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Purpose:Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions.Experimental Design:Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches.Results:In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1).Conclusions:Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.

Purpose:Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions.Experimental Design:Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches.Results:In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1).Conclusions:Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.

Advanced and metastatic tumors with complex treatment histories drive cancer mortality. Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and clinical dataset, amenable for exploration of the impacts of therapies on genomic landscapes. Previous exposure to DNA-damaging chemotherapies and mutations affecting DNA repair genes, including POLQ and genes encoding Polζ, were associated with genome-wide, therapy-induced mutagenesis. Exposure to platinum therapies coincided with signatures SBS31 and DSB5 and, when combined with DNA synthesis inhibitors, signature SBS17b. Alterations in ESR1, EGFR, CTNNB1, FGFR1, VEGFA and DPYD were consistent with drug resistance and sensitivity. Recurrent noncoding events were found in regulatory region hotspots of genes including TERT, PLEKHS1, AP2A1 and ADGRG6. Mutation burden and immune signatures corresponded with overall survival and response to immunotherapy. Our data offer a rich resource for investigation of advanced cancers and interpretation of whole-genome and transcriptome sequencing in the context of a cancer clinic. Marra and colleagues describe POG570, a pan-cancer, whole-genome, transcriptome and clinical dataset stressing the molecular interactions in advanced and post-therapy cancer patients.

Curing HIV will require eliminating the reservoir of integrated, replication-competent proviruses that persist despite antiretroviral therapy (ART). Understanding the burden, genetic diversity and longevity of persisting proviruses in diverse individuals with HIV is critical to this goal, but these characteristics remain understudied in some groups. Among them are viremic controllers, individuals who naturally suppress HIV to low levels but for whom therapy is nevertheless recommended. We reconstructed within-host HIV evolutionary histories from longitudinal single-genome amplified viral sequences in four viremic controllers who eventually initiated ART, and used this information to characterize the age and diversity of proviruses persisting on therapy. We further leveraged these within-host proviral age distributions to estimate rates of proviral turnover prior to ART. This is an important yet understudied metric, since pre-ART proviral turnover dictates reservoir composition at ART initiation (and thereafter), which is when curative interventions, once developed, would be administered. Despite natural viremic control, all participants displayed significant within-host HIV evolution pre-therapy, where overall on-ART proviral burden and diversity broadly reflected the extent of viral replication and diversity pre-ART. Consistent with recent studies of non-controllers, the proviral pools of two participants were skewed towards sequences that integrated near ART initiation, suggesting dynamic proviral turnover during untreated infection. In contrast, proviruses recovered from the two other participants dated to time-points that were more evenly spread throughout infection, suggesting slow or negligible proviral decay following deposition. HIV cure strategies will need to overcome within-host proviral diversity, even in individuals who naturally controlled HIV replication before therapy.ImportanceHIV therapy is life-long because integrated, replication-competent viral copies persist within long-lived cells. To cure HIV, we need to understand when these viral reservoirs form, how large and genetically diverse they are, and how long they endure. Elite controllers, individuals who naturally suppress HIV to undetectable levels, are being intensely studied as models of HIV remission, but viremic controllers, individuals who naturally suppress HIV to low levels, remain understudied even though they too may hold valuable insights. We combined phylogenetics and mathematical modeling to reconstruct proviral seeding and decay from infection to therapy-mediated suppression in four viremic controllers. We recovered diverse proviruses persisting during therapy that broadly reflected HIV’s within-host evolutionary history, where the estimated half-lives of the persistent proviral pool during untreated infection ranged from

Continuous (CONT) VLBI campaigns have been carried out about every 3 years since 2002. The basic idea of these campaigns is to acquire state-of-the-art VLBI data over a continuous time period of about 2 weeks to demonstrate the highest accuracy of which the current VLBI system is capable. In addition, these campaigns support scientific studies such as investigations of high-resolution Earth rotation, reference frame stability, and daily to sub-daily site motions. The size of the CONT networks and the observing data rate have increased steadily since 1994. Performance of these networks based on reference frame scale precision and polar motion/LOD comparison with global navigation satellite system (GNSS) earth orientation parameters (EOP) has been substantially better than the weekly operational R1 and R4 series. The precisions of CONT EOP and scale have improved by more than a factor of two since 2002. Polar motion precision based on the WRMS difference between VLBI and GNSS for the most recent CONT campaigns is at the 30 $$\upmu $$ as level, which is comparable to that of GNSS. The CONT campaigns are a natural precursor to the planned future VLBI observing networks, which are expected to observe continuously. We compare the performance of the most recent CONT campaigns in 2011 and 2014 with the expected performance of the future VLBI global observing system network using simulations. These simulations indicate that the expected future precision of scale and EOP will be at least 3 times better than the current CONT precision.

Advanced and metastatic tumors with complex treatment histories drive cancer mortality. Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and clinical dataset, amenable for exploration of the impacts of therapies on genomic landscapes. Previous exposure to DNA-damaging chemotherapies and mutations affecting DNA repair genes, including POLQ and genes encoding Polζ, were associated with genome-wide, therapy-induced mutagenesis. Exposure to platinum therapies coincided with signatures SBS31 and DSB5 and, when combined with DNA synthesis inhibitors, signature SBS17b. Alterations in ESR1, EGFR, CTNNB1, FGFR1, VEGFA and DPYD were consistent with drug resistance and sensitivity. Recurrent noncoding events were found in regulatory region hotspots of genes including TERT, PLEKHS1, AP2A1 and ADGRG6. Mutation burden and immune signatures corresponded with overall survival and response to immunotherapy. Our data offer a rich resource for investigation of advanced cancers and interpretation of whole-genome and transcriptome sequencing in the context of a cancer clinic.

Volume 92, no. 19, e00811-18, 2018, [https://doi.org/10.1128/JVI.00811-18][1]. Page 15, Acknowledgments, line 15: The following sentence should be added after “KwaZulu-Natal”: “J.K.M. received additional funding from the Poliomyelitis Research Foundation of South Africa." Poliomyelitis

CD8(+) T cell-mediated escape mutations in Gag can reduce HIV-1 replication capacity (RC) and alter disease progression, but less is known about immune-mediated attenuation in other HIV-1 proteins. We generated 487 recombinant viruses encoding RT-integrase from individuals with chronic (n = 406) and recent (n = 81) HIV-1 subtype C infection and measured their in vitro RC using a green fluorescent protein (GFP) reporter T cell assay. In recently infected individuals, reverse transcriptase (RT)-integrase-driven RC correlated significantly with viral load set point (r = 0.25; P = 0.03) and CD4(+) T cell decline (P = 0.013). Moreover, significant associations between RT integrase-driven RC and viral load (r = 0.28; P < 0.0001) and CD4(+) T cell count (r = −0.29; P < 0.0001) remained in chronic infection. In early HIV infection, host expression of the protective HLA-B*81 allele was associated with lower RC (P = 0.05), as was expression of HLA-B*07 (P = 0.02), suggesting early immune-driven attenuation of RT-integrase by these alleles. In chronic infection, HLA-A*30:09 (in linkage disequilibrium with HLA-B*81) was significantly associated with lower RC (P = 0.05), and all 6 HLA-B alleles with the lowest RC measurements represented protective alleles, consistent with long-term effects of host immune pressures on lowering RT-integrase RC. The polymorphisms V241I, I257V, P272K, and E297K in reverse transcriptase and I201V in integrase, all relatively uncommon polymorphisms occurring in or adjacent to optimally described HLA-restricted cytotoxic T-lymphocyte epitopes, were associated with reduced RC. Together, our data suggest that RT-integrase-driven RC is clinically relevant and provide evidence that immune-driven selection of mutations in RT-integrase can compromise RC. IMPORTANCE Identification of viral mutations that compromise HIV's ability to replicate may aid rational vaccine design. However, while certain escape mutations in Gag have been shown to reduce HIV replication and influence clinical progression, less is known about the consequences of mutations that naturally arise in other HIV proteins. Pol is a highly conserved protein, but the impact of Pol function on HIV disease progression is not well defined. Here, we generated recombinant viruses using the RT-integrase region of Pol derived from HIV-1C-infected individuals with recent and chronic infection and measured their ability to replicate in vitro. We demonstrate that RT-integrase-driven replication ability significantly impacts HIV disease progression. We further show evidence of immune-mediated attenuation in RT-integrase and identify specific polymorphisms in RT-integrase that significantly decrease HIV-1 replication ability, suggesting which Pol epitopes could be explored in vaccine development.

Tropospheric delay modeling error continues to be one of the largest sources of error in VLBI (very long baseline interferometry) analysis. For standard operational solutions, we use the VMF1 elevation-dependent mapping functions derived from European Centre for Medium-Range Weather Forecasts data. These mapping functions assume that tropospheric delay at a site is azimuthally symmetric. As this assumption is not true, we have instead determined the ray trace delay along the signal path through the troposphere for each VLBI quasar observation. We determined the troposphere refractivity fields from the pressure, temperature, specific humidity, and geopotential height fields of the NASA Goddard Space Flight Center Goddard Earth Observing System version 5 numerical weather model. When applied in VLBI analysis, baseline length repeatabilities were improved compared with using the VMF1 mapping function model for 72% of the baselines and site vertical repeatabilities were better for 11 of 13 sites during the 2 week CONT11 observing period in September 2011. When applied to a larger data set (2011–2013), we see a similar improvement in baseline length and also in site position repeatabilities for about two thirds of the stations in each of the site topocentric components.

Mycobacterium chimaera , a nontuberculous mycobacterium (NTM) belonging to the Mycobacterium avium complex (MAC), is an opportunistic pathogen that can cause respiratory and disseminated disease. We report the complete genome sequence of a strain, SJ42, isolated from an immunocompromised male presenting with MAC pneumonia, assembled from Illumina and Oxford Nanopore data.

Alternative polyadenylation (APA) of 3’ untranslated regions (3’ UTRs) has been implicated in cancer development. Earlier reports on APA in cancer primarily focused on 3’ UTR length modifications, and the conventional wisdom is that tumor cells preferentially express transcripts with shorter 3’ UTRs. Here, we analyzed the APA patterns of 114 genes, a select list of oncogenes and tumor suppressors, in 9,939 tumor and 729 normal tissue samples across 33 cancer types using RNA-Seq data from The Cancer Genome Atlas, and we found that the APA regulation machinery is much more complicated than what was previously thought. We report 77 cases (gene-cancer type pairs) of differential 3’ UTR cleavage patterns between normal and tumor tissues, involving 33 genes in 13 cancer types. For 15 genes, the tumor-specific cleavage patterns are recurrent across multiple cancer types. While the cleavage patterns in certain genes indicate apparent trends of 3’ UTR shortening in tumor samples, over half of the 77 cases imply 3’ UTR length change trends in cancer that are more complex than simple shortening or lengthening. This work extends the current understanding of APA regulation in cancer, and demonstrates how large volumes of RNA-seq data generated for characterizing cancer cohorts can be mined to investigate this process.

Aims. The IVS Working Group on Galactic Aberration (WG8) was established to investigate issues related to incorporating the effect of Galactic aberration in IVS analysis. The circular motion of the solar system barycenter around the Galactic center causes a change in aberration, which in the case of geodetic VLBI observing is over time scales of several decades. One of the specific goals was to recommend a Galactic aberration model to be applied by the IAU ICRF3 working group in the generation of ICRF3 as well as in other IVS analysis. Studies made by working group members have shown that the three-dimensional acceleration vector of the solar system barycenter can be estimated from VLBI delay observations. Methods. Among the working group members, three methods were used to estimate the acceleration vector. One is to directly estimate the acceleration vector as a global parameter. The second is to estimate the acceleration vector from source proper motions determined from estimated source position time series. A third method estimated a global reference frame scale parameter for each source and derived the acceleration vector from these estimates. The acceleration vector estimate consists of a galactocentric component along with the non-galactocentric components. Results. The geodetic reference frame VLBI estimates of the galactocentric aberration constant from the different working group members are in the range 5.1–6.4 μas yr−1. These estimates are relatively close to independent estimates of 4.8–5.4 μas yr−1 that can be derived from astrometric measurements of proper motions and parallaxes of masers in the Milky Way galaxy. Based on the most recent geodetic VLBI solutions, we find an upper bound of 0.8 μas yr−1 for the non-galactocentric component of the secular aberration. Conclusions. The working group made a recommendation only for the galactocentric component of the observed acceleration vector. For the recommended galactocentric aberration constant, the working group chose a geodetic value to be consistent with geodetic VLBI applications. The recommended value 5.8 μas yr−1 was estimated directly in a global solution that used the ICRF3 solution data set: 1979–May 2018.

Human leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989; n = 338) and modern (2001 to 2011; n = 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Phylogenies inferred from historic and modern HIV-1 Pol sequences were star-like in shape, with an inferred most recent common ancestor (epidemic founder virus) sequence nearly identical to the modern North American subtype B consensus sequence. Nevertheless, modern HIV-1 Pol sequences exhibited roughly 2-fold-higher patristic (tip-to-tip) genetic distances than historic sequences, with HLA pressures likely driving ongoing diversification. Moreover, the frequencies of published HLA-associated polymorphisms in individuals lacking the selecting HLA class I allele was on average ∼2.5-fold higher in the modern than in the historic era, supporting their spread in circulation, though some remained stable in frequency during this time. Notably, polymorphisms restricted by protective HLA alleles appear to be spreading to a greater relative extent than others, though these increases are generally of modest absolute magnitude. However, despite evidence of polymorphism spread, North American hosts generally remain at relatively low risk of acquiring an HIV-1 polymerase sequence substantially preadapted to their HLA profiles, even in the present era. IMPORTANCE HLA class I-restricted cytotoxic T-lymphocyte (CTL) escape mutations in HIV-1 that persist upon transmission may accumulate in circulation over time, potentially undermining host antiviral immunity to the transmitted viral strain. We studied >600 experimentally collected HIV-1 polymerase sequences linked to host HLA information dating back to 1979, along with phylogenetically reconstructed HIV-1 sequences dating back to the virus' introduction into North America. Overall, our results support the gradual spread of many—though not all—HIV-1 polymerase immune escape mutations in circulation over time. This is consistent with recent observations from other global regions, though the extent of polymorphism accumulation in North America appears to be lower than in populations with high seroprevalence, older epidemics, and/or limited HLA diversity. Importantly, the risk of acquiring an HIV-1 polymerase sequence at transmission that is substantially preadapted to one's HLA profile remains relatively low in North America, even in the present era.

We have compared coordinate time series from several space geodetic observing techniques to derive the kinematical motions of Ny-Alesund, Svalbard. Velocity estimates from VLBI, GPS, and DORIS scatter more than the expected error estimates from each technique, and also between individual GPS solutions with different software and analysis strategies. A statistical combination yields average topocentric velocity components of 14.3 ± 0.2 mm/year (north), 9.8 ± 0.7 mm/year (east), and 8.2 ± 0.9 mm/year (vertical) for 1993–2007. The horizontal velocity is in agreement with a combined prediction of NUVEL-NNR-1A and the effects of post-glacial rebound and present day ice melt of nearby glaciers. The observed uplift is twice that predicted by the two latter processes. The non-linear time series of both VLBI and GPS data suggest that the uplift rate increases from 7.0 mm/year before 2003 to 10.8 mm/year after 2003. We conclude that this has a geophysical origin since no monument motions have been detected. A recent sea level decrease (1993–2007) of 4.7 ± 0.9 mm/year supports an absolute sea level increase of 3.2 mm/year as determined elsewhere by satellite altimetry.

Within the International Very Long Baseline Interferometry (VLBI) Service for Geodesy and Astrometry (IVS), long time-series of zenith wet and total troposphere delays have been combined at the level of parameter estimates. The data sets were submitted by eight IVS Analysis Centers (ACs) and cover January 1984 to December 2004. In this paper, the combination method is presented and the time-series submitted by the eight IVS ACs are compared with each other. The combined zenith delays are compared with time-series provided by the International Global Navigation Satellite System (GNSS) Service (IGS), and with zenith delays derived from the European Centre for Medium-Range Weather Forecasts (ECMWF). Before the combination, outliers are eliminated from the individual time-series using the robust BIBER (bounded influence by standardized residuals) estimator. For each station and AC, relative weight factors are obtained by variance component estimation. The mean bias of the IVS ACs’ time-series with respect to the IVS combined time-series is 0.89 mm and the mean root mean square is 7.67 mm. Small differences between stations and ACs can be found, which are due to the inhomogeneous analysis options, different parameterizations, and different treatment of missing in-situ pressure records. Compared to the IGS zenith total delays, the combined IVS series show small positive mean biases and different long-term trends. Zenith wet delays from the ECMWF are used to validate the IVS combined series. Inconsistencies, e.g., long-term inhomogeneity of the in-situ pressure data used for the determination of VLBI zenith delays, are identified.

The source position time-series for many of the frequently observed radio sources in the NASA geodetic very long baseline interferometry (VLBI) program show systematic linear and non-linear variations of as much as 0.5 mas (milli-arc-seconds) to 1.0 mas, due mainly to source structure changes. In standard terrestrial reference frame (TRF) geodetic solutions, it is a common practice to only estimate a global source position for each source over the entire history of VLBI observing sessions. If apparent source position variations are not modeled, they produce corresponding systematic variations in estimated Earth orientation parameters (EOPs) at the level of 0.02–0.04 mas in nutation and 0.01–0.02 mas in polar motion. We examine the stability of position time-series of the 107 radio sources in the current NASA geodetic source catalog since these sources have relatively dense observing histories from which it is possible to detect systematic variations. We consider different strategies for handling source instabilities where we (1) estimate the positions of unstable sources for each session they are observed, or (2) estimate spline parameters or rate parameters for sources chosen to fit the specific variation seen in the position-time series. We found that some strategies improve VLBI EOP accuracy by reducing the biases and weighted root mean square differences between measurements from independent VLBI networks operating simultaneously. We discuss the problem of identifying frequently observed unstable sources and how to identify new sources to replace these unstable sources in the NASA VLBI geodetic source catalog.

SUMMARY We have analysed the Ny-Alesund very long baseline interferometry (VLBI) data over the period 1994 August to 2004 May, and we obtain secular displacement rates relative to a NNR-NUVEL-1A reference frame of 0.2 ± 0.5 mm yr −1 , −1.7 ± 0.5 mm yr −1 and 4.8 ± 1.1 mm yr −1 for the north, east and vertical directions, respectively. The corresponding global positioning system (GPS) station displacement rates relative to the same reference frame for the north, east, and vertical directions are 0.2 ± 0.6 mm yr −1 , −2.3 ± 0.6 mm yr −1 , and 6.4 ± 1.5 mm yr −1 at NYA1 and -−0.1 ± 0.5 mm yr −1 , −1.6 ± 0.5 mm yr −1 , and 6.9 ± 0.9 mm yr −1 at NALL, where these GPS rates were derived from the ITRF2000 velocity solution of Heflin. From the comparison at 25 globally distributed collocated sites, we found that the difference in uplift rate between VLBI and GPS at Ny-Alesund is mainly due to a GPS reference frame scale rate error corresponding to 1.6 mm yr −1 in the GPS vertical rates. The uplift rate was estimated to be 5.2 ± 0.3 mm yr −1 from the analysis of the tide gauge data at Ny-Alesund. Hence the uplift rates obtained from three different kinds of data are very consistent each other. The absolute gravity (AG) measurements at Ny-Alesund, which were carried out four times (period: 1998‐2002) by three different FG5 absolute gravimeters, lead to a decreasing secular rate of −2.5 ± 0.9 μGal yr −1 (1 μGal = 10 −8 ms −2 ). In this analysis, the actual data obtained from a superconducting gravimeter at Ny-Alesund were used in the corrections for the gravity tide (including the ocean tide effect) and for the air pressure effect. We have

International audience; We use very long baseline interferometry data obtained between mid-1995 and the end of 2002 May together with older data to extend and revise the International Celestial Reference Frame (ICRF). Revised positions of ICRF candidate and ``other'' sources, based on inclusion of the additional data, are presented. Positions, in the frame of the ICRF, for an additional 109 new sources are also presented. All but four of the new sources are located north of delta=-30°. Positions of the ICRF defining sources remain unchanged. We present a summary of current astrometric and geodetic observing programs and discuss the evolution and future of the ICRF.

This paper presents an extension of the Very Long Baseline Array Calibrator Survey, called VCS2, containing 276 sources. This survey fills in regions of the sky that were not completely covered by the previous VCS1 calibrator survey. The VCS2 survey includes calibrator sources near the Galactic plane, -30° < δ < -45°, and VLA calibrators. The positions have been derived from astrometric analysis of the group delays measured at 2.3 and 8.4 GHz using the Goddard Space Flight Center CALC/SOLVE package. From the VLBA snapshot observations, images of the calibrators are available, and each source is given a quality code for anticipated use. The VCS2 catalog is available from the NRAO Web site.

A catalog containing milliarcsecond--accurate positions of 1332 extragalactic radio sources distributed over the northern sky is presented - the Very Long Baseline Array Calibrator Survey (VCS1). The positions have been derived from astrometric analysis of dual-frequency 2.3 and 8.4 GHz VLBA snapshot observations; in a majority of cases, images of the sources are also available. These radio sources are suitable for use in geodetic and astrometric experiments, and as phase-reference calibrators in high-sensitivity astronomical imaging. The VCS1 is the largest high-resolution radio survey ever undertaken, and triples the number of sources available to the radio astronomy community for VLBI applications. In addition to the astrometric role, this survey can be used in active galactic nuclei, Galactic, gravitational lens and cosmological studies. The VCS1 catalog will soon be available at www.nrao.edu/vlba/VCS1 ., 25 pages, 5 figures. Accepted to ApJS

Variations in continental water storage lead to loading deformation of the crust with typical peak-to-peak variations at very long baseline interferometry (VLBI) sites of 3-15 mm in the vertical component and 1-2 mm in the horizontal component. The hydrology signal at VLBI sites has annual and semi-annual components and clear interannual variations. We have calculated the hydrology loading series using mass loading distributions derived from the global land data assimilation system (GLDAS) hydrology model and alternatively from a global grid of equal-area gravity recovery and climate experiment (GRACE) mascons. In the analysis of the two weekly VLBI 24-h R1 and R4 network sessions from 2003 to 2010 the baseline length repeatabilities are reduced in 79 % (80 %) of baselines when GLDAS (GRACE) loading corrections are applied. Site vertical coordinate repeatabilities are reduced in about 80 % of the sites when either GLDAS or GRACE loading is used. In the horizontal components, reduction occurs in 70-80 % of the sites. Estimates of the annual site vertical amplitudes were reduced for 16 out of 18 sites if either loading series was applied. We estimated loading admittance factors for each site and found that the average admittances were 1.01 0.05 for GRACE and 1.39 0.07 for GLDAS. The standard deviations of the GRACE admittances and GLDAS admittances were 0.31 and 0.68, respectively. For sites that have been observed in a set of sufficiently temporally dense daily sessions, the average correlation between VLBI vertical monthly averaged series and GLDAS or GRACE loading series was 0.47 and 0.43, respectively.

The construction of the second realization of the International Celestial Reference Frame by VLBI (ICRF2) was undertaken to take advantage of the many improvements in geodetic and astrometric VLBI and the vast increase in data since the first ICRF. The impact the switch to ICRF2 has had on the terrestrial reference frame and EOP solutions generated by VLBI is very small, at about the mm level, and should be transparent to most users of VLBI products.

Variations in the temporal length-of-day (LOD) contain information on phenomena related to the continuous evolution of Earth processes: tidal energy dissipation and core-mantle coupling (decadal, secular), meteorological and solar-lunar tide effects (annual, semi-annual). In this work, we studied an LOD time series obtained from VLBI measurements and extracted its principal components using the Singular Spectrum Analysis (SSA). After removing the long-term trend which explains 73. 8% of the signal, three remaining components explain a further 22. 0% of the signal: an annual and a semi-annual signals as well as a second trend. We compared the Multivariate ENSO index (MEI) with the variations in the amplitudes of the annual and semi-annual components and with the second trend. The correlations are significant: 0. 58 for the annual component, − 0. 48 for the semi-annual component and 0. 46 for the second trend.

IGN and DGFI both generated realizations of the terrestrial reference frame under the auspices of the IERS from combination of the same space geodetic data. We compared the IGN and DGFI TRFs with a GSFC CALC/SOLVE TRF. WRMS position and velocity differences for the 40 most frequently observed sites were 2–3mm and 0.3–0.4mm/year. There was a scale difference of −0.39/−0.09ppb between the IGN/DGFI realizations and the GSFC solution. When we fixed positions and velocities to either the IGN or DGFI values in CALC/SOLVE solutions, the resulting EOP estimates were not significantly different from the estimates from a standard TRF solution.

Atmospheric mass loading produces a primarily vertical displacement of the Earth's crust. This displacement is correlated with surface pressure and is large enough to be detected by very long baseline interferometry (VLBI) measurements. Using the measured surface pressure at VLBI stations, we have estimated the atmospheric loading term for each station location directly from VLBI data acquired from 1979 to 1992. Our estimates of the vertical sensitivity to change in pressure range from 0 to -0.6 mm/mbar depending on the station. These estimates agree with inverted barometer model calculations (Manabe et al., 1991; vanDam and Herring, 1994) of the vertical displacement sensitivity computed by convolving actual pressure distributions with loading Green's functions. The pressure sensitivity tends to be smaller for stations near the coast, which is consistent with the inverted barometer hypothesis. Applying this estimated pressure loading correction in standard VLBI geodetic analysis improves the repeatability of estimated lengths of 25 out of 37 baselines that were measured at least 50 times. In a root-sum-square (rss) sense, the improvement generally increases with baseline length at a rate of about 0.3 to 0.6 ppb depending on whether the baseline stations are close to the coast. For the 5998-km baseline from Westford, Massachusetts, to Wettzell, Germany, the rss improvement is about 3.6 mm out of 11.0 mm. The average rss reduction of the vertical scatter for inland stations ranges from 2.7 to 5.4 mm.

Time-series of zenith wet and total troposphere delays as well as north and east gradients are compared, and zenith total delays (ZTD) are combined on the level of parameter estimates. Input data sets are provided by ten Analysis Centers (ACs) of the International VLBI Service for Geodesy and Astrometry (IVS) for the CONT08 campaign (12–26 August 2008). The inconsistent usage of meteorological data and models, such as mapping functions, causes systematics among the ACs, and differing parameterizations and constraints add noise to the troposphere parameter estimates. The empirical standard deviation of ZTD among the ACs with regard to an unweighted mean is 4.6 mm. The ratio of the analysis noise to the observation noise assessed by the operator/software impact (OSI) model is about 2.5. These and other effects have to be accounted for to improve the intra-technique combination of VLBI-derived troposphere parameters. While the largest systematics caused by inconsistent usage of meteorological data can be avoided and the application of different mapping functions can be considered by applying empirical corrections, the noise has to be modeled in the stochastic model of intra-technique combination. The application of different stochastic models shows no significant effects on the combined parameters but results in different mean formal errors: the mean formal errors of the combined ZTD are 2.3 mm (unweighted), 4.4 mm (diagonal), 8.6 mm [variance component (VC) estimation], and 8.6 mm (operator/software impact, OSI). On the one hand, the OSI model, i.e. the inclusion of off-diagonal elements in the cofactor-matrix, considers the reapplication of observations yielding a factor of about two for mean formal errors as compared to the diagonal approach. On the other hand, the combination based on VC estimation shows large differences among the VCs and exhibits a comparable scaling of formal errors. Thus, for the combination of troposphere parameters a combination of the two extensions of the stochastic model is recommended.

From October 2003 to September 2005, the International VLBI Service for Geodesy and Astrometry (IVS) examined current and future requirements for geodetic VLBI, including all components from antennas to analysis. IVS Working Group 3 “VLBI 2010”, which was tasked with this effort, concluded with recommendations for a new generation of VLBI systems. These recommendations were based on the goals of achieving 1 mm measurement accuracy on global baselines, performing continuous measurements for time series of station positions and Earth orientation parameters, and reaching a turnaround time from measurement to initial geodetic results of less than 24 h. To realize these recommendations and goals, along with the need for low cost of construction and operation, requires a complete examination of all aspects of geodetic VLBI including equipment, processes, and observational strategies. Hence, in October 2005, the IVS VLBI2010 Committee (V2C) commenced work on defining the VLBI2010 system specifications. In this paper we give a summary of the recent progress of the VLBI2010 project

In April 2002 the International VLBI Service for Geodesy and Astrometry (IVS) set up the Pilot Project — Tropospheric Parameters, and the Institute of Geodesy and Geophysics (IGG), Vienna, was put in charge of coordinating the project. Seven IVS Analysis Centers have joined the project and regularly submitted their estimates of tropospheric parameters (wet and total zenith delays, horizontal gradients) for all IVS-R1 and IVS-R4 sessions since January 1st, 2002. The individual submissions are combined by a two-step procedure to obtain stable, robust and highly accurate tropospheric parameter time series with one hour resolution. The zenith delays derived by Very Long Baseline Interferometry (VLBI) are compared with those provided by the International GPS Service (IGS). At sites with co-located VLBI and GPS antennas, biases are found between the Global Positioning System (GPS) and VLBI derived zenith delays, although short-term variabilities generally show a good agreement. Possible reasons for these biases are discussed. Additionally, the time series submitted by the individual Analysis Centers are compared to the combined IGS time series for the CONT02 campaign of 15 days of continuous observations in the second half of October 2002.