Bayesian Estimation of the Time‐Varying Sensitivity of a Diagnostic Test with Application to Mother‐to‐Child Transmission of HIV

Summary We present a Bayesian model to estimate the time‐varying sensitivity of a diagnostic assay when the assay is given repeatedly over time, disease status is changing, and the gold standard is only partially observed. The model relies on parametric assumptions for the distribution of the latent time of disease onset and the time‐varying sensitivity. Additionally, we illustrate the incorporation of historical data for constructing prior distributions. We apply the new methods to data collected in a study of mother‐to‐child transmission of HIV and include a covariate for sensitivity to assess whether two different assays have different sensitivity profiles.     

Prevalence of human T‐lymphotropic virus type 1 carriers among pregnant women in Hokkaido,Japan

As there is a risk of MTCT of HTLV‐1, the HSGP HTLV‐1 MTCT was organized in 2011. To determine how many pregnant women are infected with HTLV‐1 in Hokkaido, which is the northernmost and the second largest island in Japan with a population of 5 467 000 and 39 392 newborns in 2011, the HSGP HTLV‐1 MTCT asked all facilities that may care for pregnant women in Hokkaido in July 2013 to provide information on the number of pregnant women who underwent screening for anti‐HTLV‐1 antibody using particle agglutination or chemiluminescent enzyme immunoassay, and the numbers of those with positive, equivocal, and negative test results in the screening and confirmation tests using western blotting or PCR methods in 2012, respectively. A total of 111 facilities participated in this study and provided information on 33 617 pregnant women who underwent screening in 2012, corresponding to approximately 85% of all pregnant women who gave birth in Hokkaido in 2012. Of 81 candidates for a confirmation test because of positive (n = 77) or equivocal (n = 4) results on screening, 63 (78%) underwent the confirmation test and, finally, 34 (0.1%) and 33 563 (99.8%) women were judged to be HTLV‐1 carriers and non‐carriers, respectively. It was concluded that the prevalence rate of HTLV‐1 carriers was low, one per 1000 pregnant women in Hokkaido. Approximately 40 infants are born yearly to mothers infected with HTLV‐1 in Hokkaido.     

A dynamic analysis of viral load, T lymphocyte subsets and main biochemical indexes before and after prevention of mother to child transmission (PMTCT) in HIV/AIDS

This study aims to investigate changes in viral load, T lymphocyte subsets and other main biochemical indexes of HIV/AIDS in the prevention of mother to child transmission (PMTCT). In this study, 152 pregnant women with HIV/AIDS enrolled into our hospital from January 2013 to June 2015 were chosen as objects. Changes in viral load, T lymphocyte subsets and other main biochemical indexes of HIV/AIDS were tested and compared before and after 3 months of PMTCT and in neonatals one week after birth. The CD4/CD8 examination result, and difference in CD4 before and after prevention (in the newborns after a week) was statistically significant (P < 0.05), and the rest showed no statistical significance. For the dynamic analysis of main biochemical test results: K⁺, Na⁺, Cl^-, BG, OS, BUN, BUN/Cr, UA,TDIL, DBIL, TP, ALB, CK, LDH, HDL, LDL and other indexes before and after prevention attained statistical significances (P < 0.05 or above). The same sample in the three groups was detected by repeated analysis of variance, K⁺, Na⁺, Cl^-, BG, OS, BUN/Cr, UA, DBI L, ALB, CK, LDH, HDL, LDL and other indexes also showing P at less than 0.05 or above, among which K⁺, Cl^-, CK, LDL showed homogeneity of variance, while Na⁺, BG, OS, BUN/Cr, UA, DBIL, ALB, LDH, HDL showed unequal homogeneity of variance. The study suggests that the dynamic analysis of viral load, T lymphocyte subsets and main biochemical indexes before and after PMTCT in HIV/AIDS are important means to evaluate the dose and treatment of antiretroviral drugs. Monitoring of above indexes is helpful to judge and analyze the condition of the maternal body at various stages, so antiviral drug treatment can be adjusted.     

Binding of spermine and ifenprodil to a purified,soluble regulatory domain of the N‐methyl‐d‐aspartate receptor

The binding of spermine and ifenprodil to the amino terminal regulatory (R) domain of the N‐methyl‐D ‐aspartate receptor was studied using purified regulatory domains of the NR1, NR2A and NR2B subunits, termed NR1‐R, NR2A‐R and NR2B‐R. The R domains were over‐expressed in Escherichia coli and purified to near homogeneity. The K_d values for binding of [¹⁴C]spermine to NR1‐R, NR2A‐R and NR2B‐R were 19, 140, and 33 μM, respectively. [³H]Ifenprodil bound to NR1‐R (K_d, 0.18 μM) and NR2B‐R (K_d, 0.21 μM), but not to NR2A‐R at the concentrations tested (0.1–0.8 μM). These K_d values were confirmed by circular dichroism measurements. The K_d values reflected their effective concentrations at intact NR1/NR2A and NR1/NR2B receptors. The results suggest that effects of spermine and ifenprodil on NMDA receptors occur through binding to the regulatory domains of the NR1, NR2A and NR2B subunits. The binding capacity of spermine or ifenprodil to a mixture of NR1‐R and NR2A‐R or NR1‐R and NR2B‐R was additive with that of each individual R domain. Binding of spermine to NR1‐R and NR2B‐R was not inhibited by ifenprodil and vice versa, indicating that the binding sites for spermine and ifenprodil on NR1‐R and NR2B‐R are distinct.     

Structure of HIV‐1 reverse transcriptase/d4TTP complex: Novel DNA cross‐linking site and pH‐dependent conformational changes

Stavudine (d4T, 2′,3′‐didehydro‐2′,3′‐dideoxythymidine) was one of the first chain‐terminating nucleoside analogs used to treat HIV infection. We present the first structure of the active, triphosphate form of d4T (d4TTP) bound to a catalytic complex of HIV‐1 RT/dsDNA template‐primer. We also present a new strategy for disulfide (S–S) chemical cross‐linking between N⁶ of a modified adenine at the second overhang base to I63C in the fingers subdomain of RT. The cross‐link site is upstream of the duplex‐binding region of RT, however, the structure is very similar to published RT structures with cross‐linking to Q258C in the thumb, which suggests that cross‐linking at either site does not appreciably perturb the RT/DNA structures. RT has a catalytic maximum at pH 7.5. We determined the X‐ray structures of the I63C‐RT/dsDNA/d4TTP cross‐linked complexes at pH 7, 7.5, 8, 8.5, 9, and 9.5. We found small (~0.5 Å), pH‐dependent motions of the fingers subdomain that folds in to form the dNTP‐binding pocket. We propose that the pH‐activity profile of RT relates to this motion of the fingers. Due to side effects of neuropathy and lipodystrophy, use of d4T has been stopped in most countries, however, chemical modification of d4T might lead to the development of a new class of nucleoside analogs targeting RNA and DNA polymerases.     

Identifying N‐terminal peptides by a combination of the edman procedures with a bromine isotope tag: Application to the silicateins

Silicateins are proteins found within spicules of siliceous sponges. They are analogs of proteinases cathepsins; they catalyze the transformation of silicic acid esters into biogenic silica (SiO₂·nH₂O), and are believed to take part in the processes of silicification in marine and freshwater sponges. Earlier studies by Kalyuzhnaya et al. revealed that the Baikal Sponge Lubomirskia baicalensis Pallas, 1773 (L. baicalensis) contains a gene 1988 bp long, which hosts four sequences that encode four mRNAs giving rise to silicateins α1, α2, α3 and α4 (SILα1, SILα2, SILα3, SILα4) whose predicted amino acid sequences are similar to those of the predicted sequences of marine sponge silicateins. However, the sequences of mature silicateins of L. baicalensis remained unknown, since their N‐terminal peptides were not identified. We found the sequences of these N‐terminal peptides using a combination of the Edman procedure, which involved reaction with phenylisothiocyanate, treatment with trifluoroacetic acid and trypsinolysis followed by treatment with 4‐bromine‐phenylisothiocyanate performed directly within polyacrylamide gel bands, and subsequent mass spectrometry. The N‐terminal peptides are YAESIDWR (SILα1), YVDSIDWR (SILα2 and α4), and YADSLDWR (SILα3). All mature silicateins of L. baicalensis had a length 217 amino acid residues.     

Sialic acid and sialyl‐lactose glyco‐conjugates: design,synthesis and binding assays to lectins and swine influenza H1N1 virus

The terminal parts of the influenza hemagglutinin (HA) receptors α2,6‐ and α2,3‐sialyllactoses were conjugated to an artificial carrier, named sequential oligopeptide carrier (SOC₄), to formulate human and avian receptor mimics, respectively. SOC₄, formed by the tripeptide unit Lys‐Aib‐Gly, adopts a rigid helicoids‐type conformation, which enables the conjugation of biomolecules to the Lys‐N^εH₂ groups. By doing so, it preserves their initial conformations and functionalities of the epitopes. We report that SOC₄‐glyco‐conjugate bearing two copies of the α2,6‐sialyllactose is specifically recognized by the biotinylated Sambucus nigra (elderberry) bark lectin, which binds preferentially to sialic acid in an α2,6‐linkage. SOC₄‐glyco‐conjugate bearing two copies of the α2,3‐sialyllactose was not recognized by the biotinylated Maackia amurensis lectin, despite its well‐known α2,3‐sialyl bond specificity. However, preliminary immune blot assays showed that H1N1 virus binds to both the SOC₄‐glyco‐conjugates immobilized onto nitrocellulose membrane. It is concluded that Ac‐SOC₄[(Ac)₂,(3′SL‐Aoa)₂]‐NH₂ 5 and Ac‐SOC₄[(Ac)₂,(6′SL‐Aoa)₂]‐NH₂ 6 mimic the HA receptors. These findings could be useful for easy screening of binding and inhibition assays of virus–receptor interactions. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Evaluation of Modeling Approaches to Determine End‐of‐Life Flows Associated with Buildings: A Viennese Case Study on Wood and Contaminants

Dynamic material flow analysis enables the forecasting of secondary raw material potential for waste volumes in future periods, by assessing past, present, and future stocks and flows of materials in the anthroposphere. Analyses of waste streams of buildings stocks are uncertain with respect to data and model structure. Wood construction in Viennese buildings serve as a case study to compare different modeling approaches for determining end‐of‐life (EoL) wood and corresponding contaminant flows (lead, chlorine, and polycyclic aromatic hydrocarbons). A delayed input and a leaching stock modeling approach are used to determine wood stocks and flows from 1950 until 2100. Cross‐checking with independent estimates and sensitivity analyses are used to evaluate the results’ plausibility. In the situation of the given data in the present case study, the delay approach is a better choice for historical observations of EoL wood and for analyses at a substance level. It has some major drawbacks for future predictions at the goods level, though, as the durability of a large number of historical buildings with considerably higher wood content is not reflected in the model. The wood content parameter differs strongly for the building periods and has therefore the highest influence on the results. Based on this knowledge, general recommendations can be derived for analyses on waste flows of buildings at a goods and substance level.