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Background Whole-exome sequencing (WES) has become an efficient diagnostic test for patients with likely monogenic conditions such as rare idiopathic diseases or sudden unexplained death. Yet, many cases remain undiagnosed. Here, we report the added diagnostic yield achieved for 101 WES cases re-analyzed 1 to 7 years after initial analysis. Methods Of the 101 WES cases, 51 were rare idiopathic disease cases and 50 were postmortem “molecular autopsy” cases of early sudden unexplained death. Variants considered for reporting were prioritized and classified into three groups: (1) diagnostic variants, pathogenic and likely pathogenic variants in genes known to cause the phenotype of interest; (2) possibly diagnostic variants, possibly pathogenic variants in genes known to cause the phenotype of interest or pathogenic variants in genes possibly causing the phenotype of interest; and (3) variants of uncertain diagnostic significance, potentially deleterious variants in genes possibly causing the phenotype of interest. Results Initial analysis revealed diagnostic variants in 13 rare disease cases (25.4%) and 5 sudden death cases (10%). Re-analysis resulted in the identification of additional diagnostic variants in 3 rare disease cases (5.9%) and 1 sudden unexplained death case (2%), which increased our molecular diagnostic yield to 31.4% and 12%, respectively. Conclusions The basis of new findings ranged from improvement in variant classification tools, updated genetic databases, and updated clinical phenotypes. Our findings highlight the potential for re-analysis to reveal diagnostic variants in cases that remain undiagnosed after initial WES.

The Scripps Molecular Autopsy (MA) study seeks to incorporate genetic testing into the postmortem examination of cases of sudden death in the young (< 45 years old). Here we describe the results from the first two years of the study, which consisted of whole exome sequencing (WES) of a cohort of 50 cases predominantly from San Diego County. Apart from the individual description of cases, we analyzed the data at the cohort-level, which brought new perspectives on the genetic causes of sudden death. We investigated the advantages and disadvantages of using WES compared to a gene panel for cardiac disease (usually the first genetic test used by medical examiners). In an attempt to connect complex clinical phenotypes with genotypes, we classified samples by their genetic fingerprint. Finally, we studied the benefits of analyzing the mitochondrial DNA genome. In this regard, we found that half of the cases clinically diagnosed as sudden infant death syndrome had an increased ratio of heteroplasmic variants, and that the variants were also present in the mothers. We believe that community-based data aggregation and sharing will eventually lead to an improved classification of variants. Allele frequencies for the all cases can be accessed via our genomics browser at https://genomics.scripps.edu/browser.

Training is a fundamental part of all scientific and technical disciplines. This is particularly true for all types of surgeons. For surgical procedures, a number of skills are necessary to reduce mistakes. Trainees must learn an extensive yet standardized set of problem-solving and technical skills to handle challenges as they arise. There are currently no guidelines or consistent training methods for those intending to implant electronic tags in fish; this is surprising, considering documented cases of negative consequences of fish surgeries and information from studies having empirically tested fish surgical techniques. Learning how to do fish surgery once is insufficient for ensuring the maintenance or improvement of surgical skill. Assessment of surgical skills is rarely incorporated into training, and is needed. Evaluation provides useful feedback that guides future learning, fosters habits of self-reflection and self-remediation, and promotes access to advanced training. Veterinary professionals should be involved in aspects of training to monitor basic surgical principles. We identified attributes related to knowledge, understanding, and skill that surgeons must demonstrate prior to performing fish surgery including a “hands-on” assessment using live fish. Included is a summary of common problems encountered by fish surgeons. We conclude by presenting core competencies that should be required as well as outlining a 3-day curriculum for training surgeons to conduct intracoelomic implantation of electronic tags. This curriculum could be offered through professional fisheries societies as professional development courses.

Intracoelomic implantation of transmitters into fish requires making a surgical incision, incision closure, and other surgery related techniques; however, the tools and techniques used in the surgical process vary widely. We review the available literature and focus on tools and techniques used for conducting surgery on juvenile salmonids because of the large amount of research that is conducted on them. The use of sterilized surgical instruments properly selected for a given size of fish will minimize tissue damage and infection rates, and speed the wound healing of fish implanted with transmitters. For the implantation of transmitters into small fish, the optimal surgical methods include making an incision on the ventral midline along the linea alba (for studies under 1 month), protecting the viscera (by lifting the skin with forceps while creating the incision), and using absorbable monofilament suture with a small-swaged-on swaged-on tapered or reverse-cutting needle. Standardizing the implantation techniques to be used in a study involving particular species and age classes of fish will improve survival and transmitter retention while allowing for comparisons to be made among studies and across multiple years. This review should be useful for researchers working on juvenile salmonids and other sizes and species of fish.

Fish migration represents one of the most complex and intriguing biological phenomena in the animal kingdom. How do fish migrate such vast distances? What are the costs and benefits of migration? Some of these fundamental questions have been addressed through the use of telemetry. However, telemetry alone has not and will not yield a complete understanding of the migration biology of fish a or provide solutions to problems such as identifying physical barriers to migration or understanding potential impacts of climate change. Telemetry can be coupled with other tools and techniques to yield new insights into animal biology. Using Fraser River sockeye salmon (Oncorhynchus nerka) as a model, we summarize the advances that we have made in understanding salmonid migration biology through the integration of disciplines (i.e., interdisciplinary research) including physiology, behavior, functional genomics, and experimental biology. We also discuss opportunities for using large-scale telemetry arrays an...

Knowledge of life-history traits is increasingly recognized as an important criterion for effective management and conservation. Understanding the link between physiology and life history is an important component of this knowledge and in our view is particularly relevant to understanding marine and freshwater fishes. Such linkages (i.e. the life-history/physiology nexus) have been recently advocated for avian systems and here we explore this concept for fish. This paper highlights the gap in fisheries literature with regard to understanding the relationship between physiology and life history, and proposes ways in which this integration could improve fisheries management and conservation. We use three case studies on different fishes (i.e. the Pacific salmon, the grouper complex and tuna) to explore these issues. The physiological structure and function of fish plays a central role in determining stock response to exploitation and changes in the environment. Physiological measures can provide simple indicators necessary for cost-effective monitoring in the evaluation of fisheries sustainability. The declining state of world fisheries and the need to develop and implement restoration strategies, such as hatchery production or protected areas, provides strong incentive to better understand the influence of physiology on population and reproductive dynamics and early life history. Physiology influences key population-level processes, particularly those dealing with reproduction, which must be incorporated into the design and successful implementation of specific and broadscale initiatives (e.g. aquatic protected areas and bycatch reduction). Suggestions are made for how to encourage wider application of the physiology/life-history link, in fisheries management and conservation, as well as more broadly in education and research.

We raised two populations of sockeye salmon fry from fertilized eggs in the laboratory and tested the hypothesis that outlet fry popula- tions, fish which must migrate upstream to reach rearing lakes after yolk-sac absorption, have better swimming ability and morphological char- acteristics conducive to enhanced swimming per- formance than inlet fry populations, fish which migrate downstream to rearing lakes. Despite being of identical age, fry from the outlet popu- lation were larger (approx. 6.7% longer, ~ 5m m on average) and more laterally compressed than inlet fry at the time of our initial experiments. Using an open-top box flume, we found that the burst-swimming performance (in cm s -1 ) of the outlet population was 31% better. We found no differences between populations in prolonged- swimming performance. We were unable to find any direct relationships between measures of swimming performance and size or shape vari- ables, suggesting that the larger, more robust morphology of outlet fry was not responsible for the superior burst ability. Recent biochemical studies indicate outlet fry may be metabolically better provisioned for burst swimming than inlet fry. It is possible that the morphological differ- ences between the populations of fry reflect adaptations needed by adults during their migra- tion and spawning.

Adult sockeye salmon (Oncorhynchus nerka) acquire infections with the myxosporean kidney parasite Parvicapsula minibicornis during their spawning migration in the Fraser River, British Columbia. Controlled infections with this parasite in wild sockeye salmon had no significant impact on plasma ionic status, metabolic rates, and initial maximum prolonged swimming performance (Ucrit) for fish ranked as either strongly, weakly, or noninfected by polymerase chain reaction analysis of kidney tissue. However, strongly infected fish had significantly lower second Ucritand recovery ratio (8%) values, indicating decreased ability to recover from exercise. As the present study shows that the severity of infection is affected by time and temperature, the accumulated thermal units (ATU) of exposure in this study were compared with those experienced by naturally migrating sockeye salmon. A parallel telemetry study revealed that early-timed sockeye experienced significantly more ATU (741.4 ± 29.4 °C) than normally migrating salmon (436.0 ± 20.0 °C) prior to spawning because of a significantly longer holding period in the lake system. The present data are discussed in the context of a threshold of >450 °C ATU for severe infection that would first manifest in early-timed fish in the upper reaches of the Fraser River and certainly on the spawning grounds.

A 26-day-old male infant who had been fussy and feeding poorly for a period of several hours died suddenly despite efforts at resuscitation. Postmortem examination revealed eosinophilic endomyocarditis unassociated with disease in other organs. The etiology remained unexplained after review of the medical and family histories and circumstances of death, extensive light and immunofluorescence microscopies, and microbiological, metabolic, and toxicologic testing. This appears to be the youngest reported case of eosinophilic endomyocarditis, a disorder that typically occurs in middle-age males and is often associated with benign or malignant hypereosinophilic conditions. The medical literature is reviewed.

The purpose of the present study was to characterize the surgical methods researchers use to implant telemetry transmitters in fish and obtain their opinions on fish surgical techniques. The majority of respondents (74%) use monofilament suture to close transmitter incisions, mirroring recent findings that monofilament can help reduce tissue inflammation and promote wound healing. An equal number also believe that maintaining sterile equipment between surgeries is important to preserve fish health. Despite the difficulty of maintaining sterile surgical equipment and surgery areas in field conditions, this opinion does coincide with those of veterinarians. Opinions about what component of surgery is the most hazardous for fish were mixed: 37% believed it to be the initial incision, closely followed by wound closure (23%), insertion of the transmitter and its components (22%), and anesthesia and the handling of the fish (18%). A large proportion (73%) of researchers practice at least occasionally t...

Intraperitoneal implantation of telemetry devices in fishes has become commonplace in fisheries science, yet little is known about the training and experience of practicing fish surgeons. We used a survey to characterize the training, experience, and opinions of researchers who use surgical techniques to implant telemetry devices in fishes. The experience level of the 177 respondents varied from 0 to 25 years of experience and 5 to 5,000 fish surgeries, and it was apparent that there was no consistent method of training in surgical techniques, with many of the respondents indicating they learned from trial and error. Very few of the respondents had been formally tested to assess their level of surgical competency, although the majority recognized that surgical experience was important and believed that a minimum level of experience should be required prior to engaging in fish surgery. Respondents identified a need for more effective training materials and perhaps some levels of international stan...

Using Transonic® flow probes and a uniquely designed swimming flume, we directly measured cardiac parameters ( Q , cardiac output; S V , stroke volume; and f H , heart rate) in winter flounder ( Pleuronectes americanus) before and during critical swim speed ( U crit ) tests at 4 and 10 °C. Resting Q , S V and f H averaged 9.8 ml min −1 kg −1 , 0.5 ml kg −1 (1.0 ml g ventricle −1 ) and 21 beats min −1 at 4 °C and 15.5 ml min −1 kg −1 , 0.5 ml kg −1 (0.95 ml g ventricle −1 ) and 34 beats min −1 at 10 °C ( Q 10 values of 2.13, 0.91 and 2.35, for Q , S V and f H , respectively). Cardiac output, S V and f H increased by approx. 170%, 70% and 60% at both temperatures during the U crit test. However, cardiac parameters generally reached near maximal levels almost immediately upon swimming and remained at these levels until U crit (0.65±0.06 bl s −1 at 4 °C and 0.73±0.07 bl s −1 at 10 °C). This rapid rise in cardiac function to near maximal levels did not appear to be the result of stress alone, as Q only fell slightly when flounder were swum for 75 min at −1 , speeds at which they appeared to swim comfortably. Our results suggest that both Q and U crit have been significantly overestimated in flatfishes, and that “lift-off”/slow swimming is energetically expensive. Furthermore, they show that maximum and resting stroke volume (per g of ventricle) are extremely high in the flounder as compared with other teleosts.

Repeated critical swimming performance trials (Ucrit) were performed on Atlantic salmon (Salmo salar) to test the null hypothesis that the source of dietary lipids (fish-based, poultry-based, and plant-based) does not influence exercise and recovery performance. Four diets were prepared by extensively replacing supplemental lipid from anchovy oil (AO; 100% AO at 150 g/kg) with cold pressed flaxseed oil (FO; 25% AO, 75% FO), sunflower oil (SO; 25% AO, 75% SO), or poultry fat (PF; 25% AO, 75% PF). These diets had equivalent protein and energy concentrations, but due to the different supplemental lipid sources, varied widely in their fatty acid composition. Fish fed AO had a significantly higher (P0.05) first Ucrit (2.62+/-0.07 body lenght s(-1)) than those fed PF (2.22+/-0.12 body lenght s(-1)) that had low muscle ratios of n-3 highly unsaturated fatty acids (n-3 HUFA) to saturated fatty acids (SFA) and arachidonic acid (AA), and high levels of oleic acid. Fish in the FO and SO diet groups swam as well as AO-fed fish in both swimming trials. The performance of fish fed AO decreased significantly (P0.05) during the second swimming trial (i.e. Ucrit2/Ucrit1=0.92+/-0.02). No significant differences occurred between diet groups for the second swim trial. There was a positive correlation between both n-3 HUFA/SFA and n-3 HUFA/AA ratios, and Ucrit1. A negative correlation was found between dietary AA and oleic acids, and Ucrit1. The present study suggests that low dietary n-3 HUFA/ SFA and n-3 HUFA/AA ratios may negatively affect swimming performance. The former possibly can be offset by increasing linoleic acid in the presence of nutritionally adequate n-3 HUFA (e.g. SO diet). Lipid supplements consisting largely of vegetable oils did not compromise fish cardiorespiratory physiology under the conditions of this study.

The effects of 60-mg L-1 clove oil and 60-mg L-1 tricaine methanesulphonate (MS-222) on the blood chemistry of rainbow trout were compared after exposure to handling stress via caudal puncture blood sampling. Fish sampled by caudal puncture and subsequently exposed to anaesthetics showed a typical handling stress response over a 48-h period. There were no significant differences between the responses of fish exposed to equal concentrations of clove oil and MS-222, with the following exceptions: the blood glucose at full anaesthesia, and lactate at full recovery increased significantly in the clove oil-exposed fish. In a subsequent experiment, the stress response observed in fish sampled by caudal puncture and exposed to clove oil and MS-222 was compared with a non-anaesthetized control group. The increases in plasma cortisol levels were significantly lower at recovery in fish treated with either anaesthetic compared with the control fish. Fish exposed to MS-222 had significantly higher cortisol levels at 1 h. These findings show that few differences exist between the anaesthetic effects of clove oil and MS-222 on the physiological response of fish to stress. However, clove oil is more effective at reducing the short-term stress response induced by handling and blood sampling, and is recommended as an alternative fish anaesthetic.

Context: Complementary alternative medicine therapies based on the use of cesium chloride preparations for the treatment of cancer and radiation poisoning, have generated therapeutic interest; but oral or intravenous administration of cesium chloride (CsCl) to cancer patients as an alternative mode of cancer therapy have not been approved by the U.S. Food and Drug Administration (FDA). Objective: Cesium (Cs) levels from human tissue were measured to determine exposure to an alternative medical treatment. Cesium levels are reported from two patients who were administered cesium chloride in conjunction with aloe vera as part of an alternative cancer treatment. Design: The samples were analyzed by graphite furnace atomic absorption spectrometry with Zeeman background correction. As a reference, Cs was also determined in brain, liver, kidney, and whole blood from control case materials retrieved from the National Tissue Repository of the Armed Forces Institute of Pathology. Results: High levels of cesium were found in brain, liver, kidney, bile, gastric content, and whole blood collected at autopsy as compared to reference levels. The administration of cesium chloride resulted in blood levels a factor of 1100 higher than normal. The highest Cs concentrations were found in the liver (1029 µg/g, dry wt), followed by the kidney (815 µg/g, dry wt) and brain (219 µg/g, dry wt). Conclusion: The high accumulation in the liver suggests that hepatotoxicity from Cs might be an initial presenting symptom in Cs-poisoning cases. This is the first report describing two cases with high Cs levels in human tissues.

In two separate experiments we investigated the effects of different types of suture material and patterns on wound healing in rainbow trout Oncorhynchus mykiss with and without transmitter implants. We used absorbable and nonabsorbable monofilament and braided silk sutures in simple interrupted and vertical mattress patterns to close 3-cm incisions on rainbow trout. Braided silk sutures and vertical mattress suture patterns caused significantly more tissue inflammation (P < 0.05) as shown by macroscopic analysis. However, there were no significant differences in the histology or strength of the wounds related to the type of suture material or the type of suture pattern used. Dummy radio transmitters compounded the inflammatory effect silk had on healing incisions compared with inflammation without transmitters.

We investigated the effects of preparing surgical incision sites with a topical antiseptic on wound healing and hematological response in rainbow trout Oncorhynchus mykiss. A povidone–iodine solution was applied both pre- and postsurgery to the incision sites on treated fish. Three-centimeter incisions in both treated (N = 9) and control (nontreated, N = 9) fish were closed with four nonabsorbable sutures sewn in a simple interrupted pattern. During the 42-d period of wound healing, there were no statistically significant changes in total erythrocyte counts (1.28 × 106/mm3 ± 0.05 SE), in percentage of dividing erythrocytes (0.76% ± 0.07 SE), or in differential leukocyte counts. Postmortem, pathogenic bacterial infections in the kidney or spleen were not detected in any of the fish. There was no histological difference between control and treated incisions to show either beneficial or adverse tissue reactions to the topical antiseptic treatments. Blinded histological analysis revealed both treated...

‘Sea lice' is a common name for a large number of species of marine ectoparasitic copepods, many of which are widespread and important disease-causing agents that infect both cultured and wild fish. Of these copepods, the salmon louse Lepeophtheirus salmonis is the most extensively studied because of its economic impact on the salmonid aquaculture industry and its possible impacts on wild salmonid populations. Different levels of infection by this parasite can affect the long-term survival and viability of its hosts. In this article, we review the nature of the interactions between L. salmonis and it hosts to identify crucial areas that warrant further research to aid understanding of the impact of infection with L. salmonis .

A variety of skeletal characteristics pertaining to the bony pelvis have, over the years, been of assistance as forensic markers, but the importance of the nutrient groove of the ilium has not been appreciated. During aircraft accident investigations we compared premortem anteroposterior abdominal radiographs with postmortem specimen radiographs of the ilium, with particular attention directed to the nutrient groove of the ilium. This marker can assume several configurations (i.e., parallel, V-shaped and Y-shaped) and is situated a few centimeters lateral to the sacroiliac joint. Left/right asymmetry, or absence of the nutrient grove on one side of the pelvis are possible variants within an individual. The purpose of this report is to emphasize the previously unrecognized importance of the nutrient groove of the ilium as a useful forensic radiographic marker.

We used image processing to elucidate patterned injuries in a case of assault with a police baton. Three-dimensional visualization techniques were then used to correlate the location of patterned injuries with subjacent fracture and soft tissue damage. The visualization methods are discussed. Language: en

Recent advances in image processing and visualization are of increasing use in the investigation of violent crime. The Digital Image Processing Laboratory at the Armed Forces Institute of Pathology in collaboration with groups at the University of North Carolina at Chapel Hill are actively exploring visualization applications including image processing of trauma images, 3D visualization, forensic database management and telemedicine. Examples of recent applications are presented. Future directions of effort include interactive consultation and image manipulation tools for forensic data exploration.© (1994) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

The toxicologic results from the 47 victims of the explosion on the USS Iowa are presented. Good correlation between carboxyhemoglobin saturations and cause of death was found. There were no correlations between blood cyanide concentrations and causes of death. Volatile analysis suggested postmortem ethanol production rather than antemortem ethanol ingestion. No drugs except nicotine were detected in any of the victims.

Chloroquine concentrations in blood and tissues were examined in overdose and non-overdose cases to determine appropriate ranges for interpretation. Twenty-nine literature overdose cases and 8 non-overdose literature cases were compared with this laboratory's findings. The results indicate significant postmortem redistribution of chloroquine. Combining this laboratory's results and the literature results indicates that using a liver concentration of 150 mg/kg as a cutoff between overdose and non-overdose concentrations properly identified 30 of the 34 published cases containing liver chloroquine and 19 of the 20 presented cases.

Although child abuse and neglect continue to appear in the medical literature frequently, little regarding scene investigation in such cases has been discussed. Many explanations have been offered for this deficit, the most common one is based on the time delay between infliction of the injury and discovery. At the Armed Forces Institute of Pathology, child-abuse cases submitted for consultation repeatedly show deficits in the scene investigation and its documentation. Since the discovery of child abuse is dependent on either physical evidence of repetitive punitive measures or an injury pattern not in agreement with the alleged circumstances, it behooves the assigned investigator to make every attempt to document the scene(s) as in any other criminal investigation.

The tissue adhesive butyl cyanoacrylate was evaluated in the repair of injured porcine kidneys following low-velocity ballistic trauma. This technique was compared to the classic renal repair using chromic suture and a patch of perirenal fat. The repair with butyl cyanoacrylate was less time consuming (four minutes vs. 28 minutes for the controls) and decreased blood loss (67 cc vs. 180 cc for the controls). Ten days post injury the kidneys repaired with tissue adhesive showed minimal intraparenchymal hemorrhage or perirenal bleeding, while two of the four (50%) suture-repaired kidneys showed intrarenal microhemorrhages and one (25%) developed a perirenal hematoma. Perirenal adhesions were noted in both groups. Vital signs, IVP’s, creatinine clearance, and serum and urine chemistries were nearly identical in the two groups. The results show that low-velocity ballistic injuries of renal tissue can be repaired effectively and more efficiently with the use of butyl cyanoacrylate when compared to conventional suturing methods.

A cloud of carbon dioxide gas, with an estimated volume of 1 km3 was released from Lake Nyos, a volcanic crater lake in Cameroon, Africa, causing 1700 to 2000 human fatalities as well as killing thousands of livestock and wild animals. At the request of the Cameroonian Government, the Office of Foreign Disaster Assistance of the U.S. Department of State sent a multidisciplinary team which included 2 forensic pathologists to assist the Government of Cameroon in investigating this natural disaster. The medical evaluation was concentrated in 3 areas: the autopsy of human and animal fatalities, examination and interview of survivors, and examination of the scene of the disaster. Toxicologic specimens were obtained at autopsy, and numerous samples of lake water were collected. The autopsy findings were consistent with asphyxia. The results of chemical analyses excluded many volatiles but not carbon dioxide as the toxic agent. The exact source of this gas continues to be a subject of a heated geologic debate, but fermentation of organic materials in the lake water has been eliminated on the basis of C14 isotope studies. This investigation underlines the value of forensic pathologists in epidemiological studies and in the examination of living persons.

This is a study of commercially available .22 caliber rimfire ammunition manufactured to explode on bullet impact. Factors considered were bullet velocity, angle of impact, missile deformation, and depth of penetration and cavitation in ordnance gelatin. Microscopic, radiographic, and high speed motion picture photographic techniques were employed. This study found that the angle of impact was critical for detonation of the bullet.