Combined modelling of mRNA decay dynamics and single-molecule imaging in the Drosophila embryo uncovers a role for P-bodies in 5' to 3' degradation.

Regulation of mRNA degradation is critical for a diverse array of cellular processes and developmental cell fate decisions. Many methods for determining mRNA half-lives rely on transcriptional inhibition or metabolic labelling. Here, we use a non-invasive method for estimating half-lives for hundreds of mRNAs in the early Drosophila embryo. This approach uses the intronic and exonic reads from a total RNA-seq time series and Gaussian process regression to model the dynamics of premature and mature mRNAs. We show how regulation of mRNA stability is used to establish a range of mature mRNA dynamics during embryogenesis, despite shared transcription profiles. Using single-molecule imaging, we provide evidence that, for the mRNAs tested, there is a correlation between short half-life and mRNA association with P-bodies. Moreover, we detect an enrichment of mRNA 3' ends in P-bodies in the early embryo, consistent with 5' to 3' degradation occurring in P-bodies for at least a subset of mRNAs. We discuss our findings in relation to recently published data suggesting that the primary function of P-bodies in other biological contexts is mRNA storage.

Cardiopulmonary Resuscitation Induced Posterior Rib Fractures in Nontraumatic Pediatric Deaths.

ABSTRACT: Posterior rib fractures are considered suspicious for nonaccidental injury when observed in infants without significant trauma history or underlying bone disease. The biomechanical mechanism postulated for causing posterior rib fractures is anterior/posterior compression of the chest with posterior levering of the rib head over the transverse process of the vertebra creating a focal area of stress. The recommended "2-thumb" cardiopulmonary resuscitation method involves the administrator placing both thumbs on the sternum of the patient, encircling the chest with the hands, and placing the finger tips lateral to the spine. From this position, the administrator compresses the chest in an anterior/posterior direction by pressing on the sternum. Theoretically, the 2-thumb method should focus all force on the sternum while the back is supported by the fingers limiting posterior levering of the ribs and reducing the risk of posterior rib fractures. However, posterior rib fractures have been found during the autopsy of infants who received 2-thumb cardiopulmonary resuscitation, had no traumatic history, had a nontraumatic cause of death, and had no indication of underlying bone disease. This case study series presents the demographics, birth histories, circumstances surrounding death, and autopsy findings of four such medical examiner cases.

The first step in an investigation of quantitative ultrasound as a technique for evaluating infant bone strength.

This study's purpose is to evaluate whether bone speed of sound (SOS) data, a parameter of quantitative ultrasound, collected from an infant autopsy sample are comparable to data collected from healthy, living infants. We hypothesize that SOS values obtained from deceased term-born infants will fall within the normal range for healthy, living infants. The study sample consists of 351 deceased infants between the ages of 30 weeks gestation at birth to 1 year postnatal at the time of death receiving autopsies at the Harris County Institute of Forensic Sciences or Texas Children's Hospital in Houston, TX. Various multivariate and univariate statistics were used to examine the relationship between SOS and age, prematurity, and chronic illness. The results of an ANOVA comparing the study sample data to published data from healthy, living infants indicate the SOS data are comparable. Additionally, a MANOVA indicated significant differences in SOS related to prematurity (p = 0.001) and age (p < 0.001). Mean SOS was significantly greater among term-born infants (M = 3065.66, SD =165.05) than premature infants (M = 2969.71, SD =192.72). Age had a significant polynomial (cubic) relationship with SOS for both the premature and term groups (p < 0.001). Results suggest that bone from an infant autopsy sample is an appropriate surrogate to examine the relationship between SOS and determinants of bone strength. Therefore, future research will use this study sample to investigate the relationship between SOS and determinants of bone strength in infants.

The Infant Injury Database: A Tool for the Study of Injury Patterns in Medicolegal Investigations of Child Abuse.

In 2012, the Harris County Institute of Forensic Sciences began prospectively collecting injury data from pediatric autopsies. These data and associated case information from 635 pediatric cases are archived in the Infant Injury Database (IID). This paper introduces the IID to the forensic community and demonstrates its potential utility for child abuse and infant fatality investigations. The database is intended to be a source of evidence-based research for coroners/medical examiners and clinicians in the recognition and diagnosis of child abuse. RR estimates were employed to quantify the relationship between individual autopsy findings to trauma-related and nontrauma-related causes of death. For example, unsurprisingly, the RR of trauma cases with multiple injury types is significantly greater than other causes of death, but the RR results provide a quantitative representation of the relationship. ROC curve modeling of the presence/absence of various injury types performed well at discriminating trauma from other causes of death (AUC = 0.96).

Sharp force trauma analysis in bone and cartilage: A literature review.

Sharp force trauma (SFT) in bone and cartilage has been studied extensively. This literature review summarizes knife and saw mark research. Researchers have documented several features of cut surfaces and successfully associated them with various tool characteristics. Most study designs are based on light microscopic examination, but other technologies such as micro-computed scanning, scanning electron microscope, and epifluorescence microscopy have been investigated. Researchers have worked with human and non-human material, and found that the presentation of SFT differs between the two. Furthermore, they have designed studies to control the parameters surrounding SFT (e.g., tool angle, force, direction) as well as not to control these parameters (real-world scenario) and have found that the trauma produced in the two scenarios differ considerably. Researchers have attempted to calculate the error rate associated with cut and saw mark analysis and have reported very different results. Several high profile cases of successful SFT analysis have been published and are briefly reviewed. Expert testimony based on cut and saw mark analysis has been found admissible, but not in all cases. Unfortunately, researchers have not consistently used standard terminology, a list of terms gathered from the literature is provided. Despite the extensive research, more work is needed. Methods that mitigate potential sources of error that are not dependent on analyst's experience must be developed.

The Utility of Forensic Anthropology in the Medical Examiner's Office.

Over the past few decades, the field of forensic anthropology has seen major advancements and experienced a considerable growth of professionals in medical examiner/coroner offices. Despite this expansion, misconceptions regarding the role and utility of the anthropologist in the medicolegal setting still exist. This article brings together practitioners employed full-time in four medical examiner's offices, with each practitioner providing a unique perspective and emphasis regarding their role as an anthropologist. Discussed is the history of the anthropology division in each office as well as the types of casework and ancillary duties completed by the anthropologists. Consistently, the anthropologists are involved in the search and recovery of human remains, managing long-term unidentified cases, facilitating disposition of unclaimed decedents, and developing mass disaster protocols for their respective agency. Also consistent across the four offices is the fact that the anthropologists receive far more consult requests for trauma evaluation of nonskeletonized cases than any other type of case.

Skeletal Trauma: An Anthropological Review.

As anthropologists take on a larger role in medical examiner's offices, the incorporation of bone trauma analysis into the autopsy increases. The purpose of this invited review is to summarize recent anthropological literature that exemplifies the value of forensic anthropology in medicolegal death investigation, concentrating in the area of skeletal trauma analysis. Forensic anthropologists have a strong understanding of bone's response to trauma, gained through research and case studies. With this body of knowledge they are able to examine and interpret skeletal injury resulting from blunt, sharp, firearm, and thermal trauma. For example, toolmark class characteristics are recognized through sharp force injury examination, and fracture pattern analysis provides details of the impacting surface area. Interpretation of skeletal trauma allows for reconstruction of events surrounding death, and may inform the manner of death classification.

The Value of Anthropology in Medicolegal Death Investigation of Pediatric Nonaccidental Injury.

Forensic anthropologists have made remarkable contributions to the medicolegal investigation of nonaccidental injury in pediatric cases. They have created standard nomenclature for fracture descriptions. Anthropologists have developed novel techniques that increase the sensitivity of the pediatric autopsy. They have performed biomechanical research that enables reconstruction of events surrounding death. Also, anthropology practitioners have developed several reference guides on the subject of nonaccidental injury that are of value to forensic pathologists. These advancements assist forensic pathologists in the accurate classification of cause and manner of death in pediatric cases.

A Novel Method for Removing a Spinal Cord with Attached Cervical Ganglia from a Pediatric Decedent.

A diagnosis of child abuse is dependent on a comprehensive and accurate assessment of injury in the context of a thorough investigation. However, signatures of trauma are often subtle and interpretation can be very difficult. Recently, researchers have refocused their attention from the head to the neck in search of traumatic signatures of abusive head trauma. HCIFS has developed a technique to remove the cervical spinal cord with the ganglia attached that is less destructive and more time and cost efficient than alternative methods previously published. Once removed, the dorsal nerve roots and ganglia are evaluated for the presence of hemorrhage. The authors performed a small pilot study using the novel method to evaluate 20 decedents with a history of blunt force trauma and eight without a traumatic history. Fifteen of the traumatic deaths and two of the nontraumatic deaths were found to have dorsal nerve root and/or ganglia hemorrhage.

Microscopic saw mark analysis: an empirical approach.

Microscopic saw mark analysis is a well published and generally accepted qualitative analytical method. However, little research has focused on identifying and mitigating potential sources of error associated with the method. The presented study proposes the use of classification trees and random forest classifiers as an optimal, statistically sound approach to mitigate the potential for error of variability and outcome error in microscopic saw mark analysis. The statistical model was applied to 58 experimental saw marks created with four types of saws. The saw marks were made in fresh human femurs obtained through anatomical gift and were analyzed using a Keyence digital microscope. The statistical approach weighed the variables based on discriminatory value and produced decision trees with an associated outcome error rate of 8.62-17.82%.

A proposed scheme for classifying pediatric rib head fractures using case examples.

Pediatric rib head fractures are typically described as "posterior" or "costovertebral," terms lacking specificity. To resolve this issue, a scheme was developed to describe the location of rib head fractures observed in a pediatric forensic population. The scheme uses three anatomical landmarks, terminus (tip), tubercle, and costovertebral articular surface to divide the rib head into two subregions, costovertebral and costotransverse. Examples of five cases of infants with rib head fractures are presented using this scheme. Forty-eight rib head fractures were observed in these infants with the following frequencies: 56% (three infants) at the terminus; 21% (three infants) in the costovertebral subregion; 21% (one infant) at the costovertebral articular facet; and 2% (one infant) in the costotransverse subregion. Due to the small number of cases assessed, statistical analyses could not be performed; however, the data demonstrate the variation in distribution of pediatric rib head fractures.

Development of a computer-assisted forensic radiographic identification method using the lateral cervical and lumbar spine.

Medical examiners and coroners (ME/C) in the United States hold statutory responsibility to identify deceased individuals who fall under their jurisdiction. The computer-assisted decedent identification (CADI) project was designed to modify software used in diagnosis and treatment of spinal injuries into a mathematically validated tool for ME/C identification of fleshed decedents. CADI software analyzes the shapes of targeted vertebral bodies imaged in an array of standard radiographs and quantifies the likelihood that any two of the radiographs contain matching vertebral bodies. Six validation tests measured the repeatability, reliability, and sensitivity of the method, and the effects of age, sex, and number of radiographs in array composition. CADI returned a 92-100% success rate in identifying the true matching pair of vertebrae within arrays of five to 30 radiographs. Further development of CADI is expected to produce a novel identification method for use in ME/C offices that is reliable, timely, and cost-effective.

Standardized descriptive method for the anthropological evaluation of pediatric skull fractures.

The literature pertaining to pediatric skull fracture is primarily clinically based and thus motivated by the need for effective assessment of both fracture characteristics (type, frequency, location, and mechanics) and context (severity of injury, associated soft tissue damage, and prognosis). From a strictly descriptive standpoint, these schemas employ overlapping levels of detail that confound the nonclinical description of fractures in the forensic context. For this reason, application of these schemas in the forensic anthropological interpretation of skull fractures is inappropriate. We argue that forensic anthropological interpretation of skull fractures requires a standard classification system that reflects fracture morphology alone, and we suggest a three-stepped classification system that conveys increasing detail with each additional step. A retrospective application of the method to a sample of 31 children aged 1 month to 2 years demonstrated its efficacy in the description of pediatric skull fractures.

Manual and automated cardiopulmonary resuscitation (CPR): a comparison of associated injury patterns.

The purpose of this study was to identify and compare patterns of trauma associated with AutoPulse(®) CPR and manual CPR. Finalized autopsy records from 175 decedents brought to the Harris County Institute of Forensic Sciences were reviewed, 87 received manual-only CPR, and 88 received AutoPulse(®) CPR (in combination with manual CPR as per standard protocol). The characteristic pattern observed in manual-only CPR use included a high frequency of anterior rib fractures, sternal fractures, and midline chest abrasions along the sternum. The characteristic pattern observed in AutoPulse(®) CPR use included a high frequency of posterior rib fractures, skin abrasions located along the anterolateral chest and shoulder, vertebral fractures, and a few cases of visceral injuries including liver lacerations, splenic lacerations, and hemoperitoneum. Knowledge of the AutoPulse(®) CPR injury pattern can help forensic pathologists differentiate therapeutic from inflicted injuries and therefore avoid an erroneous assessment of cause and manner of death.

Novel classification system of rib fractures observed in infants.

Rib fractures are considered highly suspicious for nonaccidental injury in the pediatric clinical literature; however, a rib fracture classification system has not been developed. As an aid and impetus for rib fracture research, we developed a concise schema for classifying rib fracture types and fracture location that is applicable to infants. The system defined four fracture types (sternal end, buckle, transverse, and oblique) and four regions of the rib (posterior, posterolateral, anterolateral, and anterior). It was applied to all rib fractures observed during 85 consecutive infant autopsies. Rib fractures were found in 24 (28%) of the cases. A total of 158 rib fractures were identified. The proposed schema was adequate to classify 153 (97%) of the observed fractures. The results indicate that the classification system is sufficiently robust to classify rib fractures typically observed in infants and should be used by researchers investigating infant rib fractures.

Validation of tool mark analysis of cut costal cartilage.

This study was designed to establish the potential error rate associated with the generally accepted method of tool mark analysis of cut marks in costal cartilage. Three knives with different blade types were used to make experimental cut marks in costal cartilage of pigs. Each cut surface was cast, and each cast was examined by three analysts working independently. The presence of striations, regularity of striations, and presence of a primary and secondary striation pattern were recorded for each cast. The distance between each striation was measured. The results showed that striations were not consistently impressed on the cut surface by the blade's cutting edge. Also, blade type classification by the presence or absence of striations led to a 65% misclassification rate. Use of the classification tree and cross-validation methods and inclusion of the mean interstriation distance decreased the error rate to c. 50%.

Recognition of skeletal fractures in infants: an autopsy technique.

Complete recognition and documentation of injury pattern is crucial in the diagnosis of child abuse. Skeletal fractures regarded as highly specific to nonaccidental injury in infants include posterior rib, scapular, metaphyseal, and spinous process fractures. These injuries are often occult, especially when acute, to standard radiologic and autopsy procedures. The presented autopsy technique requires incising and reflecting skeletal muscles to expose the bones and costal osseous joints in situ, increasing the opportunity to recognize skeletal injury. Fractured or atypical appearing bones are removed and processed for complete evaluation. The bones are processed by macerating the soft tissue in a water soap bath at an elevated temperature. To aid in reconstruction of the decedent, long bones are replaced with wooden dowels and the chest cavity is packed with the organ bag. The technique is invasive and recommended for cases in which the pathologist has reasonable suspicion of acute or remote trauma.

Understanding rib fracture patterns: incomplete and buckle fractures.

Reconstructing traumatic thoracic events, especially when soft tissues are absent, requires an advanced understanding of ribcage fracture patterns. The morphology and orientation of ribs complicate the fracture pattern, as a single blow often causes multiple fractures at various locations. Furthermore, fracture types observed in ribs are not explained easily by current bone biomechanic literature. Using evidential skeletal material archived at the Regional Forensic Center, Memphis, the ribs of 43 blunt force trauma cases were analyzed. A total of 195 incomplete fractures and 63 buckle fractures were noted. Incomplete fractures, previously thought to be common in children but rare in adults, were found among individuals ranging in age from 21-76 years. A buckle fracture, failure resulting from compressive instability, has been undefined previously in bone trauma literature but was repeatedly observed in this sample. This study elucidates recognizable rib fracture patterns while emphasizing gross bone examination for force and mechanical factors.

Decomposition chemistry of human remains: a new methodology for determining the postmortem interval.

This study was conducted to characterize the chemistry associated with the decomposition of human remains with the objective of identifying time-dependent biomarkers of decomposition. The purpose of this work was to develop an accurate and precise method for measuring the postmortem interval (PMI) of human remains. Eighteen subjects were placed within a decay research facility throughout a four-year time period and allowed to decompose naturally. Field autopsies were performed and tissue samples were regularly collected until the tissues decomposed to the point where they were no longer recognizable (encompassing a cumulative degree hour (CDH) range of approximately 1000 (approximately 3 weeks)). Analysis of the biomarkers (amino acids, neurotransmitters, and decompositional by-products) in various organs (liver, kidney, heart, brain, muscle) revealed distinct patterns useful for determining the PMI when based on CDHs. Proper use of the methods described herein allow for PMIs so accurate that the estimate is limited by the ability to obtain correct temperature data at a crime scene rather than sample variability.