Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning

BACKGROUND

Rapidly and efficiently identifying critically ill infants for whole genome sequencing (WGS) is a costly and challenging task currently performed by scarce, highly trained experts and is a major bottleneck for application of WGS in the NICU. There is a dire need for automated means to prioritize patients for WGS.

METHODS

Institutional databases of electronic health records (EHRs) are logical starting points for identifying patients with undiagnosed Mendelian diseases. We have developed automated means to prioritize patients for rapid and whole genome sequencing (rWGS and WGS) directly from clinical notes. Our approach combines a clinical natural language processing (CNLP) workflow with a machine learning-based prioritization tool named Mendelian Phenotype Search Engine (MPSE).

RESULTS

MPSE accurately and robustly identified NICU patients selected for WGS by clinical experts from Rady Children's Hospital in San Diego (AUC 0.86) and the University of Utah (AUC 0.85). In addition to effectively identifying patients for WGS, MPSE scores also strongly prioritize diagnostic cases over non-diagnostic cases, with projected diagnostic yields exceeding 50% throughout the first and second quartiles of score-ranked patients.

CONCLUSIONS

Our results indicate that an automated pipeline for selecting acutely ill infants in neonatal intensive care units (NICU) for WGS can meet or exceed diagnostic yields obtained through current selection procedures, which require time-consuming manual review of clinical notes and histories by specialized personnel.

The Genomic landscape of short tandem repeats across multiple ancestries

Short Tandem Repeats (STRs) have been found to play a role in a myriad of complex traits and genetic diseases. We examined the variability in the lengths of over 850,000 STR loci in 996 children with suspected genetic disorders and 1,178 parents across six separate ancestral groups: Africans, Europeans, East Asians, Admixed Americans, Non-admixed Americans, and Pacific Islanders. For each STR locus we compared allele length between and within each ancestry group. In relation to Europeans, admixed Americans had the most similar STR lengths with only 623 positions either significantly expanded or contracted, while the divergence was highest in Africans, with 4,933 chromosomal positions contracted or expanded. We also examined probands to identify STR expansions at known pathogenic loci. The genes TCF4, AR, and DMPK showed significant expansions with lengths 250% greater than their various average allele lengths in 49, 162, and 11 individuals respectively. All 49 individuals containing an expansion in TCF4 and six individuals containing an expansion in DMPK presented with allele lengths longer than the known pathogenic length for these genes. Next, we identified individuals with significant expansions in highly conserved loci across all ancestries. Eighty loci in conserved regions met criteria for divergence. Two of these individuals were found to have exonic STR expansions: one in ZBTB4 and the other in SLC9A7, which is associated with X-linked mental retardation. Finally, we used parent-child trios to detect and analyze de novo mutations. In total, we observed 3,219 de novo expansions, where proband allele lengths are greater than twice the longest parental allele length. This work helps lay the foundation for understanding STR lengths genome-wide across ancestries and may help identify new disease genes and novel mechanisms of pathogenicity in known disease genes.

A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases

Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.

An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases

While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases.

An RCT of Rapid Genomic Sequencing among Seriously Ill Infants Results in High Clinical Utility, Changes in Management, and Low Perceived Harm

The second Newborn Sequencing in Genomic Medicine and Public Health (NSIGHT2) study was a randomized, controlled trial of rapid whole-genome sequencing (rWGS) or rapid whole-exome sequencing (rWES) in infants with diseases of unknown etiology in intensive care units (ICUs). Gravely ill infants were not randomized and received ultra-rapid whole-genome sequencing (urWGS). Herein we report results of clinician surveys of the clinical utility of rapid genomic sequencing (RGS). The primary end-point-clinician perception that RGS was useful- was met for 154 (77%) of 201 infants. Both positive and negative tests were rated as having clinical utility (42 of 45 [93%] and 112 of 156 [72%], respectively). Physicians reported that RGS changed clinical management in 57 (28%) infants, particularly in those receiving urWGS (p = 0.0001) and positive tests (p < 0.00001). Outcomes of 32 (15%) infants were perceived to be changed by RGS. Positive tests changed outcomes more frequently than negative tests (p < 0.00001). In logistic regression models, the likelihood that RGS was perceived as useful increased 6.7-fold when associated with changes in management (95% CI 1.8-43.3). Changes in management were 10.1-fold more likely when results were positive (95% CI 4.7-22.4) and turnaround time was shorter (odds ratio 0.92, 95% CI 0.85-0.99). RGS seldom led to clinician-perceived confusion or distress among families (6 of 207 [3%]). In summary, clinicians perceived high clinical utility and low likelihood of harm with first-tier RGS of infants in ICUs with diseases of unknown etiology. RGS was perceived as beneficial irrespective of whether results were positive or negative.

Postmortem diagnosis of PPA2-associated sudden cardiac death from dried blood spot in a neonate presenting with vocal cord paralysis

Biallelic variants in inorganic pyrophosphatase 2 (PPA2) are known to cause infantile sudden cardiac failure (OMIM #617222), but relatively little is known about phenotypic variability of these patients prior to their death. We report a 5-wk-old male with bilateral vocal cord paralysis and hypertension who had a sudden unexpected cardiac death. Subsequently, molecular autopsy via whole-genome sequencing from newborn dried blood spot identified compound heterozygous mutations in PPA2, with a paternally inherited, pathogenic missense variant (c.514G > A; p.Glu172Lys) and a novel, maternally inherited missense variant of uncertain significance (c.442A > T; p.Thr148Ser). This report expands the presenting phenotype of patients with PPA2 variants. It also highlights the utility of dried blood spots for postmortem molecular diagnosis.

Clinical utility of ultra-rapid whole-genome sequencing in an infant with atypical presentation of WT1-associated nephrotic syndrome type 4

Relatively little is known about phenotypic variability in nonsyndromic nephropathy associated with the gene encoding the WT1 transcription factor. We report a 12-mo-old female who presented with vomiting, diarrhea, and fatigue in the setting of renal failure and malignant hypertension. Trio ultra-rapid whole-genome sequencing identified a novel, likely pathogenic, de novo missense variant (c.485T > A, p.Val162Asp) in WT1 in 46 h, consistent with a diagnosis of nephrotic syndrome type 4 (NPHS4; OMIM 256370). This disorder typically presents with nephrotic syndrome (gross proteinuria, hypoalbuminemia, and edema). Rapid diagnosis had an immediate impact on her clinical management in the pediatric intensive care unit. Diagnostic renal biopsy was avoided, and placement of permanent dialysis access, a gastrostomy tube, and bilateral nephrectomy were accelerated. This report expands the presenting phenotype of nonsyndromic nephrotic syndrome and/or renal failure due to heterozygous variants in WT1 (NPHS4). It also highlights the relationship between time to genomic diagnosis and clinical utility in critically ill infants.

Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation

By informing timely targeted treatments, rapid whole-genome sequencing can improve the outcomes of seriously ill children with genetic diseases, particularly infants in neonatal and pediatric intensive care units (ICUs). The need for highly qualified professionals to decipher results, however, precludes widespread implementation. We describe a platform for population-scale, provisional diagnosis of genetic diseases with automated phenotyping and interpretation. Genome sequencing was expedited by bead-based genome library preparation directly from blood samples and sequencing of paired 100-nt reads in 15.5 hours. Clinical natural language processing (CNLP) automatically extracted children's deep phenomes from electronic health records with 80% precision and 93% recall. In 101 children with 105 genetic diseases, a mean of 4.3 CNLP-extracted phenotypic features matched the expected phenotypic features of those diseases, compared with a match of 0.9 phenotypic features used in manual interpretation. We automated provisional diagnosis by combining the ranking of the similarity of a patient's CNLP phenome with respect to the expected phenotypic features of all genetic diseases, together with the ranking of the pathogenicity of all of the patient's genomic variants. Automated, retrospective diagnoses concurred well with expert manual interpretation (97% recall and 99% precision in 95 children with 97 genetic diseases). Prospectively, our platform correctly diagnosed three of seven seriously ill ICU infants (100% precision and recall) with a mean time saving of 22:19 hours. In each case, the diagnosis affected treatment. Genome sequencing with automated phenotyping and interpretation in a median of 20:10 hours may increase adoption in ICUs and, thereby, timely implementation of precise treatments.

A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants

The second Newborn Sequencing in Genomic Medicine and Public Health study was a randomized, controlled trial of the effectiveness of rapid whole-genome or -exome sequencing (rWGS or rWES, respectively) in seriously ill infants with diseases of unknown etiology. Here we report comparisons of analytic and diagnostic performance. Of 1,248 ill inpatient infants, 578 (46%) had diseases of unknown etiology. 213 infants (37% of those eligible) were enrolled within 96 h of admission. 24 infants (11%) were very ill and received ultra-rapid whole-genome sequencing (urWGS). The remaining infants were randomized, 95 to rWES and 94 to rWGS. The analytic performance of rWGS was superior to rWES, including variants likely to affect protein function, and ClinVar pathogenic/likely pathogenic variants (p < 0.0001). The diagnostic performance of rWGS and rWES were similar (18 diagnoses in 94 infants [19%] versus 19 diagnoses in 95 infants [20%], respectively), as was time to result (median 11.0 versus 11.2 days, respectively). However, the proportion diagnosed by urWGS (11 of 24 [46%]) was higher than rWES/rWGS (p = 0.004) and time to result was less (median 4.6 days, p < 0.0001). The incremental diagnostic yield of reflexing to trio after negative proband analysis was 0.7% (1 of 147). In conclusion, rapid genomic sequencing can be performed as a first-tier diagnostic test in inpatient infants. urWGS had the shortest time to result, which was important in unstable infants, and those in whom a genetic diagnosis was likely to impact immediate management. Further comparison of urWGS and rWES is warranted because genomic technologies and knowledge of variant pathogenicity are evolving rapidly.

Concomitant diagnosis of immune deficiency and Pseudomonas sepsis in a 19 month old with ecthyma gangrenosum by host whole-genome sequencing

X-linked agammaglobulinemia (XLA, OMIM#300300) is a rare monogenic primary immunodeficiency caused by mutations in the Bruton tyrosine kinase (BTK) gene. XLA is characterized by insufficient immunoglobulin levels and susceptibility to life-threatening bacterial infections. We report on a patient that presented with ecthyma gangrenosum and septicemia. Rapid trio whole-genome sequencing (rWGS) revealed an apparently de novo hemizygous pathogenic variant (c.726dupT; p.Ile243TyrfsTer15) in the BTK gene. Metagenomic analysis of rWGS sequences that did not align to the human genome revealed 770 aligned to the Pseudomonas aeruginosa PAO1 genome. The patient was diagnosed with XLA and pseudomonal sepsis.

Rapid whole-genome sequencing identifies a novel AIRE variant associated with autoimmune polyendocrine syndrome type 1

Autoimmune polyendocrine syndrome type 1 (APS-1; OMIM #240300), also referred to as autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), is a rare monogenic autoimmune disorder caused by mutations in the autoimmune regulator (AIRE) gene. APS-1 is classically characterized by a triad of chronic mucocutaneous candidiasis, autoimmune hypoparathyroidism, and autoimmune adrenocortical insufficiency. We report a 5-yr-old female who presented with symptoms of tetany due to hypocalcemia and was subsequently found to be secondary to hypoparathyroidism. Rapid trio whole-genome sequencing revealed compound heterozygous variants in AIRE in the proband, with a paternally inherited, pathogenic, frameshift variant (c.1265delC; p.Pro422LeufsTer58) and a novel, likely pathogenic, maternally inherited missense variant (c.268T>C; p.Tyr90His).

Comprehensive genomic profiling of anal squamous cell carcinoma reveals distinct genomically defined classes

BACKGROUND

Squamous cell cancers of the anal canal (ASCC) are increasing in frequency and lack effective therapies for advanced disease. Although an association with human papillomavirus (HPV) has been established, little is known about the molecular characterization of ASCC. A comprehensive genomic analysis of ASCC was undertaken to identify novel genomic alterations (GAs) that will inform therapeutic choices for patients with advanced disease.

PATIENTS AND METHODS

Hybrid-capture-based next-generation sequencing of exons from 236 cancer-related genes and intronic regions from 19 genes commonly rearranged in cancer was performed on 70 patients with ASCC. HPV status was assessed by aligning tumor sequencing reads to HPV viral genomes. GAs were identified using an established algorithm and correlated with HPV status.

RESULTS

Sixty-one samples (87%) were HPV-positive. A mean of 3.5 GAs per sample was identified. Recurrent alterations in phosphoinositol-3-kinase pathway (PI3K/AKT/mTOR) genes including amplifications and homozygous deletions were present in 63% of cases. Clinically relevant GAs in genes involved in DNA repair, chromatin remodeling, or receptor tyrosine kinase signaling were observed in 30% of cases. Loss-of-function mutations in TP53 and CDKN2A were significantly enhanced in HPV-negative cases (P < 0.0001).

CONCLUSIONS

This is the first comprehensive genomic analysis of ASCC, and the results suggest new therapeutic approaches. Differing genomic profiles between HPV-associated and HPV-negative ASCC warrants further investigation and may require novel therapeutic and preventive strategies.

Epidemiological, social, diagnostic and economic evaluation of population screening for genital chlamydial infection

OBJECTIVES

To investigate epidemiological, social, diagnostic and economic aspects of chlamydia screening in non-genitourinary medicine settings.

METHODS

Linked studies around a cross-sectional population-based survey of adult men and women invited to collect urine and (for women) vulvovaginal swab specimens at home and mail these to a laboratory for testing for Chlamydia trachomatis. Specimens were used in laboratory evaluations of an amplified enzyme immunoassay (PCE EIA) and two nucleic acid amplification tests [Cobas polymerase chain reaction (PCR), Becton Dickinson strand displacement amplification (SDA)]. Chlamydia-positive cases and two negative controls completed a risk factor questionnaire. Chlamydia-positive cases were invited into a randomised controlled trial of partner notification strategies. Samples of individuals testing negative completed psychological questionnaires before and after screening. In-depth interviews were conducted at all stages of screening. Chlamydia transmission and cost-effectiveness of screening were investigated in a transmission dynamic model.

SETTING AND PARTICIPANTS

General population in the Bristol and Birmingham areas of England. In total, 19,773 women and men aged 16-39 years were randomly selected from 27 general practice lists.

RESULTS

Screening invitations reached 73% (14,382/19,773). Uptake (4731 participants), weighted for sampling, was 39.5% (95% CI 37.7, 40.8%) in women and 29.5% (95% CI 28.0, 31.0%) in men aged 16-39 years. Chlamydia prevalence (219 positive results) in 16-24 year olds was 6.2% (95% CI 4.9, 7.8%) in women and 5.3% (95% CI 4.4, 6.3%) in men. The case-control study did not identify any additional factors that would help target screening. Screening did not adversely affect anxiety, depression or self-esteem. Participants welcomed the convenience and privacy of home-sampling. The relative sensitivity of PCR on male urine specimens was 100% (95% CI 89.1, 100%). The combined relative sensitivities of PCR and SDA using female urine and vulvovaginal swabs were 91.8% (86.1, 95.7, 134/146) and 97.3% (93.1, 99.2%, 142/146). A total of 140 people (74% of eligible) participated in the randomised trial. Compared with referral to a genitourinary medicine clinic, partner notification by practice nurses resulted in 12.4% (95% CI -3.7, 28.6%) more patients with at least one partner treated and 22.0% (95% CI 6.1, 37.8%) more patients with all partners treated. The health service and patients costs (2005 prices) of home-based postal chlamydia screening were 21.47 pounds (95% CI 19.91 pounds, 25.99) per screening invitation and 28.56 pounds (95% CI 22.10 pounds, 30.43) per accepted offer. Preliminary modelling found an incremental cost-effectiveness ratio (2003 prices) comparing screening men and women annually to no screening in the base case of 27,000 pounds/major outcome averted at 8 years. If estimated screening uptake and pelvic inflammatory disease incidence were increased, the cost-effectiveness ratio fell to 3700 pounds/major outcome averted.

CONCLUSIONS

Proactive screening for chlamydia in women and men using home-collected specimens was feasible and acceptable. Chlamydia prevalence rates in men and women in the general population are similar. Nucleic acid amplification tests can be used on first-catch urine specimens and vulvovaginal swabs. The administrative costs of proactive screening were similar to those for opportunistic screening. Using empirical estimates of screening uptake and incidence of complications, screening was not cost-effective.

The chlamydia screening studies: rationale and design

BACKGROUND

Screening has been recommended to reduce the prevalence and morbidity associated with genital chlamydia infection in the United Kingdom.

METHODS

We describe the rationale and study design of the Chlamydia Screening Studies (ClaSS), a collaborative project designed to evaluate screening outside genitourinary medicine clinics. A non-selective, active screening approach in 16-39 year olds randomly sampled from 27 general practice lists in the Bristol and Birmingham areas formed the basis of interlinked studies: a case-control study was used to investigate factors to improve the targeting of screening; participants with chlamydia were invited to enroll in a randomised controlled trial to evaluate partner notification conducted in primary care; and laboratory based studies were used to assess the best specimens and tests. We also explored psychosocial effects of screening and partner notification and modelled the cost effectiveness of the programme.

CONCLUSION

Results from four pilot practices show that mailing of specimens for chlamydia testing is feasible but that it is difficult to achieve high response rates with postal screening. The high prevalence of asymptomatic infection in men suggests that efforts to screen men for chlamydia should be strengthened.

Assessment of satisfaction with care after inpatient treatment for oesophageal and gastric cancer

BACKGROUND

Patients' views are becoming increasingly important in the current health system. They provide information on effectiveness of healthcare and how it may be improved. This study aimed to measure patients' satisfaction with care received for treatment of oesophageal and gastric cancer, and to identify areas that contribute most to overall satisfaction scores.

METHODS

Consecutive inpatients with oesophageal and gastric cancer treated in one surgical unit were recruited prospectively during a 2-year period. The European Organization for Research and Treatment of Cancer 'satisfaction with in-hospital care' questionnaire (QLQ-SAT32) was completed following discharge. Scores ranged from 0 to 100 for each satisfaction scale. Univariable and multivariable analysis was used to define the relationships between the different dimensions of satisfaction with care and the overall score.

RESULTS

Ninety-one patients (mean age 67 years, 60 men) completed the questionnaire a mean of 40 days after treatment. The highest scores were for doctors (mean 72), nurses (mean 67) and overall satisfaction (mean 68). Univariable analysis showed that all dimensions of satisfaction with care contributed significantly to overall satisfaction (P < 0.001). Multivariable analyses, however, showed that most of the variation in overall satisfaction could be attributed to levels of satisfaction with doctors, nurses, and hospital comfort and cleanliness.

CONCLUSION

Satisfaction with care in these surgical patients was high and could be measured using a multidimensional instrument. Overall satisfaction was not influenced equally by all aspects of care. The strongest contributors to overall satisfaction in this study were doctors, nurses and hospital cleanliness.

Public trust in health care: the system or the doctor?

OBJECTIVES

To examine how the public assess trust in health care in England and Wales.

DESIGN

Postal structured questionnaire in cross sectional survey.

SETTING

Random sample of people on the electoral register in England and Wales.

SUBJECTS

People aged 18 and over.

MAIN OUTCOME MEASURES

General levels of trust and confidence in health care.

RESULTS

The response rate was 48% (n = 1187). The mean level of confidence (trust) in the healthcare system was 6.0 out of a score of 10. Levels of distrust appeared relatively high with at least 356 (30%) respondents reporting little or very little trust for 28 of 32 specific aspects of health care. The highest levels of distrust were found in relation to how the health service was run and financed, particularly waiting times and the implication of cost cutting for patients. Statistical analysis by univariable linear regression of the specific determinants of generic assessments of public trust (confidence) suggested that the key aspects were patient centred care and levels of professional expertise. Being covered by private health insurance was also a key determinant of levels of public trust.

CONCLUSION

Public assessment of trust tends to address the views of care at the micro level. Policy makers concerned with the erosion of public trust need to target aspects associated with patient centred care and professional expertise.

Functional and Evolutionary Implications of Opposed Bands, Big Mouths, and Extensive Oral Ciliation in Larval Opheliids and Echiurids (Annelida)

Larvae of two annelids, the opheliid Armandia brevis and the echiurid Urechis caupo, captured small particles between opposed prototrochal and metatrochal ciliary bands and also captured large particles with wide ciliated mouths. The body volume of larval A. brevis increased more rapidly than the estimated maximum clearance rate as segments were added. Capture of larger particles by late-stage larvae may compensate for this potentially unfavorable allometry. The existence of larvae that use two feeding mechanisms at once, not previously known in annelids, suggests possible evolutionary routes between larval forms that feed only with opposed bands (e.g., serpulids and oweniids) and those that use complex oral ciliature to feed primarily on large particles (e.g., polynoids and nephtyids). In particular, the metatroch and food groove of opposed-band feeders may have arisen as expansions of oral ciliation in ancestral large-particle feeders; alternatively, extensive oral ciliation in large-particle feeders may have originated as a modification of metatroch and food-groove cilia in ancestral opposed-band feeders.

Regulation of keystone predation by small changes in ocean temperature

Key species interactions that are sensitive to temperature may act as leverage points through which small changes in climate could generate large changes in natural communities. Field and laboratory experiments showed that a slight decrease in water temperature dramatically reduced the effects of a keystone predator, the sea star Pisaster ochraceus, on its principal prey. Ongoing changes in patterns of cold water upwelling, associated with El Nino events and longer term geophysical changes, may thus have far-reaching impacts on the composition and diversity of these rocky intertidal communities.

Glial cell line-derived neurotrophic factor improves intrastriatal graft survival of stored dopaminergic cells

Glial cell line-derived neurotrophic factor, the newest member of the transforming growth factor-beta superfamily, has been shown to promote the survival and differentiation of dopaminergic neurons in the ventral mesencephalon. Glial cell line-derived neurotrophic factor has been implicated in both the in vitro and in vivo recovery of mesencephalic dopaminergic cells challenged with the neurotoxins 1-methyl-4-phenylpyridinium and 6-hydroxydopamine. Previous studies have shown increased survival of intrastriatally transplanted dopaminergic cells when followed by infusion of neurotrophic factors such as basic fibroblast growth factor, brain-derived neurotrophic factor and glial cell line-derived neurotrophic factor. However, the effects of glial cell line-derived neurotrophic factor co-administered with dopaminergic cells prior to implantation in the host striatum have not been studied. In the present study, the hypothesis was that treating fetal ventral mesencephalic tissue containing the dopaminergic substantia nigra with glial cell line-derived neurotrophic factor either during storage or at the time of transplantation, would enhance grafted dopaminergic cell survival and functional reinnervation of the host striatum in the unilaterally 6-hydroxydopamine-lesioned rat. To test this hypothesis, two experiments were performed. In the first experimental group (n = 7), fetal ventral mesencephalons from embryonic day 14 rats were maintained in hibernation medium containing glial cell line-derived neurotrophic factor (1 migrogram/ml) at 4 degrees C for six days prior to dissociation and stereotactic implantation into the host striatum: the control group (n = 5) received tissue hibernated without glial cell line-derived neurotrophic factor. The second experimental group (n = 8) received fresh fetal ventral mesencephalic tissue treated with glial cell line-derived neurotrophic factor (0.2 microgram/microliter) while the control group (n = 5) received the fresh graft with no glial cell line-derived neurotrophic factor. Transplantation success was assessed by behavioural analysis (rotometry) and tyrosine hydroxylase immunohistochemistry. Cell counts of tyrosine hydoxylase-stained sections revealed a statistically significant increase in tyrosine hydroxylase-positive neurons in grafts exposed to glial cell line-derived neurotrophic factor during hibernation as compared to control grafts. In addition, there was a statistically significant enhancement of fibre density in the glial cell line-derived neurotrophic factor hibernation graft group as compared to the glial cell line-derived neurotrophic factor fresh graft group. Behavioural analysis three weeks post-grafting exhibited a statistically significant decrease in amphetamine-induced rotations in animals transplanted with glial cell line-derived neurotrophic factor grafts as compared to control grafts. These findings suggest that storing dopaminergic cells in a glial cell line-derived neurotrophic factor-containing medium prior to transplantation increases graft survival, graft derived fibre outgrowth, and behavioural recovery in the adult host. This observation has potential implications for enhancing the efficacy of neural transplantation in the treatment of Parkinson's disease.

Benthic-pelagic links and rocky intertidal communities: bottom-up effects on top-down control?

Insight into the dependence of benthic communities on biological and physical processes in nearshore pelagic environments, long considered a "black box," has eluded ecologists. In rocky intertidal communities at Oregon coastal sites 80 km apart, differences in abundance of sessile invertebrates, herbivores, carnivores, and macrophytes in the low zone were not readily explained by local scale differences in hydrodynamic or physical conditions (wave forces, surge flow, or air temperature during low tide). Field experiments employing predator and herbivore manipulations and prey transplants suggested top-down (predation, grazing) processes varied positively with bottom-up processes (growth of filter-feeders, prey recruitment), but the basis for these differences was unknown. Shore-based sampling revealed that between-site differences were associated with nearshore oceanographic conditions, including phytoplankton concentration and productivity, particulates, and water temperature during upwelling. Further, samples taken at 19 sites along 380 km of coastline suggested that the differences documented between two sites reflect broader scale gradients of phytoplankton concentration. Among several alternative explanations, a coastal hydrodynamics hypothesis, reflecting mesoscale (tens to hundreds of kilometers) variation in the interaction between offshore currents and winds and continental shelf bathymetry, was inferred to be the primary underlying cause. Satellite imagery and offshore chlorophyll-a samples are consistent with the postulated mechanism. Our results suggest that benthic community dynamics can be coupled to pelagic ecosystems by both trophic and transport linkages.

Cost consequences of surveillance, medical management or surgery for benign prostatic hyperplasia

PURPOSE

The cost consequences of alternative treatment modalities for benign prostatic hyperplasia (BPH) were investigated. The present lifetime costs of watchful waiting, medical management and surgery alone and in various combinations were estimated for a synthetic cohort of men comprised of 5 age groupings.

MATERIALS AND METHODS

Synthetic cohort models were constructed to follow men at different ages "analytically" for specific intervals and to calculate the cumulative health care costs associated with alternative BPH treatment regimens during those periods. These models accounted explicitly for survival probabilities, the use of different types of health care services and products, price changes for those services and products, failure rates of some therapies and a discount factor needed to compute the present value of the cost streams. The models were implemented with hospital discharge and other data on BPH incident cases in the state of Florida in approximately 1989.

RESULTS

The addition of medical management to the mix of therapies is likely to increase overall health care spending on BPH treatment, perhaps by a considerable amount. The cost-effectiveness of each type of BPH therapy differs by the age of the patient at which it is first initiated. All other parameters being equal, surgery appears to be more cost-effective at younger patient ages, while medical management has a cost advantage at older ages.

CONCLUSIONS

The cost implications of alternative BPH therapies are substantial, and warrant more detailed consideration by clinicians and health policy specialists.

Tunica vaginalis flap for the management of disabling Peyronie's disease: surgical technique, results, and complications

OBJECTIVES

To discuss the surgical technique for tunica vaginalis flap (TVF) in the management of disabling Peyronie's disease and to evaluate the results and complications.

METHODS

Twelve patients underwent the TVF technique. Through a scrotal incision, the most dependent part of the tunica was dissected from the testicle and epididymis. The flap measured at least 4 cm in width and its upper extremity was left attached to the cremasteric muscle. Subsequently, the flap was brought underneath a groin skin bridge to cover the dorsal penile defect.

RESULTS

All patients were pain free. Seven patients (58.3%) were able to achieve a satisfactory erection with good vaginal penetration. Five patients (41.7%) were unable to perform sexually secondary to disabling chordee in 3 patients, glanular hypoesthesia in 1 patient, and venous leakage in 1 patient.

CONCLUSIONS

TVF is an adequate alternative for correction of distortions of Peyronie's plaque in patients with disabling disease. TVF is at present our first choice in the management of this disease. If penetration is still impaired following recurrent curvature, a Nesbit ventral plication can be used as a secondary procedure.

A trans-reservoir technique for correction of ureterointestinal obstruction in continent urinary diversion

Following construction of a continent colonic urinary reservoir, 5 uretero-colonic reimplantations became obstructed at the anastomotic site. In these obstructed units previous percutaneous balloon dilation and stent placement had failed and they were subsequently treated by a new reimplantation procedure. Preoperatively, in all ureteral units a percutaneous ureteral stent was inserted to facilitate intraoperative recognition of the ureteral meatus. The technique included a trans-reservoir approach, which allowed easy localization of the stent and anastomotic site. The ureter was dissected free from the intestinal wall and then was mobilized into the lumen of the reservoir. After excision of the scarred distal ureteral segment and spatulation of the proximal healthy ureter, a new direct mucosa-to-mucosa reimplantation was performed leaving the ureter stented. This trans-reservoir approach (occasionally done through an abdominal transverse muscle splitting incision) allows for shortening of the operation, and avoids the time-consuming and more complicated transabdominal lysis of adhesions. All newly reimplanted ureters (100%) showed evidence of adequate ureteral drainage without residual obstruction on followup excretory urography or furosemide renography up to 45 months postoperatively. The trans-reservoir approach for refractory ureteral reimplantation obstruction in continent colonic reservoirs has been associated with no morbidity or mortality, and facilitates the solution to a difficult clinical problem.

Prostate cancer imaging with a new monoclonal antibody: a preliminary report

BACKGROUND

Optimal treatment of prostate cancer depends on accurate staging. Computed tomography (CT) and magnetic resonance imaging have severe limitations, and standard bone scanning can show only destructive osseous metastases. A radiolabeled antibody specific to prostatic adenocarcinoma could theoretically find evidence of soft-tissue metastases and lymph node involvement.

METHODS

An immunoconjugate (CYT-356) consisting of a murine monoclonal antibody against human prostatic adenocarcinoma bound to a linker-chelator and radiolabeled with indium 111 was administered intravenously to seven patients with documented Stage D adenocarcinoma of the prostate. Planar imaging was done on days 1, 2, and 3 after injection. The CYT-356 scans were compared with standard technetium Tc99m sulfur colloid bone scans and CT scans.

RESULTS

Optimal imaging results were obtained on the 72-h scans. All patients had lesions on both the 99mTc-sulfur colloid bone scan and the CYT-356 scan. The location of the lesions correlated to a great extent. Two patients had positive lesions biopsied, and both biopsies showed the presence of metastatic prostatic carcinoma. There were no side effects from administration of the antibody.

CONCLUSION

In this preliminary study, CYT-356 scanning appears to be a promising agent to accomplish specific staging of prostatic carcinoma.

Experimental investigation of an infolded bowel segment as an anti-incontinence mechanism without interposing the ileo-cecal valve

A technique for using bowel segment as an anti-incontinence mechanism was developed in an animal model and evaluated urodynamically. Variously modified bowel segments were investigated alone and later attached to a colonic reservoir to establish their value in preventing urinary incontinence while allowing easy catheterization. Using careful surgical technique, intussuscepted, tapered and plicated bowel segments were constructed. The maximum segmental closure pressure and functional length were evaluated in all preparations. The three bowel segments remained continent during slow filling and up to reservoir capacity. The recordings demonstrated both highest maximal closure pressure and longest functional length in the plicated system when evaluated both alone and following reservoir attachment. These recording differences occurred both with the reservoir full and empty. These results demonstrate the value of a plicated bowel segment in the maintenance of urinary continence when attached to a compliant urinary reservoir without using the ileo-cecal valve in this model.

Direct (nontunneled) ureterocolonic reimplantation in association with continent reservoirs

A total of 190 patients underwent continent urinary diversion using the Florida pouch. Direct mucosa-to-mucosa ureterocolonic reimplantation was used in 165 patients (326 ureters). Of the first 30 ureters in patients who underwent antireflux tunneled reimplantation obstruction occurred in 4 (13.3%). Obstruction developed directly in 16 of the ureters reimplanted (4.9%), and 3 of the 6 plicated and reimplanted megaureters (50%). Among the obstructed units 3 (13%) were treated unexpectedly by autonephrectomy, while the other 20 units (87%) were treated with percutaneous balloon dilation and internal stenting for 6 to 8 weeks. In the latter group 12 units (60%) recovered function, 3 (15%) had pyelonephritis requiring nephrectomy and 5 (25%) stabilized following a new reimplantation. Reflux was demonstrated in 23 units (7%). All units with reflux are being followed conservatively and renal deterioration has not been demonstrated. The incidence of ureteral obstruction with direct reimplantation is lower compared to a tunneled technique. This reimplantation procedure is technically simpler than others and is safe in adults when performed in association with a large volume, continent colonic reservoir.

Conversion from external appliance wearing or internal urinary diversion to a continent urinary reservoir (Florida pouch I and II): surgical technique, indications and complications

A total of 20 patients with diversion requiring an external appliance or internal urinary diversion underwent conversion to a continent urinary reservoir (Florida pouch I or II). All patients subsequently reported an improvement in the quality of life and expressed satisfaction with the new urinary diversion procedure. Of the patients 15 (75%) previously had an ileal conduit, while 1 (5%) had undergone ureterosigmoidostomy, 1 (5%) had cutaneous ureterostomy, 1 (5%) had a suprapubic tube, 1 (5%) had a sigmoid conduit and 1 (5%) had a cecal conduit. After the original diversion 3 patients (15%) had recurrent urinary infections, 3 had complications related to the stoma and external appliance (stenosis and skin dermatitis) and 5 (25%) had ureteral obstruction in 7 ureters. A total of 17 patients with conduits (85%) underwent conversion via different surgical technical aspects depending on the status of the intestinal segment from the conduit and the function of the ureteral reimplantation: in 14 the conduit was discarded or was used only to patch the newly created Florida I colonic pouch, while in 6 the conduit was preserved and 9 ureterointestinal reimplantations were left undisturbed (Florida pouch II). Among 7 ureters preoperatively obstructed (original diversion), reimplanting them into the pouch failed to prevent further renal damage in 5 (71%). Three renal units required nephrectomy, 2 kidneys deteriorated and 2 recovered renal function after percutaneous balloon dilation and stenting. Among 31 preoperatively nonobstructed renoureteral units (original diversion), 22 were reimplanted into the colonic reservoir. One of these units (4.2%) became obstructed postoperatively and 3 (13.5%) presently have reflux. The 10 reimplantations left undisturbed in the detubularized conduit drain satisfactorily without postoperative obstruction and in 6 reflux has not been demonstrated. Renal function (serum creatinine) is preserved in all patients but 15 (75%) have hyperchloremia of mild degree. Two patients (10%) have acidosis and 1 (5%) of these had low red blood cell folic acid. Conversion of an external or internal diversion to a continent colonic urinary reservoir (Florida pouch I or II) can be successful and improve the quality of life of the patient. The functioning renal units that were preoperatively obstructed were associated with a high failure rate (71%) after reimplantation. Metabolic alterations will require long-term followup, and are particularly worrisome in children and young adults.

Results, complications and surgical indications of the Florida pouch

One hundred and seven patients underwent continent urinary diversion using an extended, detubularized right colonic segment as the urinary reservoir and the distal part of the ileum as a continent catheterized efferent system. This reservoir allows the accommodation of a large volume of urine; urodynamics in 28 patients demonstrated a maximum reservoir capacity varying between 550 and 1,200 milliliters (an average of 747 milliliters). The reservoir maximal volume and pressure remains unchanged in six patients studied urodynamically three to four years postoperatively. Maximal reservoir pressures ranged between 10 and 58 centimeters of H2O (an average of 35 centimeters). Of 201 ureterocolonic reimplantations, four ureters were initially reimplanted using a modified Le Duc procedure, 26 ureters were subsequently managed using the Goodwin transcolonic approach and 165 reimplantations were done with a direct (nontunneled) mucosa to mucosal anastomosis. The over-all success rates with each of the three techniques (absence of reflux and obstruction) have been 75.0, 84.7 and 87.4 per cent, respectively. However, the incidence of obstruction was 13.3 per cent for the tunneled and 4.2 per cent for the non-tunneled reimplantations. Six megaureters underwent imbrication and direct reimplantation, and three of these became obstructed. One patient died of pulmonary embolism. Medical and surgical complications markedly predominated in the group who underwent simultaneous cystectomies, and in this group, the over-all complication rate was comparable with that for previously reported series with ileal conduits. The double row plication of the distal part of the ileum and ileocecal valve allows easy catheterization every four to six hours and 105 patients (97.2 per cent) remained continent between catheterizations. The stoma is covered using a small gauze, cap or sterile adhesive strip. This protects clothing from mucus production by the stoma and an occasional episode of urinary dribbling. Seven patients required reoperation for correction of incontinence or other complications. Our satisfactory experience with these patients makes this technique an excellent approach to achieving continent urinary diversion.

A continent colonic urinary reservoir: the Florida pouch

A total of 92 patients underwent continent urinary diversion with an extended, detubularized right colonic segment as the urinary reservoir and the distal ileum as a continent catheterizable efferent system. In this series 65 patients were followed for 6 to 46 months (average 17 months). Our reservoir allows the accommodation of a large volume of urine; urodynamic studies in 28 patients demonstrated a maximum reservoir capacity varying between 550 and 1,200 cc (average 747 cc). Maximal reservoir pressures ranged from 10 to 58 cm. water (average 35 cm. water). Of the 127 ureterocolonic reimplantations 4 ureters were initially reimplanted with a modified Le Duc procedure, 26 ureters were managed subsequently with the Goodwin transcolonic approach and 91 reimplantations were done with a direct (nontunneled) mucosa-to-mucosa anastomosis. The overall success rates with each of the 3 techniques (absence of reflux and obstruction) were 75, 88.6 and 90.1%, respectively. Six megaureters underwent imbrication and direct reimplantation, and 3 of these (50%) became obstructed. Two converted ileal conduits were opened at the antimesenteric edge and were patched to the reservoir while the ureteroileal anastomosis was left undisturbed. One patient (1.5%) died of pulmonary embolism. Medical and surgical complications occurred only in the group who underwent simultaneous cystectomy and the over-all rate of complication was comparable to previous series with ileal conduits. The double row plication of the distal ileum and ileocecal valve allows for easy catheterization every 4 to 6 hours and 63 patients (97%) remain continent between catheterization. Four patients (6%) required reoperation for correction of incontinence or other complications. Our satisfactory experience with these patients makes this technique an excellent approach to achieving continent urinary diversion.

Case report: An outbreak of herpesvirus myeloencephalitis in vaccinated horses

In the foaling season of 1977, five vaccinated horses in a Standardbred breeding stable were affected with herpesvirus myeloencephalitis. Respiratory and abortigenic forms also occurred in other individuals on the premises. Equine herpesvirus type 1 was isolated from the brain of one case of myeloencephalitis and from lungs of two aborted fetuses. Twelve of 16 horses demonstrated fourfold or greater increases in titres to equine herpesvirus type 1.

Clinical and radiographic findings of focally infected polycystic kidneys

Three patients with localized polycystic kidney infections are presented with the pertinent clinical, laboratory, and radiographic findings. Gallium-67 citrate and angiography play an important role in evaluation of these patients. Angiography in particular is valuable in the diagnosis and the exact localization of the inflammatory disease. Localization is extremely important in planning surgical treatment should conservative therapy fail.