Semi‐Markov Models with Phase‐Type Sojourn Distributions

Summary Continuous‐time multistate models are widely used for categorical response data, particularly in the modeling of chronic diseases. However, inference is difficult when the process is only observed at discrete time points, with no information about the times or types of events between observation times, unless a Markov assumption is made. This assumption can be limiting as rates of transition between disease states might instead depend on the time since entry into the current state. Such a formulation results in a semi‐Markov model. We show that the computational problems associated with fitting semi‐Markov models to panel‐observed data can be alleviated by considering a class of semi‐Markov models with phase‐type sojourn distributions. This allows methods for hidden Markov models to be applied. In addition, extensions to models where observed states are subject to classification error are given. The methodology is demonstrated on a dataset relating to development of bronchiolitis obliterans syndrome in post‐lung‐transplantation patients.     

Phase‐Field Model of Electrothermal Breakdown in Flexible High‐Temperature Nanocomposites under Extreme Conditions

Polymer‐based dielectrics are attracting increasing attention due to their high‐density energy storage. However, mitigating the heat generation in real capacitors has been a challenge. Here an electrothermal breakdown phase‐field model is developed to fundamentally understand the thermal effects on the dielectric breakdown of polymer‐based dielectrics in real capacitor configurations including the increase in the dielectric loss and the decrease in the breakdown strength. While both enhancing the thermal conductivity and reducing the electrical conductivity of the polymer nanocomposites can reduce the thermal effects, it is found that reducing the electrical conductivity is more effective. This work is expected to not only stimulate attention to the thermal effects in polymer‐based dielectrics but also provide a fundamental guidance to mitigate the heat‐induced deterioration of breakdown strength.     

A Cyclin D1‐Specific Single‐Chain Variable Fragment Antibody that Inhibits HepG2 Cell Growth and Proliferation

Cyclin D1 is a key regulatory factor of the G1 to S transition during cell cycle progression. Aberrant cyclin D gene amplification and abnormal protein expression have been linked to hepatocellular carcinoma (HCC) tumorigenesis. Intrabodies, effective anticancer therapies that specifically inhibit target protein function within all intracellular compartments, may block cyclin D1 function. Here, a single‐chain variable fragment (scFv) antibody against cyclin D1 (ADκ) selected from a human semi‐synthetic phage display scFv library is expressed in Escherichia coli as soluble ADκ. Purified ADκ specifically binds to recombinant and endogenous cyclin D1 with high affinity. To enable blocking of intracellular cyclin D1 activity, an endoplasmic reticulum (ER) retention signal sequence is added to the ADκ sequence to encode anti‐cyclin D1 intrabody ER‐ADκ. Transfection of HepG2 cells with expression vector encoding ER‐ADκ elicited intracellular ER‐ADκ expression leading to cyclin D1 binding, significant G1 phase arrest, and apoptosis that are mechanistically tied to decreased intracellular phosphorylated retinoblastoma protein (Rb) levels. Meanwhile, ER‐ADκ dramatically inhibited subcutaneous human HCC xenografts growth in nude mice in vivo after injection of tumors with expression vector encoding ER‐ADκ. These results demonstrate the potential of intrabody‐based cyclin D1 targeting therapy as a promising treatment for HCC.     

Microglial Depletion Causes Region‐Specific Changes to Developmental Neuronal Cell Death in the Mouse Brain

Developmental neuronal cell death has been characterized as a cell autonomous “suicide” program, but recent findings suggest that microglia play an active role in determining the survival of developing neurons. Results have been contradictory, however, with some studies concluding that microglia promote cell death, while others report that microglia are neuroprotective. Here, we depleted microglia throughout the newborn mouse brain using intracerebroventricular injections of clodronate liposomes, and examined effects on naturally occurring cell death across multiple brain areas. Microglial density varied significantly by brain region, and clodronate liposome treatment at birth reduced the number of microglia in all regions examined. The effect of microglia reduction on cell death, however, varied by region: the number of dying cells was reduced in the medial septum and medial amygdala in clodronate treated animals, but was increased in the oriens layer of the hippocampus, and unchanged in several other brain regions. In most brain regions, the average size of microglia was greater in microglia‐depleted than in control animals, suggesting that the remaining microglia compensate to some extent for a reduction in microglial number. The hippocampal oriens was exceptional in this regard, in that microglial size was reduced following treatment with clodronate. Microglia produce cytokines which mediate many of their effects, and we found higher expression of inflammatory cytokines in the hippocampus than in the septum, independent of clodronate treatment. Thus, microglial depletion has opposite effects on cell death in different brain regions of the newborn brain, which may be related to regional heterogeneity in microglia.     

Synthesis of Novel Diselenide‐Linked Porphyrin Dimers under Phase‐Transfer Catalysis Condition and Their Interactions with DNA

Novel diselenide‐linked porphyrin dimers were synthesized under phase‐transfer catalysis conditions. The targeted compounds were characterized by ¹H‐NMR, high‐resolution mass spectrometry, UV/VIS and fluorescence spectroscopies, redox‐potential measurements, and elemental analysis. The interaction of the title compounds with DNA was studied using UV/VIS, fluorescence, and circular dichroism (CD) spectroscopies. The relative rates of singlet‐oxygen production from the diselenide‐linked porphyrin dimers upon photoirradiation were also measured.     

Phase‐sensitive fluorescence detector for parathyroid glands during thyroidectomy: A preliminary report

Despite advances in medical technology, the parathyroid glands are still damaged during thyroid surgery. Our previous studies exploring methods for locating the parathyroid glands using autofluorescence have limitations, such as turning off the surgical light or requiring additional matching between the autofluorescence image and real‐surgical field‐of‐view. We developed a probe‐type parathyroid autofluorescence detector using a phase‐sensitive process and optical filtering to overcome these limitations. A preliminary clinical trial was performed on eight parathyroid glands in four patients. The normalized mean signal of the normal parathyroid glands was 332% stronger than that of the thyroid, and 384%, 459% and 286% stronger than the signal of the muscle, trachea and fat, respectively. Additionally, the device also detected fluorescence from indocyanine green.     

Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity,Low Intra‐Specific Genetic Variation,and the Rare Occurrence of Inter‐Specific Hybrids in the Wild

Foliose Ulva spp. have become increasingly important worldwide for their environmental and financial impacts. A large number of such Ulva species have rapid reproduction and proliferation habits, which explains why they are responsible for Ulva blooms, known as “green tides”, having dramatic negative effects on coastal ecosystems, but also making them attractive for aquaculture applications. Despite the increasing interest in the genus Ulva, particularly on the larger foliose species for aquaculture, their inter‐ and intra‐specific genetic diversity is still poorly described. We compared the cytoplasmic genome (chloroplast and mitochondrion) of 110 strains of large distromatic foliose Ulva from Ireland, Brittany (France), the Netherlands and Portugal. We found six different species, with high levels of inter‐specific genetic diversity, despite highly similar or overlapping morphologies. Genetic variation was as high as 82 SNPs/kb between Ulva pseudorotundata and U. laetevirens, indicating considerable genetic diversity. On the other hand, intra‐specific genetic diversity was relatively low, with only 36 variant sites (0.03 SNPs/kb) in the mitochondrial genome of the 29 Ulva rigida individuals found in this study, despite different geographical origins. The use of next‐generation sequencing allowed for the detection of a single inter‐species hybrid between two genetically closely related species, U. laetevirens, and U. rigida, among the 110 strains analyzed in this study. Altogether, this study represents an important advance in our understanding of Ulva biology and provides genetic information for genomic selection of large foliose strains in aquaculture.     

Quantitation and Visualization of Ultraviolet‐Induced DNA Damage Using Specific Antibodies: Application to Pigment Cell Biology

The major types of DNA damage induced by sunlight in the skin are DNA photoproducts, such as cyclobutane pyrimidine dimers (CPDs), (6‐4)photoproducts (6‐4PPs) and Dewar isomers of 6‐4PPs. A sensitive method for quantitating and visualizing each type of DNA photoproduct induced by biologically relevant doses of ultraviolet (UV) or sunlight is essential to characterize DNA photoproducts and their biological effects. We have established monoclonal antibodies specific for CPDs, 6‐4PPs or Dewar isomers. Those antibodies allow one to quantitate photoproducts in DNA purified from cultured cells or from the skin epidermis using an enzyme‐linked immunosorbent assay. One can also use those specific antibodies with in situ laser cytometry to visualize and measure DNA photoproducts in cultured cells or in the skin, using indirect immunofluorescence and a laser‐scanning confocal microscope. This latter method allows us to reconstruct three‐dimensional images of nuclei containing DNA photoproducts and to simultaneously examine DNA photoproducts and histology in multilayered epidermis. Using those techniques, one can determine the induction and repair of these three distinct types of DNA photoproducts in cultured cells and in the skin exposed to sublethal or suberythematous doses of UV or solar simulated radiation. As examples of the utility of these techniques and antibodies, we describe the DNA repair kinetics following irradiation of human cell nuclei and the photoprotective effect of melanin against DNA photoproducts in cultured pigmented cells and in human epidermis.     

Cell memory‐based therapy

Current cell therapies, despite all of the progress in this field, still faces major ethical, technical and regulatory hurdles. Because these issues possibly stem from the current, restricted, stereotypical view of cell ultrastructure and function, we must think radically about the nature of the cell. In this regard, the author's theory of the cell memory disc offers ‘memory‐based therapy’, which, with the help of immune system rejuvenation, nervous system control and microparticle‐based biodrugs, may have substantial therapeutic potential. In addition to its potential value in the study and prevention of premature cell aging, age‐related diseases and cell death, memory therapy may improve the treatment of diseases that are currently limited by genetic disorders, risk of tumour formation and the availability and immunocompatibility of tissue transplants.     

Characterization of the Site‐Specific Acid‐Base Equilibria of 3‐Nitrotyrosine

The complete macro‐ and microequilibrium analyses of 3‐nitrotyrosine, a biomarker of oxidative stress damage, are presented for the first time. The protonation macroconstants were determined by ¹H‐NMR‐pH titration, while microconstants were elucidated by a combination of deductive and NMR methods, in which properties of the methyl ester derivative as an auxiliary compound were also studied. Combination of the NMR‐pH characterization of the title and auxiliary compounds and the pair‐interactivity parameters of 3‐iodotyrosine provided the sufficient system to evaluate all the microconstants. NMR‐pH profiles, macroscopic and microscopic protonation schemes, and species‐specific distribution diagrams are included. The phenolate basicity of 3‐nitrotyrosine is 500 times below that of tyrosine, and it is even lower than that of 3‐iodotyrosine. This phenomenon can be explained by the stronger electron withdrawing and the negative mesomeric effect of the nitro group. Based on our results, 89 % of the phenolic OH groups are deprotonated in 3‐NT molecules at the pH of the blood plasma.     

Specific DNA G‐quadruplexes bind to ethanolamines

A significant number of G‐quadruplex‐forming sequences have been revealed in human genome by bioinformatic searches, implying that G‐quadruplexes may be involved in important biological processes and may be new chemotherapeutic targets. Therefore, it is important to discover the potential interactions of G‐quadruplexes with other molecules or groups. Here we describe a class of G‐quadruplexes, which can bind to ethanolamine groups that widely exist in biomolecules and drug molecules. The specific interaction of these G‐quadruplexes with ethanolamine groups was identified by high performance affinity chromatography (HPAC) using immobilized ethanolamine and diethanolamine as stationary phase reagents. The circular dichroism (CD) spectra and native polyacrylamide gel electrophoresis (PAGE) show that these ethanolamine binding quadruplexes adopt an intramolecularly parallel structure. The relationship of ethanolamine binding and G‐quadruplexe structure provides new clues for the G‐quadruplex‐related studies as well as for the molecular designs of therapeutic reagents. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 874–883, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Risk‐Group‐Specific Dose Finding Based on an Average Toxicity Score

Summary We propose a Bayesian dose‐finding design that accounts for two important factors, the severity of toxicity and heterogeneity in patients' susceptibility to toxicity. We consider toxicity outcomes with various levels of severity and define appropriate scores for these severity levels. We then use a multinomial‐likelihood function and a Dirichlet prior to model the probabilities of these toxicity scores at each dose, and characterize the overall toxicity using an average toxicity score (ATS) parameter. To address the issue of heterogeneity in patients' susceptibility to toxicity, we categorize patients into different risk groups based on their susceptibility. A Bayesian isotonic transformation is applied to induce an order‐restricted posterior inference on the ATS. We demonstrate the performance of the proposed dose‐finding design using simulations based on a clinical trial in multiple myeloma.     

Child‐Specific Thoracic Gas Volume Prediction Equations for Air‐Displacement Plethysmography

Objective: To develop child‐specific thoracic gas volume (TGV) prediction equations for use in air‐displacement plethysmography in 6‐ to 17‐year‐old children. Research Methods and Procedures: Study 1 developed TGV prediction equations using anthropometric variables after completing a measured TGV and air‐displacement plethysmography test in 224 healthy boys and girls (11.2 ± 3.2 years, 45.3 ± 18.7 kg, 149.9 ± 18.5 cm). Study 2 cross‐validated the prediction equations in a separate cohort of 62 healthy boys and girls (11.2 ± 3.4 years, 44.2 ± 15.3 kg, 149.4 ± 19.3 cm). Results: In Study 1 (development of TGV prediction equations), the quadratic relationship using height as the independent variable and the measured TGV as the dependent variable yielded the highest adjusted R² and the lowest SE of estimate in both genders, thus producing the following prediction equations: TGV = 0.00056 × H² ? 0.12422 × H + 8.15194 (boys) and TGV = 0.00044 × H² ? 0.09220 × H + 6.00305 (girls). In Study 2 (cross‐validation), no significant difference between the predicted and measured TGVs (?0.018 ± 0.377 liters) was observed. The regression between the measured TGV and the predicted TGV yielded a slope and intercept that did not significantly differ from the line of identity. Prediction accuracy was good as indicated by a high R² (0.862) and low SE of estimate (0.369 liters). Discussion: The new child‐specific TGV prediction equations accurately, precisely, and without bias estimated the actual TGV of 6‐ to 17‐year‐old children.     

A Stand‐Alone Si‐Based Porous Photoelectrochemical Cell

Wireless photoelectrochemical (PEC) devices promise easy device fabrication as well as reduced losses. Here, the design and fabrication of a stand‐alone ion exchange material‐embedded, Si membrane‐based, photoelectrochemical cell architecture with micron‐sized pores is shown, to overcome the i) pH gradient formation due to long‐distance ion transport, ii) product crossover, and iii) parasitic light absorption by application of a patterned catalyst. The membrane‐embedded PEC cell with micropores utilizes a triple Si junction cell as the light absorber, and Pt and IrO_x as electrocatalysts for the hydrogen evolution reactions and oxygen evolution reactions, respectively. The solar‐to‐hydrogen efficiency of 7% at steady‐state operation, as compared to an unpatterned η_PV of 10.8%, is mainly attributed to absorption losses by the incorporation of the micropores and catalyst microdots. The introduction of the Nafion ion exchange material ensures an intrinsically safe PEC cell, by reducing the total gas crossover to <0.1%, while without a cation exchange membrane, a crossover of >6% is observed. Only in a pure electrolyte of 1 m H₂SO₄, a pH gradient‐free system is observed thus completely avoiding the build‐up of a counteracting potential.