SMaRT-PCR: sampling using masks and RT-PCR, a non-invasive diagnostic tool for paediatric pulmonary TB

BACKGROUND

Key challenges in paediatric TB diagnosis are invasive sampling and poor sensitivity of standard methods. This study demonstrates the diagnostic potential of non-invasive sampling of bioaerosols from children using SMaRT-PCR, comprising mask sampling combined with reverse transcriptase-polymerase chain reaction (RT-PCR) for TB.

METHODS

Exhaled bioaerosols were captured on modified N-95 masks in a 10-min talk-cough-breathe process from 51 children (30 with TB confirmed using standard sampling methods and 21 without TB) aged 2-15 years. All mask samples were tested using in-house RT-PCR for 16s and rpoB RNA transcripts. Additional mask samples from children with TB were tested using Xpert® MTB/RIF (n = 3) and Xpert® MTB/RIF Ultra (n = 27).

RESULTS

SMaRT-PCR sensitivity for detecting TB among treatment-naïve children was 96% if 16s or rpoB was present, and 75% if both genes were present, comparable to standard methods (71%) in the same cohort. Specificity was better for both genes, at 95%, than 85% for a single gene detection. Mask sampling with Xpert MTB/RIF or Ultra had a sensitivity of only 13%.

CONCLUSION

This is the first study to provide evidence for testing bioaerosols as a promising alternative for detecting paediatric TB. Sampling is non-invasive and simple, with the potential for point-of-care applications. This pilot study also suggests that RNA transcript-based detection may improve TB diagnostic sensitivity in children; however, further investigation is required to establish its adaptability in clinical settings..

Evaluating structure-based activity in a high-throughput assay for steroid biosynthesis

Data from a high-throughput human adrenocortical carcinoma assay (HT-H295R) for steroid hormone biosynthesis are available for >2000 chemicals in single concentration and 654 chemicals in multi-concentration (mc). Previously, a metric describing the effect size of a chemical on the biosynthesis of 11 hormones was derived using mc data referred to as the maximum mean Mahalanobis distance (maxmMd). However, mc HT-H295R assay data remain unavailable for many chemicals. This work leverages existing HT-H295R assay data by constructing structure-activity relationships to make predictions for data-poor chemicals, including: (1) identification of individual structural descriptors, known as ToxPrint chemotypes, associated with increased odds of affecting estrogen or androgen synthesis; (2) a random forest (RF) classifier using physicochemical property descriptors to predict HT-H295R maxmMd binary (positive or negative) outcomes; and, (3) a local approach to predict maxmMd binary outcomes using nearest neighbors (NNs) based on two types of chemical fingerprints (chemotype or Morgan). Individual chemotypes demonstrated high specificity (85-98%) for modulators of estrogen and androgen synthesis but with low sensitivity. The best RF model for maxmMd classification included 13 predicted physicochemical descriptors, yielding a balanced accuracy (BA) of 71% with only modest improvement when hundreds of structural features were added. The best two NN models for binary maxmMd prediction demonstrated BAs of 85 and 81% using chemotype and Morgan fingerprints, respectively. Using an external test set of 6302 chemicals (lacking HT-H295R data), 1241 were identified as putative estrogen and androgen modulators. Combined results across the three classification models (global RF model and two local NN models) predict that 1033 of the 6302 chemicals would be more likely to affect HT-H295R bioactivity. Together, these in silico approaches can efficiently prioritize thousands of untested chemicals for screening to further evaluate their effects on steroid biosynthesis.

Differing radiation exposure in scrub technicians and rotating staff in cardiac catheterization laboratory: occupation matters

Funding Acknowledgements

Type of funding sources: None.

Background

Radiation exposure of cardiac catheterization lab personnel is an evolving area of concern, due to long term, repetitive exposure causing deterministic and stochastic effects(1,2). Current radiation protection measures are based on increasing distance, shielding from fluoroscopy source and depend on primary operator behavior(3)

Effective dose(ED) in micro Sieverts( μSv) as a measure of individual absorbed radiation dose provides feedback as to occupational exposure and risks. Dosimeter badges worn over equipment measure ED correlating with radiation exposure of areas unprotected by standard lead apron such as head, neck, lens and upper limbs. (4)

Most studies focus on primary operator exposure (5,6,7), overlooking non physician staff comprising scrub technicians working as assistants to primary operator physicians, and rotating staff involved in peri-procedural care of patients.

Purpose

This study aimed to find out ED acquired by scrub technicians(ED.S) and rotating staff(ED.R) in interventional cardiology and invasive electrophysiology procedures, utilizing external dosimeters worn over lead aprons.

Methods

We prospectively collected radiation data over forty six invasive Cardiology procedures from 15th March 2021 to 1st June 2021 comprising fourteen diagnostic coronary and graft angiograms, seventeen combined diagnostic and interventional cardiology procedures, nine sole percutaneous coronary interventions and six electrophysiology procedures. Nine staff members: two female and seven male members participated as scrub technicians and rotating staff, provided with external dosimeter badges. ED was obtained by logging in dosimeter badges into pre calibrated monitors.

Results

Significantly high mean ED was acquired by rotating staff as compared to scrub technicians, mean ED.R:21.04 μSv( SD: +/-39.64) and mean ED.S: 7.54 μSv( SD:+/- 17.23), this three fold difference in radiation exposure was statistically significant with a p-value of 0.03.

This was consistent across procedure groups, with rotating staff acquiring higher ED compared to their scrub technician colleagues in diagnostic, interventional and electrophysiology cases. Statistically significant differences in radiation exposure of both staff groups were demonstrated in diagnostic and interventional cardiology procedures, with p-values of 0.04 and 0.01 respectively.(See Table)

Conclusion

This small, single center study highlights occupational role as a significant factor in varying radiation exposure amongst non-physician staff . Higher ED was attributed to rotating staff duties involving proximity and mobility around fluoroscopy source and patient, devoid of protective lead shields.

Based on these findings, avoiding fluoroscopy use while staff performs duties involving proximity to patient such is mandatory. Other essential measures should include accessory left sided leads shields, mandatory protective lens and head shields for rotating staff. Abstract Table

The family planning "know-do" gap among married women of reproductive age in urban Pakistan

OBJECTIVE

To examine the prevalence and predictors of family planning (FP) know-do gaps among married women of reproductive age (MWRA) in low socio-economic urban areas of Karachi, Pakistan.

DESIGN

This was a cross-sectional survey of randomly selected 7288 MWRA (16-49 years) to identify predictors of the know-do gap in FP using a logistic regression model.

RESULTS

More than one third (35.5%) of MWRA had FP know-do gap, i.e., despite having a knowledge of contraceptives and desire to limit or delay childbearing, they were not using contraceptives. Women were less likely to use FP if they were getting older (25-35 years: OR 1.45, 95% CI 1.09-1.94; >35 years: OR 3.02, 95% CI 1.90-4.80), from certain ethnicities (Sindhi: OR 1.64, 95% CI 1.11-2.42; Saraiki: OR 1.66, 95% CI 1.01-2.71; other minorities: OR 2.37, 95% CI 1.63-3.44); did not receive FP counselling: OR 1.43, 95% CI 1.13-1.80; and had not made a joint decision on FP: OR 1.44, 95% CI 1.06-1.98). Conversely, women were more likely to use contraceptives if they had >10 years of schooling (OR 0.66, 95% CI 0.46-0.94), with each increasing number of a living child (OR 0.68, 95% CI 0.62-0.75) and each increasing number of contraceptive method known (OR 0.93, 95% CI 0.88-0.98).

CONCLUSION

The predictors associated with the FP know-do gap among MWRA should be considered when planning future strategies to improve the contraceptive prevalence rate in Pakistan.

New TB drugs for the treatment of children and adolescents with rifampicin-resistant TB in Mumbai, India

SETTING: Médecins Sans Frontières (MSF) clinic in Mumbai, India.OBJECTIVE: To determine the final treatment outcomes, culture conversion and adverse events (AEs) during treatment among children and adolescents (0-19 years) with rifampicin-resistant tuberculosis (RR-TB) who received ambulatory injectable-free treatment, including bedaquiline (BDQ) and/or delamanid (DLM) during September 2014-January 2020.DESIGN: This was a retrospective cohort study based on review of routinely collected programme data.RESULTS: Twenty-four patients were included; the median age was 15.5 years (min-max 3-19) and 15 (63%) were females. None were HIV-coinfected. All had fluoroquinolone resistance. Twelve received treatment, including BDQ and DLM, 11 received DLM and one BDQ. The median exposure to BDQ (n = 13) and DLM (n = 23) was 82 (IQR 80-93) and 82 (IQR 77-96) weeks, respectively. Seventeen (94%) patients with positive culture at baseline (n = 18) had negative culture during treatment; median time for culture-conversion was 7 weeks (IQR 5-11). Twenty-three (96%) had successful treatment outcomes: cured (n = 16) or completed treatment (n = 7); one died. Eleven (46%) had 17 episodes of AEs. Two of 12 serious AEs were associated with new drugs (QTcF >500 ms).CONCLUSION: Based on one of the largest global cohorts of children and adolescents to receive new TB drugs, this study has shown that injectable-free regimens containing BDQ and/or DLM on ambulatory basis were effective and well-tolerated among children and adolescents and should be made routinely accessible to these vulnerable groups.

Profile of osteoarticular tuberculosis in children

OBJECTIVE

To determine clinical profile of osteoarticular tuberculosis (TB) in children.

METHODS

Cross-sectional analysis from 2007 to 2013. All patients diagnosed with bone TB, spinal TB or TB abscesses were included.

RESULTS

Out of 1318 children with TB, 39 (2.96%) had osteoarticular TB, of which 16 (42%) had osteomyelitis, 8 (20.5%) had spinal involvement, 7 (17.9%) had TB synovitis, 2 (5.1%) had psoas abscess and 6 (15.4%) had abscesses. The mean age of presentation was 7.1 ± 3.5 years (range 2-14 years). Of the 33 cases in which a culture was done, 25 (64%) showed a positive culture. Drug sensitivity tests were done in 21 patients of which 10 (47.6%) tested were drug resistant, of which 4 (36.4%) were multidrug resistant (MDR), 2 (18.2%) were extensively drug resistant (XDR), 3 were pre-XDR (27.3%) and 1 was polyresistant (9.1%). Nine (23.1%) patients had TB in the past with a treatment duration of 8.3 ± 5.3 months. Contact with a TB patient had occurred in 10 (25.6%) cases. Associated pulmonary TB were seen in 6 (15.39%) and TB meningitis were seen in 1 (2.6%) patients. Surgical intervention was needed in 11 (28.2%) patients of which 5 (45.5%) underwent curettage, drainage was done in 1 (9.1%), arthrotomy in 4 (36.4%) and spinal surgery in 1 (9.1%) patient.

CONCLUSION

Drug resistant osteoarticular TB is an emerging problem in children.

Quantitative prediction of repeat dose toxicity values using GenRA

Computational approaches have recently gained popularity in the field of read-across to automatically fill data-gaps for untested chemicals. Previously, we developed the generalized read-across (GenRA) tool, which utilizes in vitro bioactivity data in conjunction with chemical descriptor information to derive local validity domains to predict hazards observed in in vivo toxicity studies. Here, we modified GenRA to quantitatively predict point of departure (POD) values obtained from US EPA's Toxicity Reference Database (ToxRefDB) version 2.0. To evaluate GenRA predictions, we first aggregated oral Lowest Observed Adverse Effect Levels (LOAEL) for 1,014 chemicals by systemic, developmental, reproductive, and cholinesterase effects. The mean LOAEL values for each chemical were converted to log molar equivalents. Applying GenRA to all chemicals with a minimum Jaccard similarity threshold of 0.05 for Morgan fingerprints and a maximum of 10 nearest neighbors predicted systemic, developmental, reproductive, and cholinesterase inhibition min aggregated LOAEL values with R² values of 0.23, 0.22, 0.14, and 0.43, respectively. However, when evaluating GenRA locally to clusters of structurally-similar chemicals (containing 2 to 362 chemicals), average R² values for systemic, developmental, reproductive, and cholinesterase LOAEL predictions improved to 0.73, 0.66, 0.60 and 0.79, respectively. Our findings highlight the complexity of the chemical-toxicity landscape and the importance of identifying local domains where GenRA can be used most effectively for predicting PODs.

Be Careful Where You Smile: Culture Shapes Judgments of Intelligence and Honesty of Smiling Individuals

Smiling individuals are usually perceived more favorably than non-smiling ones—they are judged as happier, more attractive, competent, and friendly. These seemingly clear and obvious consequences of smiling are assumed to be culturally universal, however most of the psychological research is carried out in WEIRD societies (Western, Educated, Industrialized, Rich, and Democratic) and the influence of culture on social perception of nonverbal behavior is still understudied. Here we show that a smiling individual may be judged as less intelligent than the same non-smiling individual in cultures low on the GLOBE’s uncertainty avoidance dimension. Furthermore, we show that corruption at the societal level may undermine the prosocial perception of smiling—in societies with high corruption indicators, trust toward smiling individuals is reduced. This research fosters understanding of the cultural framework surrounding nonverbal communication processes and reveals that in some cultures smiling may lead to negative attributions.

Eosinophilic meningitis: a case series and review of literature of Angiostrongylus cantonensis and Gnathostoma spinigerum

Eosinophilic meningitis is defined as the presence of >10 eosinophils/μL in cerebrospinal fluid (CSF) or at least 10% eosinophils in the total CSF leukocyte count. Eosinophilic meningitis has been reported in two case series and two case reports in India till date and has not been reported in children below 15 years of age. We present two children with eosinophilic meningitis with peripheral eosinophilia and the proposed etiologic agents based on the clinical setting and their response to antihelminthic agents.

Adolescent conduct problems and premature mortality: follow-up to age 65 years in a national birth cohort

BACKGROUND

Severe youth antisocial behaviour has been associated with increased risk of premature mortality in high-risk samples for many years, and some evidence now points to similar effects in representative samples. We set out to assess the prospective association between adolescent conduct problems and premature mortality in a population-based sample of men and women followed to the age of 65 years.

METHOD

A total of 4158 members of the Medical Research Council National Survey of Health and Development (the British 1946 birth cohort) were assessed for conduct problems at the ages of 13 and 15 years. Follow-up to the age of 65 years via the UK National Health Service Central Register provided data on date and cause of death.

RESULTS

Dimensional measures of teacher-rated adolescent conduct problems were associated with increased hazards of death from cardiovascular disease by the age of 65 years in men [hazard ratio (HR) 1.17, 95% confidence interval (CI) 1.04-1.32], and of all-cause and cancer mortality by the age of 65 years in women (all-cause HR 1.16, 95% CI 1.07-1.25). Adjustment for childhood cognition and family social class did little to attenuate these risks. Adolescent conduct problems were not associated with increased risks of unnatural/substance-related deaths in men or women in this representative sample.

CONCLUSIONS

Whereas previous studies of high-risk delinquent or offender samples have highlighted increased risks of unnatural and alcohol- or substance abuse-related deaths in early adulthood, we found marked differences in mortality risk from other causes emerging later in the life course among women as well as men.

Using a birth cohort to study ageing: representativeness and response rates in the National Survey of Health and Development

Britain's oldest birth cohort study, the MRC National Survey of Health and Development (NSHD) provides data to explore life time influences on ageing. The latest data collection was undertaken between 2006 and 2011 when study members were aged 60-64 and consisted of postal and pre-assessment questionnaires to eligible study members, followed by invitation to attend one of six clinical research facilities (CRFs) across the UK for clinical assessments, and dietary diaries and activity monitors in the days following the CRF visit. The option of a home visit for clinical assessments was provided if the study member refused or was unable to attend the CRF. We examined response and attrition, here describing rates overall and for postal and clinical assessment modes of data collection, identifying socioeconomic and health-related predictors of response, and assessing the continued representativeness of the sample. In total, 2,661 (84 % of the target sample) responded. Lower educational attainment, lower childhood cognition and lifelong smoking independently predicted lower likelihood of both overall response and CRF cooperation. At 53 years, not owning one's home and not being married predicted lower likelihood of overall response whereas manual social class and obesity predicted lower likelihood of CRF cooperation. Providing for collection of biomedical data in the home and use of assessment instruments and modes to retain study members with lower education attainment, lower cognition and poorer health behaviours should be priorities for helping reduce attrition amongst vulnerable ageing study members.

Kawasaki's disease: An unusual presentation

Atypical presentations of Kawasaki's disease have been described in the form of intestinal pseudo-obstruction, tonsillitis, hemorrhagic serous effusions, thrombocytopenia, and non-fulfillment of all criteria for diagnosis of Kawasaki's disease. However, presentation of Kawasaki's disease with shock and need for ionotropic support have been rarely described. We present a 4-year-old girl with Kawasaki's disease who presented with anasarca, oliguria, shock, and presence of dilated coronary arteries within 5 days of fever and responded to intravenous immunoglobulin (IVIG) and inotropic support.

Reliability of absolute lymphocyte count as a marker to assess the need to initiate antiretroviral therapy in HIV-infected children

BACKGROUND

CD4 counts are a standard laboratory measure of disease progression in HIV-infected children. However, CD4 counting is done by flow cytometry and may not always be possible in every centre treating HIV-infected children in resource-limited countries. Absolute Lymphocyte Count (ALC) can be derived easily by performing a routine white blood cell count. The World Health Organization (WHO) in 2006 had recommended ALC to identify HIV-infected children in need of ART in resource-limited settings, when CD4 cell count is not available.

AIMS

This study aims to assess the reliability of using ALC as a marker for starting antiretroviral therapy (ART) in HIV-infected children in a tertiary hospital setting.

SETTINGS AND DESIGN

Retrospective analysis of 46 HIV-infected children who presented at a pediatric HIV clinic at a tertiary referral centre from 2002-2005.

MATERIALS AND METHODS

Using WHO 2006 guidelines for cutoff values of ALC and 2008 guidelines for CD4% as a comparative standard, a retrospective analysis was done on ART-naοve HIV-infected children who underwent baseline CD4% and ALC, and sensitivity and specificity of ALC was calculated.

STATISTICAL ANALYSIS

Fischer exact two-tailed analysis was used to correlate ALC and CD4 and need for starting ART.

RESULTS

Sensitivity of ALC was 27.6% (72.4% were false negatives), specificity was 70.6%, with positive predictive value of 61.5%. On comparison across all clinical stages of disease, only 13/46 children (28.2%) would have been started on ART according to ALC cutoffs versus 29/46 children (63.04%) using CD4 criteria (P value=0.0015). In children with WHO clinical Stage 1 or 2 of disease, only 1/11 (9.1%) children were identified by ALC as requiring ART as opposed to 6/11 (54.5%) children by CD4% (P=0.0635).

CONCLUSIONS

ALC is an unreliable marker to determine the need for starting ART in HIV-infected children.

Budd-Chiari disease in infancy: three cases

Budd-Chiari syndrome (BCS) is rare in infancy. Three cases are presented. Case 1, an 8-month-old boy, presented with abdominal distension and oliguria. Doppler study of the abdomen showed ascites, hepatomegaly and normal hepatic veins. However, a CT scan demonstrated hepatic vein thrombosis. Case 2, a 5-month-old boy, presented with abdominal distension and diarrhoea. Ultrasound of the abdomen showed hepatic vein thrombosis and hepatomegaly. Case 3, a 7-month-old girl, presented with abdominal distension, diarrhoea and oliguria. Ultrasound of the abdomen showed hepatomegaly and obstructed hepatic veins. None of the cases had fever or jaundice before presentation. Case 1 developed fungal septicaemia and was lost to follow-up. Cases 2 and 3 succumbed to the disease before further intervention.

Preliminary Phytochemical Screening and Antispasmodic Activity of Artemisia macrocephala Jacquem

The current work describes the antispasmodic action of Artemisia macrocephala, which is achieved via blocking of the calcium channels. This explains its traditional use as an antispasmodic.The crude methanolic extract of A. macrocephala was studied for possible relaxant effect(s) on spontaneous rabbits' jejunum preparations. Analytical-grade chemicals were used in the experimental protocols. A. macrocephala gave positive tests for flavonoids, saponins, glycosides, alkaloids, and terpenes. A. macrocephala caused relaxation of spontaneous rabbits' jejunum preparations (n=6) at a dose of 10.0 mg/mL (EC(50) = 6.95 ± 0.20 mg/mL; 95% CI: 6.2 to 7.5). Contractions induced by 80 mM potassium chloride (KCl) were also relaxed by the A. macrocephala at dose of 10.0 mg/mL. Attempting to find an explanation for the possible mode of action, we found that, A. macrocephala at concentration of 1.0 mg/mL produced rightward shift in the calcium chloride curves, with EC(50) value of -1.65 ± 0.02 log [Ca(++)] M vs control with EC(50) value of -2.44 ± 0.043 for calcium chloride curves. At a concentration of 1.0 mg/mL it could produce 52.4% of the control response at log [Ca(++)] M = -1.6. Similarly, verapamil at a concentration of 0.1 μM produced a rightward shift, with EC(50) value of -1.74 ± 0.026 log [Ca(++)] M (95% CI: -1.66 to -1.82; n=6) vs control with EC(50) value of -2.45 ± 0.05 log [Ca(++)] M (95% CI: - 2.23 to -2.91; n=6). The right shift of the EC(50) values is justification for the folkloric use of A. macrocephala as an antispasmodic, suggesting that the possible mode of action is through calcium channel blockade.

Ileal perforation in a child with abdominal tuberculosis

A 6-year-old boy presented with a 1-month history of fever followed by abdominal distension, constipation and bilious vomiting for 2 days. The clinical impression was of intestinal obstruction. At exploratory laparotomy, there was an ileal perforation secondary to tuberculosis. There are many case reports of tubercular ileal perforation in adults but in children it is very rare.

Maternal and biochemical predictors of antepartum stillbirth among nulliparous women in relation to gestational age of fetal death

OBJECTIVE

To determine whether maternal serum levels of alphafetoprotein (alpha-FP) and human chorionic gonadotrophin (hCG) at 15-21 weeks provided clinically useful prediction of stillbirth in first pregnancies.

DESIGN

Retrospective study of record linkage of a regional serum screening laboratory to national registries of pregnancy outcome and perinatal death.

SETTING

West of Scotland, 1992-2001.

POPULATION

A total of 84,769 eligible primigravid women delivering an infant at or beyond 24 weeks of gestation.

METHODS

The risk of stillbirth between 24 and 43 weeks was assessed using the Cox proportional hazards model. Logistic regression models within gestational windows were then used to estimate predicted probability. Screening performance was assessed as area under the receiver operating characteristic (ROC) curve.

MAIN OUTCOME MEASURE

Antepartum stillbirth unrelated to congenital abnormality.

RESULTS

The odds ratio (95% CI) for stillbirth at 24-28 weeks for women in the top 1% were 11.97 (5.34-26.83) for alpha-FP and 5.80 (2.19-15.40) for hCG. The corresponding odds ratios for stillbirth at or after 37 weeks were 2.44 (0.74-8.10) and 0.79 (0.11-5.86), respectively. Adding biochemical to maternal data increased the area under the ROC curve from 0.66 to 0.75 for stillbirth between 24 and 28 weeks but only increased it from 0.64 to 0.65 for stillbirth at term and post-term. Women in the top 5% of predicted risk had a positive likelihood ratio of 7.8 at 24-28 weeks, 3.7 at 29-32 weeks, 5.1 at 33-36 weeks and 3.4 at 37-43 weeks, and the corresponding positive predictive values were 0.97, 0.33, 0.47 and 0.63%, respectively.

CONCLUSIONS

Maternal serum levels of alpha-FP and hCG were statistically associated with stillbirth risk. However, the predictive ability was generally poor except for losses at extreme preterm gestations, where prevention may be difficult and interventions have the potential to cause significant harm.

Seroprevalence of HIV infection in hospitalized paediatric patients at a tertiary care centre in western India

The prevalence of HIV infection in children in India is not known. In this study, a total of 270 children admitted to paediatric wards in Mumbai were screened for HIV infection by enzyme-linked immunosorbent assay (ELISA). Eight patients (2.96%) had a positive HIV ELISA. Of these two patients (25%) were less than 15 months of old and hence HIV infection in them could not be confirmed. The prevalence of HIV was 2.3%. Three out of 11 patients with tuberculosis (27.3%) and four out of 15 patients with nutritional anaemia (26.7%) had HIV infection (P<0.0001 in each case). Vertical transmission was the cause in all children, suggesting that implementation of Prevention of Parent to Child Transmission of HIV (PPTCT) is required to reduce the rate of paediatric HIV infection.

Genes Induced by Reovirus Infection Have a Distinct Modular Cis-Regulatory Architecture

The availability of complete genomes and global gene expression profiling has greatly facilitated analysis of complex genetic regulatory systems. We describe the use of a bioinformatics strategy for analyzing the cis-regulatory design of genes diferentially regulated during viral infection of a target cell. The large-scale transcriptional activity of human embryonic kidney (HEK293) cells to reovirus (serotype 3 Abney) infection was measured using the Affymetrix HU-95Av2 gene array. Comparing the 2000 base pairs of 5' upstream sequence for the most differentially expressed genes revealed highly preserved sequence regions, which we call "modules". Higher-order patterns of modules, called "super-modules", were significantly over-represented in the 5' upstream regions of transcriptionally responsive genes. These supermodules contain binding sites for multiple transcription factors and tend to define the role of genes in processes associated with reovirus infection. The supermodular design encodes a cis-regulatory logic for transducing upstream signaling for the control of expression of genes involved in similar biological processes. In the case of reovirus infection, these processes recapitulate the integrated response of cells including signal transduction, transcriptional regulation, cell cycle control, and apoptosis. The computational strategies described for analyzing gene expression data to discover cis-regulatory features and associating them with pathological processes represents a novel approach to studying the interaction of a pathogen with its target cells.

Symbolic inference of xenobiotic metabolism

We present a new symbolic computational approach to elucidate the biochemical networks of living systems de novo and we apply it to an important biomedical problem: xenobiotic metabolism. A crucial issue in analyzing and modeling a living organism is understanding its biochemical network beyond what is already known. Our objective is to use the available metabolic information in a representational framework that enables the inference of novel biochemical knowledge and whose results can be validated experimentally. We describe a symbolic computational approach consisting of two parts. First, biotransformation rules are inferred from the molecular graphs of compounds in enzyme-catalyzed reactions. Second, these rules are recursively applied to different compounds to generate novel metabolic networks, containing new biotransformations and new metabolites. Using data for 456 generic reactions and 825 generic compounds from KEGG we were able to extract 110 biotransformation rules, which generalize a subset of known biocatalytic functions. We tested our approach by applying these rules to ethanol, a common substance of abuse and to furfuryl alcohol, a xenobiotic organic solvent, which is absent in metabolic databases. In both cases our predictions on the fate of ethanol and furfuryl alcohol are consistent with the literature on the metabolism of these compounds.

PathMiner: predicting metabolic pathways by heuristic search

MOTIVATION

Automated methods for biochemical pathway inference are becoming increasingly important for understanding biological processes in living and synthetic systems. With the availability of data on complete genomes and increasing information about enzyme-catalyzed biochemistry it is becoming feasible to approach this problem computationally. In this paper we present PathMiner, a system for automatic metabolic pathway inference. PathMiner predicts metabolic routes by reasoning over transformations using chemical and biological information.

RESULTS

We build a biochemical state-space using data from known enzyme-catalyzed transformations in Ligand, including, 2917 unique transformations between 3890 different compounds. To predict metabolic pathways we explore this state-space by developing an informed search algorithm. For this purpose we develop a chemically motivated heuristic to guide the search. Since the algorithm does not depend on predefined pathways, it can efficiently identify plausible routes using known biochemical transformations.

Flexural strength of heat-polymerized polymethyl methacrylate denture resin reinforced with glass, aramid, or nylon fibers

STATEMENT OF PROBLEM

Despite the favorable properties of conventional PMMA used as a denture base material, its fracture resistance could be improved.

PURPOSE

This in vitro study was performed to determine whether the flexural strength of a commercially available, heat-polymerized acrylic denture base material could be improved through reinforcement with 3 types of fibers.

MATERIAL AND METHODS

Ten specimens of similar dimensions were prepared for each of the 4 experimental groups: conventional acrylic resin and the same resin reinforced with glass, aramid, or nylon fibers. Flexural strength was evaluated with a 3-point bending test. The results were analyzed with a 1-way analysis of variance.

RESULTS

All reinforced specimens showed better flexural strength than the conventional acrylic resin. Specimens reinforced with glass fibers showed the highest flexural strength, followed by aramid and nylon.

CONCLUSION

Within the limitations of this study, the flexural strength of heat-polymerized PMMA denture resin was improved after reinforcement with glass or aramid fibers. It may be possible to apply these results to distal extension partial denture bases and provisional fixed partial dentures.

Primary pancreatic lymphoma: a case report, literature review, and proposal for nomenclature

Primary neoplasms of the pancreas are most often adenocarcinoma. Non-Hodgkin's lymphoma (NHL) involving the pancreas is less common but well documented; the pancreas as the primary site of NHL is rare. The majority of patients with pancreatic cancer, whether it is adenocarcinoma or lymphoma, present with a mass in the head of the gland. Pancreatic lymphoma is often described as a large homogeneous mass with extra-pancreatic extension, with or without associated lymphadenopathy. Less common presentations are masses in the body or tail, or more rarely diffuse involvement of the pancreas. We present a case of diffuse pancreatic lymphoma with extra-pancreatic dissemination to the spleen and lymph nodes, and review the literature on pancreatic lymphoma. Because the definition of pancreatic lymphoma and primary pancreatic lymphoma varies, we also propose a nomenclature system to make future studies of pancreatic lymphoma more comparable.

Visual management of large scale data mining projects

This paper describes a unified framework for visualizing the preparations for, and results of, hundreds of machine learning experiments. These experiments were designed to improve the accuracy of enzyme functional predictions from sequence, and in many cases were successful. Our system provides graphical user interfaces for defining and exploring training datasets and various representational alternatives, for inspecting the hypotheses induced by various types of learning algorithms, for visualizing the global results, and for inspecting in detail results for specific training sets (functions) and examples (proteins). The visualization tools serve as a navigational aid through a large amount of sequence data and induced knowledge. They provided significant help in understanding both the significance and the underlying biological explanations of our successes and failures. Using these visualizations it was possible to efficiently identify weaknesses of the modular sequence representations and induction algorithms which suggest better learning strategies. The context in which our data mining visualization toolkit was developed was the problem of accurately predicting enzyme function from protein sequence data. Previous work demonstrated that approximately 6% of enzyme protein sequences are likely to be assigned incorrect functions on the basis of sequence similarity alone. In order to test the hypothesis that more detailed sequence analysis using machine learning techniques and modular domain representations could address many of these failures, we designed a series of more than 250 experiments using information-theoretic decision tree induction and naive Bayesian learning on local sequence domain representations of problematic enzyme function classes. In more than half of these cases, our methods were able to perfectly discriminate among various possible functions of similar sequences. We developed and tested our visualization techniques on this application.

Leptospirosis - an under-diagnosed clinical condition

Leptospirosis is a zoonotic disease caused by leptospiral spirochaete. Two cases in children are described presenting with hepatorenal dysfunction.

Identification of divergent functions in homologous proteins by induction over conserved modules

Homologous proteins do not necessarily exhibit identical biochemical function. Despite this fact, local or global sequence similarity is widely used as an indication of functional identity. Of the 1327 Enzyme Commission defined functional classes with more than one annotated example in the sequence databases, similarity scores alone are inadequate in 251 (19%) of the cases. We test the hypothesis that conserved domains, as defined in the ProDom database, can be used to discriminate between alternative functions for homologous proteins in these cases. Using machine learning methods, we were able to induce correct discriminators for more than half of these 251 challenging functional classes. These results show that the combination of modular representations of proteins with sequence similarity improves the ability to infer function from sequence over similarity scores alone.

Visualization based on the Enzyme Commission nomenclature

We developed a tool for visualizing data related to protein function, based on the nomenclature defined by the International Enzyme Commission. The method represents the 1327 specific reaction types and three additional levels of abstract classifications in the nomenclature as an interactive graph. Each node and link in the graph can have associated with it stored or computed data values of various types, each of which can be assigned to any of a set of visualization methods, including color, size, various chart types and text. Visualizations can then be interactively created for single nodes, groups of nodes or the entire graph. This visualization tool is particularly useful for exploring the distribution of quantitative attributes across protein function classes. As a test of this tool, we developed a visualization of data measuring the effectiveness of sequence similarity for prediction of EC class. Using this tool, it was possible to rapidly scan hundreds of functional classes, and to correlate predictability from sequence with other attributes, facilitating the generation of hypotheses about the causes of predictive failure.

Chloroquine resistance in Pakistan and the upsurge of falciparum malaria in Pakistani and Afghan refugee populations

Surveys conducted in Pakistan during the last decade show that falciparum malaria has become resistant to chloroquine in Pakistani and Afghan refugee populations throughout the country. Although RI resistance is common everywhere (with a frequency of 30%-84%), RII is rarer (2%-36%), and RIII resistance has yet to be detected. The national policy is to prescribe chloroquine as first-line treatment of malaria. A repeated in-vivo survey in a sentinel village indicated that prescription of chloroquine can lead to a 15% increase in the frequency of resistance in a single year, and similar trends were observed in other districts. Coinciding with the spread of resistance is a 6-fold increase in the number of falciparum cases recorded nationally between 1982 and 1992 and a parallel, 5-fold increase in the number of cases recorded in the Afghan refugee population. Resistance contributes to this trend in various ways. Firstly, patients with resistant malaria make repeated visits to health centres. In the sentinel village, for example, where resistance was measured at 71%, recrudescent infections inflated by 66% the genuine incidence of new infections recorded at the health centre. Secondly, owing to ineffective treatment, resistant infections are often still patent during the post-transmission season. This may enlarge the 'overwintering' parasite reservoir, leading to a surge of new cases when transmission resumes. Other factors potentially contributing to the upsurge in falciparum include the decrease availability of insecticide for indoor spraying. Despite the problems posed by resistance for case management, the evidence from the vector-control programme among the refugees is that malaria control through well-targeted campaigns of insecticide spraying is still able to reduce the incidence of falciparum malaria to a level that existed before the advent of resistance.

Fertility and contraception in Europe: the case of low fertility in southern Europe

Demographic trends in Europe can be summarized in terms of a declining proportion of its population in the world total, low fertility, and a slow population growth. Fertility in Western Europe was already below the replacement level in 1970-75 and has remained low. Fertility has substantially declined in Eastern and Southern Europe, with Italy and Spain recording one of the lowest levels (1.2 children per woman) in 1994. Some explanations of the dramatic fertility decline in Southern Europe are: (1) The emancipation of women and their increased participation in the labor force; (2) Economic aspects such as costs for child care and education; and (3) The couple's motivation for low fertility because of the expanded choices for travel and leisure and their concerns for improving their standard of living. Social pressures on childbearing outside marriage remain quite strong; cohabitation and extramarital births is Southern Europe are not as prevalent as in other European regions and there is a trend toward delaying the birth of the first child rather than foregoing childbearing.