs can be developed by studying their molecular activation mechanisms and selecting proper targeting methods.