Protein design using structure-based residue preferences

Recent developments in protein design rely on large neural networks with up to 100s of millions of parameters, yet it is unclear which residue dependencies are critical for determining protein function. Here, we show that amino acid preferences at individual residues-without accounting for mutation interactions-explain much and sometimes virtually all of the combinatorial mutation effects across 8 datasets (R2 ~ 78-98%). Hence, few observations (~100 times the number of mutated residues) enable accurate prediction of held-out variant effects (Pearson r > 0.80). We hypothesized that the local structural contexts around a residue could be sufficient to predict mutation preferences, and develop an unsupervised approach termed CoVES (Combinatorial Variant Effects from Structure). Our results suggest that CoVES outperforms not just model-free methods but also similarly to complex models for creating functional and diverse protein variants. CoVES offers an effective alternative to complicated models for identifying functional protein mutations.

Machine learning for functional protein design

Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. New methods promise to escape the constraints of natural and laboratory evolution, accelerating the generation of proteins for applications in biotechnology and medicine. To make sense of the exploding diversity of machine learning approaches, we introduce a unifying framework that classifies models on the basis of their use of three core data modalities: sequences, structures and functional labels. We discuss the new capabilities and outstanding challenges for the practical design of enzymes, antibodies, vaccines, nanomachines and more. We then highlight trends shaping the future of this field, from large-scale assays to more robust benchmarks, multimodal foundation models, enhanced sampling strategies and laboratory automation.

ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction

Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins that can address our most pressing challenges in climate, agriculture and healthcare. Despite a surge in machine learning-based protein models to tackle these questions, an assessment of their respective benefits is challenging due to the use of distinct, often contrived, experimental datasets, and the variable performance of models across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high-quality expert annotations about mutation effects. We devise a robust evaluation framework that combines metrics for both fitness prediction and design, factors in known limitations of the underlying experimental methods, and covers both zero-shot and supervised settings. We report the performance of a diverse set of over 70 high-performing models from various subfields (eg., alignment-based, inverse folding) into a unified benchmark suite. We open source the corresponding codebase, datasets, MSAs, structures, model predictions and develop a user-friendly website that facilitates data access and analysis.

Exploring targeting peptide-shell interactions in encapsulin nanocompartments

Encapsulins are recently discovered protein compartments able to specifically encapsulate cargo proteins in vivo. Encapsulation is dependent on C-terminal targeting peptides (TPs). Here, we characterize and engineer TP-shell interactions in the Thermotoga maritima and Myxococcus xanthus encapsulin systems. Using force-field modeling and particle fluorescence measurements we show that TPs vary in native specificity and binding strength, and that TP-shell interactions are determined by hydrophobic and ionic interactions as well as TP flexibility. We design a set of TPs with a variety of predicted binding strengths and experimentally characterize these designs. This yields a set of TPs with novel binding characteristics representing a potentially useful toolbox for future nanoreactor engineering aimed at controlling cargo loading efficiency and the relative stoichiometry of multiple concurrently loaded cargo proteins.

Attitudes and perceptions about breastfeeding among female and male informal workers in India and South Africa

BACKGROUND

Worldwide, over 740 million women make their living in the informal economy and therefore lack formal employment benefits, such as maternity leave, that can improve infant feeding practices. Returning to work is one of the biggest challenges women face to maintaining breastfeeding. This study aimed to explore attitudes and perceptions towards breastfeeding in the informal work environment among male and female informal workers.

METHODS

The study used a qualitative research design. Purposive and snowball sampling was employed. Focus group discussions (FGDs) were conducted among men and women working in different types of informal jobs, in India and South Africa. Data was analysed using a thematic approach and the framework method.

RESULTS

Between March and July 2017, 14 FGDs were conducted in South Africa and nine in India. Most women were knowledgeable about the benefits of breastfeeding and reported initiating breastfeeding. However, pressures of family responsibilities and household financial obligations frequently forced mothers to return to work soon after childbirth. Upon return to work many mothers changed their infant feeding practices, adding breastmilk substitutes like formula milk, buffalo milk, and non-nutritive fluids like Rooibos tea. Some mothers expressed breastmilk to feed the infant while working but many mothers raised concerns about expressed breastmilk becoming 'spoilt'. Breastfeeding in the workplace was challenging as the work environment was described as unsafe and unhygienic for breastfeeding. Mothers also described being unable to complete work tasks while caring for an infant. In contrast, the flexibility of informal work allowed some mothers to successfully balance competing priorities of childcare and work. Sociocultural challenges influenced breastfeeding practices. For example, men in both countries expressed mixed views about breastfeeding. Breastfeeding was perceived as beneficial for both mother and child, however it was culturally unacceptable for women to breastfeed in public. This affected working mothers' ability to breastfeed outside the home and contributed to a lack of respect for women who chose to breastfeed in the workplace.

CONCLUSION

Mothers working in the informal sector face multiple challenges to maintaining breastfeeding. Interventions are required to support feeding and childcare if global nutrition and development goals are to be met.

Prospective research on infants with mild encephalopathy: the PRIME study

OBJECTIVE

To determine short-term outcomes of infants with evidence of hypoxia-ischemia at birth and classified as mild neonatal encephalopathy (NE) at <6 h of age.

STUDY DESIGN

Prospective multicenter study. Mild NE was defined as ⩾1 abnormal category in modified Sarnat score. Primary outcome was any abnormality on early amplitude integrated electroencephalogram (aEEG) or seizures, abnormal brain magnetic resonance imaging (MRI) or neurological exam at discharge.

RESULTS

A total of 54/63 (86%) of enrolled infants had data on components of the primary outcome, which was abnormal in 28/54 (52%): discontinuous aEEG (n=4), MRI (n=9) and discharge exam (n=22). Abnormal tone and/or incomplete Moro were the most common findings. MRI abnormalities were confined to cerebral cortex but two infants had basal ganglia and/or thalamus involvement. The 18 to 24 months follow-up is ongoing.

CONCLUSIONS

A larger than expected proportion of mild NE infants with abnormal outcomes was observed. Future research should evaluate safety and efficacy of neuroprotection for mild NE.

Improving public health information: a data quality intervention in KwaZulu-Natal, South Africa

OBJECTIVE

To evaluate the effect of an intervention to improve the quality of data used to monitor the prevention of mother-to-child transmission (PMTCT) of the human immunodeficiency virus in South Africa.

METHODS

The study involved 58 antenatal clinics and 20 delivery wards (37 urban, 21 rural and 20 semi-urban) in KwaZulu-Natal province that provided PMTCT services and reported data to the District Health Information System. The data improvement intervention, which was implemented between May 2008 and March 2009, involved training on data collection and feedback for health information personnel and programme managers, monthly data reviews and data audits at health-care facilities. Data on six data elements used to monitor PMTCT services and recorded in the information system were compared with source data from health facility registers before, during and after the intervention. Data completeness (i.e. their presence in the system) and accuracy (i.e. being within 10% of their true value) were evaluated.

FINDINGS

The level of data completeness increased from 26% before to 64% after the intervention. Similarly, the proportion of data in the information system considered accurate increased from 37% to 65% (P < 0.0001). Moreover, the correlation between data in the information system and those from facility registers rose from 0.54 to 0.92.

CONCLUSION

A simple, practical data improvement intervention significantly increased the completeness and accuracy of the data used to monitor PMTCT services in South Africa.

Hyperlipidemia resulting in abnormal density and signal intensity of blood in a neonate with lipoprotein lipase deficiency

We present the imaging findings in an 8-week-old infant with LPL deficiency. Due to markedly increased lipoproteins in the serum, abnormal hypodensity and abnormal T1-weighted hyperintensity were identified in the dural venous sinuses and medullary veins.

Infant feeding in the time of HIV: rapid assessment of infant feeding policy and programmes in four African countries scaling up prevention of mother to child transmission programmes

OBJECTIVE

To assess the infant feeding components of prevention of mother to child HIV transmission (PMTCT) programmes.

METHODS

Assessments were performed across Botswana, Kenya, Malawi and Uganda. 29 districts offering PMTCT were selected by stratified random sampling with rural and urban strata. All health facilities in the selected PMTCT district were assessed. The facility level manager and the senior nurse in charge of maternal care were interviewed. 334 randomly selected health workers involved in the PMTCT programme completed self-administered questionnaires. 640 PMTCT counselling observations were carried out and 34 focus groups were conducted amongst men and women.

RESULTS

Most health workers (234/334, 70%) were unable to correctly estimate the transmission risks of breastfeeding irrespective of exposure to PMTCT training. Infant feeding options were mentioned in 307 of 640 (48%) observations of PMTCT counselling sessions, and in only 35 (5.5%) were infant feeding issues discussed in any depth; of these 19 (54.3%) were rated as poor. Several health workers also reported receiving free samples of infant formula in contravention of the International Code on Breastmilk Substitutes. National HIV managers stated they were unsure about infant feeding policy in the context of HIV. Finally, there was an almost universal belief that an HIV positive mother who breastfeeds her child will always infect the child and intentional avoidance of breastfeeding by the mother indicates that she is HIV positive.

CONCLUSION

These findings underline the need to implement and support systematic infant feeding policies and programme responses in the context of HIV programmes.

Messages about dual contraception in areas of high HIV prevalence are not heeded

BACKGROUND

Dual protection is recommended for prevention of unwanted pregnancies and protection against sexually transmitted infections, including HIV. It is critical for HIV-negative women to prevent seroconversion and HIV transmission to their infants during pregnancy and breastfeeding.

METHODS

Women were followed up after delivery, monthly for the first 9 months and then 3-monthly to 24 months, in a cohort study investigating postnatal HIV transmission. Study nurses discussed family planning, including condom use, at each visit. Contraceptive methods used since the last visit were recorded. All women knew their HIV status, and most women breastfed for a minimum of 6 months.

RESULTS

Among 1,137 HIV-positive and 1 220 HIV-negative women the most common contraceptive method was the hormonal injectable; few women used condoms alone or as dual contraception (0-3 months 6.8%; 7-12 months 16.3%; 19-24 months 14.4%). Compared with uninfected women, HIV-positive women were more likely to use condoms in years 1 and 2 after delivery (adjusted odds ratio (AOR) 1.72, 95% confidence interval (CI) 1.38-2.14, p<0.001; AOR 1.61, 95% CI 1.15-2.25, p=0.006 respectively). Compared with women with a flush toilet, those with a pit latrine were less likely to use condoms in years 1 and 2 (AOR 0.22, 95% CI 01.7-0.28, p<0.001; AOR 0.27, 95% CI 0.19-0.39, p<0.001). Older women were more likely to use condoms in the first postpartum year (AOR 1.78, 95% CI 1.03-3.09, p=0.040).

CONCLUSIONS

More creative ways of promoting condoms and dual contraception need to be found if new HIV infections, in women and children, are to be prevented.

Micronutrient supplementation in children and adults with HIV infection

BACKGROUND

The scale and impact of the HIV/AIDS pandemic has made the search for simple, affordable, safe, and effective public health interventions all the more urgent. Micronutrient supplements hold the promise of meeting these criteria, but their widespread use needs to be based on sound scientific evidence of effectiveness and safety.

OBJECTIVES

To assess whether micronutrient supplements are effective in reducing morbidity and mortality in adults and children with HIV infection.

SEARCH STRATEGY

The Cochrane Library (CENTRAL), EMBASE, MEDLINE, AIDSearch, CINAHL, and conference proceedings were searched, and pharmaceutical manufacturers and researchers in the field were contacted to locate any ongoing or unpublished trials.

SELECTION CRITERIA

Randomised controlled trials comparing the effects of micronutrient supplements (vitamins, trace elements, and combinations of these) with placebo or no treatment on mortality and morbidity in HIV-infected individuals.

DATA COLLECTION AND ANALYSIS

Two reviewers independently appraised trial quality and extracted data. Study authors were contacted for additional data where necessary. A meta-analysis was not deemed appropriate due to significant heterogeneity between trials.

MAIN RESULTS

Fifteen trials were included. Six trials comparing vitamin A/beta-carotene with placebo in adults failed to show any effects on mortality, morbidity, CD4 and CD8 counts, or on viral load. Four trials of other micronutrients in adults did not affect overall mortality, although there was a reduction in mortality in a low CD4 subgroup. In a large Tanzanian trial in pregnant and lactating women, daily multivitamin supplementation was associated with a number of benefits to both mothers and children: a reduction in maternal mortality from AIDS-related causes; a reduced risk of progression to stage four disease; fewer adverse pregnancy outcomes; less diarrhoeal morbidity; and a reduction in early-child mortality among immunologically- and nutritionally-compromised women. Vitamin A alone reduced all-cause mortality and improved growth in a small sub-group of HIV-infected children in one hospital-based trial, and reduced diarrhoea-associated morbidity in a small HIV-infected sub-group of infants in another trial.

AUTHORS' CONCLUSIONS

There is no conclusive evidence at present to show that micronutrient supplementation effectively reduces morbidity and mortality among HIV-infected adults. It is reasonable to support the current WHO recommendations to promote and support adequate dietary intake of micronutrients at RDA levels wherever possible. There is evidence of benefit of vitamin A supplementation in children. The long-term clinical benefits, adverse effects, and optimal formulation of micronutrient supplements require further investigation.

Free formula milk for infants of HIV-infected women: blessing or curse?

There is vigorous controversy around whether HIV-infected women in developing countries should choose formula or breastfeeding for their infants. Formula eliminates HIV transmission but incurs risk of increased mortality, whereas breastfeeding has multiple benefits but entails risk of HIV transmission. International guidelines are available but need to be strengthened. This commentary summarizes data on the scale and rate of mother-to-child transmission (MTCT) of HIV through breastfeeding, and the hazards and benefits of breast- and formula-feeding. The case against providing free or subsidized formula to HIV-infected mothers is based on the following: it exacerbates disadvantages of formula feeding; compromises free choice; targets beneficiaries erroneously; creates a false perception of endorsement by health workers; compromises breastfeeding; results in disclosure of HIV status; ignores hidden costs of preparation of formula; increases mixed breastfeeding, which is an unsatisfactory method for all women; requires organization and management of programmes that are complicated and costly; and finally increases the 'spill-over' effect into the normal breastfeeding population. Recommendations to minimize these drawbacks include use of affordable antiretrovirals to reduce MTCT; investments in high-quality, widely available HIV counselling; support for choice of feeding; and exclusive breastfeeding for those who choose to breastfeed.

Catheter-related thrombosis in children with cancer

OBJECTIVE

The prevalence of asymptomatic catheter-related thrombosis of the upper venous system in children with cancer has not been determined. We evaluated patients with cancer and implantable central venous catheters (ports) for this complication.

STUDY DESIGN

Children with cancer undergoing port removal were eligible for this study. Vessel patency was evaluated by contrast venography. We examined each child for physical stigmata of thrombosis and retrospectively assessed catheter-related mechanical difficulties and infections.

RESULTS

Thirty-one ports had been placed in 24 children (aged 20 months to 18 years; median age, 9 years) with diagnoses of leukemia/lymphoma (n = 10), solid tumor (n = 12), and histiocytosis (n = 2). Venography showed abnormalities in 12 of the 24 patients. Physical examination revealed dilated superficial veins on the chest in 3 patients. Venograms showed abnormalities in all 3 children with prominent superficial thoracic veins. Nine of the 21 other patients had clinically occult central venous occlusion.

CONCLUSION

Fifty percent (95% CI, 30% to 70%) of children who had implantable ports removed during or after treatment of cancer exhibited deep venous thrombosis at the site of catheter placement. Future studies should determine the contribution of inherited and other acquired risk factors for thrombosis and assess measures to prevent and/or treat catheter-related thrombosis in this population.

The use of gated cine phase contrast and MR venography in achondroplasia

OBJECTS

Foramen magnum and jugular foramen stenosis, well-known problems in achondroplasia, may result in brain stem compression and venous outflow obstruction, respectively. We studied a series of children with achondroplasia using gated cine phase contrast (PC) CSF flow studies to evaluate CSF dynamics across the foramen magnum and MR venography (MRV) to depict obstructed venous drainage.

METHODS

Ten patients (9 months to 11 years, mean 2.85 years) were referred for possible brain stem compression. MRI included routine sequences, cine PC with velocity encoding (VENC) = 5 cm/s, and MRV. Six patients, including the asymptomatic patient, had brain stem compression without tonsillar herniation; two had tonsillar herniation; and two had neither brain stem compression nor tonsillar herniation. Abnormal tonsillar movement was seen only with tonsillar herniation. MRV showed steno-occlusive disease of the internal jugular vein (IJV) in nine patients, sigmoid sinus in four, and absent or hypoplastic transverse sinus in seven. Veno-occlusive disease was not progressive. No patient had massive hydrocephalus, although larger ventricles were associated with more profuse venous collateral formation and more severe degrees of IJV stenosis. Three patients have undergone CSF diversion.

CONCLUSIONS

MR imaging may be useful in defining the pathophysiology of brain stem compression and hydrocephalus in achondroplasia.

Surveillance protocol for the detection of intracranial abnormalities in premature neonates

OBJECTIVE

To determine the optimal timing of cranial ultrasound scans (USs) for identifying preterm neonates weighing less than 1500 g at birth who develop intracranial complications of prematurity.

DESIGN/SETTING

Observational study at an urban county hospital.

METHODS

Serial USs from neonates with less than 1500-g birth weight (BW) admitted to the neonatal intensive care unit between January 1995 and December 1996 were reviewed by a pediatric neuroradiologist in a blinded random manner.

RESULTS

Two hundred forty-eight neonates (78%) underwent at least 3 USs, 32 (10%) had 2 USs and 37 (12%) only 1 US. The initial US was normal in 156 neonates (49%) and abnormal in 161 (57%). The principal abnormalities included intraventricular hemorrhage (IVH) (n = 74), periventricular echogenicity (PVE) (n = 68), ventriculomegaly (n = 7), and solitary cysts (n = 9). Severe IVH (n = 17) occurred in 13 (11.4%) of 114 neonates at less than 1000-g BW and 4 (5%) of 79 neonates of BW 1000 to 1250 g. In 11 cases (65%), the severe IVH was clinically unsuspected. For neonates weighing less than 1000 g, IVH was diagnosed by days 3 to 5 in 10 (77%) of 13, by days 10 to 14 in 11 (84%) of 13, and by day 28 in all neonates; for neonates 1001 to 1250 g, IVH was diagnosed in 1 (24%) of 4 by days 3 to 5, 2 (50%) of 4 by days 10 to 14, and 3 (75%) of 4 by day 28. One infant's condition was diagnosed on routine US before discharge from the hospital. Cystic periventricular leukomalacia (PVL) was noted in 9 neonates; in 4 of the 9 cases, increased PVE was present on the initial US and cyst formation was obvious by the second US. For 4 neonates (3 with BW <1000 g), all routine USs were negative and cystic PVL was noted on the predischarge US in these cases. Nonobstructive ventriculomegaly in the absence of IVH or cystic PVL was observed in 14 neonates. In 6, it was noted on the initial screening US; in 4 of the cases, it evolved after the third screening US. Two hundred fifty-six neonates had a US before discharge from the hospital; 181 (72%) were normal and 75 (28%) abnormal. Nine significant lesions were identified by the US before discharge from the hospital (ie, severe IVH [n = 1], cystic PVL [n = 4], and ventriculomegaly [n = 4]).

CONCLUSIONS

The following screening protocol is recommended: (1) Neonates of less than 1000-g BW: initial US on days 3 to 5 (should identify at least 75% of cases of IVH and some PVE abnormalities); second US on days 10 to 14 (should detect at least 84% of IVH and identify early hydrocephalus and early cyst formation); third scan on day 28 (should detect all cases of IVH, as well as assess PVE and ventricular size); and final scan before discharge from the hospital (should detect approximately 20% of significant late-onset lesions). (2) Neonates of 1000- to 1250-g BW: initial US at days 3 to 5 (should detect at least 40% of significant abnormalities); a second scan at day 28 (should detect at least 70% of significant abnormalities); and a predischarge scan (should detect all late-onset significant lesions). (3) Neonates of 1251- to 1500-g BW: an initial scan at days 3 to 5; and a second scan before discharge from the hospital if the clinical course is complicated. Arch Pediatr Adolesc Med. 2000;154:822-826

MR venography in children with complex craniosynostosis

PURPOSE

Chronic venous hypertension due to jugular foramen stenosis has been proposed as an etiology for the hydrocephalus and tonsillar herniation seen in some patients with complex craniosynostosis. We report the use of MR venography (MRV) to evaluate venous outflow obstruction in this clinical setting.

MATERIALS AND METHODS

We studied 17 patients, (ages 4 months to 34 years; mean 7.3 years) with complex craniosynostosis; 8 patients with Crouzon's syndrome, 2 with Apert's, 1 with Pfeiffer's and 6 patients without an eponymous classification. MR imaging included routine imaging sequences and axial 2D TOF MRV. Patterns of venous drainage and the presence of hydrocephalus and tonsillar herniation were noted.

RESULTS

Jugular vein obstruction was seen in 12/17 patients; in 5/8 patients with Crouzon's, 1/2 with Apert's, the single patient with Pfeiffer's and 5/6 patients with nonsyndromic craniosynostosis. The predominant collateral drainage was via the posterior condylar veins. Nine of 12 (75%) of the patients with abnormal MRV had hydrocephalus; 3/8 patients with Crouzon's, 1/2 patients with Apert's, and 5/6 nonsyndromic patients. Two patients had hydrocephalus with normal MRV. Ten patients had tonsillar herniation, which was associated with shunted hydrocephalus in 7/10 patients, and hydrocephalus seen prior to shunt placement in 3/9. Nine of 10 patients with tonsillar herniation had an abnormal MRV, while 1 patient had a normal MRV. Venous pressures measured in 1 patient showed an 8-mm-Hg differential across the skull base.

CONCLUSIONS

The posterior condylar veins appear pivotal in maintaining venous drainage when the jugular bulbs are occluded. Although the association between venous outflow obstruction, hydrocephalus and tonsillar herniation is intriguing, evidence of venous outflow obstruction by MRV may not be indicative of significant intracranial venous hypertension.

Idiopathic ischemic cerebral infarction in childhood: depiction of arterial abnormalities by MR angiography and catheter angiography

BACKGROUND AND PURPOSE

We report our experience with MR imaging, MR angiography, and catheter angiography in children with acute idiopathic cerebral infarction and suggest that catheter angiography may still play an important role in this setting.

METHODS

During the past 8 years, 18 children with idiopathic cerebral infarction underwent MR imaging and catheter angiography; 17 were also studied with MR angiography. MR imaging was done within 34 hours after onset of hemiplegia or seizures or both. Sixteen patients underwent catheter angiography within 36 hours of MR imaging; 12 studies were performed within 22 hours. Two patients underwent catheter angiography, in both cases within 72 hours. Infarcts were compared with arterial abnormalities seen at catheter angiography, and the results of MR angiography were compared with those seen at catheter angiography.

RESULTS

Comparing MR angiography with catheter angiography, we found the positive predictive value of MR angiography for arteriopathy was 100%, with a negative predictive value of 88%. MR angiography was equivalent to catheter angiography in the detection and depiction of proximal middle cerebral artery disease; however, depiction of disease in the internal carotid artery (ICA) and detection of peripheral embolic disease were better with catheter angiography than MR angiography.

CONCLUSION

Basal ganglia lesions associated with ICA disease by MR angiography should probably be studied with digital subtraction angiography, as MR angiography did not depict the length and severity of ICA disease as well as catheter angiography did. Hemispheric infarcts should be studied with catheter angiography, as emboli may occur in the absence of heart disease; the circle of Willis may be uninvolved with embolic disease, and MR angiography is not sensitive to emboli in small peripheral intracranial arteries.

Coexistent holoprosencephaly and Chiari II malformation

Chiari II malformations and holoprosencephaly have been considered to be brain malformations that differ with respect to teratogenic insult, embryologic mechanism, and morphology. We herein describe coexistent Chiari II malformation and holoprosencephaly that occurred in a viable infant. A review of the literature regarding Chiari II malformations and holoprosencephaly suggests that a disturbance to the mesenchyme in early embryologic life may be the cause of both malformations.

Surgical lessons learned from the Shigella dysenteriae type I epidemic

An epidemic of Shigella dysenteriae type I is spreading through Africa. It is a particularly infectious and virulent form of dysentery which can cause clinical confusion with other endemic diseases and may present to the surgeon as a result of its complications. A total of 140 children with Shigella dysenteriae type I presented to the paediatricians at King Edward VIII Hospital in 1995; 35 were referred to the surgeons because of abdominal tenderness, distension, peritonitis or perforation. Ten children underwent laparotomy--four for peritonitis and six for perforation. Of the four children with peritonitis, three had transmural colitis. Therefore laparotomy was only performed for objective evidence of perforation. Of the subsequent non-operated group with the clinical features of peritonitis, none developed further surgical problems in the acute phase and none died. It is suggested that surgery in the acute phase should be avoided unless there is evidence of perforation.

Basal ganglia and thalamic infarction in children. Cause and clinical features

BACKGROUND

We present the signs, symptoms, and radiographic features of 36 children with ischemic infarctions of the basal ganglia, internal capsule, or thalamus.

PATIENTS AND METHODS

The series includes 14 males and 22 females ranging in age from newborn to 13 years. Twenty-seven patients were evaluated with computed tomography, 34 with magnetic resonance imaging, 16 with magnetic resonance angiography, and 10 with conventional cerebral angiography. Thirty patients had unilateral lesions (16 left, 14 right) and 6 had bilateral infarctions.

RESULTS

The most common presenting symptom was hemiplegia (30 of 36). Other children presented with aphasia (5 of 36), seizures (5 of 36), altered consciousness (5 of 36), and hemisensory changes (5 of 36). Four of 6 patients with bilateral lesions presented with altered mental status, but the location of a unilateral infarction within the thalamus or basal ganglia did not predict the clinical presentation.

CONCLUSIONS

The risk factors for basal ganglia infarction in children are diverse, but systemic hypertension does not play a major role in children. The vascular occlusion often occurred in the large arteries, with secondary occlusion of the smaller penetrating arteries. Most children with a single unilateral infarction have a good prognosis.

Factitious lambdoid perisutural sclerosis: does the "sticky suture" exist?

We report a patient with occipital flattening attributed to lambdoid synostosis on the basis of perisutural sclerosis. The lambdoid suture was patent at surgery and by histology. Specimen radiography showed no perisutural sclerosis. This case questions the validity of peri- sutural sclerosis as a radiographic indicator of impending lambdoid synostosis.

Neurologic manifestations of in utero cocaine exposure in near-term and term infants

OBJECTIVE

To determine whether the incidence of neurosonographic and neurologic abnormalities is higher in cocaine-exposed infants at birth.

METHODS

In utero exposure to cocaine was investigated in 39 term and near-term infants with positive urine screens for cocaine only and 39 matched control infants without drug exposure admitted to the regular term newborn nursery. Serial evaluations were performed on each infant on postnatal days 1 and 2 and included a cranial sonogram, a neurologic and behavioral assessment for drug withdrawal, and Doppler interrogation of the anterior and middle cerebral arteries.

RESULTS

There were no differences between groups in neurosonographic abnormalities. Grade I or II intraventricular hemorrhage occurred in 11% of cocaine-exposed and 11% of control infants. There were no cases of grade III intraventricular hemorrhage, cystic periventricular leukomalacia, or neonatal stroke. Head size was smaller in cocaine-exposed infants, ie, 32.7 +/- 0.1 cm versus 33.8 +/- 0.1 cm. The neurologic examination was similar between groups with regard to tone, reflexes, and cranial nerves. Behavioral scores were higher on both days, in cocaine-exposed versus control infants, ie, 4.4 +/- 0.5 versus 2.7 +/- 0.03 on day 1 and 5.0 +/- 0.5 versus 1.71 +/- 0.31 on day 2. Cerebral blood flow velocity measurements in the anterior cerebral artery were similar between groups on both days of examination. However, cocaine-exposed infants demonstrated a significant increase in flow velocity from day 1 to day 2, ie, 0.48 +/- 0.03 to 0.57 +/- 0.04. There was a concomitant decrease in the pulsatility index from day 1 to day 2 in the cocaine-exposed, ie, 0.74 +/- 0.02 to 0.69 +/- 0.02, but not in the control infants. No differences were noted in the flow velocities in the middle cerebral arteries between groups.

CONCLUSIONS

Term and near-term infants admitted to a regular nursery who are exposed to cocaine in utero: (1) do not exhibit an increased incidence of neurosonographic abnormalities; (2) do exhibit altered behavior consistent with drug withdrawal; and (3) do demonstrate changes in flow velocity in the anterior cerebral artery consistent with the vasoconstrictive effects of the drug. However, these changes were not accompanied by changes in the neurologic examination or altered care. The long-term neurodevelopmental implications of these subtle abnormalities in the neonatal period remain to be determined.

Treatment of dural sinus thrombosis using selective catheterization and urokinase

Thrombosis of the cerebral dural venous sinuses, cortical draining veins, and deep cerebral veins is a rare clinical finding. Because of its low incidence and multiple etiologies, the optimum therapy for this condition will only be elucidated by a multicenter, randomized prospective study. At our institution, we favor early and aggressive management of cerebral venous sinus thrombosis with transfemoral, venous intradural infusions of the fibrinolytic agent urokinase. To date, treatment of only 13 patients using this technique has been reported in the English literature. This report adds 12 more such treated patients. Despite the presence of preinfusion infarcts in 5 patients, four of which were hemorrhagic, we incurred no major therapeutic morbidity. Functional sinus patency was achieved in 11 of 12 patients, with our only true failure occurring in an individual with symptoms of at least 2 months' duration. Good to excellent clinical outcome was achieved in 10 of 11 patients (one newborn had inadequate follow-up).

Leptomyxid amebic meningoencephalitis mimicking brain stem glioma

An 11-month-old infant presented with cranial nerve palsy and ataxia. MR revealed a large, enhancing pontine mass and small, nonenhancing parafalcial lesions; no organisms were seen in cerebrospinal fluid. After empiric treatment for brain stem glioma, the patient died. Autopsy revealed meningoencephalitis caused by leptomyxid amebae.

Use of distal splenorenal shunt in children referred for liver transplant evaluation

Variceal bleeding remains a common cause of morbidity for children with both intrahepatic and extrahepatic portal hypertension. Occasionally, patients referred for liver transplant evaluation have significant variceal bleeding, despite adequate synthetic liver function. During a 7-year period, 322 children were referred for liver transplant evaluation. Six underwent distal splenorenal shunt surgery after evaluation. There were four boys and two girls. The average age was 11 +/- 4 years, and the average weight was 39 +/- 15 kg. The etiology of variceal bleeding was intrahepatic portal hypertension in five (1 biliary atresia, 2 chronic hepatitis, 2 congenital hepatic fibrosis) and extrahepatic portal vein thrombosis in one. Two patients had no previous attempts at sclerotherapy (one because of an abnormality in platelet function, the other because of extensive gastric varices), and four had multiple previous sclerotherapy treatments. No patient had preoperative encephalopathy. Three cases were Child's class A, and three were Child's class B. Preoperative evaluation of the portasystemic system was performed with magnetic resonance (MR) imaging or splenoportography. All patients underwent a distal splenorenal shunt procedure, four of whom also had splenopancreatic disconnection. One patient required 100 mL of blood replacement, and five required no blood. The average length of hospital stay was 9.8 +/- 2.2 days. Postoperative complications were minimal. All patients are alive, without recurrent gastrointestinal bleeding or encephalopathy, and they have patent shunts, which was confirmed by MR or Doppler ultrasound at a mean of 25 +/- 20 months after shunt surgery.(ABSTRACT TRUNCATED AT 250 WORDS)

Congenital defects of the posterior arch of the atlas: a report of seven cases including an affected mother and son

PURPOSE

To describe our experience with congenital anomalies of the posterior arch of the atlas, with a review and classification of these defects and a note on their clinical significance.

METHODS

We report six children and one adult, the mother of one of the children, with an anomalous posterior arch of the atlas. The diagnosis was made on lateral films of the neck. Three patients also had axial CT of the cervical spine.

RESULTS

The anomalies encountered in the seven patients were absence of the posterior arch of the atlas (four patients), bilateral clefts (two patients), and unilateral cleft (one patient). In three patients the anomaly was discovered as an incidental asymptomatic finding; three other patients presented with transient neck pain or transient neurologic symptoms after head and neck trauma, and one patient (an adult woman) described neck symptoms of 1-year duration.

CONCLUSIONS

On the basis of these seven cases we conclude that congenital defects of the posterior arch of the atlas may be discovered as incidental asymptomatic findings, but symptoms occurring after trauma to the head and neck or spontaneously also may be encountered.

Relationship between periventricular intraparenchymal echodensities and germinal matrix-intraventricular hemorrhage in the very low birth weight neonate

The pathogenesis of the periventricular intraparenchymal echodense lesion (IPE) observed in association with germinal matrix-intraventricular hemorrhage (GM-IVH) in premature neonates is unclear. The objectives of this study were to determine (1) the temporal characteristics of GM-IVH and IPE, (2) the basic characteristics of the IPE, and (3) the relationship of clinical events, including surfactant administration, to IPE. One hundred twenty-four neonates of less than 1250 g birth weight were prospectively evaluated. IPE was defined as an echodensity greater than 1 cm in diameter by cranial sonography. Fifteen (12%) neonates developed IPE in association with GM-IVH (group 1); 33 neonates developed GM-IVH only (group 2) and 76 neonates without GM-IVH served as comparison group (group 3). IPE was essentially an asymmetrical lesion; both sides of cerebrum were equally affected. The lesion was diffuse in 9 neonates and focal in 5. IPE occurred both early, at 36 hours or before (n = 8), and later, ie, between 48 and 96 hours (n = 6). In one neonate IPE was diagnosed at autopsy. GM-IVH and IPE were noted simultaneously in neonate with the earlier onset IPE (diagnosed within 36 hours); GM-IVH preceded the IPE by 6 to 48 hours when the lesion was of a later onset. Surfactant was administered to 13 (87%) group 1, 24 (73%) group 2, and 35 (46%) group 3 neonates. Pulmonary hemorrhage developed in 9 (60%) of group 1, 3 (9%) group 2, and no group 3 neonates. Symptomatic patent ductus arteriosus occurred in 12 (75%) group 1, 15 (45%) group 2, and 15 (20%) group 3 neonates. The onset of symptoms associated with patent ductus arteriosus was earlier in group 1 vs group 2 or group 3 neonates, ie, 70 vs 172 hours. Nine (60%) group 1 neonates, 6 (18%) group 2, and 5 (7%) group 3 neonates died. The cranial sonogram was markedly abnormal in all 6 group 1 survivors. Stepwise polytomous logistic regression indicated that birth weight, gestational age, and emergent cesarean section were the best predictors of GM-IVH + IPE.(ABSTRACT TRUNCATED AT 250 WORDS)

Late-onset meningitis in sick, very-low-birth-weight infants. Clinical and sonographic observations

OBJECTIVES

To determine the clinical and sonographic features of late-onset meningitis (after 7 days of life) in sick, very-low-birth-weight infants.

DESIGN

Retrospective study of a patient series.

SETTING

Neonatal intensive care nursery at Parkland Memorial Hospital in Dallas, Tex.

PARTICIPANTS

Ten preterm infants with birth weights of more than 1750 g who developed late-onset meningitis during a 42-month study period.

INTERVENTIONS

None.

RESULTS

Ten preterm infants developed meningitis at a mean (+/- SD) postnatal age of 20 +/- 14 days. Eight of the infants survived. Initial clinical signs were nonspecific, eg, apnea and bradycardia (eight infants), abdominal distention (five infants), hyponatremia (serum sodium level, < 130 mmol/L), and a decrease in urine output with an increase in weight (three infants). Specific neurologic signs occurred in three infants (seizures [n = 2] and third-nerve palsy [n = 1]). Sonographic abnormalities noted in seven (70%) of the 10 infants included progressive ventriculomegaly (n = 6), thalamic echodensities (n = 3), ventriculitis (n = 4), and cystic leukomalacia (n = 1). The progressive ventriculomegaly developed from 1 to 2 weeks after diagnosis; permanent shunting was required in all six infants. The thalamic echodensities were linear or punctate and developed from 1 to 2 weeks after diagnosis in two infants.

CONCLUSIONS

The data indicate the need for a high index of suspicion of meningitis in very-low-birth-weight infants suspected of having sepsis because of the nonspecific clinical presentation of meningitis. Because both progressive ventriculomegaly and thalamic echodensities are late and frequent findings, serial sonograms are essential for careful monitoring of sequelae of disease.

Unexpected acute neurologic toxicity in the treatment of children with acute lymphoblastic leukemia

BACKGROUND

Our current protocol for treatment of childhood acute lymphoblastic leukemia (ALL) was designed to assess the efficacy of methotrexate (MTX) plus L-asparaginase and of etopisode (VP-16) plus cytarabine (ARA-C) during intensive consolidation and continuation therapies and to determine the feasibility of intensifying MTX therapy by the use of divided oral doses of MTX. The protocol was associated with unexpected acute neurotoxicity. There are few reports of such toxic effects during therapy for ALL.

PURPOSE

This report describes these toxic effects and outlines our successful approach to the problem.

METHODS

The standard four-drug induction regimen consisted of vincristine, L-asparaginase, daunorubicin, and prednisone. In consolidation therapy, oral MTX was given in divided doses (dMTX) of 25 mg/m2 every 6 hours four times daily in four weekly courses concomitant with weekly triple intrathecal therapy--MTX, ARA-C, and hydrocortisone--plus one dose of leucovorin 24 hours after triple intrathecal therapy. Consolidation treatment ended with three daily doses of intravenous VP-16 and ARA-C. The first 16 months of continuation therapy included 6-week cycles of dMTX and L-asparaginase, both given every other week for 5 weeks, with 6-mercaptopurine nightly, and then two doses of VP-16 plus ARA-C and one dose of triple intrathecal therapy.

RESULTS

Twenty-five of the 138 patients evaluated had acute neurotoxicity. Ten of the first 72 experienced a seizure or episode of transient neurological deficit 9-11 days following the administration of intravenous ARA-C, VP-16, and triple intrathecal therapy. Despite discontinuation of intrathecal ARA-C, which eliminated simultaneous intravenous and intrathecal treatment with ARA-C, acute neurotoxicity was observed in six previously unaffected patients and six of 42 patients treated after the elimination of intrathecal ARA-C. Therefore, as a second amendment, oral leucovorin was given 24 and 36 hours after dMTX and intrathecal MTX in continuation therapy. No acute neurotoxicity has been seen in 24 patients subsequently entered in the study.

CONCLUSION

These findings suggest that folate replacement due to administration of leucovorin modulated MTX toxicity and/or modified an interaction among VP-16, ARA-C, intrathecal therapy, and the central nervous system.

The yield of routine chest radiography in children with cancer hospitalized for fever and neutropenia

A routine admission chest radiograph (CXR) in pediatric patients with cancer who are admitted to the hospital for fever and neutropenia has been advised because the signs and symptoms of pneumonia may be absent. The authors studied 131 consecutive patient admissions for fever and neutropenia to evaluate the diagnostic yield of routine CXR. All patients had a complete history, physical examination, complete blood count, blood culture, urinalysis, urine culture, and CXR. Patients routinely started ceftazidime monotherapy. Results of the CXR were correlated with the presence or absence of signs and symptoms of respiratory disease. Of 128 CXR results, 26 (20%) were abnormal (13 with known malignant disease, 2 with atelectasis, 3 with peribronchial cuffing, and 8 with pneumonia [6%]). Three patients with pneumonia were asymptomatic. Therefore, only 3 of 128 patients (2.3%) had pneumonia on CXR not suspected by physical examination. None would have had initial therapy modified based on the CXR finding alone. The authors concluded that the incidence of pneumonia in a child with fever and neutropenia is low and that routine CXR at diagnostic evaluation is unnecessary in the asymptomatic ambulatory patient.

Systemic neonatal candidiasis

Forty-five cases of systemic neonatal candidiasis were diagnosed over a 9-year period in a neonatal intensive care unit; 42 infants weighted less than 1.5 kg. All had been very ill with preceding bacterial sepsis and other complications of low birthweight. Where treatment was instituted the mortality was low (4 out of 39 dying) and complications of treatment were transitory. We therefore recommend diligent examination for the presence of this infection, and treatment with a combination of amphotericin B and 5-flucytosine.

Rapid detection of Pneumocystis carinii using a direct fluorescent monoclonal antibody stain

A collaborative study was undertaken at two institutions to assess the performance of a direct fluorescent-antibody stain for the detection of Pneumocystis carinii in respiratory specimens from patients with known or suspected human immunodeficiency virus type 1 infections. A total of 163 specimens (125 induced sputa, 37 bronchoalveolar lavage fluids, and 1 tracheal aspirate) from 124 patients were examined by using modified Giemsa (Diff-Quik; Baxter American Scientific Products, Chicago, Ill.) and direct fluorescent-antibody stains. A total of 73 specimens contained P. carinii, which was detected in 66 (92%) of the specimens by using the modified Giemsa and in 71 (97%) of the specimens by using the fluorescent-antibody stain. One bronchoalveolar lavage fluid specimen in which P. carinii was detected only with the fluorescent-antibody stain was determined to be a false-positive based on subsequent clinical evaluation of the patient. Although the overall time for processing and examining specimens stained with either stain was not significantly different for those specimens containing P. carinii, considerably less time was required for microscopic examination of those fluorescent-antibody-stained specimens lacking P. carinii.

Recurrent medulloblastoma: frequency of tumor enhancement on Gd-DTPA MR imaging

Thirty-two children with medulloblastoma were evaluated postoperatively with conventional and gadolinium-enhanced MR imaging. Eleven patients had abnormal cranial MR studies; nine of these had recurrent tumor. In six patients recurrent tumor enhanced with Gd, while in the other three patients recurrent tumor did not enhance. The remaining two patients had areas of abnormal Gd enhancement that were caused by radiation-induced breakdown of the blood-brain barrier rather than by recurrent tumor. This study shows that not all recurrent medulloblastoma enhances and that the absence of Gd enhancement does not necessarily indicate the absence of recurrent tumor.

Recurrent medulloblastoma: frequency of tumor enhancement on Gd-DTPA MR imaging

Thirty-two children with medulloblastoma were evaluated postoperatively with conventional and gadolinium-enhanced MR imaging. Eleven patients had abnormal cranial MR studies; nine of these had recurrent tumor. In six patients recurrent tumor enhanced with Gd, while in the other three patients recurrent tumor did not enhance. The remaining two patients had areas of abnormal Gd enhancement that were caused by radiation-induced breakdown of the blood-brain barrier rather than by recurrent tumor. This study shows that not all recurrent medulloblastoma enhances and that the absence of Gd enhancement does not necessarily indicate the absence of recurrent tumor.

Clinical evaluation of a direct fluorescent monoclonal antibody test for detection of Pseudomonas aeruginosa in blood cultures

A direct fluorescent monoclonal antibody test (DFA; Genetic Systems Corp., Seattle, Wash.) was evaluated for the detection of Pseudomonas aeruginosa in 178 blood culture broths obtained from 128 patients. The DFA identified 44 (98%) of 45 blood cultures positive for P. aeruginosa and was negative in 131 (98%) of 133 blood cultures which grew gram-negative rods other than P. aeruginosa. Upon further investigation, saline suspensions of the organism from the false-negative blood culture were strongly (4+) DFA positive. The false-positive reactions were not due to cross-reactivity, as shown by lack of DFA staining of the non-P. aeruginosa isolates following subculture to agar media. The specificity of the reagent was further demonstrated by directly staining culture isolates including 10 serotypes of P. aeruginosa (all positive) and 57 selected gram-negative bacilli including eight species of Pseudomonas that were not P. aeruginosa (all negative). DFA staining of blood culture broths was easy to perform and read with minimal background fluorescence. The DFA method can be performed in 50 min and appears promising as a rapid method for the identification of P. aeruginosa bacteremia.

Self-expanding metallic stents: preliminary evaluation in an atherosclerotic model

The performance of the self-expanding stainless steel (Gianturco) stent in atherosclerotic arteries was examined in a rabbit model. Atherosclerosis was induced by supplementing rabbit chow with 6% peanut oil and 2% cholesterol followed by endothelial disruption of the abdominal aorta with a balloon catheter and continuation on the atherogenic diet for the remainder of the study. Eighteen stents, 1 cm in length and 4 or 5 mm in diameter when fully expanded, were placed in atherosclerotic stenotic lesions in six rabbits. Luminal distention was consistently achieved. At 8 weeks follow-up, no luminal narrowing, stent migration, thrombus formation or branch vessel occlusion had occurred. Atherosclerotic neointimal proliferation occurred around the stent wires following placement, but did not cause significant luminal narrowing.

Monoclonal antibodies to cell surface antigens shared by chemically induced mouse bladder carcinomas

Rats were immunized with cultured cells from chemically induced transitional cell carcinomas of the mouse urinary bladder, and their spleen cells were hybridized with NS-1 mouse myeloma cells. Following initial screening of antibodies made by hybridoma clones, the tissue distribution of antigens defined by the antibodies was established by using a peroxidase-antiperoxidase technique with frozen sections of a variety of mouse tumors, as well as normal adult and embryonic tissues. Two antibodies were identified which detected antigens with bladder carcinoma specificity. One antibody (3B12) reacted weakly with epithelial cells from several sources, including normal bladder, while the second antibody (6.10), which bound strongly to bladder carcinoma cells, was negative on bladder epithelium and bound (weakly) to only a small fraction of all epithelial cells tested except for epidermal cells and periosteum from embryos. Both antibodies should be useful to assess the immunotherapeutic and immunoprophylactic effects of monoclonal antibodies to tumor-type specific oncofetal antigens.

Monoclonal antibodies to two mouse bladder carcinoma antigens

Carcinomas of the urinary bladder of mice were induced by 3-methyl-cholanthrene or fanft [(4-5-nitro-2-furyl)-2-thioazolyl formamide]. On transplantation in vivo, tumor lines consisting of well-differentiated transitional-cell carcinomas were established. Some tumors were also explanted in vitro. A rat was immunized with a pool of carcinomas and normal bladder tissue and its spleen cells were hybridized with NS-l mouse myeloma cells. Supernatants of hybrid cells ("hybridomas") were screened for antibody binding to antigens present in bladder carcinomas but not in normal syngeneic urinary bladder, with cell extracts as targets. Hybridomas that appeared to have the required specificity were cloned, tested further against transitional-cell bladder carcinomas, an anaplastic bladder tumor, rhabdomyosarcomas, a mammary carcinoma, myelomas and lymphomas, and normal adult urinary bladder, kidney, lung, spleen, heart, brain, thymus, and whole embryo. Antibody formed by one hybridoma, 2H5, gave significant binding to membranes from five of seven transitional-cell carcinomas but not to membranes from many other tissues. A second hybridoma, IE6, formed antibody to an antigen present in bladder carcinomas and normal liver and, in smaller amounts, in several other normal and neoplastic tissues. Fluorescence microscopy established that both antigens were present at the cell surface of transitional-cell bladder carcinomas. Immunoprecipitation and SDS-polyacrylamide gel electrophoresis were used to identify the target antigens from 125I-labelled cell membrane proteins. The antibody formed by 2H5 was found to identify a protein with a molecular weight in the range of 140 kilodaltons, which was detected in transitional-cell bladder. The molecular nature of the antigen defined by hybridoma IE6 is not known.

Soviet and American youth in a changing world

This study explores some relationships between culture, adolescent personality styles, and psychopathology in the USA and the USSR. The broader macrosocial level includes characteristics of the epoch. The more restricted macrosocial level includes one sociopolitical system and cultural features. In Soviet society, the conformist type of personality is prevalent; in the United States, “Protean man” is common. Soviet and American youth diverge in their attitudes toward technology and achievement.

These personality styles are related to the restricted macrosocial level, while the broader epochal level is related to prevailing types of psychopathology. In the USSR, the distinction between normality and psychopathology is sharper than it is in the USA.