Extraction of Pharmacokinetic Evidence of Drug–Drug Interactions from the Literature

Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases. Though DDI is investigated in domains ranging in scale from intracellular biochemistry to human populations, literature mining has not been used to extract specific types of experimental evidence, which are reported differently for distinct experimental goals. We focus on pharmacokinetic evidence for DDI, essential for identifying causal mechanisms of putative interactions and as input for further pharmacological and pharmacoepidemiology investigations. We used manually curated corpora of PubMed abstracts and annotated sentences to evaluate the efficacy of literature mining on two tasks: first, identifying PubMed abstracts containing pharmacokinetic evidence of DDIs; second, extracting sentences containing such evidence from abstracts. We implemented a text mining pipeline and evaluated it using several linear classifiers and a variety of feature transforms. The most important textual features in the abstract and sentence classification tasks were analyzed. We also investigated the performance benefits of using features derived from PubMed metadata fields, various publicly available named entity recognizers, and pharmacokinetic dictionaries. Several classifiers performed very well in distinguishing relevant and irrelevant abstracts (reaching F1≈0.93, MCC≈0.74, iAUC≈0.99) and sentences (F1≈0.76, MCC≈0.65, iAUC≈0.83). We found that word bigram features were important for achieving optimal classifier performance and that features derived from Medical Subject Headings (MeSH) terms significantly improved abstract classification. We also found that some drug-related named entity recognition tools and dictionaries led to slight but significant improvements, especially in classification of evidence sentences. Based on our thorough analysis of classifiers and feature transforms and the high classification performance achieved, we demonstrate that literature mining can aid DDI discovery by supporting automatic extraction of specific types of experimental evidence.     

Host–Parasite Interactions and the Evolution of Gene Expression

Interactions between hosts and parasites provide an ongoing source of selection that promotes the evolution of a variety of features in the interacting species. Here, we use a genetically explicit mathematical model to explore how patterns of gene expression evolve at genetic loci responsible for host resistance and parasite infection. Our results reveal the striking yet intuitive conclusion that gene expression should evolve along very different trajectories in the two interacting species. Specifically, host resistance loci should frequently evolve to co-express alleles, whereas parasite infection loci should evolve to express only a single allele. This result arises because hosts that co-express resistance alleles are able to recognize and clear a greater diversity of parasite genotypes. By the same token, parasites that co-express antigen or elicitor alleles are more likely to be recognized and cleared by the host, and this favours the expression of only a single allele. Our model provides testable predictions that can help interpret accumulating data on expression levels for genes relevant to host−parasite interactions.     

Does Poor Quality Schooling and/or Teacher Quality Hurt Black South African Students Enrolling for a Degree at the University of KwaZulu-Natal?

AbstractWealthy schools appoint better qualified teachers, less wealthy schools under qualified teachers. Added to this mix is a powerful teacher’s union whose policies attempt to entrench the job security of teachers in the less wealthy schools irrespective of whether they can teach their subjects or not. Can one isolate these effects from that of other socio-demographic factors that may also be affecting the performance of students when they enrol for a degree at the University of KwaZulu-Natal (UKZN)? An outcome variable that subtracts the number of courses that have been failed from the number of courses that have been passed, dividing this by the total number of years that they have spent studying for a particular degree will be used as a response variable for this paper.ObjectivesThe system of secondary education in South Africa is highly polarized. On the one hand, we have a group of mainly Black African students, forming about 80% of the total student population, that come from a vastly under-resourced rural or township based community. On the other hand, we have a group of predominantly White and Indian students who are able to attend a far better resourced set of private schools. Added to this mix, we have 240,000 of South Africa’s total number of 390,000 primary and secondary school teachers who belong to a powerful teacher’s union which enjoys a strong political alliance with the ruling party in South Africa. With most of their union members teaching in the less wealthy schools in South Africa, `school background’ now includes a politically motivated component that focuses on teacher self–interest rather than the education of the child. What sort of effect does school background have on the performance of students when they enter an institution of higher learning? More importantly, can one isolate the effect of school background from that of other possibly confounding factors such as gender, financial aid and the receipt of some form of residence based accommodation that will also impact on their performance while at university?MethodA total of 6,183 students enrolling for a degree at the University of KwaZulu-Natal (UKZN) over the period 2008 to 2012 were used a dataset for this study. Permission to use this dataset was given by the Teaching and Learning Office at UKZN. The database that was used for this study was obtained from the Division of Management Information (DMI) office at UKZN. The percentage based marks that students have managed to record for Mathematics, English, Biology and Accounting in their school leaving exams together with some other important but observable socio-economic factors were included in a regression model to determine how students will perform at UKZN. Socio-economic variables relating to gender, race and whether they have receivd some form of financial aid or residence based accommodation while studying at university were also included as predictor variables in our regression based model structure.

Results and Conclusions

An interaction effect associated with being a Black African student who has been privileged enough to attend a quintile five school was found to be significant. A main effect associated with being able to attend a more privileged quintile 5 school however was found to be nonsignificant even after an adjustment has been made for gender, race, the receipt of some form of financial aid and residence based accommodation. Given that UKZN already has a number of bridging programs in place that target students who have come from a less privileged background, for university based policymakers, this result may help to justify the targeted selection of Black African students from the less privileged schools that is taking place. Because some of the disparity in matric performance that we are observing may also be associated with teacher competency and the protective influence of a powerful teacher’s union, this paper may also help to highlight some of the economic costs related with having under-prepared students. “A mind is a terrible thing to waste”–United Negro College Fund.     

Predicting the structure and vibrational frequencies of ethylene using harmonic and anharmonic approaches at the Kohn–Sham complete basis set limit

In this work, regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn–Sham complete basis set (KS CBS) limit are demonstrated for the first time. The performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with two Pople basis sets (6-311++G** and 6-311++G(3df,2pd)), the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n?=?0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X?=?D, T, Q, 5, 6) was tested.The BLYP-calculated harmonic frequencies were found to be markedly closer than the B3LYP-calculated harmonic frequencies to the experimentally derived values, while the calculated anharmonic frequencies consistently underestimated the observed wavenumbers. The different basis set families gave very similar estimated values for the CBS parameters. The anharmonic frequencies calculated with B3LYP/aug-pc-3 were consistently significantly higher than those obtained with the pc-3 basis set; applying the aug-pcseg-n basis set family alleviated this problem. Utilization of B3LYP/aug-pcseg-n basis sets instead of B3LYP/aug-cc-pVXZ, which is computationally less expensive, is suggested for medium-sized molecules. Harmonic BLYP/pc-2 calculations produced fairly accurate ethylene frequencies.

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Graphical Abstract In this study, the performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n?=?0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X?=?D, T, Q, 5, and 6) was tested. For the first time, we demonstrated regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn–Sham complete basis set (KS CBS) limit

     

Comparison of the Nucleotide Sequence at the 5′ End of RNAs from Nine Aphthoviruses, Including Representatives of the Seven Serotypes

The sequence of about 70 nucleotides at the 5' end of the RNAs of nine different aphthoviruses (foot-and-mouth disease viruses), including representatives of the seven serotypes of the virus, has been determined by partial enzyme digestion of (32)P-end-labeled S fragment-that part of the RNA lying to the 5' side of the poly(C) tract and including the 5' end of the molecule. The S fragments were prepared from polyadenylated virus-specific RNA extracted from infected cells by digestion with RNase H in the presence of oligo(dG)(12-18). The first 27 nucleotides from the 5' end were highly conserved in all the RNAs. This region was followed by a more variable region of about 15 nucleotides, showing some length and sequence heterogeneity and including potential but probably nonutilized initiation codons. In agreement with previous homology studies, the sequencing results showed that the European serotypes A, O, and C form a group distinct from the SAT serotypes and that the Asia 1 serotype is closely related to the European group. The lengths of the S fragments of two different RNAs were confirmed as containing 360 to 400 nucleotides by gel electrophoresis with reference to nucleotide markers of known size.     

Do Strategies to Improve Quality of Maternal and Child Health Care in Lower and Middle Income Countries Lead to Improved Outcomes? A Review of the Evidence

Objectives

Efforts to scale-up maternal and child health services in lower and middle income countries will fail if services delivered are not of good quality. Although there is evidence of strategies to increase the quality of health services, less is known about the way these strategies affect health system goals and outcomes. We conducted a systematic review of the literature to examine this relationship.

Methods

We undertook a search of MEDLINE, SCOPUS and CINAHL databases, limiting the results to studies including strategies specifically aimed at improving quality that also reported a measure of quality and at least one indicator related to health system outcomes. Variation in study methodologies prevented further quantitative analysis; instead we present a narrative review of the evidence.

Findings

Methodologically, the quality of evidence was poor, and dominated by studies of individual facilities. Studies relied heavily on service utilisation as a measure of strategy success, which did not always correspond to improved quality. The majority of studies targeted the competency of staff and adequacy of facilities. No strategies addressed distribution systems, public-private partnership or equity. Key themes identified were the conflict between perceptions of patients and clinical measures of quality and the need for holistic approaches to health system interventions.

Conclusion

Existing evidence linking quality improvement strategies to improved MNCH outcomes is extremely limited. Future research would benefit from the inclusion of more appropriate indicators and additional focus on non-facility determinants of health service quality such as health policy, supply distribution, community acceptability and equity of care.     

Formation of Multilayers at the Interface of Oil-in-Water Emulsion via Interactions between Lactoferrin and β-Lactoglobulin

The interactions between negatively charged β-lactoglobulin and the positively charged lactoferrin at the droplet surface to form a multi-protein surface layer were examined. Addition of lactoferrin to the aqueous phase of emulsions formed with β-lactoglobulin at pH 7.0 caused an increase in the ζ-potential of emulsion droplets, and the ζ-potential became positive as the concentration of added lactoferrin was higher than 1% in the system. It is found that lactoferrin binds to adsorbed β-lactoglobulin at droplet surface probably via electrostatic interactions. The amount of lactoferrin at interface increased with increasing the concentration of added lactoferrin, but it decreased with a decrease in the pH. No lactoferrin was observed at interface at pH 3 and 4. By contrast, when β-lactoglobulin was added in the emulsions formed with lactoferrin at pH 7.0, the ζ-potential of emulsions changed from positive to negative as the concentration of added β-lactoglobulin increased. The amount of β-lactoglobulin at surface increased correspondingly with increasing the concentration of added β-lactoglobulin. However, in this case, β-lactoglobulin remained bound at interface even at pH 3 and 4 where both lactoferrin and β-lactoglobulin are positively charged. The association of lactoferrin or β-lactoglobulin with the surface proteins that have oppositely charge is probably mainly through electrostatic interactions between the two proteins. It appears that alternative layers of these proteins could be created at the droplet surface.     

Un-Separate and Still Unequal? Three Books about American Education and Race at the End of the Liberal Century

Multicultural Education, Transformative Knowledge, and Action: Historical and Contemporary Perspectives. James Banks, ed. New York: Teachers College Press, 1996. 352 pp.
Other People's Children: Cultural Conflict in the Classroom. Lisa Delpit. New York: The New Press, 1995. 206 pp.
Beyond Desegregation: The Politics of Quality in African American Schooling. Mwalimu J. Shujaa, ed. Thousand Oaks, CA: Corwin Press, 1996. 268 pp.     

Synthesis and Activity of Oligonucleotides Containing a Biologically Active Nucleoside at the 2′End

Abstract

The antiviral activity of (E)-5-(2-bromovinyl)-2′-deoxyuridine (BVdUrd), acyclovir and other antiherpetic nucleosides depends on a selective phosphorylation by the herpesvirus-induced thymidine kinase in the infected cells. Viruses not encoding a specific thymidine kinase (TK) activity are resistant to the action of these nucleoside analogues. The nucleoside monophosphates are as such poorly taken up by the cells. In order to circumvent the necessity of intracellular phosphorylation, we synthesized four core oligonucleotides bearing a biological active nucleoside at the 2′end. It was hypothesized that these core oligonucleotides, like core 2–5A itself, would be taken up within the cell and that, following intracellular 2′-5′ phosphodiesterase cleavage, the 5′-monophosphate of the active product would be formed. In these circumstances, activity against TK- strains could be expected.     

Predicting Neuropathy and Reactions in Leprosy at Diagnosis and Before Incident Events—Results from the INFIR Cohort Study

Background

Leprosy is a disease of skin and peripheral nerves. The process of nerve injury occurs gradually through the course of the disease as well as acutely in association with reactions. The INFIR (ILEP Nerve Function Impairment and Reactions) Cohort was established to identify clinically relevant neurological and immunological predictors for nerve injury and reactions.

Methodology/Principal Findings

The study, in two centres in India, recruited 188 new, previously untreated patients with multi-bacillary leprosy who had no recent nerve damage. These patients underwent a series of novel blood tests and nerve function testing including motor and sensory nerve conduction, warm and cold detection thresholds, vibrometry, dynamometry, monofilament sensory testing and voluntary muscle testing at diagnosis and at monthly follow up for the first year and every second month for the second year. During the 2 year follow up a total of 74 incident events were detected. Sub-clinical changes to nerve function at diagnosis and during follow-up predicted these new nerve events. Serological assays at baseline and immediately before an event were not predictive; however, change in TNF alpha before an event was a statistically significant predictor of that event.

Conclusions/Significance

These findings increase our understanding of the processes of nerve damage in leprosy showing that nerve function impairment is more widespread than previously appreciated. Any nerve involvement, including sub-clinical changes, is predictive of further nerve function impairment. These new factors could be used to identify patients at high risk of developing impairment and disability.     

End of the Trend? A 12-year Study of Age at Menarche

A 12-year study of menarchial age in all girls entering the University College of Swansea (1959-70) suggests that the downward trend in age at menarche has ceased in Britain. The turning point appears to have occurred in girls born about 1946.