Corona, Lime, Sun, Rash: A Case Report of Severe Phytophotodermatitis in an Active Duty Soldier.

Dermatological complaints constitute a large portion of patient visits to both emergency departments and military clinics. Proper assessment to separate the benign diagnoses from life-threatening may prove challenging based on seemingly non-specific history and physical examination. Similarly, reflexive specialty consultation may delay treatment and overload the health care system. Phytophotodermatitis is caused by contact with sensitizing agents, including lime juice, which triggers localized skin reactions when exposed to ultraviolet A light. The resulting progression of erythema, edema, pain, and non-pruritic skin lesions presents a unique pattern limited to the area of initial psoralen contact. This uniquely limited pattern coupled with specific historical context provides evidence for diagnosis. We highlight the case of a 24-year- old otherwise healthy female returning from a leisure trip to Mexico with progressive worsening of erythematous bullae limited to her hands and wrists bilaterally, ultimately attributed to phytophotodermatitis from lime wedge exposure in her alcoholic beverages, commonly referred to as "Mexican Beer Hand." Despite the severity of her initial appearance, her symptoms resolved without complication from limited supportive care.

The importance of sound to the Atlantic cod, Gadus morhua, and the Atlantic haddock, Melanogrammus aeglefinus.

The gadoid fishes, including the Atlantic cod and haddock, are currently being exploited close to their safe biological limits, requiring restrictions upon the human activities that may harm them. This has prompted interest in the biology of such fishes. Studies of the cod and haddock have shown highly complex behavior, involving prolonged and energetic visual and acoustic displays. Different sounds are produced in different behavioral contexts and are emitted almost continuously by cod and haddock, especially throughout the spawning season (February to May). The distinctive characteristics of these sounds make it possible to locate spawning cod and haddock at their marine spawning grounds. Human activities in these areas may affect their spawning adversely and have deleterious effects upon their stocks. Man-made sounds in water do have an adverse effect upon cod and haddock, and other fishes. Listening for the cod and haddock sounds provides a reliable, non-invasive technique for detecting their locations, and especially their spawning areas, and enables them to be protected well.

Fish hearing "specialization" - a re-evaluation.

Investigators working with fish bioacoustics used to refer to fishes that have a narrow hearing bandwidth and poor sensitivity as "hearing generalists" (or "non-specialists"), while fishes that could detect a wider hearing bandwidth and had greater sensitivity were referred to as specialists. However, as more was learned about fish hearing mechanism and capacities, these terms became hard to apply since it was clear there were gradations in hearing capabilities. Popper and Fay, in a paper in Hearing Research in 2011, proposed that these terms be dropped because of the gradation. While this was widely accepted by investigators, it is now apparent that the lack of relatively concise terminology for fish hearing capabilities makes it hard to discuss fish hearing. Thus, in this paper we resurrect the terms specialist and non-specialist but use them with modifiers to express the specific structure of function that is considered a specialization. Moreover, this resurrection recognizes that hearing specializations in fishes may not only be related to increased bandwidth and/or sensitivity, but to other, perhaps more important, aspects of hearing such as sound source localization, discrimination between sounds, and detection of sounds in the presence of masking signals.

Substrate vibrations and their potential effects upon fishes and invertebrates.

This paper reviews the nature of substrate vibration within aquatic environments where seismic interface waves may travel along the surface of the substrate, generating high levels of particle motion. There are, however, few data on the ambient levels of particle motion close to the seabed and within the substrates of lakes and rivers. Nor is there information on the levels and the characteristics of the particle motion generated by anthropogenic sources in and on the substrate, which may have major effects upon fishes and invertebrates, all of which primarily detect particle motion. We therefore consider how to monitor substrate vibration and describe the information gained from modeling it. Unlike most acoustic modeling, we treat the substrate as a solid. Furthermore, we use a model where the substrate stiffness increases with depth but makes use of a wave that propagates with little or no dispersion. This shows the presence of higher levels of particle motion than those predicted from the acoustic pressures, and we consider the possible effects of substrate vibration upon fishes and invertebrates. We suggest that research is needed to examine the actual nature of substrate vibration and its effects upon aquatic animals.

Sound detection by Atlantic cod: An overview.

The Atlantic cod (Gadus morhua) is among the commercially most important fish species in the world. Since sound plays such an important role in the lives of Atlantic cod and its related species, understanding of their bioacoustics is of great importance. Moreover, since cod are amenable to studies of hearing, especially in open bodies of water, they have the potential to become a "model species" for investigations of fish hearing. To serve as the basis for future studies, and to bring together what is now known about cod hearing, this paper reviews the literature to date. While there is some discussion of other species in the paper, the focus is upon what is already known about cod hearing, and what now needs to be known. An additional focus is on what knowledge of cod hearing tells about hearing in fishes in general.

Introduction to the special issue on the effects of sound on aquatic life.

The effects of anthropogenic (man-made) underwater sound on aquatic life have become an important environmental issue. One of the focal ways to present and to share knowledge on the topic has been the international conference on The Effects of Noise on Aquatic Life ("Aquatic Noise"). The conferences have brought together people from diverse interests and backgrounds to share information and ideas directed at understanding and solving the challenges of the potential effects of sound on aquatic life. The papers published here and in a related special issue of Proceedings of Meetings on Acoustics present a good overview of the many topics and ideas covered at the meeting. Indeed, the growth in studies on anthropogenic sound since the first meeting in 2007 reflects the increasing use of oceans, lakes, rivers, and other waterways by humans. However, there are still very substantial knowledge gaps about the effects of sound on all aquatic animals, and these gaps lead to there being a substantial need for a better understanding of the sounds produced by various sources and how these sounds may affect animals.

Taking the Animals' Perspective Regarding Anthropogenic Underwater Sound.

Anthropogenic (man-made) sound has the potential to harm marine biota. Increasing concerns about these effects have led to regulation and mitigation, despite there being few data on which to base environmental management, especially for fishes and invertebrates. We argue that regulation and mitigation should always be developed by looking at potential effects from the perspectives of the animals and ecosystems exposed to the sounds. We contend that there is currently a need for far more data on which to base regulation and mitigation, as well as for deciding on future research priorities. This will require a process whereby regulators and researchers come together to identify and implement a strategy that links key scientific and regulatory questions.

How to set sound exposure criteria for fishes.

Underwater sounds from human sources can have detrimental effects upon aquatic animals, including fishes. Thus, it is important to establish sound exposure criteria for fishes, setting out those levels of sound from different sources that have detrimental effects upon them, in order to support current and future protective regulations. This paper considers the gaps in information that must be resolved in order to establish reasonable sound exposure criteria for fishes. The vulnerability of fishes is affected by the characteristics of underwater sounds, which must be taken into account when evaluating effects. The effects that need to be considered include death and injuries, physiological effects, and changes in behavior. Strong emphasis in assessing the effects of sounds has been placed upon the hearing abilities of fishes. However, although hearing has to be taken into account, other actual effects also have to be considered. This paper considers the information gaps that must be filled for the development of future guidelines and criteria.

The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia.

Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy, and implementation of risk-adapted therapy has been instrumental in the dramatic improvements in clinical outcomes. A key to risk-adapted therapies includes the identification of genomic features of individual tumors, including chromosome number (for hyper- and hypodiploidy) and gene fusions, notably ETV6-RUNX1, TCF3-PBX1, and BCR-ABL1 in B-cell ALL (B-ALL). RNA-sequencing (RNA-seq) of large ALL cohorts has expanded the number of recurrent gene fusions recognized as drivers in ALL, and identification of these new entities will contribute to refining ALL risk stratification. We used RNA-seq on 126 ALL patients from our clinical service to test the utility of including RNA-seq in standard-of-care diagnostic pipelines to detect gene rearrangements and IKZF1 deletions. RNA-seq identified 86% of rearrangements detected by standard-of-care diagnostics. KMT2A (MLL) rearrangements, although usually identified, were the most commonly missed by RNA-seq as a result of low expression. RNA-seq identified rearrangements that were not detected by standard-of-care testing in 9 patients. These were found in patients who were not classifiable using standard molecular assessment. We developed an approach to detect the most common IKZF1 deletion from RNA-seq data and validated this using an RQ-PCR assay. We applied an expression classifier to identify Philadelphia chromosome-like B-ALL patients. T-ALL proved a rich source of novel gene fusions, which have clinical implications or provide insights into disease biology. Our experience shows that RNA-seq can be implemented within an individual clinical service to enhance the current molecular diagnostic risk classification of ALL.

The importance of underwater sounds to gadoid fishes.

The codfish family includes more than 500 species that vary greatly in their abundance in areas like the North Sea and are widely fished. Gadoids (codfish) gather at particular locations to spawn, where they exhibit complex reproductive behavior with visual and acoustic displays. Calls have been described from seven species, including the Atlantic cod and haddock. They vocalize by means of a specialized apparatus, consisting of rapidly contracting striated muscles (the drumming muscles) attached to the gas-filled swim bladder. Several gadoids, such as the ling and the Greenland cod, possess drumming muscles and are likely to make sounds. Non-vocal gadoids, such as the poor cod, lack these muscles. It is suggested that the sonic apparatus was present in the early species of the gadoids, with some species having lost their sonic ability. Interestingly, silent gadoids are mainly small schooling fishes. Gadoid species are most sensitive to sounds from 30 to 500 Hz. Gadoid hearing can be masked by ambient sound but also by anthropogenic sounds, which may therefore adversely affect their reproduction, with potential effects upon discrete local stocks. Listening for gadoid sounds provides a reliable, non-invasive way of locating spawning sites, which can enhance the protection of reproducing fish from human impacts.

Effects of sound exposure from a seismic airgun on heart rate, acceleration and depth use in free-swimming Atlantic cod and saithe.

Airguns used for offshore seismic exploration by the oil and gas industry contribute to globally increasing anthropogenic noise levels in the marine environment. There is concern that the omnidirectional, high intensity sound pulses created by airguns may alter fish physiology and behaviour. A controlled short-term field experiment was performed to investigate the effects of sound exposure from a seismic airgun on the physiology and behaviour of two socioeconomically and ecologically important marine fishes: the Atlantic cod (Gadus morhua) and saithe (Pollachius virens). Biologgers recording heart rate and body temperature and acoustic transmitters recording locomotory activity (i.e. acceleration) and depth were used to monitor free-swimming individuals during experimental sound exposures (18-60 dB above ambient). Fish were held in a large sea cage (50 m diameter; 25 m depth) and exposed to sound exposure trials over a 3-day period. Concurrently, the behaviour of untagged cod and saithe was monitored using video recording. The cod exhibited reduced heart rate (bradycardia) in response to the particle motion component of the sound from the airgun, indicative of an initial flight response. No behavioural startle response to the airgun was observed; both cod and saithe changed both swimming depth and horizontal position more frequently during sound production. The saithe became more dispersed in response to the elevated sound levels. The fish seemed to habituate both physiologically and behaviourally with repeated exposure. In conclusion, the sound exposures induced over the time frames used in this study appear unlikely to be associated with long-term alterations in physiology or behaviour. However, additional research is needed to fully understand the ecological consequences of airgun use in marine ecosystems.

An overview of fish bioacoustics and the impacts of anthropogenic sounds on fishes.

Fishes use a variety of sensory systems to learn about their environments and to communicate. Of the various senses, hearing plays a particularly important role for fishes in providing information, often from great distances, from all around these animals. This information is in all three spatial dimensions, often overcoming the limitations of other senses such as vision, touch, taste and smell. Sound is used for communication between fishes, mating behaviour, the detection of prey and predators, orientation and migration and habitat selection. Thus, anything that interferes with the ability of a fish to detect and respond to biologically relevant sounds can decrease survival and fitness of individuals and populations. Since the onset of the Industrial Revolution, there has been a growing increase in the noise that humans put into the water. These anthropogenic sounds are from a wide range of sources that include shipping, sonars, construction activities (e.g., wind farms, harbours), trawling, dredging and exploration for oil and gas. Anthropogenic sounds may be sufficiently intense to result in death or mortal injury. However, anthropogenic sounds at lower levels may result in temporary hearing impairment, physiological changes including stress effects, changes in behaviour or the masking of biologically important sounds. The intent of this paper is to review the potential effects of anthropogenic sounds upon fishes, the potential consequences for populations and ecosystems and the need to develop sound exposure criteria and relevant regulations. However, assuming that many readers may not have a background in fish bioacoustics, the paper first provides information on underwater acoustics, with a focus on introducing the very important concept of particle motion, the primary acoustic stimulus for all fishes, including elasmobranchs. The paper then provides background material on fish hearing, sound production and acoustic behaviour. This is followed by an overview of what is known about effects of anthropogenic sounds on fishes and considers the current guidelines and criteria being used world-wide to assess potential effects on fishes. Most importantly, the paper provides the most complete summary of the effects of anthropogenic noise on fishes to date. It is also made clear that there are currently so many information gaps that it is almost impossible to reach clear conclusions on the nature and levels of anthropogenic sounds that have potential to cause changes in animal behaviour, or even result in physical harm. Further research is required on the responses of a range of fish species to different sound sources, under different conditions. There is a need both to examine the immediate effects of sound exposure and the longer-term effects, in terms of fitness and likely impacts upon populations.

Clinker: visualizing fusion genes detected in RNA-seq data.

Background: Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for identifying fusion genes from RNA-sequencing (RNA-seq) data, visualizing these transcripts and their supporting reads remains challenging. Findings: Clinker is a bioinformatics tool written in Python, R, and Bpipe that leverages the superTranscript method to visualize fusion genes. We demonstrate the use of Clinker to obtain interpretable visualizations of the RNA-seq data that lead to fusion calls. In addition, we use Clinker to explore multiple fusion transcripts with novel breakpoints within the P2RY8-CRLF2 fusion gene in B-cell acute lymphoblastic leukemia. Conclusions: Clinker is freely available software that allows visualization of fusion genes and the RNA-seq data used in their discovery.

The importance of particle motion to fishes and invertebrates.

This paper considers the importance of particle motion to fishes and invertebrates and the steps that need to be taken to improve knowledge of its effects. It is aimed at scientists investigating the impacts of sounds on fishes and invertebrates but it is also relevant to regulators, those preparing environmental impact assessments, and to industries creating underwater sounds. The overall aim of this paper is to ensure that proper attention is paid to particle motion as a stimulus when evaluating the effects of sound upon aquatic life. Directions are suggested for future research and planning that, if implemented, will provide a better scientific basis for dealing with the impact of underwater sounds on marine ecosystems and for regulating those human activities that generate such sounds. The paper includes background material on underwater acoustics, focusing on particle motion; the importance of particle motion to fishes and invertebrates; and sound propagation through both water and the substrate. Consideration is then given to the data gaps that must be filled in order to better understand the interactions between particle motion and aquatic animals. Finally, suggestions are provided on how to increase the understanding of particle motion and its relevance to aquatic animals.

Directional hearing and sound source localization by fishes.

Directional hearing may enable fishes to seek out prey, avoid predators, find mates, and detect important spatial cues. Early sound localization experiments gave negative results, and it was thought unlikely that fishes utilized the same direction-finding mechanisms as terrestrial vertebrates. However, fishes swim towards underwater sound sources, and some can discriminate between sounds from different directions and distances. The otolith organs of the inner ear detect the particle motion components of sound, acting as vector detectors through the presence of sensory hair cells with differing orientation. However, many questions remain on inner ear functioning. There are problems in understanding the actual mechanisms involved in determining sound direction and distance. Moreover, very little is still known about the ability of fishes to locate sound sources in three-dimensional space. Do fishes swim directly towards a source, or instead "sample" sound levels while moving towards the source? To what extent do fishes utilize other senses and especially vision in locating the source? Further behavioral studies of free-swimming fishes are required to provide better understanding of how fishes might actually locate sound sources. In addition, more experiments are required on the auditory mechanism that fishes may utilize.

Snapshot recordings provide a first description of the acoustic signatures of deeper habitats adjacent to coral reefs of Moorea.

Acoustic recording has been recognized as a valuable tool for non-intrusive monitoring of the marine environment, complementing traditional visual surveys. Acoustic surveys conducted on coral ecosystems have so far been restricted to barrier reefs and to shallow depths (10-30 m). Since they may provide refuge for coral reef organisms, the monitoring of outer reef slopes and describing of the soundscapes of deeper environment could provide insights into the characteristics of different biotopes of coral ecosystems. In this study, the acoustic features of four different habitats, with different topographies and substrates, located at different depths from 10 to 100 m, were recorded during day-time on the outer reef slope of the north Coast of Moorea Island (French Polynesia). Barrier reefs appeared to be the noisiest habitats whereas the average sound levels at other habitats decreased with their distance from the reef and with increasing depth. However, sound levels were higher than expected by propagation models, supporting that these habitats possess their own sound sources. While reef sounds are known to attract marine larvae, sounds from deeper habitats may then also have a non-negligible attractive potential, coming into play before the reef itself.