Next-generation vaccines for tropical infectious diseases

Tropical infectious diseases inflict an unacceptable burden of disease on humans living in developing countries. Although anti-pathogenic drugs have been widely used, they carry a constant threat of selecting for resistance. Vaccines offer a promising means by which to enhance the global control of tropical infectious diseases; however, these have been difficult to develop, mostly because of the complex nature of the pathogen lifecycles. Here, we present recently developed vaccine candidates for five tropical infectious diseases in the form of a catalog that have either entered clinical trials or have been licensed for use. We deliberate on recently licensed dengue vaccines, provide evidence why combination vaccination could have a synergistic impact on schistosomiasis, critically appraise the value of typhoid conjugate vaccines, and discuss the potential of vaccines in the efforts to eliminate vivax malaria and hookworms.

M. tuberculosis Infection Attributable to Exposure in Social Networks of Tuberculosis Cases in an Urban African Community

Background

The persistence of tuberculosis today and its global disparity send a powerful message that effective tuberculosis control must respond to its regional epidemiology. Active case finding through contact investigation is a standard protocol used for tuberculosis control, but its effectiveness has not been established, especially in endemic areas.

Methods

To quantify the potential effectiveness of contact investigation in Kampala, Uganda, we used a cross-sectional design to evaluate the social networks of 123 tuberculosis index cases and 124 controls without tuberculosis.

Results

Tuberculous infection was present in 515 of 989 tuberculosis case contacts (52.1%) and 396 of 1026 control contacts (38.6%; adjusted prevalence ratio, 1.4; 95% CI, 1.3-1.6). The proportion of infected participants with known exposure within the social network of the tuberculosis case was 35%. The population-attributable fraction was 11.1% for any known exposure, with 7.3% attributable to household exposure and 3.4% attributable to extrahousehold exposure.

Conclusions

This low population-attributable fraction indicates that contact tracing in the social networks of index cases will have only a modest effect in reducing tuberculous infection in a community. New approaches to community-level active case finding are needed.

Incidence and risk factors for travellers' diarrhoea among short-term international adult travellers from high-income countries: a systematic review with meta-analysis of cohort studies

BACKGROUND

Travellers' Diarrhoea (TD) continues to be the most common travel-related medical event in international travellers. Updated incidence and risk factor data will improve pre-travel medical advice for travellers from high-income countries (HIC), providing an opportunity for disease prevention, and appropriate disease management.

METHODS

A systematic search for cohort studies of TD incidence published between 1 January 1997 and 2 March 2023 was performed using Ovid Medline, SCOPUS, and Google Scholar databases. Study quality was assessed with a modified Newcastle-Ottawa scale (NOS). We extracted incidence data for adults travelling less than 100 days from HIC and available risk factor data. The overall random-effects pooled incidence and the corresponding 95% confidence intervals (95% CI) were estimated. Heterogeneity was assessed using the I2 statistic, tau and the 95% prediction intervals. Subgroup analyses were conducted to identify sources of heterogeneity. Risk factor studies were reviewed qualitatively and described.

RESULTS

Ten studies were included in the meta-analysis, containing 8478 participants. Two of the studies measured as high quality and eight as good quality as assessed by the modified NOS. The TD incidence was 36.1% (95% CI 24-41%; I2 94%), with a prediction interval ranging from 20.3% to 55.8%. The pooled incidence of mild, moderate, and severe TD was 23.6%, 8.1% and 2.9%, respectively. Subgroup analysis showed that the incidence increased with increasing average data collection period. Risk factors for TD in travellers from HIC identified include younger age, longer travel periods, low and middle-income destinations, travelling for tourism, backpacking travel styles and pre-travel health status.

CONCLUSION

It is estimated that between 20 to 56% of international travellers can expect to develop TD in travel of under 100 days. While most cases are mild, approximately 3% of all travellers will experience a disease that prevents usual activities or requires medical attention.

Patient satisfaction among persons living with HIV/AIDS and receiving antiretroviral therapy in urban Uganda: A factor analysis

INTRODUCTION

Patient satisfaction is an important predictor of health outcomes among patients in HIV/AIDS treatment and care, yet it is rarely measured in routine clinic settings in most of Africa. The aims of our study were to evaluate the internal validity and reliability of the Consumer Assessment of Healthcare Providers and Systems instrument for measuring satisfaction, assess the general level of patient satisfaction, and identify the factors associated with the level of satisfaction among patients receiving antiretroviral therapy in Uganda.

MATERIALS AND METHODS

We conducted a cross-sectional study of 475 HIV/AIDS-infected patients from July to August 2015 in Kampala, Uganda. Eligible participants were 18 years or older, consented to the study and receiving antiretroviral therapy and outpatient care at the selected public health clinic. This study used a modified version of the validated Consumer Assessment of Healthcare Providers and Systems (CAHPS) instrument to assess the level of satisfaction among HIV/AIDS patients receiving outpatient care. We collected data on socio-demographics, clinical variables and 18-items adapted from the CAHPS instrument rating satisfaction with aspects of health services. We conducted an exploratory factor analysis to assess the internal validity of the 18 items and multiple linear regression analysis of factors associated with patient satisfaction with care.

RESULTS

Majority of the respondents were females (76.8%), and the mean age was 37 years (SD = 10). The modified CAHPS instrument had high internal consistency (Cronbach's α = 0.94) for measuring satisfaction with HIV/AIDS care. Female sex (p = 0.016), perceived providers' technical and interpersonal skills (p = 0.022), emotional health (p = 0.032), and quality of reception services (p<0.001) were significantly associated with satisfaction in this urban HIV/AIDS public clinic.

CONCLUSION

The reliability of the CAHPS instrument was high for measuring satisfaction. Providers' technical and interpersonal skills, and the quality of reception services are key to achieving patient satisfaction. Health system interventions to address the gaps identified will enhance the quality of patient-centered HIV/AIDS care in the Ugandan setting.

Travel-Related Monkeypox Outbreaks in the Era of COVID-19 Pandemic: Are We Prepared?

Several neglected infectious pathogens, such as the monkeypox virus (MPXV), have re-emerged in the last few decades, becoming a global health burden. Despite the incipient vaccine against MPXV infection, the global incidence of travel-related outbreaks continues to rise. About 472 confirmed cases have been reported in 27 countries as of 31 May 2022, the largest recorded number of cases outside Africa since the disease was discovered in the early 1970s.

A Comprehensive Study of the Epidemiology of Haematological Malignancies in North Queensland

BACKGROUND

There is an absence of clinically relevant epidemiological data in regional Australia pertaining to haematological malignancies.

AIM

To determine the incidence and geographical variation of haematological malignancies in North Queensland using a clinically appropriate disease classification.

METHODS

Retrospective, observational study of individual patient data records of all adults diagnosed with a haematological malignancy between 2005-2014 and residing within The Townsville Hospital Haematology catchment region. We report descriptive summaries, incidence rates and incidence-rate ratios of haematologic malignancies by geographic regions.

RESULTS

1581 haematological malignancies (69% lymphoid, 31% myeloid) were diagnosed over the 10-year study period. Descriptive data is presented for 58 major subtypes as per the WHO diagnostic classification of tumours of haematopoietic and lymphoid tissues. The overall median age at diagnosis was 66 years with a male predominance (60%). We demonstrate a temporal increase in the incidence of haematologic malignancies over the study period. We observed geographical variations in the age-standardised incidence rates per 100,000 ranging from 0.5 to 233.5. Our data suggests an increased incidence rate ratio for haematological malignancies in some postcodes within the Mackay area compared to other regions.

CONCLUSION

This study successfully reports on the incidence of haematological malignancies in regional Queensland using a clinically meaningful diagnostic classification system and identifies potential geographic hotspots. We advocate for such contemporary, comprehensive, and clinically meaningful epidemiological data reporting of blood cancer diagnoses in wider Australia. Such an approach will have significant implications toward developing appropriate data-driven management strategies and public health responses for haematological malignancies. This article is protected by copyright. All rights reserved.

Excess Risk of Tuberculous Infection among Extra-Household Contacts of Tuberculosis Cases in an African City

RATIONALE

Although households of tuberculosis cases represent a setting for intense transmission of M. tuberculosis, household exposure accounts for less than 20% of transmission within a community.

OBJECTIVES

To estimate excess risk of M. tuberculosis infection among household and extra-household contacts of index cases.

METHODS

We performed a cross-sectional study in Kampala, Uganda, to delineate social networks of tuberculosis cases and matched controls without tuberculosis. We estimated the age-stratified prevalence difference of tuberculous infection between case and control networks, partitioned as household and extra-household contacts.

RESULTS

We enrolled 123 index cases, 124 index controls, and 2415 first-degree network contacts. The prevalence of infection was highest among household contacts of cases (61.5%), lowest among household contacts of controls (25.2%), and intermediary among extra-household tuberculosis contacts (44.9%) and extra-household control contacts (41.2%). The age-adjusted prevalence difference between extra-household contacts of cases and their controls was 5.4%. The prevalence of infection was similar among the majority of extra-household case contacts and corresponding controls (47%).

CONCLUSIONS

Most first-degree social network members of tuberculosis cases do not have adequate contact with the index case to experience additional risk for infection but appear instead to acquire infection through unrecognized exposures with infectious cases in the community.

Transmission Dynamics in Tuberculosis Patients with Human Immunodeficiency Virus: A Systematic Review and Meta-Analysis of 32 Observational Studies

BACKGROUND

There are large knowledge gaps on the transmission dynamics of Mycobacterium tuberculosis in settings where both tuberculosis and HIV are endemic. We aimed to assess the infectiousness of tuberculosis patients coinfected with HIV.

METHODS

We systematically searched for studies of contacts of both HIV-positive and negative tuberculosis index cases. Our primary outcome was Mycobacterium tuberculosis infection in contacts. Data on sputum smear and lung cavitation status of index cases was extracted from each study to assess effect modification. Secondary outcomes included prevalent tuberculosis and HIV in contacts of HIV-positive and negative index cases.

RESULTS

Of 5,255 original citations identified, 32 studies met inclusion criteria including 25 studies investigating M. tuberculosis infection (Nparticipants=36,893), 13 on tuberculosis (Nparticipants=18,853), and 12 on HIV positivity (Nparticipants=18,424). Risk of M. tuberculosis infection was lower in contacts of HIV-positive index cases (Odds Ratio [OR], 0.67, 95% CI, 0.58-0.77) but was heterogeneous (I2=75.1%). Two factors modified this relationship: the lung cavitary status of the index case and immunosuppression (measured through CD4 counts or HIV or AIDS diagnoses) among index patients living with HIV. Rates of HIV were consistently higher in contacts of coinfected index cases (OR, 4.9, 95% CI, 3.0-8.0). This was modified by whether the study was in sub-Saharan Africa (OR, 2.8, 1.6-4.9) or in another global region (OR, 9.8, 5.9-16.3).

CONCLUSIONS

Tuberculosis patients coinfected with HIV are less infectious than HIV-uninfected cases when they have severe immunosuppression or paucibacillary disease. Contacts of coinfected index cases are almost five times more likely to also have HIV.

Performance of the QuantiFERON®-TB Gold In-Tube assay in tuberculin skin test converters: a prospective cohort study

OBJECTIVE

To investigate diagnostic agreement of the QuantiFERON®-TB Gold In-Tube (QFT-GIT) test in adult tuberculin skin test (TST) converters in a high tuberculosis (TB) burden setting.

SETTING AND DESIGN

We performed a case-cohort study from 2014 to 2016 in Uganda among residents who were not infected with Mycobacterium tuberculosis. Participants were followed up for 1 year, when they were retested to determine TST conversion. All TST converters and a random sample of participants from baseline were offered QFT-GIT testing.

RESULTS

Of 368 enrolled participants, 61 (17%) converted their TST by 1 year. Among 61 converters, 42 were tested using QFT-GIT, 64% of whom were QFT-GIT-positive. Of 307 participants with a persistent negative TST, 48 were tested using QFT-GIT, 83% of whom were QFT-negative. Overall concordance of TST and QFT-GIT was moderate (κ = 0.48, 95%CI 0.30-0.66). Converters with a conversion of 15 mm had a higher proportion of concordant QFT-GIT results (79%) than converters with increments of 10-14.9 mm (52%).

CONCLUSION

Concordance between TST and QFT-GIT was moderate among TST converters in this urban African population. These findings call for improved tests that more accurately measure conversion to tuberculous infection.

Blood cytokine, chemokine and growth factor profiling in a cohort of pregnant women from tropical countries

The immune status of women changes during and after pregnancy, differs between blood compartments at delivery and is affected by environmental factors particularly in tropical areas endemic for multiple infections. We quantified the plasma concentration of a set of thirty-one T_H1, T_H2, T_H17 and regulatory cytokines, pro-inflammatory and anti-inflammatory cytokines and chemokines, and growth factors (altogether biomarkers), in a cohort of 540 pregnant women from five malaria-endemic tropical countries. Samples were collected at recruitment (first antenatal visit), delivery (periphery, cord and placenta) and postpartum, allowing a longitudinal analysis. We found the lowest concentration of biomarkers at recruitment and the highest at postpartum, with few exceptions. Among them, IL-6, HGF and TGF-β had the highest levels at delivery, and even higher concentrations in the placenta compared to peripheral blood. Placental concentrations were generally higher than peripheral, except for eotaxin that was lower. We also compared plasma biomarker concentrations between the tropical cohort and a control group from Spain at delivery, presenting overall higher biomarker levels the tropical cohort, particularly pro-inflammatory cytokines and growth factors. Only IL-6 presented lower levels in the tropical group. Moreover, a principal component analysis of biomarker concentrations at delivery showed that women from Spain grouped more homogenously, and that IL-6 and IL-8 clustered together in the tropical cohort but not in the Spanish one. Plasma cytokine concentrations correlated with Plasmodium antibody levels at postpartum but not during pregnancy. This basal profiling of immune mediators over gestation and in different compartments at delivery is important to subsequently understand response to infections and clinical outcomes in mothers and infants in tropical areas.

P-value calibration in multiple hypotheses testing

As p-values are the most common measures of evidence against a hypothesis, their calibration with respect to null hypothesis conditional probability is important in order to match frequentist unconditional inference with the Bayesian ones. The Selke, Bayarri and Berger calibration is one of the most popular attempts to obtain such a calibration. This relies on the theoretical sampling null distribution of p-values, which is the well-known Uniform(0,1), but arising only for specific sampling models. We generalize this calibration by considering a sampling null distribution estimated from the data. It is possible to obtain such an empirical null distribution, for instance, in the context of multiple testing in which many p-values come from the null model. Such a context is purely instrumental for the purposes of p-value calibration, and multiple testing still needs to be considered with appropriate techniques. The new calibration proposed here still remains a simple analytic formula like the original one under the Uniform(0,1) and basically provides a stronger interpretation framework for the widely used p-value. Copyright © 2017 John Wiley & Sons, Ltd.

Ethnic Disparities of Perceived Safety Climate Among Construction Workers in Georgia, 2015

BACKGROUND

Safety climate involves worker perception about the relative importance where they work and safety climate and has been shown to be a reliable predictor of safety-related outcomes.

METHODS

The primary objective of this study is to investigate ethnic differences in perceived safety climate among construction workers. Surveys (n = 179) that included a 10-item safety climate scale were administered in Athens, Georgia (GA), at local construction sites and home improvement stores during June-August, 2015.

RESULTS

The majority of respondents were carpenters or roofers (39%), followed by laborers (22%), painters and dry wall workers (14%), other skilled trades (14%), and supervisors (11%); 32% were Hispanic. Hispanic ethnicity (p < 0.0001), drinking two or more alcoholic beverages per day (p < 0.0001), working for a company that does not provide health insurance (p = 0.0022), and working for a company with fewer than ten employees (p < 0.0001) were significantly associated with lower perceived safety climate scores.

CONCLUSION

The lower perceived safety climate scores among Hispanic workers indicate that the perception of the importance of safety on the job site is lower among Hispanics construction workers than non-Hispanics construction workers.

Reverse ethnopharmacology and drug discovery

ETHNOPHARMACOLOGICAL RELEVANCE

Ethnopharmacological investigations of traditional medicines have made significant contributions to plant-derived drugs, as well as the advancement of pharmacology. Drug discovery from medicinal flora is more complex than generally acknowledged because plants are applied for different therapeutic indications within and across cultures. Therefore we propose the concept of "reverse ethnopharmacology" and compare biomedical uses of plant taxa with their ethnomedicinal and popular uses and test the effect of these on the probability of finding biomedical and specifically anticancer drugs.

MATERIALS AND METHODS

For this analysis we use data on taxonomy and medical indications of plant derived biomedical drugs, clinical trial, and preclinical trial drug candidates published by Zhu et al. (2011) and compare their therapeutic indications with their ethnomedicinal and popular uses as reported in the NAPRALERT^® database. Specifically, we test for increase or decrease of the probability of finding anticancer drugs based on ethnomedicinal and popular reports with Bayesian logistic regression analyses.

RESULTS

Anticancer therapy resulted as the most frequent biomedicinal indication of the therapeutics derived from the 225 drug producing higher plant taxa and showed an association with ethnomedicinal and popular uses in women's medicine, which was also the most important popular use-category. Popular remedies for dysmenorrhoea, and uses as emmenagogues, abortifacients and contraceptives showed a positive effect on the probability of finding anticancer drugs. Another positive effect on the probability of discovering anticancer therapeutics was estimated for popular herbal drugs associated with the therapy of viral and bacterial infections, while the highest effect was found for popular remedies used to treat cancer symptoms. However, this latter effect seems to be influenced by the feedback loop and divulgence of biomedical knowledge on the popular level.

CONCLUSION

We introduce the concept of reverse ethnopharmacology and show that it is possible to estimate the probability of finding biomedical drugs based on ethnomedicinal uses. The detected associations confirm the classical ethnopharmacological approach where a popular remedy for disease category X results in a biomedical drug for disease category X but does also point out the existence of cross-over relationships where popular remedies for disease category X result in biomedical therapeutics for disease category Y (Zhu et al., 2011).

Naturally Acquired Binding-Inhibitory Antibodies to Plasmodium vivax Duffy Binding Protein in Pregnant Women Are Associated with Higher Birth Weight in a Multicenter Study

A vaccine to eliminate malaria would need a multi-stage and multi-species composition to achieve robust protection, but the lack of knowledge about antigen targets and mechanisms of protection precludes the development of fully efficacious malaria vaccines, especially for Plasmodium vivax (Pv). Pregnant women constitute a risk population who would greatly benefit from a vaccine preventing the adverse events of Plasmodium infection during gestation. We hypothesized that functional immune responses against putative targets of naturally acquired immunity to malaria and vaccine candidates will be associated with protection against malaria infection and/or poor outcomes during pregnancy. We measured (i) IgG responses to a large panel of Pv and Plasmodium falciparum (Pf) antigens, (ii) the capacity of anti-Pv ligand Duffy binding protein (PvDBP) antibodies to inhibit binding to Duffy antigen, and (iii) cellular immune responses to two Pv antigens, in a subset of 1,056 pregnant women from Brazil, Colombia, Guatemala, India, and Papua New Guinea (PNG). There were significant intraspecies and interspecies correlations for most antibody responses (e.g., PfMSP1₁₉ versus PfAMA1, Spearman’s rho = 0.81). Women from PNG and Colombia had the highest levels of IgG overall. Submicroscopic infections seemed sufficient to boost antibody responses in Guatemala but not antigen-specific cellular responses in PNG. Brazil had the highest percentage of Duffy binding inhibition (p-values versus Colombia: 0.040; Guatemala: 0.047; India: 0.003, and PNG: 0.153) despite having low anti-PvDBP IgG levels. Almost all antibodies had a positive association with present infection, and coinfection with the other species increased this association. Anti-PvDBP, anti-PfMSP1, and anti-PfAMA1 IgG levels at recruitment were positively associated with infection at delivery (p-values: 0.010, 0.003, and 0.023, respectively), suggesting that they are markers of malaria exposure. Peripheral blood mononuclear cells from Pv-infected women presented fewer CD8⁺IFN-γ⁺ T cells and secreted more G-CSF and IL-4 independently of the stimulus used in vitro. Functional anti-PvDBP levels at recruitment had a positive association with birth weight (difference per doubling antibody levels: 45 g, p-value: 0.046). Thus, naturally acquired binding-inhibitory antibodies to PvDBP might confer protection against poor outcomes of Pv malaria in pregnancy.

Plasmodium vivax VIR Proteins Are Targets of Naturally-Acquired Antibody and T Cell Immune Responses to Malaria in Pregnant Women

P. vivax infection during pregnancy has been associated with poor outcomes such as anemia, low birth weight and congenital malaria, thus representing an important global health problem. However, no vaccine is currently available for its prevention. Vir genes were the first putative virulent factors associated with P. vivax infections, yet very few studies have examined their potential role as targets of immunity. We investigated the immunogenic properties of five VIR proteins and two long synthetic peptides containing conserved VIR sequences (PvLP1 and PvLP2) in the context of the PregVax cohort study including women from five malaria endemic countries: Brazil, Colombia, Guatemala, India and Papua New Guinea (PNG) at different timepoints during and after pregnancy. Antibody responses against all antigens were detected in all populations, with PNG women presenting the highest levels overall. P. vivax infection at sample collection time was positively associated with antibody levels against PvLP1 (fold-increase: 1.60 at recruitment -first antenatal visit-) and PvLP2 (fold-increase: 1.63 at delivery), and P. falciparum co-infection was found to increase those responses (for PvLP1 at recruitment, fold-increase: 2.25). Levels of IgG against two VIR proteins at delivery were associated with higher birth weight (27 g increase per duplicating antibody levels, p<0.05). Peripheral blood mononuclear cells from PNG uninfected pregnant women had significantly higher antigen-specific IFN-γ T_H1 responses (p=0.006) and secreted less pro-inflammatory cytokines TNF and IL-6 after PvLP2 stimulation than P. vivax-infected women (p<0.05). These data demonstrate that VIR antigens induce the natural acquisition of antibody and T cell memory responses that might be important in immunity to P. vivax during pregnancy in very diverse geographical settings.

Naturally-acquired antibody responses to novel recombinant proteins and synthetic peptides based on sequences from P. vivax VIR antigens were evaluated in women from five distinct geographical regions endemic for malaria, during and after pregnancy. Levels of IgG to VIR antigens were indicative of cumulative malaria exposure and increased with current P. vivax infection and P. falciparum co-infection. Antibody data were consistent with levels of malaria endemicity and current prevalence in the diverse geographical areas studied. In addition, the magnitude of IgG response to two VIR antigens at delivery was associated with higher birth weight. Furthermore, T cell responses to VIR antigens were naturally induced and their magnitude varied according to P. vivax infectious status. Peripheral blood mononuclear cells from uninfected pregnant women from a highly endemic area produced higher T_H1 (IFN-γ) and lower pro-inflammatory cytokines (TNF and IL-6) upon stimulation with a long synthetic peptide representing conserved globular domains of VIR antigens than P. vivax-infected women. Data suggest that further investigation on these antigens as potential targets of immunity in naturally-exposed individuals is warranted.

From cumulative cultural transmission to evidence-based medicine: evolution of medicinal plant knowledge in Southern Italy

In Mediterranean cultures written records of medicinal plant use have a long tradition. This written record contributed to building a consensus about what was perceived to be an efficacious pharmacopeia. Passed down through millennia, these scripts have transmitted knowledge about plant uses, with high fidelity, to scholars and laypersons alike. Herbal medicine's importance and the long-standing written record call for a better understanding of the mechanisms influencing the transmission of contemporary medicinal plant knowledge. Here we contextualize herbal medicine within evolutionary medicine and cultural evolution. Cumulative knowledge transmission is approached by estimating the causal effect of two seminal scripts about materia medica written by Dioscorides and Galen, two classical Greco-Roman physicians, on today's medicinal plant use in the Southern Italian regions of Campania, Sardinia, and Sicily. Plant-use combinations are treated as transmissible cultural traits (or “memes”), which in analogy to the biological evolution of genetic traits, are subjected to mutation and selection. Our results suggest that until today ancient scripts have exerted a strong influence on the use of herbal medicine. We conclude that the repeated empirical testing and scientific study of health care claims is guiding and shaping the selection of efficacious treatments and evidence-based herbal medicine.

Comparison of objective Bayes factors for variable selection in parametric regression models for survival analysis

This paper considers the problem of selecting a set of regressors when the response variable is distributed according to a specified parametric model and observations are censored. Under a Bayesian perspective, the most widely used tools are Bayes factors (BFs), which are undefined when improper priors are used. In order to overcome this issue, fractional (FBF) and intrinsic (IBF) BFs have become common tools for model selection. Both depend on the size, Nt , of a minimal training sample (MTS), while the IBF also depends on the specific MTS used. In the case of regression with censored data, the definition of an MTS is problematic because only uncensored data allow to turn the improper prior into a proper posterior and also because full exploration of the space of the MTSs, which includes also censored observations, is needed to avoid bias in model selection. To address this concern, a sequential MTS was proposed, but it has the drawback of an increase of the number of possible MTSs as Nt becomes random. For this reason, we explore the behaviour of the FBF, contextualizing its definition to censored data. We show that these are consistent, providing also the corresponding fractional prior. Finally, a large simulation study and an application to real data are used to compare IBF, FBF and the well-known Bayesian information criterion.

Bioprospecting: evolutionary implications from a post-olmec pharmacopoeia and the relevance of widespread taxa

ETHNOPHARMACOLOGICAL RELEVANCE

"Nothing in biology makes sense except in the light of evolution" The historical legacy and relevance of ethnopharmacology in drug discovery is undisputed. Here we connect the parameters influencing the selection of plant derived medicines by human culture with the concept of evolution.

AIM OF THE STUDY

In the present contribution we compare global data with local data and try to answer the questions, to what extent are the taxonomic clades included in indigenous pharmacopoeias associated with certain ailment groups, and to what extent can ecology and phylogeny, which we consider a proxy for chemical relatedness and convergence, account for the observed bias?

MATERIALS AND METHODS

We use an approximated chi-square test (χ(2)) to check for associations between 12 ethnomedical use-categories and 15 taxonomical clades. With cluster analyses we test for correlations between phylogeny and use-categories. We compare the 67 drug-productive families identified by Zhu et al. with the medicinal flora of the Popoluca and the APG database and compare our results with the phylogenetic target classes evidenced by Zhu et al. Furthermore, we compare the medicinal flora of the Popoluca with the world's weeds (cf. Holm et al.) and discuss our results in relation to anthropological rationales for plant selection.

RESULTS

The null-hypothesis "species from the 15 taxonomic clades are selected proportionally to their share in the treatment of the twelve organ- and symptom-defined use-categories" is rejected. The cluster dendrogram for the clades shows that the use patterns are to a certain extent associated with Angiosperm phylogeny. With the occurrence of 53 families the 67 drug-productive families are overrepresented in the regional flora of the Popoluca. The importance of these families in terms of their share is even more pronounced with the medicinal flora holding around 70% of all individual Popoluca informant responses.

CONCLUSIONS

The overall phylogenetic use pattern is influenced by both the inherent pharmacological properties, which depend on phylogeny, biogeography, ecology and ultimately allelopathy, and on culture-specific perception of organoleptic properties. The comparison of the 67 drug-productive Viridiplantae families with the ethnopharmacopoeia of the Popoluca and the APG database, shows that "traditional" pharmacopoeias and plant-derived drugs are obtained from widespread and species-rich taxa. This is not a function of family size alone. We put forward the theory that as a function of evolution, widespread taxa contain a broader range of accumulated ecological information and response encoded in their genes relative to locally occurring taxa. This information is expressed through the synthesis of allelochemicals with a wide ecological radius, showing broad-spectrum biota-specific interactions, including the targeting of proteins of mammals and primates.

IMP-3 expression in keratoacanthomas and squamous cell carcinomas of the skin: an immunohistochemical study

The protein insulin-like growth factor II mRNA binding protein 3 (IMP-3) is an important factor for cell migration and adhesion in malignancies. Recent studies have shown a remarkable overexpression of IMP-3 in different human malignant neoplasms and also revealed it as an important prognostic marker in some tumor entities. The purpose of this study is to compare IMP-3 immunostaining in cutaneous squamous cell tumors and determine whether IMP-3 can aid in the differential diagnosis of these lesions. To our knowledge, IMP-3 expression has not been investigated in skin squamous cell proliferations thus far. Immunohi-stochemical staining for IMP-3 was performed on slides organized by samples from 67 patients, 34 with keratoacanthoma (KA) and 33 with primary cutaneous squamous cell carcinoma (SCC) (16 invasive and 17 in situ). Seventyfour percent of KAs (25/34) were negative for IMP-3 staining, while 57% of SCCs (19/33) were positive for IMP-3 staining. The percentage of IMP-3 positive cells increased significantly in the invasive SCC group (P=0.0111), and particularly in the SCC in situ group (P=0.0021) with respect to the KA group. IMP-3 intensity staining was significantly higher in invasive SCCs (P=0.0213), and particularly in SCCs in situ (P=0.008) with respect to KA. Our data show that IMP-3 expression is different in keratoacanthoma with respect to squamous cell carcinoma. IMP-3 assessment and staining pattern, together with a careful histological study, can be useful in the differential diagnosis between KA e SCC.

Bayesian analysis of a disability model for lung cancer survival

Bayesian reasoning, survival analysis and multi-state models are used to assess survival times for Stage IV non-small-cell lung cancer patients and the evolution of the disease over time. Bayesian estimation is done using minimum informative priors for the Weibull regression survival model, leading to an automatic inferential procedure. Markov chain Monte Carlo methods have been used for approximating posterior distributions and the Bayesian information criterion has been considered for covariate selection. In particular, the posterior distribution of the transition probabilities, resulting from the multi-state model, constitutes a very interesting tool which could be useful to help oncologists and patients make efficient and effective decisions.

An imprecise probability approach for the detection of over and underused taxonomic groups with the Campania (Italy) and the Sierra Popoluca (Mexico) medicinal flora

AIM OF THE STUDY

We use the IDM model to test for over- and underuse of plant taxa as source for medicine. In contrast to the Bayes approach, which only considers the uncertainty around the data of medicinal plant surveys, the IDM model also takes the uncertainty around the inventory of the flora into account, which is used for the comparison between medicinal and local floras.

MATERIALS AND METHODS

Statistical analysis of the medicinal flora of Campania (Italy) and of the medicinal flora used by the Sierra Popoluca (Mexico) was performed with the IDM model and the Bayes approach. For Campania 423 medicinal plants and 2237 vascular plant species and for the Sierra Popoluca 605 medicinal plants and 2317 vascular plant species were considered.

RESULTS

The IDM model (s=4) indicates for Campania the Lamiaceae and Rosaceae as overused, and the Caryophyllaceae, Poaceae, and Orchidaceae as underused. Among the Popoluca the Asteraceae and Piperaceae turn out to be overused, while Cyperaceae, Poaceae, and Orchidaceae are underused. In comparison with the Bayes approach, the IDM approach indicates fewer families as over- or underused.

CONCLUSIONS

The IDM model leads to more conservative results compared to the Bayes approach. Only relatively few taxa are indicated as over- or underused. The larger the families (n(j)'s) are, the more similar do the results of the two approaches turn out. In contrast to the Bayes approach, small taxa with most or all species used as medicine (e.g., n(j)=2, x(j)=2) tend not to be indicated as overused with the IDM model.

Unscaled Bayes factors for multiple hypothesis testing in microarray experiments

Multiple hypothesis testing collects a series of techniques usually based on p-values as a summary of the available evidence from many statistical tests. In hypothesis testing, under a Bayesian perspective, the evidence for a specified hypothesis against an alternative, conditionally on data, is given by the Bayes factor. In this study, we approach multiple hypothesis testing based on both Bayes factors and p-values, regarding multiple hypothesis testing as a multiple model selection problem. To obtain the Bayes factors we assume default priors that are typically improper. In this case, the Bayes factor is usually undetermined due to the ratio of prior pseudo-constants. We show that ignoring prior pseudo-constants leads to unscaled Bayes factor which do not invalidate the inferential procedure in multiple hypothesis testing, because they are used within a comparative scheme. In fact, using partial information from the p-values, we are able to approximate the sampling null distribution of the unscaled Bayes factor and use it within Efron's multiple testing procedure. The simulation study suggests that under normal sampling model and even with small sample sizes, our approach provides false positive and false negative proportions that are less than other common multiple hypothesis testing approaches based only on p-values. The proposed procedure is illustrated in two simulation studies, and the advantages of its use are showed in the analysis of two microarray experiments.

Quantitative methods in ethnobotany and ethnopharmacology: considering the overall flora--hypothesis testing for over- and underused plant families with the Bayesian approach

ETHNOPHARMACOLOGICAL RELEVANCE

We introduce and explain the advantages of the Bayesian approach and exemplify the method with an analysis of the medicinal flora of Campania, Italy. The Bayesian approach is a new method, which allows to compare medicinal floras with the overall flora of a given area and to investigate over- and underused plant families. In contrast to previously used methods (regression analysis and binomial method) it considers the inherent uncertainty around the analyzed data.

MATERIALS AND METHODS

The medicinal flora with 423 species was compiled based on nine studies on local medicinal plant use in Campania. The total flora comprises 2237 species belonging to 128 families. Statistical analysis was performed with the Bayesian method and the binomial method. An approximated χ(2)-test was used to analyze the relationship between use categories and higher taxonomic groups.

RESULTS

Among the larger plant families we find the Lamiaceae, Rosaceae, and Malvaceae, to be overused in the local medicine of Campania and the Orchidaceae, Caryophyllaceae, Poaceae, and Fabaceae to be underused compared to the overall flora. Furthermore, do specific medicinal uses tend to be correlated with taxonomic plant groups. For example, are the Monocots heavily used for urological complaints.

CONCLUSIONS

Testing for over- and underused taxonomic groups of a flora with the Bayesian method is easy to adopt and can readily be calculated in excel spreadsheets using the excel function Inverse beta (INV.BETA). In contrast to the binomial method the presented method is also suitable for small datasets. With larger datasets the two methods tend to converge. However, results are generally more conservative with the Bayesian method pointing out fewer families as over- or underused.

A strategy analysis for genetic association studies with known inbreeding

Background

Association studies consist in identifying the genetic variants which are related to a specific disease through the use of statistical multiple hypothesis testing or segregation analysis in pedigrees. This type of studies has been very successful in the case of Mendelian monogenic disorders while it has been less successful in identifying genetic variants related to complex diseases where the insurgence depends on the interactions between different genes and the environment. The current technology allows to genotype more than a million of markers and this number has been rapidly increasing in the last years with the imputation based on templates sets and whole genome sequencing. This type of data introduces a great amount of noise in the statistical analysis and usually requires a great number of samples. Current methods seldom take into account gene-gene and gene-environment interactions which are fundamental especially in complex diseases. In this paper we propose to use a non-parametric additive model to detect the genetic variants related to diseases which accounts for interactions of unknown order. Although this is not new to the current literature, we show that in an isolated population, where the most related subjects share also most of their genetic code, the use of additive models may be improved if the available genealogical tree is taken into account. Specifically, we form a sample of cases and controls with the highest inbreeding by means of the Hungarian method, and estimate the set of genes/environmental variables, associated with the disease, by means of Random Forest.

Results

We have evidence, from statistical theory, simulations and two applications, that we build a suitable procedure to eliminate stratification between cases and controls and that it also has enough precision in identifying genetic variants responsible for a disease. This procedure has been successfully used for the beta-thalassemia, which is a well known Mendelian disease, and also to the common asthma where we have identified candidate genes that underlie to the susceptibility of the asthma. Some of such candidate genes have been also found related to common asthma in the current literature.

Conclusions

The data analysis approach, based on selecting the most related cases and controls along with the Random Forest model, is a powerful tool for detecting genetic variants associated to a disease in isolated populations. Moreover, this method provides also a prediction model that has accuracy in estimating the unknown disease status and that can be generally used to build kit tests for a wide class of Mendelian diseases.

The usefulness of c-Kit in the immunohistochemical assessment of melanocytic lesions

C-Kit (CD117), the receptor for the stem cell factor, a growth factor for melanocyte migration and proliferation, has shown differential immunostaining in various benign and malignant melanocytic lesions. The purpose of this study is to compare c-Kit immunostaining in benign nevi and in primary and metastatic malignant melanomas, to determine whether c-Kit can aid in the differential diagnosis of these lesions. c-Kit immunostaining was performed in 60 cases of pigmented lesions, including 39 benign nevi (5 blue nevi, 5 intradermal nevi, 3 junctional nevi, 15 cases of primary compound nevus, 11 cases of Spitz nevus), 18 cases of primary malignant melanoma and 3 cases of metastatic melanoma. The vast majority of nevi and melanomas examined in this study were positive for c-Kit, with minimal differences between benign and malignant lesions. C-Kit cytoplasmatic immunoreactivity in the intraepidermal proliferating nevus cells, was detected in benign pigmented lesions as well as in malignant melanoma, increasing with the age of patients (P=0.007) in both groups. The patient's age at presentation appeared to be the variable able to cluster benign and malignant pigmented lesions. The percentage of c-Kit positive intraepidermal nevus cells was better associated with age despite other variables (P=0.014). The intensity and percentage of c-Kit positivity in the proliferating nevus cells in the dermis was significantly increased in malignant melanocytic lesions (P=0.015 and P=0.008) compared to benign lesions (compound melanocytic nevi, Spitz nevi, intradermal nevi, blue nevi). Immunostaning for c-Kit in metastatic melanomas was negative. Interestingly in two cases of melanoma occurring on a pre-existent nevus, the melanoma tumor cells showed strong cytoplasmatic and membranous positivity for c-kit, in contrast with the absence of any immunoreactivity in pre-existent intradermal nevus cells. C-Kit does not appear to be a strong immunohistochemical marker for distinguishing melanoma from melanocytic nevi, if we consider c-Kit expression in intraepidermal proliferating cells. The c-Kit expression in proliferating melanocytes in the dermis could help in the differential diagnosis between a superficial spreading melanoma (with dermis invasion) and a compound nevus or an intradermal nevus. Finally, c-Kit could be a good diagnostic tool for distinguishing benign compound nevi from malignant melanocytic lesions with dermis invasion and to differentiate metastatic melanoma from primary melanoma.

The role of genomic and antigenomic HCV-RNA strands as predictive factors of response to pegylated interferon plus ribavirin therapy

BACKGROUND

Hepatitis C virus replicates by the synthesis of an antigenomic HCV-RNA. As the end point of anti-viral therapy is to decrease viral replication, the amount of antigenomic HCV-RNA could influence the response.

AIM

To study if amounts of genomic and antigenomic HCV-RNA in the baseline liver biopsy are predictive factors of response to anti-viral therapy.

METHODS

Eighty-eight patients with chronic HCV infection (anti-HIV-negative) treated with pegyltaed-interferon-alpha2b plus ribavirin for 12 months were included. Intrahepatic genomic and antigenomic HCV-RNA concentrations were determined by real-time polymerase chain reaction and percentage of infected hepatocytes by in situ hybridization.

RESULTS

Of the 88 patients, 31% were responders while 69% were not. Median of antigenomic HCV-RNA in liver of responders and non-responders was 120 000 copies/microg RNA (range: 10,000-775,000) vs. 150,000 copies/microg RNA (range: 100-3,200,000; P = 0.38). Median of genomic HCV-RNA in liver of responders was 1,250,000 copies/microg RNA (range: 5000-9,000,000) and in non-responders 3,180,000 copies/microg RNA (range: 4600-18,000,000; P = 0.0191). Predictive factors of response in the logistic regression were: intrahepatic amount of genomic HCV-RNA, percentage of infected hepatocytes and previous therapy.

CONCLUSION

Response to 12 months of therapy with pegylated interferon-alpha2b plus ribavirin depends on the amount of genomic HCV-RNA in the pre-treatment liver biopsy.

[Partial breast irradiation: high dose rate peroperative brachytherapy technique using the MammoSite]

In the conservative management of breast cancer, radiation therapy delivering 45 to 50 Gy to the whole breast, in 4.5 to 5 weeks, followed by a booster dose of 10 to 20 Gy is the standard of care. Based on the numerous studies which have reported that the local recurrences occurs within and surrounding the primary tumor site and in order to decrease the treatment duration and its morbidity, partial breast irradiation using several techniques has been developed. Partial irradiation may be considered as an alternative local adjuvant treatment for selected patients with favorable prognostic factors. Using external beam radiation therapy, the 3D-conformal technique is appropriate to deliver the whole dose to a limited volume. In UK, an intraoperative technique using a miniature beam of low energy of x-ray (50 Kv) has been developed (Targit). Milan's team have developed an intraoperative electrons beam radiotherapy using a dedicated linear accelerator in the operative room. In USA and Canada the MammoSite has been advised for clinical use in per-operative brachytherapy of the breast. These two last techniques are currently compared in phase III randomised studies to the standard whole breast irradiation followed by a tumour bed booster dose. In this review we will focus on the MammoSite technique and will describe the per-operative implantation procedure, radiological controls ad dosimetric aspects.

[Impact of medical counselling on giving up smoking during pregnancy]

OBJECTIVE

Women s tobacco consumption has increased in Spain in recent years, especially among women of reproductive age. This study aims to evaluate the impact of medical counselling integrated into pre-natal care on tobacco consumption during pregnancy and the period after delivery.

DESIGN

Quasi-experimental intervention study.Setting. Hospital del Mar, Barcelona.

PATIENTS

219 patients who attended the Hospital del Mar for delivery during 1996 (control group) and 169 patients seen during their pregnancies at the same hospital in 1997 (intervention group).

INTERVENTIONS

The control group patients had received normal care. The pregnant women in the intervention group received systematic structured counselling on giving up smoking, backed up by a special brochure composed for this purpose.

MEASUREMENTS AND RESULTS

The intervention and control groups showed no statistically significant differences either in their social or demographic variables or in their tobacco consumption. In both groups the evolution of their smoking during pregnancy was determined during their pre-natal visits and six months after delivery through a telephone interview. 44 of the women in the control group (20.1%) gave up smoking before their first pre-natal visit, and 11 (5%) gave up during pregnancy. In the intervention group 26 (17.7%) had given up spontaneously and 16 (10.9%) gave up during pregnancy. Of those who gave up completely during pregnancy, 36.4% of women in the control group and 64.3% in the intervention group remained abstinent at six months (P=.002).

CONCLUSIONS

Counselling at pre-natal check-ups to give up smoking lightly increases the number of women who give up and reduces significantly the number of post-delivery backsliders.

[Validity of the declared tobacco consumption in pregnancy]

OBJECTIVES

To analyse the relationship between the stated consumption of tobacco by pregnant women who say they smoked before pregnancy and the levels of cotinine in their urine at the start and end of pregnancy.

DESIGN

Observational, longitudinal study.

PARTICIPANTS

During 1997.

STUDY GROUP

147 pregnant women at their first pre-natal visit to outclinics of the Hospital del Mar.

CONTROL GROUP

50 non-smoker pregnant women monitored during their pregnancy.

MEASUREMENTS AND MAIN RESULTS

The numbers of cigarettes per day that they said they smoked on their first monitoring visit to our centre and at the last attendance before giving birth were recorded. Cotinine levels in the urine samples taken on these visits were measured. Mean cotinine in pregnant women who said they had given up smoking was higher than in non-smokers. There was a statistically significant linear relationship between the number of cigarettes stated and cotinine levels at the first and last pregnancy monitoring visits, as well as between the variation in the number of cigarettes and cotinine levels at these two visits. The negative predictive value of what they said about their tobacco habit was 82.9%.

CONCLUSIONS

There was a certain under-declaration by pregnant smokers, although their statements of consumption and cotinine levels correlated closely. The under-declaration did not increase despite reiterated advice to stop smoking, which means that, despite its limitations, it could be a useful indicator for evaluating the effect of interventions aimed at stopping women smoking during pregnancy.

[Use of a multileaf collimator for the production of intensity-modulated beams]

In external radiotherapy, the use of intensity modulated fields has been proposed for tissue and non-homogeneity compensation or for the generation of conformal dose distributions. Multileaf collimators can be employed dynamically for the modulation of the X-ray field in two dimensions. Efficient dynamic collimation became possible due to advances in computer and linear accelerator technology. It presents a number of advantages over conventional methods such as the use of compensators. We have developed a program which calculates, from a given intensity distribution, the motion of the MLC leaves as a function of monitor units, and we have applied it on a Varian linear accelerator with a 40 pair multileaf collimator. The analysis of the experimental results demonstrates the feasibility and the potential of the method.

Evaluation of the scatter field for high-energy photon beam attenuators

Based upon sector integration, a method has been developed to evaluate the scatter from attenuating beam modulators at any point in the field for arbitrarily shaped fields and attenuators with variable thickness. The method requires preliminary measurements of narrow and broad beam transmission fractions as a function of filter thickness and field size. The ratio Sp of the contribution from photons scattered by the attenuator to the non-attenuated primary contribution was derived from these measurements. Sp was determined for x-ray beam energies between 4 and 23 MV with brass and lead attenuators. This quantity was found to be practically independent of beam energy for a given field size and material. The variation of Sp as a function of slab thickness for attenuators covering the entire beam showed a maximum for a thickness of approximately one mean free path. This maximum represents about 6.0% of the transmitted primary dose for an extreme case of a very heavily (1.6 cm thick lead slab) attenuated 15 cm x 15 cm field. The 'scatter field', corresponding to the scatter contribution from the attenuator across the field, was calculated for different partial attenuators and wedges. The results show that this component has a limited influence on calculation of dose distribution, but should be taken into account in absolute dosimetry analysis for large fields and thick wedge filters.