Escape Event Research Articles

Behavior of Trapped Molecules in Lantern-Like Carcerand Superphanes.

Superphanes are a group of organic molecules from the cyclophane family. They are characterized by the presence of two parallel benzene rings joined together by six bridges. If these bridges are sufficiently long, the superphane cavity can be large enough to trap small molecules or ions. Using ab initio (time scale of 80 ps) and classical (up to 200 ns) molecular dynamics (MD) methods, we study the behavior of five fundamental molecules (M = H2O, NH3, HF, HCN, MeOH) encapsulated inside the experimentally reported lantern-like superphane and its two derivatives featuring slightly modified side bridges. The main focus is studying the dynamics of hydrogen bonds between the trapped M molecule and the imino nitrogen atoms of the side chains of the host superphane. The length of the N···H hydrogen bond increases in the following order: HF < HCN < H2O < MeOH < NH3. The mobility of the trapped molecule and its preferred position inside the superphane cage depend not only on the type of this molecule but also largely on the in/out conformational arrangement of the imino nitrogens in the side chains of the superphane. Their inward-pointing positions allow the formation of strong N···H hydrogen bonds. For this reason, these nitrogens are the preferred sites of interaction. The mobility of the molecules and their residence times on each side of the superphane have been explained by referring to the symmetry and conformation of the given superphane cage. All force field MD simulations have shown that the encapsulated molecule remained inside the superphane cage for 200 ns without any escape event to the outside. Moreover, our simulations based on some endohedral complexes in the water box also showed no exchange event. Thus, the superphanes we study are true carcerand molecules. We attribute this property to the hydrophobic side chains and their pinwheel arrangement, which makes the side walls of the studied superphanes fairly impenetrable to small molecules.

CORRECTION: Fish dispersal from a sabotage-mediated massive escape event

CORRECTION: Fish dispersal from a sabotage-mediated massive escape event

Fish dispersal from a sabotage-mediated massive escape event

Farm sabotage can cause massive fish escape events with significant ecological and socio-economic risks. This study examined the fate of Mediterranean seabass Dicentrarchus labrax escapees following a large-scale escape event caused by sabotage in the Western Mediterranean Sea. We monitored the escapee density and size structure over 3 mo after the escape at increasing distances from the escape point, up to 45 km away. Fish density adjacent to the escape location 5 d after the sabotage was, on average, 114 ± 44.7 (SE) fish per 100 m2. Our analyses showed that fish density decreased by 17% for every km away from the location, dropping to 2 and 1% after 1 and 2 mo, respectively, following the escape event. As escapee density declined throughout time and space, the size distribution of seabass shifted towards larger sizes. The rapid decrease in fish densities highlights the need for contingency plans focusing on fishing efforts in the coastal areas near the escape location (&lt;20 km) within the first 24 h. These results are paramount to mitigating the risks associated with escape events cost-effectively. We emphasise the importance of sabotage prevention measures, such as security systems that can quickly detect intruders and trigger an immediate response to deter them. Additionally, enforcing appropriate sanctions based on the severity of the damage caused could help to discourage future sabotage attempts.

Socioecology of farmed salmon escapes: 'Commons' and de-privatization of escaped salmon for better management of a potentially invasive species

Aquaculture is increasingly important in a growing and hungry world. However, it is also associated with several socio-ecological problems such as non-native fish escaping from aquaculture. A particular issue in Chile is that escaped fish remain the property of the aquaculture operation, resulting in socio-ecological conflict. This article analyzes the opinions of artisanal fishermen from various locations across the Seno de Reloncaví in the Los Lagos region of Chile regarding salmonid escape events. To this end, we collected approaches and governance proposals about salmon escapes raised by fishers, allowing for a debate on the legal property status of escaped salmonids and the limits that this situation represents for better socio-environmental escape management. Empirically, the work is based on data gathering done between June 2019 and February 2020, immediately after a well-publicized and large-scale escape event (∼700,000 fish) from an aquaculture facility. Based on the case, we propose some elements for better socio-ecological governance of escapes from the theory of common and common-use resources.

Mediterranean Aquaculture and Genetic Pollution: A Review Combined with Data from a Fish Farm Evaluating the Ecological Risks of Finfish Escapes

Mediterranean finfish aquaculture is mainly represented by the production of the gilthead sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax) growing in marine cage farms. Despite the numerous benefits of fish farming, the ecological risk potentially caused by fish escapes to the wild populations is occasionally high. In the current study, an integrated review of fish escapes is presented regarding S. aurata and D. labrax escapes and their potential effect on the genetic composition of wild populations. The collected data from the literature are combined and discussed along with recorded escapes in a fish farm located in the Aegean Sea, Greece. According to these records, fish escapes present a generally stable rate, ranging between 0 and 2% in each escape event, which occur 5–8 times per year. Although for other farmed fish species worldwide, the ecological risk may be higher, this risk is probably lower in Mediterranean finfish populations, which are characterized by generally low levels of genetic differentiation. Nevertheless, the risk of genetic introgression still exists. Particularly in sea bream and sea bass farming, genetic structure and differentiation in wild populations seem to be unaffected for now. Nevertheless, suitable management measurements would be a useful strategy to avoid future negative effects of fish escapes. These strategies should be focused on further efforts towards recapture program development, reduced escapees’ survival, and proper legislation. Furthermore, more data on escapees’ survival percentage, their migration pathways, and the way these pathways relate to mortality, the type of escape event, and the season of release would be also valuable.

Causal analysis of escapement of farmed salmonids in southern Chile

Escaped salmonids are considered among the most serious threats to the aquatic environment. One hundred and nine escape incidents were reported in Chile from 2004-2021, representing some 8.53 million escaped salmonids. Of this total, 5.73 million were Atlantic salmon Salmo salar (67.2%), 0.83 million coho salmon Oncorhynchus kisutch (9.8%), and 1.96 million were rainbow trout O. mykiss (23.0%). It is estimated that 70.1% of the escaped salmonids were recorded in the Los Lagos Region, 23% in the Aysén Region, and 4.6% in the Magallanes Region. In total, 80.5% of the escapes were recorded from seawater facilities, while freshwater units accounted for 19.5%. The highest percentage of escaped salmon recorded in seawater over 2004-2021 was 1.71% of harvested salmonids in 2013. Some 39.5% of the escapes in 2015-2021 were attributed to rupturing of net cages, mainly due to adverse climatic conditions. The additional regulations introduced in 2020 by the Chilean authority, has helped to minimize the escape of farmed salmonids. As a consequence, just one escape event was reported in 2021, corresponding to 3.85% of the total number of escapees recorded from 2004-2021.

The escape of CRISPR-mediated gene editing in Zymomonas mobilis.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems have been widely applied for gene or genome editing. Adequate checking is important to screen mutants after CRISPR-mediated editing events. Here, we report gene escape cases after the knock-out by Type I-F native CRISPR system in Zymomonas mobilis. Through amplifying both the gene of interest and its flanking homologous arms, followed by curing the editing plasmid, we found different destinies for gene editing events. Some genes were readily knocked out and followed by the easy plasmid curing. In some other cases, however, the editing plasmid was difficult to remove from the cell, or the deleted genes were transferred into the editing plasmid. For example, the targeted region of fur can be integrated into the editing plasmid after the knockout, resulting in a spurious editing event. We supposed that the transfer of the gene was may attributed to bacterial insertion sequences. Searching for literatures on the gene knockout using CRISPR in bacteria reveals that the escape event is likely underestimated due to inadequate validation in other microbes. Hence several strategies are proposed to enhance gene knockout and plasmid curing.

Raddeanin A synergistically enhances the anti-tumor effect of MAP30 in multiple ways, more than promoting endosomal escape

Biomacromolecules such as proteins and nucleic acids are very attractive due to their high efficiency and specificity as cancer therapeutics. In fact, the endocytosed macromolecules are often trapped in the endosomes and cannot exhibit pharmacological effects well. Many strategies have been used to address this bottleneck, and one promising approach is to exploit the endosomal escape-promoting effect of triterpenoid saponins to aid in the release of biomacromolecules. Here, Raddeanin A (RA, an oleanane-type triterpenoid saponin) was proved to significantly promote endosomal escape as it recruited Galectin-9, an endosomal escape event reporter. As expected, RA effectively enhanced the anti-tumor effect of MAP30 (a type I ribosome-inactivating protein derived from Momordica charantia). However, based on the results of fluorescent colocalization, RA did not significantly promote MAP30 release from endosomes, suggesting that RA enhances MAP30 activity not only by promoting endosomal escape. Furthermore, it was found that the inhibitors of micropinocytosis and caveolae could almost completely inhibit the cytotoxicity of MAP30 combined with RA without affecting the cytotoxicity of MAP30 alone, indicating that RA may regulate the endocytic pathway of MAP30. Meanwhile, the effect of RA is related to the intra vesicular pH and cholesterol content on cell membrane, and is also cell-type dependent. Therefore, RA enhanced the anti-tumor effect of MAP30 in multiple ways, not just by promoting endosomal escape. Our findings will help to further decipher the possible mechanisms by which triterpenoid saponins enhance drug activity, and provide a new perspective for improving the activity of endocytosed drugs.

Precocial male maturation contributes to the introgression of farmed Atlantic salmon into wild populations

The escape of domesticated Atlantic salmon Salmo salar from aquaculture facilities represents a continued threat to the genetic and demographic stability of wild salmon stocks. Escaped farm-origin salmon have been shown to hybridize with wild conspecifics, yet the long-term genetic impacts are generally unknown. Theoretically, life history variation, specifically precocial maturation of male hybrids, could fast-track introgression, but evidence for this has been sparse. Here, we used empirical and experimental data to examine the role of precocious male maturation in introgression. We examined hybrid class composition using juvenile sampling and genetic assignment over a 5 yr period following an escape event in southern Newfoundland, a region with high rates of natural male precocial maturation. Initially following the escape, the proportion of first-generation (F1) hybrids was high and then decreased annually, contrasting the proportion of backcross wild individuals, which increased over time. The presence and temporal distribution of backcross wild individuals supports the hypothesis that high rates of precocial maturation can fast-track the long-term impacts of escaped farmed salmon on wild populations via interbreeding. This was experimentally tested using lab-created wild, farmed, and F1 parr released and recaptured from a Newfoundland river to assess levels of precocious male maturation. Observed rates of maturation of F1 hybrids were high and similar to wild parr (77 vs. 73%, respectively), indicating that most F1 hybrids mature precocially. Our results suggest that rates of precocial male maturation should be explicitly considered in risk assessments evaluating the genetic impacts of escaped farmed salmon on wild populations.

Immunogenetic, Molecular and Clinical Determinants of Clonal Evolution in Aplastic Anemia and Paroxysmal Nocturnal Hemoglobinuria

Immunogenetic, Molecular and Clinical Determinants of Clonal Evolution in Aplastic Anemia and Paroxysmal Nocturnal Hemoglobinuria

Optical Flow-Based Weighted Magnitude and Direction Histograms for the Detection of Abnormal Visual Events Using Combined Classifier

Movement information of persons is a very vital feature for abnormality detection in crowded scenes. In this paper, a new method for detection of crowd escape event in video surveillance system is proposed. The proposed method detects abnormalities based on crowd motion pattern, considering both crowd motion magnitude and direction. Motion features are described by weighted-oriented histogram of optical flow magnitude (WOHOFM) and weighted-oriented histogram of optical flow direction (WOHOFD), which describes local motion pattern. The proposed method uses semi-supervised learning approach using combined classifier (KNN and K-Means) framework to detect abnormalities in motion pattern. The authors validate the effectiveness of the proposed approach on publicly available UMN, PETS2009, and Avanue datasets consisting of events like gathering, splitting, and running. The technique reported here has been found to outperform the recent findings reported in the literature.

The Iris billiard: Critical geometries for global chaos.

We introduce the Iris billiard that consists of a point particle enclosed by a unit circle around a central scattering ellipse of fixed elongation (defined as the ratio of the semi-major to the semi-minor axes). When the ellipse degenerates to a circle, the system is integrable; otherwise, it displays mixed dynamics. Poincaré sections are presented for different elongations. Recurrence plots are then applied to the long-term chaotic dynamics of trajectories launched from the unstable period-2 orbit along the semi-major axis, i.e., one that initially alternately collides with the ellipse and the circle. We obtain numerical evidence of a set of critical elongations at which the system undergoes a transition to global chaos. The transition is characterized by an endogenous escape event, E, which is the first time a trajectory launched from the unstable period-2 orbit misses the ellipse. The angle of escape, θesc, and the distance of the closest approach, dmin, of the escape event are studied and are shown to be exquisitely sensitive to the elongation. The survival probability that E has not occurred after n collisions is shown to follow an exponential distribution.

Escape history and proportion of farmed Atlantic salmon Salmo salar on the coast and in an adjacent salmon fjord in Norway

To gain more knowledge about escaped farmed salmon Salmo salar in the wild, we investigated the proportion of escapees, body length at escape, proportion escaped as smolts/post-smolts (≤300 mm) and number of winters in the wild (winter zones in the growth pattern in the scale samples) in catches on the Norwegian coast and in an adjacent fjord from 2013 to 2017. The mean proportion of escapees was higher on the coast (26%) than in the fjord (4%), and escapees caught on the coast had a slightly larger mean body length at escape (607 mm) than in the fjord (557 mm). However, the mean proportion escaped as smolts/post-smolts did not differ significantly between the coast (8%) and the fjord (11%). There was also no significant difference in the mean proportion of farmed salmon with 1 or more winter zones after escape (50% on the coast and 56% in the fjord). The proportions of escapees with 1, 2, 3 or 4 winter zones after escape were 28, 20, 2 and 0.4% in catches on the coast and 30, 21 and 4% in catches in the fjord, respectively. This study found that the proportion of escapees was considerably higher in coastal waters than in the fjord. Escapees consisted of farmed salmon from several escape events over several years, and approximately 50% of the escapees had one or more winter zones after escape. Thus, escaped farmed salmon may pose a threat to wild salmon populations for several years after the escape event.

Distinct genomic and immune microenvironment between thymomas and thymic carcinomas.

e13529 Background: Thymomas and thymic carcinomas which uniformly known as thymic epithelial tumors (TETs) are rare intrathoracic malignancies and a limited studies have been reported addressing the molecular biology and immune discrepancy. The main purpose of this study was to depict the genomic and transcriptomic landscape of thymomas and thymic carcinomas, as well as elucidate the differentiated immune microenvironment. Methods: Totally 15 thymomas and 7 thymic carcinomas patients were enrolled from January 2014 to July 2018. Treatment-naïve tissue samples were collected, and we also obtained matched peripheral blood mononucleocytes as negative control. DNA and RNA were co-extracted and performed with whole exon and transcriptome sequencing. The immune cell infiltration scores were estimated using ssGSEA algorithm. Results: Exome sequencing revealed that GTF2I mutation occurred in all of type A thymomas but was absent in the aggressive subtypes. The median tumor mutation burden of thymomas was 0.12/Mb, significantly lower than thymic carcinomas (median: 1.02/Mb, p = 0.001). Copy number variation was more common in thymic carcinomas than thymomas (83.3% vs 9.1%, p = 0.005). Top mutational signatures enriched in both thymomas and thymic carcinomas included age and Aristolochic acid exposure, while the APOBEC signature was more common in thymomas than thymic carcinomas (81.8% vs 16.7%, p = 0.03). As a confirmed immune escape event, loss of heterozygosity of human leukocyte antigen was identified in 9.1% of thymomas and 50% of thymic carcinomas. Via unsupervised clustering of immune infiltration, all tissue samples were classified into high- and low-infiltration subgroups. Remarkably, up to 71.4% of samples from thymic carcinomas and only 6.7% of samples from thymomas were defined as low immune cell infiltration. In consideration of specific immune cell types, macrophage ( p = 0.01) and neutrophil ( p = 0.02) were enriched in thymic carcinomas while CD56+ NK cell ( p = 0.005) was enriched in thymomas, indicating the evidential discrepancy about immune cell infiltration between two subtypes of TETs. Conclusions: This study elucidated the molecular and immune microenvironment discrepancy between two subtypes of TETs. From molecular perspective, thymomas and thymic carcinomas are entirely different diseases with different etiology and characterized by distinct immune infiltration, and thus should be managed with disparate therapeutic strategies. Findings in this study may also be useful in future targets development and exploration of immunotherapies in TETs.

Estimating the relative fitness of escaped farmed salmon offspring in the wild and modelling the consequences of invasion for wild populations.

Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net‐pen salmon aquaculture. Although domestic–wild hybrid offspring have shown reduced fitness in laboratory and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context‐dependent. Here, we follow a single large escape event of farmed Atlantic salmon in southern Newfoundland and monitor changes in the in‐river proportions of hybrids and feral individuals over time using genetically based hybrid identification. Over a three‐year period following the escape, the overall proportion of wild parr increased consistently (total wild proportion of 71.6%, 75.1% and 87.5% each year, respectively), with subsequent declines in feral (genetically pure farmed individuals originating from escaped, farmed adults) and hybrid parr. We quantify the strength of selection against parr of aquaculture ancestry and explore the genetic and demographic consequences for populations in the region. Within‐cohort changes in the relative proportions of feral and F1 parr suggest reduced relative survival compared to wild individuals over the first (0.15 and 0.81 for feral and F1, respectively) and second years of life (0.26, 0.83). These relative survivorship estimates were used to inform an individual‐based salmon eco‐genetic model to project changes in adult abundance and overall allele frequency across three invasion scenarios ranging from short‐term to long‐term invasion and three relative survival scenarios. Modelling results indicate that total population abundance and time to recovery were greatly affected by relative survivorship and predict significant declines in wild population abundance under continued large escape events and calculated survivorship. Overall, this work demonstrates the importance of estimating the strength of selection against domestic offspring in the wild to predict the long‐term impact of farmed salmon escape events on wild populations.

Crowd escape event detection based on Direction-Collectiveness Model

Crowd escape event detection based on Direction-Collectiveness Model

The fish farm of origin is assigned by the element profile of Atlantic salmon (Salmo salar L.) scales in a simulated escape event

The Norwegian aquaculture management authorities require that the sea farm of origin for escaped salmon can be identified. As a contribution to develop a reliable and feasible method for tracing escaped salmon to their sea cage of origin the proof-of-concept of the case-based red alert method ‘FarmSalmTrack’ is demonstrated through a simulated escape event. The ‘FarmSalmTrack’ method uses the trace element distribution in the scale hydroxyapatite, HAP-layer, to discriminate between groups of salmon. The case-based approach can primarily be used for larger escapes and preferably where the escaped fish are caught relatively soon after the time of escape. The method is dependent on baseline data being available from all sea farm cages potentially responsible for the escape. Classification of the escapees towards the baseline material collected from nearby sea cages holding salmon of same age and size is done in a three-step process; (1) analysis of the Sr/Ba ratio which reveals if seawater or salt are added to the hatchery tanks, (2) analysis of element profiles in the juvenile section of the scale and (3) analysis of trace element profile of the scale HAP-layer formed in seawater. Step (1) reduced the number of suspected sea cages by one half, step (2) identified the escapees’ hatchery of origin and step (3) identified the sea cage of origin. The classification was based on the concentration of the elements B, Ba, Li, Mg, Mn, Na, S, Sr, U and Zn along selected sclerites. Barium was the most important element for correct classification using the elemental profile of the juvenile section of the scale, while Zn showed the strongest influence on the classification using the seawater section of the scale. Improved understanding of the incorporation of non-essential life elements and essential life elements into the bio-mineralised structures of the fish scale HAP-layer would be highly beneficial for further development of the ‘FarmSalmTrack-method’.

Forward, backward, and weighted stochastic bridges.

We define stochastic bridges as conditional distributions of stochastic paths that leave a specified point in phase-space in the past and arrive at another one in the future. These can be defined relative to either forward or backward stochastic differential equations and with the inclusion of arbitrary path-dependent weights. The underlying stochastic equations are not the same except in linear cases. Accordingly, we generalize the theory of stochastic bridges to include time-reversed and weighted stochastic processes. We show that the resulting stochastic bridges are identical, whether derived from a forward or a backward time stochastic process. A numerical algorithm is obtained to sample these distributions. This technique, which uses partial stochastic equations, is robust and easily implemented. Examples are given, and comparisons are made to previous work. In stochastic equations without a gradient drift, our results confirm an earlier conjecture, while generalizing this to cases with path-dependent weights. An example of a two-dimensional stochastic equation with no potential solution is analyzed and numerically solved. We show how this method can treat unexpectedly large excursions occurring during a tunneling or escape event, in which a system escapes from one quasistable point to arrive at another one at a later time.

Predicting Non-Stationary and Stochastic Activation of Saddle-Node Bifurcation

Accurately predicting the onset of large behavioral deviations associated with saddle-node bifurcations is imperative in a broad range of sciences and for a wide variety of purposes, including ecological assessment, signal amplification, and microscale mass sensing. In many such practices, noise and non-stationarity are unavoidable and ever-present influences. As a result, it is critical to simultaneously account for these two factors toward the estimation of parameters that may induce sudden bifurcations. Here, a new analytical formulation is presented to accurately determine the probable time at which a system undergoes an escape event as governing parameters are swept toward a saddle-node bifurcation point in the presence of noise. The double-well Duffing oscillator serves as the archetype system of interest since it possesses a dynamic saddle-node bifurcation. The stochastic normal form of the saddle-node bifurcation is derived from the governing equation of this oscillator to formulate the probability distribution of escape events. Non-stationarity is accounted for using a time-dependent bifurcation parameter in the stochastic normal form. Then, the mean escape time is approximated from the probability density function (PDF) to yield a straightforward means to estimate the point of bifurcation. Experiments conducted using a double-well Duffing analog circuit verifies that the analytical approximations provide faithful estimation of the critical parameters that lead to the non-stationary and noise-activated saddle-node bifurcation.

Recapturing escaped fish from marine aquaculture is largely unsuccessful: alternatives to reduce the number of escapees in the wild

AbstractFarmed fish that escape and mix with wild fish populations can have significant ecological and genetic consequences. To reduce the number of escaped fish in the wild, recapture is often attempted. Here, we review the behaviours of escapees post‐escape, and how recapture success varies with escaped fish size, the size of the initial escape event and recapture methods. Success rates of fishing gears varied among species, with gill‐nets and coastal barrier nets most effective for recapture of salmonids. Recapture success was strongly negatively correlated with both fish size and the number of fish escaped, regardless of species. Recapture success was universally low across all studied species (8%). Numerous tracking studies of escaped fish indicate that recapture efforts should be initiated within 24 h of an escape incident for highest recapture success. However, most large escape events are due to storms, which mean recapture efforts rarely start within this timeframe. Recapture of escaped fish is broadly ineffective in marine habitats, with rare exception. High bycatch rates during ineffective recapture attempts imply that large‐scale recapture efforts should be weighed against the possibility of affecting wild fish populations negatively. We suggest three alternative approaches to reduce escapee numbers in wild habitats: (i) protect populations of predatory fish around sea‐cage farms from fishing, as they prey upon smaller escapees; (ii) construct impact offset programmes to target recapture in habitats where escapees can be efficiently caught; and (iii) ensure technical standards are legislated so that fish farmers invest in preventative technologies to minimize escapes.