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Robert Sheridan

Publications and source records attributed to Robert Sheridan.

18 recordsLinked to original sources
PubMed2006

A novel class of small RNAs bind to MILI protein in mouse testes.

Small RNAs bound to Argonaute proteins recognize partially or fully complementary nucleic acid targets in diverse gene-silencing processes. A subgroup of the Argonaute proteins--known as the 'Piwi family'--is required for germ- and stem-cell development in invertebrates, and two Piwi members--MILI and MIWI--are essential for spermatogenesis in mouse. Here we describe a new class of small RNAs that bind to MILI in mouse male germ cells, where they accumulate at the onset of meiosis. The sequences of the over 1,000 identified unique molecules share a strong preference for a 5' uridine, but otherwise cannot be readily classified into sequence families. Genomic mapping of these small RNAs reveals a limited number of clusters, suggesting that these RNAs are processed from long primary transcripts. The small RNAs are 26-31 nucleotides (nt) in length--clearly distinct from the 21-23 nt of microRNAs (miRNAs) or short interfering RNAs (siRNAs)--and we refer to them as 'Piwi-interacting RNAs' or piRNAs. Orthologous human chromosomal regions also give rise to small RNAs with the characteristics of piRNAs, but the cloned sequences are distinct. The identification of this new class of small RNAs provides an important starting point to determine the molecular function of Piwi proteins in mammalian spermatogenesis.

Animals↗
PubMed2006

SPA: a probabilistic algorithm for spliced alignment.

Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of the repertoire of splice variants, and to gain insight into the mechanisms of alternative splicing, it is essential that cDNAs are very accurately mapped to their respective genomes. Currently available algorithms for cDNA-to-genome alignment do not reach the necessary level of accuracy because they use ad hoc scoring models that cannot correctly trade off the likelihoods of various sequencing errors against the probabilities of different gene structures. Here we develop a Bayesian probabilistic approach to cDNA-to-genome alignment. Gene structures are assigned prior probabilities based on the lengths of their introns and exons, and based on the sequences at their splice boundaries. A likelihood model for sequencing errors takes into account the rates at which misincorporation, as well as insertions and deletions of different lengths, occurs during sequencing. The parameters of both the prior and likelihood model can be automatically estimated from a set of cDNAs, thus enabling our method to adapt itself to different organisms and experimental procedures. We implemented our method in a fast cDNA-to-genome alignment program, SPA, and applied it to the FANTOM3 dataset of over 100,000 full-length mouse cDNAs and a dataset of over 20,000 full-length human cDNAs. Comparison with the results of four other mapping programs shows that SPA produces alignments of significantly higher quality. In particular, the quality of the SPA alignments near splice boundaries and SPA's mapping of the 5' and 3' ends of the cDNAs are highly improved, allowing for more accurate identification of transcript starts and ends, and accurate identification of subtle splice variations. Finally, our splice boundary analysis on the human dataset suggests the existence of a novel non-canonical splice site that we also find in the mouse dataset. The SPA software package is available at http://www.biozentrum.unibas.ch/personal/nimwegen/cgi-bin/spa.cgi.

Algorithms↗
PubMed2006

Acute stress symptoms in young children with burns.

OBJECTIVE: Posttraumatic stress disorder symptoms are a focus of much research with older children, but little research has been conducted with young children, who account for about 50% of all pediatric burn injuries. This is a 3-year study of 12- to 48-month-old acutely burned children to assess acute traumatic stress outcomes. The aims were to (1) assess the prevalence of acute traumatic stress symptoms and (2) develop a model of risk factors for these symptoms in these children. METHOD: Acute stress symptoms were measured using the Posttraumatic Stress Disorder Semi-Structured Interview and Observational Record for Infants and Young Children. Children's responses were then assessed, including behavior and physiological measures for developmental/functional consequences. A path analysis strategy was used to build a model of risk factors. Risk factors assessed in this model included observed pain (Visual Analogue Scale), parent symptoms (Stanford Acute Stress Reaction Questionnaire), and magnitude of trauma (total body surface area burned). RESULTS: Of the 64 subjects meeting inclusion criteria, 52 subjects agreed to participate. These children were highly symptomatic; almost 30% of these children had acute stress symptoms. A path analysis model yielded two independent pathways to acute stress symptoms: (1) from the size of the burn to the mean pulse rate in the hospital to acute stress symptoms and (2) from the child's pain to the parents' stress symptoms to acute stress symptoms. This model accounted for 39% of the variance of acute stress symptoms and yielded excellent fit indexes. CONCLUSIONS: A high percentage of acute stress symptoms were identified in young children with burns. A model of risk factors, including the size of the burn, pain, pulse rate, and parents' symptoms, was identified.

Burns↗
PubMed2005

The developmental miRNA profiles of zebrafish as determined by small RNA cloning.

MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a developmental and cell-type-specific manner. The profiles were obtained from larger-scale sequencing of small RNA libraries prepared from developmentally staged zebrafish, and two adult fibroblast cell lines derived from the caudal fin (ZFL) and the liver epithelium (SJD). We identified a total of 154 distinct miRNAs expressed from 343 miRNA genes. Other experimental/computational sources support an additional 10 miRNAs encoded by 19 genes. The miRNAs can be classified into 87 distinct families. Cross-species comparison indicates that 81 families are conserved in mammals, 17 of which also have at least one member conserved in an invertebrate. Our analysis reveals that the zygotes are essentially devoid of miRNAs and that their expression begins during the blastula period with a zebrafish-specific family of miRNAs encoded by closely spaced multicopy genes. Computational predictions of zebrafish miRNA targets are provided that take into account the depth of evolutionary conservation. Besides miRNAs, we identified a prominent class of repeat-associated small interfering RNAs (rasiRNAs).

Animals↗
PubMed2005

Identification of microRNAs of the herpesvirus family.

Epstein-Barr virus (EBV or HHV4), a member of the human herpesvirus (HHV) family, has recently been shown to encode microRNAs (miRNAs). In contrast to most eukaryotic miRNAs, these viral miRNAs do not have close homologs in other viral genomes or in the genome of the human host. To identify other miRNA genes in pathogenic viruses, we combined a new miRNA gene prediction method with small-RNA cloning from several virus-infected cell types. We cloned ten miRNAs in the Kaposi sarcoma-associated virus (KSHV or HHV8), nine miRNAs in the mouse gammaherpesvirus 68 (MHV68) and nine miRNAs in the human cytomegalovirus (HCMV or HHV5). These miRNA genes are expressed individually or in clusters from either polymerase (pol) II or pol III promoters, and share no substantial sequence homology with one another or with the known human miRNAs. Generally, we predicted miRNAs in several large DNA viruses, and we could neither predict nor experimentally identify miRNAs in the genomes of small RNA viruses or retroviruses.

Chromosome Mapping↗
PubMed2005

Gender differences in etiology and outcome of open globe injuries.

PURPOSE: Patterns of injury and outcomes after multi-system trauma differ between men and women. Few data exist regarding the epidemiology of gender differences in severe eye trauma. We hypothesized that the incidence and patterns of open globe injuries might differ between men and women. METHODS: Charts of 220 patients with open globe injuries presenting to the Massachusetts Eye and Ear Infirmary during a three-year period were retrospectively reviewed. The data were analyzed with respect to gender, type of open globe injury (penetrating, perforating, or rupture), and mechanism of globe injury (projectile, non-projectile, assault, fall, sports, motor vehicle crash). RESULTS: The majority (78.6%) of patients were men. Women with open globe injuries were older (median age 73 years) than men (median age 36 years). Men were more likely to suffer from penetrating injuries (69.9%) while women were more likely to experience blunt globe rupture (68.1%). Projectile objects accounted for the majority of open globe injuries in men (54.9%) and were an infrequent cause in women (4.3%). Nearly one-third (31.8%) of the projectile injuries in men were work-related, and 19.7% occurred during home improvement projects. Compared with men, falls were more frequently responsible for globe injuries in women (55.3% versus 8.1%). Injuries limited to the cornea were more common in men than women (46.2% versus 23.4%), while more posterior globe injuries were more common among women (46.8% versus 28.3% men). Women were more likely than men to have poor visual acuity at 3 months after injury. CONCLUSIONS: The causes and patterns of open globe injuries differ between men and women. In this series, the majority of injuries to men were caused by projectile objects related to work or home improvement projects. Open globe injuries in women were most often resulted from fall, and were more likely to cause rupture posterior to the limbus.

Adult↗
PubMed2005

Pathways to PTSD, part I: Children with burns.

OBJECTIVE: The goal of this study was to develop a model of risk factors for posttraumatic stress disorder (PTSD) in a group of acutely burned children. METHOD: Seventy-two children between the ages of 7 and 17 who were admitted to the hospital for an acute burn were eligible for study. Members of families who consented completed the Child PTSD Reaction Index, the Multidimensional Anxiety Scale for Children, and other self-report measures of psychopathology and environmental stress both during the hospitalization and 3 months following the burn. A path analytic strategy was used to build a model of risk factors for PTSD. RESULTS: Two pathways to PTSD were discerned: 1) from the size of the burn and level of pain following the burn to the child's level of acute separation anxiety, and then to PTSD, and 2) from the size of the burn to the child's level of acute dissociation following the burn, and then to PTSD. Together these pathways accounted for almost 60% of the variance in PTSD symptoms and constituted a model with excellent fit indices. CONCLUSIONS: These findings support a model of complex etiology for childhood PTSD in which two independent pathways may be mediated by different biobehavioral systems.

Age Factors↗
PubMed2005

Risk factors for acute stress disorder in children with burns.

The purpose of this study was to (1) estimate the prevalence of acute stress disorder (ASD) in a sample of burned children, and (2) determine risk factors for ASD in these children. Seventy-two children were assessed for acute stress disorder approximately 10 days after being hospitalized for a burn. Variables hypothesized to predict ASD symptoms (i.e., size of the burn, prior behavioral symptoms, body image, parents' symptoms, heart rate) were also assessed. Based on a diagnosis derived from the ASD module of the Diagnostic Interview for Children and Adolescents (DICA), 31% of children met criteria for ASD. Path analyses revealed that the variables of heart rate, body image, and parents' acute stress symptoms were directly related to the development of ASD symptoms and accounted for 41% of its variance. These variables also mediated the relationship between the size of the burn and ASD symptoms. ASD is found in almost one third of children hospitalized for a burn. A high resting heart rate, lowered body image, and parent's acute stress symptoms were found to be significant risk factors for ASD symptoms.

Adolescent↗
PubMed2003

Sodium bromide by instrumental neutron activation analysis quantifies change in extracellular water space with wound closure in severely burned children.

BACKGROUND: The ability to measure extracellular water (ECW) in critically ill patients can significantly enhance current methods of assessing fluid homeostasis, body composition, and response to nutritional therapy. We measured corrected bromide space to determine change in ECW with wound closure among acutely burned children. METHODS: Fifteen children with burns over 30% of their total body surface area had their ECW determined following hemodynamic stabilization and when wound closure was complete. Plasma samples were obtained at baseline and 4 hours after receiving 25 mg/kg of sodium bromide. Plasma bromide was quantified by instrumental neutron activation analysis. RESULTS: Mean CBS decreased with wound closure (9.1 +/- 4.1 vs 7.9 +/- 3.9 liters; P =.04), indicating a significant decrease in ECW over the course of recovery. A decline in weight also occurred over the same period (32.4 +/- 15.2 vs 29.1 +/- 13.5 kg; P =.007); however, change in corrected bromide space as a proportion of weight was not statistically significant. CONCLUSION: A significant decrease in ECW accompanies the weight loss observed in patients following wound closure. Measurement of bromide dilution space is a convenient method for monitoring ECW that can be done at the bedside.

Acute Disease↗
PubMed2003

Child Stress Disorders Checklist: a measure of ASD and PTSD in children.

OBJECTIVE: To assess the psychometric properties of the Child Stress Disorders Checklist (CSDC), a 36-item observer-report instrument that measures acute stress and posttraumatic symptoms in children. METHOD: The CSDC was administered to parents of 43 children with acute burns and 41 children who had experienced a traffic crash. This instrument was also administered to the burned children's primary nurse to estimate interrater reliability. The CSDC was completed again by parents of burned children, 2 days and 3 months later. Convergent validity was determined by correlating scores on the CSDC with scores on instruments of known validity for assessing posttraumatic stress disorder (PTSD) in children. Concurrent validity was determined through an examination of the relationship between CSDC scores and an index of trauma severity (percentage of body surface area burned). Discriminant validity was assessed by administering the Child Behavior Checklist (CBCL): it was hypothesized that PTSD symptoms would be more closely related to the PTSD scale of the CBCL than the Thought Problems scale of the CBCL. RESULTS: The CSDC has reliable and valid psychometric properties. CONCLUSIONS: The CSDC, an observer-report instrument of ASD and PTSD in children, has important utility in clinical and research settings.

Accidents, Traffic↗
PubMed2003

Reformatted visceral protocol helical computed tomographic scanning allows conventional radiographs of the thoracic and lumbar spine to be eliminated in the evaluation of blunt trauma patients.

BACKGROUND: Patients suffering high-energy injuries are at risk for occult thoracic and lumbar spine fractures, and the standard of care includes radiographic spine screening. Most such patients require computed tomographic (CT) scanning to screen for chest and/or abdominal visceral injury. Helical CT (HCT) scanning represents a major technologic change that allows data to be reformatted after the patient has left the radiology suite. We explored the possibility of using reformatted visceral protocol HCT scanning to replace radiographs of the thoracic and lumbar spine in the evaluation of seriously injured patients. METHODS: A prospective evaluation of consecutive patients with thoracic and lumbar spine fractures admitted over a 12-month period to an urban Level I trauma center was completed. The ability of conventional radiography and reformatted HCT scanning to detect spine fractures was compared. RESULTS: Of 1,915 trauma patients admitted, 78 (4.1%), with an average Injury Severity Score of 21.3 +/- 1.2, sustained one or more thoracic (n = 35 patients) or lumbar (n = 43 patients) spine fractures. The sensitivity of reformatted HCT scanning as a screening test for spine fractures was 97% for thoracic and 95% for lumbar spine fractures, compared with a sensitivity of 62% for thoracic and 86% for lumbar conventional radiographs. CONCLUSION: Data obtained from HCT scanning performed to evaluate seriously injured multiple trauma patients for thoracic and abdominal visceral injury can be reformatted to screen for thoracic and lumbar spine fractures, providing accurate screening while eliminating the time, expense, and radiation exposure associated with conventional film radiography.

Adolescent↗
PubMed2002

Genetic and immunological comparison of anti-botulinum type A antibodies from immune and non-immune human phage libraries.

Understanding the antibody response in botulinum intoxication is important for vaccine design and passive prophylaxis. To investigate this activity, we have studied the immune response to BoNT/A (botulinum neurotoxin serotype A) binding domain (HC) at the molecular level using phage display. The scFv antibodies were isolated from V-gene repertoires prepared from (a) human volunteer immunized with pentavalent botulinum toxoid and (b) non-immune human peripheral blood lymphocytes and spleenocytes. A large panel of serotype specific phage expressing botulinum binding scFv could be selected from both libraries. Epitope mapping of immune scFv binders towards BoNT/A HC revealed surprisingly a limited number of scFv recognizing conformational epitopes that corresponded to two distinct groups, clusters I and II. Only scFv from cluster I exhibited neutralizing activity in the mouse hemidiaphragm assay. Anti- BoNT/A HC clones derived from a non-immune library could be conveniently grouped into clusters III-XI and appeared to share no overlapping epitopes with cluster I or II. In addition they showed no neutralization of toxin at biologically significant concentrations. We therefore suggest that a vaccine based on the pentavalent botulinum toxoid directs the humoral immune response to a limited number of immunodominant epitopes exposed on the binding domain HC.

Antibodies, Bacterial↗
PubMed2002

Management of the burned trauma patient: balancing conflicting priorities.

PURPOSE: Approximately 5% of multiple trauma patients sustain concomitant burns. Complicated management issues arise in these patients as burn and trauma care often conflict. This study reviews 53 consecutive burned multiple trauma patients in order to examine common management conflicts and recommend appropriate compromises in caring for these difficult patients. PROCEDURE: A retrospective review of 53 consecutive burn patients with coincident trauma admitted to The Massachusetts General Hospital (MGH) from 1993-2001 was performed. FINDINGS: In the study period, 53 patients were admitted to the Massachusetts General Hospital with concomitant burns and trauma. Of this group, 42 (79%) were male. Average age was 31.5 +/- 15.0. Mechanisms included 11 motor vehicle collisions (MVC), 10 explosions, 10 electrocutions with subsequent falls, nine house fires, four motorcycle collisions (MCC), three pedestrian versus car accidents, two falls into fires, two plane crashes, and one each of a lawnmower accident and a patient drawn into a machine. Average burn size was 25.4% +/- 22.4. The most common traumatic injury was fracture (52). Management of fractures in burn patients and resuscitation in head injured burn patient represented the most common conflicts in patient care. There were five deaths (9.4%) in this series. CONCLUSIONS: Burns are a rare but significant complication in the trauma patient. Outcomes are dependent on rapid trauma evaluation as well as effective resuscitation and wound management. Given the complexities of their problems, these patients necessitate a balanced multidisciplinary approach to maximize their potential for full recovery. Thoughtful compromise between trauma and burn priorities is frequently necessary.

Adolescent↗
PubMedDate not supplied

Body water in children during recovery from severe burn injury using a combined tracer dilution method.

Useful information about hydration and the size of the body cell mass (BCM) can be obtained by monitoring changes in the amount of total body water (TBW) and its components, extracellular water (ECW) and intracellular water (ICW). A combined tracer dilution method with deuterium to measure TBW and bromide to measure ECW was used to assess changes in ICW (as a proxy for the BCM) and in the ECW/ICW ratio (an indicator of water distribution) over the course of recovery in nine severely burned children. During the acute phase of recovery, ICW losses averaged (mean +/- SD) 2.2 +/- 2.0 liters (P = .02) or 18.5 +/- 0.4%. During the rehabilitative phase, mean ICW increased by 3.4 +/- 3.7 liters or 31.9 +/- 14%. The ECW/ICW ratio varied widely both between patients and during the course of the study. During the acute phase of recovery, the mean ECW/ICW ratio increased from 1.06 +/- 0.15 liters to 1.20 +/- 0.14 liters because the ECW compartment had expanded relative to the ICW compartment. During rehabilitation, the ECW/ICW ratio decreased from 1.20 +/- 0.14 liters to 0.86 +/- 0.20 liters, with a recoup of ICW and continued ECW losses. Tracking ICW and the ECW/ICW ratio using the combined tracer dilution method is practical for monitoring BCM and water distribution in severely burned children. Taken together, the indices provide useful information about hydration and nutritional status in individuals recovering from severe burn injury.

Adolescent↗
PubMedDate not supplied

Trauma severity influences acute stress in young burned children.

The purpose of this study was to assess the role of trauma severity on subsequent symptoms of posttraumatic stress disorder (PTSD) and physiological reactivity in a total of 70 children, ranging from 12 to 48 months of age, who were acutely burned. Parents were interviewed shortly after the child was admitted to the hospital. PTSD symptoms were measured using the Posttraumatic Stress Disorder Semi-Structured Interview and Observational Record for Infants and Young Children and the Diagnostic Interview for Children and Adolescents. Nurses completed a questionnaire about the child's symptoms and recorded the child's physiological data throughout the hospital stay. Significant relationships were found between severity of childhood trauma and the total number of PTSD symptoms and physiological reactivity. This study supports the hypothesis that severity of trauma experienced by young children influences psychological and physiological stress indicators after burn injuries. These findings provide new directions for the assessment and prevention of PTSD in this age group.

Age Factors↗
PubMedDate not supplied

Determination of abamectin, doramectin, emamectin, eprinomectin, ivermectin, and moxidectin in milk by liquid chromatography electrospray tandem mass specrometry.

The avermectin and milbemycin families of compounds are derived from naturally occurring yeasts. They have proven to be potent preventatives against a variety of pests such as insects and parasites. Only eprinomectin and moxidectin are currently approved for use on lactating cattle with tolerances in milk of 12 microg/kg for eprinomectin and 40 microg/kg for moxidectin. Detection of misuse or inadvertent contamination in milk requires a sensitive and definitive analytical method. A method has been developed for the determination of 5 avermectins and 1 milbemycin in milk using a simple liquid-liquid extraction and liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis. Ivermectin (IVR), doramectin (DOR), abamectin (ABA), eprinomectin (EPR), emamectin (EMA), and moxidectin (MOX) were extracted from whole milk by partitioning into acetonitrile with a subsequent solvent exchange into methanol-water. Simultaneous confirmation and quantification were achieved with LC separation, positive electrospray ionization (ESI+), and MS/MS. The limits of detection ranged from 16 pg/g (ppt) for EMA to 1.7 microg/g (ppb) for MOX.

Acetonitriles↗