Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM

The HIV-1 epidemic in Europe is primarily sustained by a dynamic topology of sexual interactions among MSM who have individual immune systems and behavior. This epidemiological process shapes the phylogeny of the virus population. Both fields of epidemic modeling and phylogenetics have a long history, however it remains difficult to use phylogenetic data to infer epidemiological parameters such as the structure of the sexual network and the per-act infectiousness. This is because phylogenetic data is necessarily incomplete and ambiguous. Here we show that the cluster-size distribution indeed contains information about epidemiological parameters using detailed numberical experiments. We simulate the HIV epidemic among MSM many times using the Monte Carlo method with all parameter values and their ranges taken from literature. For each simulation and the corresponding set of parameter values we calculate the likelihood of reproducing an observed cluster-size distribution. The result is an estimated likelihood distribution of all parameters from the phylogenetic data, in particular the structure of the sexual network, the per-act infectiousness, and the risk behavior reduction upon diagnosis. These likelihood distributions encode the knowledge provided by the observed cluster-size distrbution, which we quantify using information theory. Our work suggests that the growing body of genetic data of patients can be exploited to understand the underlying epidemiological process.     

Detailed experimental and kinetic modeling study of 3-carene pyrolysis

3-Carene is an important potential biofuel with properties similar to the jet-propellant JP-10. Its thermal decomposition and combustion behavior is to date unknown, which is essential to assess its quality as a fuel. A combined experimental and kinetic modeling study has been conducted to understand the initial decomposition of 3-carene. The pyrolysis of 3-carene was investigated in a jet-stirred quartz reactor at atmospheric pressure, at temperatures varying from 650 to 1050 K, covering the complete conversion range. The decomposition of 3-carene was observed to start around 800 K, and it is almost complete at 970 K. Online gas chromatography shows that primarily aromatics are generated which suggests that 3-carene is not a good fuel candidate. The potential energy surface for the initial decomposition pathways determined by KinBot shows that a hydrogen elimination reaction dominates, giving primarily cara-2,4-diene. Next to this molecular pathway, radical pathways lead to aromatics via ring opening. The kinetic model was automatically generated with Genesys and consists of 2565 species and 9331 reactions. New quantum chemical calculations at the CBS-QB3 level of theory were needed to calculate rate coefficients and thermodynamic properties relevant for the primary decomposition of 3-carene. Both the conversion of 3-carene and the yields of the primary products (ie, benzene and hydrogen gas) are well predicted with this kinetic model. Rate of production analyses shows that the dominant pathways to convert 3-carene are hydrogen elimination reaction and radical chemistry.     

Transmission of HIV in sexual networks in sub-Saharan Africa and Europe

We are reviewing the literature regarding sexual networks and HIV transmission in sub-Saharan Africa and Europe. On Likoma Island in Malawi, a sexual network was reconstructed using a sociometric survey in which individuals named their sexual partners. The sexual network identified one giant component including half of all sexually active individuals. More than 25% of respondents were linked through independent chains of sexual relations. HIV was more common in the sparser regions of the network due to over-representation of groups with higher HIV prevalence. A study from KwaZulu-Natal in South-Africa collected egocentric data about sexual partners and found that new infections in women in a particular area was associated with the number of life-time partners in men. Data about sexual networks and HIV transmission are not reported in Europe. It is, however, found that the annual number of sexual partners follows a scale-free network. Phylogenetic studies that determine genetic relatedness between HIV isolates obtained from infected individuals, found that patients in the early stages of infections explain a high number of new infections. In conclusion, the limited information that is available suggest that sexual networks play a role in spread of HIV. Obtaining more information about sexual networks can be of benefit for modeling studies on HIV transmission and prevention.     

White-light toxicity, resulting from systemically administered 5-aminolevulinic acid, under normal operating conditions

This study has investigated damage to the intraperitoneal organs of the rat after systemic (intraperitoneal and intravenous) administration of low doses of 5-aminolevulinic acid (ALA) and illumination with a standard white-light operating-room (o.r.) lamp. The study has been done within the framework of a larger study in which the possibility of using ALA for localization of small-volume macroscopically nonvisible peritoneal metastasis of ovarian tumors is being investigated. Fluorescence diagnostics are done in addition to the standard staging and localization procedures, either through a laparoscope or during laparotomy. In these circumstances, fluorescence diagnostics involve some risk of photosensitization of critical organs since a broad-band (o.r.) light source is used during the surgical procedures for illumination of the operating area. The drug dose and the time interval between administration of ALA and illumination are varied and normal tissues are examined both macroscopically and microscopically for damage. A relationship is demonstrated between the maximum tolerable dose (MTD) of ALA (defined as the dose that does not cause any tissue damage) and the time interval between administration and illumination. The white light that is used for illumination of the operating area is sufficient to induce damage to the peritoneal organs at relatively low ALA doses. The MDTs for 2, 6 and 16 h intervals are found to be respectively 1, 10 and 100 mg kg⁻¹. The results are similar for both intraperitoneal and intravenous administration.     

Symmetry calculation for molecules and transition states

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three‐dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label‐stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules. © 2014 Wiley Periodicals, Inc.     

Podand and macrocyclic amine receptors with urea functionalities for potentiometric detection of organic acids in HPLC

Ten synthetic receptors were tested in potentiometric coated wire electrodes. The electrodes were used as sensing devices in classical reversed phase HPLC determinations of dicarboxylic acids present in food materials. All receptors contained amine functionalities. Four of them were podand urea derivatives. The other six were macrocyclic polyamines with lipophilic groups. Three of them had urea functionalities in their side-chains. Glassy carbon (GC) substrate electrodes were coated with PVC-based “liquid membranes” containing plasticizers and receptors. All tested compounds strongly enhanced the detection limits for the dicarboxylic acids (low pg detection limits), in comparison to a non-specific electrode based on methyltridodecylammonium chloride (MTDDACl). Receptors of the podand urea type yielded high sensitivity, but the electrodes had a lower long-time stability (a few weeks) than the electrodes based on macrocyclic polyamines (at least 3 months).     

Automatic Mechanism and Kinetic Model Generation for Gas‐ and Solution‐Phase Processes: A Perspective on Best Practices,Recent Advances,and Future Challenges

Completely automated mechanism generation of detailed kinetic models is within reach in the coming decade. The recent developments in this field of chemical reaction engineering are anticipated to lead to some groundbreaking discoveries in the future, extending our fundamental understanding and resolving many of today's society problems such as energy production and conversion, emission reduction, greener chemical production processes, etc. In the present review, the focus is on the core of these automated mechanism generation for gas‐phase and solution‐phase processes that is on how the reaction kinetics and thermodynamic and transport properties of species are estimated and calculated starting from the fundamental elements of the software. With tasks such as the definition of reaction rules and reaction families, the unambiguous representation of species, and the choice of different termination criteria, generating a good reaction mechanism is still not as simple as pressing a “run” button. One of the main challenges that still needs to be overcome is how to deal with data scarcity and the combination with affordable computational chemistry calculations seems the logical step forward. The best practices are illustrated in a butane pyrolysis case study, which also exposes the challenges in the field of automatic kinetic model generation.     

Intraperitoneal Photodynamic Therapy: Comparison of Red and Green Light Distribution and Toxicity

Abstract— The aim of this study was to compare red (652 nm) and green (514 nm) light for photodynamic therapy (PDT) of the peritoneal cavity with emphasis on light distribution and toxicity. Red-light PDT was limited by intestinal toxicity and it was hypothesized that less penetrating green light would allow higher light doses to be used in the peritoneal cavity. Female non-tumor-bearing rats were photosensitized with mTHPC (meta-tetrahydroxyphenylchlorin, Foscan®) intravenously or intraperitoneally and the peritoneum was illuminated using a minimally invasive technique. For both red and green light, the time of illumination was varied to give the required dose. Light fluence rate was measured in situ at multiple sites within the abdominal cavity. The toxicity experiments were carried out with a total of 160 J incident red or 640 J incident green light and a drug dose of 0.15 mg/kg Foscan® For red light a mean fluence rate of 55.2 38.5 mW cm ₂ was measured, with a peak fluence rate of 128 mW cm ₂ on the intestines. For green light the mean and peak fluence rates were 8.2 9.0 (i.e. including zero fluence rate measurements) and 28 mW cm ₂, respectively. Intestines were most vulnerable to red light illumination. The intravenous injection route resulted in increased toxicity for red light, but for green light there were no major differences between intravenous and intraperitoneal routes. The 4 h interval between drug and illumination resulted in very little toxicity for both wavelengths. We conclude that for intraperitoneal PDT green light allows higher light doses than red light, but the light distribution over the peritoneum is much less favorable and may not be suitable for whole peritoneal illumination using a minimal-access technique.     

Combustion of ethylamine,dimethylamine and diethylamine: Theoretical and kinetic modeling study

Aliphatic amines are an important class of nitrogen-containing compounds present in renewable fuels such as bio-oils. Conversion of this fuel-bound nitrogen can lead to the formation of HCN and NH₃, as well as NO_x emissions. In this work, the combustion chemistry of small aliphatic amines is investigated via a combination of quantum chemical calculations, chemical kinetic modeling and experimental validation. The influence of the degree of substitution on the nitrogen atom and the alkyl chain length on the reactivity and product distribution is studied via three model compounds, i.e. ethylamine (EA, CH₃CH₂NH₂), dimethylamine (DMA, (CH₃)₂NH) and diethylamine (DEA, (CH₃CH₂)₂NH). A detailed kinetic model containing 258 species and 2274 reactions is developed to describe their combustion over a wide range of conditions. The proposed model captures the trends in ignition delay times and species concentrations over a temperature range from 500 to 2000 K and pressures from 4 to 170 kPa. The ignition delay data are predicted with an average deviation of 10%. The difference between experimental and simulated species concentrations from laminar premixed flames is for the major species on average 50%, while the agreement for the JSR is even better, with an average deviation of 10%. The dominant decomposition pathway under all the studied conditions is a set of hydrogen abstractions from the C_α and N positions followed by β-scission of the fuel radicals. Among the unimolecular decomposition pathways, the homolytic CC and CN scissions and four-centered elimination play a minor role. HCN is the main intermediate and at temperatures above 1100 K the amines are completely converted to N₂ and NO.     

Application of an omonasteine ligation strategy for the total chemical synthesis of the BRD7 bromodomain

The use of omonasteine (Omo) in sequential peptide ligation strategies extends the scope of homocysteine (Hcy) ligation to longer, methionine-rich proteins. Hcy-to-Omo conversion can be performed on-resin, while the Omo-to-Hcy deprotection can be performed in situ after peptide ligation. This strategy was successfully applied in the synthesis of the BRD7 bromodomain.