This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. A powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.

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The HITRAN 2008 molecular spectroscopic database

Changes in Atmospheric Constituents and in Radiative Forcing

An improved method for computing potential-derived charges is described which is based upon the CHELP program available from QCPE.1 This approach (CHELPG) is shown to be considerably less dependent upon molecular orientation than the original CHELP program. In the second part of this work, the CHELPG point selection algorithm was used to analyze the changes in the potential-derived charges in formamide during rotation about the CN bond. In order to achieve a level of rotational invariance less than 10% of the magnitude of the electronic effects studied, an equally-spaced array of points 0.3 A apart was required. Points found to be greater than 2.8 A from any nucleus were eliminated, along with all points contained within the defined VDW distances from each of the atoms. The results are compared to those obtained by using CHELP. Even when large numbers of points (ca. 3000) were sampled using the CHELP selection routine, the results did not indicate a satisfactory level of rotatational invariance. On the basis of these results, the original CHELP program was found to be inadequate for analyzing internal rotations.

Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis

Secondary organic aerosol (SOA) accounts for a significant fraction of ambient tropospheric aerosol and a detailed knowledge of the formation, properties and transformation of SOA is therefore required to evaluate its impact on atmospheric processes, climate and human health. The chemical and physical processes associated with SOA formation are complex and varied, and, despite considerable progress in recent years, a quantitative and predictive understanding of SOA formation does not exist and therefore represents a major research challenge in atmospheric science. This review begins with an update on the current state of knowledge on the global SOA budget and is followed by an overview of the atmospheric degradation mechanisms for SOA precursors, gas-particle partitioning theory and the analytical techniques used to determine the chemical composition of SOA. A survey of recent laboratory, field and modeling studies is also presented. The following topical and emerging issues are highlighted and discussed in detail: molecular characterization of biogenic SOA constituents, condensed phase reactions and oligomerization, the interaction of atmospheric organic components with sulfuric acid, the chemical and photochemical processing of organics in the atmospheric aqueous phase, aerosol formation from real plant emissions, interaction of atmospheric organic components with water, thermodynamics and mixtures in atmospheric models. Finally, the major challenges ahead in laboratory, field and modeling studies of SOA are discussed and recommendations for future research directions are proposed.

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The formation, properties and impact of secondary organic aerosol: current and emerging issues

The present paper reviews existing knowledge with regard to Organic Aerosol (OA) of importance for global climate modelling and defines critical gaps needed to reduce the involved uncertainties. All pieces required for the representation of OA in a global climate model are sketched out with special attention to Secondary Organic Aerosol (SOA): The emission estimates of primary carbonaceous particles and SOA precursor gases are summarized. The up-to-date understanding of the chemical formation and transformation of condensable organic material is outlined. Knowledge on the hygroscopicity of OA and measurements of optical properties of the organic aerosol constituents are summarized. The mechanisms of interactions of OA with clouds and dry and wet removal processes parameterisations in global models are outlined. This information is synthesized to provide a continuous analysis of the flow from the emitted material to the atmosphere up to the point of the climate impact of the produced organic aerosol. The sources of uncertainties at each step of this process are highlighted as areas that require further studies.

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Organic aerosol and global climate modelling: a review

BACKGROUND In Denmark, 300 new individuals are diagnosed with HIV every year, despite decades of public health campaigns aimed to raise awareness of potential risk behavior for HIV transmission. It is important to identify the driving forces of the epidemic, to enable more targeted campaigns. The role of very late presenters (VLPs, defined by a CD4 T-cell count of <200 cells/μL at the time of diagnosis) in driving the epidemic is currently not known and was investigated in this study. METHODS We performed phylogenetic analysis to identify potential transmission clusters. One thousand five hundred fifteen partial polymerase sequences from 1515 newly diagnosed individuals in Denmark for whom clinical and epidemiological data existed were included in the study. RESULTS We identified 46 epidemic clusters, including a total of 502 patients. Median cluster size was 7 patients (range, 4-82). Of the 460 VLPs, 20% were included in a cluster. Through multivariate analysis, it was found that the clusters mainly consisted of Danish individuals with homosexual and intravenous drug use risk behavior, infected in Denmark with subtype B. Large clusters contained significantly more homosexual transmission events, characterized by primary infections, younger age, higher CD4 cell count, and lower viral load compared with the small clusters that contained mostly heterosexual transmission events and VLP. CONCLUSION Danish HIV epidemic is driven mainly by younger homosexual men diagnosed during primary HIV infection. VLPs appear more frequently in smaller clusters or as single branches in the phylogeny. The VLP contribution is not of significant importance from a transmission standpoint.

Phylogenetics of the Danish HIV epidemic: the role of very late presenters in sustaining the epidemic.

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Phase analyses of potassium, rubidium and cesium tungsten bronzes

A systematic theoretical study of imines formation from the atmospheric reactions of RnNH2−n with O2 and NO2 (R = CH3 and CH3CH2; n = 1 and 2)

To improve the immunogenicity of epitopes from the envelope protein of HIV-1, we have developed gene gun-delivered subunit DNA vaccines by inserting the sequences encoding the V3 region into the hepatitis B virus (HBV) envelope gene, often called the surface antigen (HBsAg). We have examined the possibility of modifying the immune response to V3 by introducing modifications into the carrier HBsAg in gene gun DNA immunization of mice. In some plasmid constructions, the V3 sequence was introduced into the preS2 region of the HBsAg. Although this region is not present in all protein subunits of the HBsAg particles produced, abolishing the internal translational initiation site for the S protein had no effect on the immune response to V3. Expression of V3 at the N-terminal or C-terminal part of the HBsAg protein resulted in equal anti-V3 antibody and cytotoxic T-lymphocyte (CTL) responses. However, elimination of secretion by single amino-acid mutations in the HBsAg decreased the anti-HBsAg antibody response ...

Improved Immunogenicity of HIV-1 Epitopes in HBsAg Chimeric DNA Vaccine Plasmids by Structural Mutations of HBsAg

So far codon-optimized HIV-1 envelope genes have been investigated for the T cell line-adapted strain MN, which differs in several aspects from primary isolates. Envelopes of primary isolates may be more relevant for vaccine purposes. This article describes for the first time the engineering and characterization of four "humanized" genes encoding the secreted gp120/gp140, or the membrane-bound gp150/gp160, of a primary CCR5 tropic, clade B, clinical isolate HIV-1BX08. The genes were built in fragments for easy cassette exchange of regions important for immunogenicity, function, and expression. The transcription and expression of the synthetic genes in mammalian cell lines were Rev independent and highly increased. Increased expression of membrane-bound gp160 induced a high cytopathic effect in U87.CD4.CCR5 cells. Gene gun and intramuscular DNA vaccination in mice induced a strong specific cytotoxic T lymphocyte response independent of the gene construct, expression level, or DNA immunization route. In con...

Construction, biological activity, and immunogenicity of synthetic envelope DNA vaccines based on a primary, CCR5-tropic, early HIV type 1 isolate (BX08) with human codons.

Claus J. Nielsen

Papers

Phylogenetics of the Danish HIV epidemic: the role of very late presenters in sustaining the epidemic.

Phase analyses of potassium, rubidium and cesium tungsten bronzes

A systematic theoretical study of imines formation from the atmospheric reactions of RnNH2−n with O2 and NO2 (R = CH3 and CH3CH2; n = 1 and 2)

Improved Immunogenicity of HIV-1 Epitopes in HBsAg Chimeric DNA Vaccine Plasmids by Structural Mutations of HBsAg

Construction, biological activity, and immunogenicity of synthetic envelope DNA vaccines based on a primary, CCR5-tropic, early HIV type 1 isolate (BX08) with human codons.