Spatiotemporal genotype replacement of H5N8 avian influenza viruses contributed to H5N1 emergence in 2021/2022 panzootic

Since 2020, clade 2.3.4.4b highly pathogenic avian influenza H5N8 and H5N1 viruses have swept through continents, posing serious threats to the world. Through comprehensive analyses of epidemiological, genetic, and bird migration data, we found that the dominant genotype replacement of the H5N8 viruses in 2020 contributed to the H5N1 outbreak in the 2021/2022 wave. The 2020 outbreak of the H5N8 G1 genotype instead of the G0 genotype produced reassortment opportunities and led to the emergence of a new H5N1 virus with G1's HA and MP genes. Despite extensive reassortments in the 2021/2022 wave, the H5N1 virus retained the HA and MP genes, causing a significant outbreak in Europe and North America. Furtherly, through the wild bird migration flyways investigation, we found that the temporal-spatial coincidence between the outbreak of the H5N8 G1 virus and the bird autumn migration may have expanded the H5 viral spread, which may be one of the main drivers of the emergence of the 2020-2022 H5 panzootic.IMPORTANCESince 2020, highly pathogenic avian influenza (HPAI) H5 subtype variants of clade 2.3.4.4b have spread across continents, posing unprecedented threats globally. However, the factors promoting the genesis and spread of H5 HPAI viruses remain unclear. Here, we found that the spatiotemporal genotype replacement of H5N8 HPAI viruses contributed to the emergence of the H5N1 variant that caused the 2021/2022 panzootic, and the viral evolution in poultry of Egypt and surrounding area and autumn bird migration from the Russia-Kazakhstan region to Europe are important drivers of the emergence of the 2020-2022 H5 panzootic. These findings provide important targets for early warning and could help control the current and future HPAI epidemics.

BAG6 inhibits influenza A virus replication by inducing viral polymerase subunit PB2 degradation and perturbing RdRp complex assembly

The interaction between influenza A virus (IAV) and host proteins is an important process that greatly influences viral replication and pathogenicity. PB2 protein is a subunit of viral ribonucleoprotein (vRNP) complex playing distinct roles in viral transcription and replication. BAG6 (BCL2-associated athanogene 6) as a multifunctional host protein participates in physiological and pathological processes. Here, we identify BAG6 as a new restriction factor for IAV replication through targeting PB2. For both avian and human influenza viruses, overexpression of BAG6 reduced viral protein expression and virus titers, whereas deletion of BAG6 significantly enhanced virus replication. Moreover, BAG6-knockdown mice developed more severe clinical symptoms and higher viral loads upon IAV infection. Mechanistically, BAG6 restricted IAV transcription and replication by inhibiting the activity of viral RNA-dependent RNA polymerase (RdRp). The co-immunoprecipitation assays showed BAG6 specifically interacted with the N-terminus of PB2 and competed with PB1 for RdRp complex assembly. The ubiquitination assay indicated that BAG6 promoted PB2 ubiquitination at K189 residue and targeted PB2 for K48-linked ubiquitination degradation. The antiviral effect of BAG6 necessitated its N-terminal region containing a ubiquitin-like (UBL) domain (17-92aa) and a PB2-binding domain (124-186aa), which are synergistically responsible for viral polymerase subunit PB2 degradation and perturbing RdRp complex assembly. These findings unravel a novel antiviral mechanism via the interaction of viral PB2 and host protein BAG6 during avian or human influenza virus infection and highlight a potential application of BAG6 for antiviral drug development.

Genetic and Biological Characteristics of Duck-Origin H4N6 Avian Influenza Virus Isolated in China in 2022

The interaction between migratory birds and domestic waterfowl facilitates viral co-infections, leading to viral reassortment and the emergence of novel viruses. In 2022, samples were collected from duck farms around Poyang Lake in Jiangxi Province, China, which is located within the East Asia-Australasia flyway. Three strains of H4N6 avian influenza virus (AIV) were isolated. Genetic and phylogenetic analyses showed that the isolated H4N6 avian influenza viruses (AIVs) belonged to new genotypes, G23 and G24. All isolated strains demonstrated dual receptor binding properties. Additionally, the isolated strains were able to replicate efficiently not only in avian cells but also in mammalian cells. Furthermore, the H4N6 AIV isolates could infect chickens, with viral replication detected in the lungs and extrapulmonary organs, and could transmit within chicken flocks through contact, with viral shedding detected only in oropharyngeal swabs from chickens in the contact group. Notably, the H4N6 AIV could infect mice without prior adaptation and replicate in the lungs with high viral titers, suggesting that it is a potential threat to humans. In conclusion, this study provides valuable insight into the characteristics of H4N6 strains currently circulating in China.

Wideband Direct Detection Constraints on Hidden Photon Dark Matter with the QUALIPHIDE Experiment

We report direction detection constraints on the presence of hidden photon dark matter with masses between 20-30  μeV c^{-2}, using a cryogenic emitter-receiver-amplifier spectroscopy setup designed as the first iteration of QUALIPHIDE (quantum limited photons in the dark experiment). A metallic dish sources conversion photons, from hidden photon kinetic mixing, onto a horn antenna which is coupled to a C band kinetic inductance traveling wave parametric amplifier, providing for near quantum-limited noise performance. We demonstrate a first probing of the kinetic mixing parameter χ to the 10^{-12} level for the majority of hidden photon masses in this region. These results not only represent stringent constraints on new dark matter parameter space, but are also the first demonstrated use of wideband quantum-limited amplification for astroparticle applications.

Different cellular landscape of four types of non-diseased cardiac valves contributes to their differences in susceptibility of pathological remodeling and disease

Funding Acknowledgements

Type of funding sources: Foundation. Main funding source(s): National Natural Science Foundation of China

Background

Exploring the mechanisms of valvular heart disease (VHD) at the cellular level may be useful to identify new therapeutic targets; however, the comprehensive cellular landscape of non-diseased human cardiac valve leaflets remains unclear.

Methods

The cellular landscapes of non-diseased human cardiac valve leaflets (five aortic valves, five pulmonary valves, five tricuspid valves, and three mitral valves) from end-stage heart failure patients undergoing heart transplantation were explored using single-cell RNA sequencing (scRNA-seq). Bioinformatics was used to identify the cell types, describe the cell functions, and investigate cellular developmental trajectories and interactions. Differences among the four types of cardiac valve at the cellular level were summarized. Pathological staining was performed to validate the key findings of scRNA-seq. An integrative analysis of our single-cell data and published genome-wide association study-based and bulk RNA sequencing-based data provided insights into the cell-specific contributions to calcific aortic valve diseases.

Results

Six cell types were identified among 128,412 cells from non-diseased human cardiac valve leaflets. Valvular interstitial cells were the largest population, followed by myeloid cells, lymphocytes, valvular endothelial cells, mast cells, and myofibroblasts. The four types of cardiac valve had distinct cellular compositions. The intercellular communication analysis revealed that valvular interstitial cells were at the center of the communication network. The integrative analysis of our scRNA-seq data revealed key cellular subpopulations involved in the pathogenesis of calcific aortic valve diseases.

Conclusions

The cellular landscape differed among the four types of non-diseased cardiac valve, which might explain their differences in susceptibility to pathological remodeling and VHD.

Development of Superconducting On-chip Fourier Transform Spectrometers

Superconducting On-chip Fourier Transform Spectrometers (SOFTS) are broadband, ultra-compact and electronic interferometers. SOFTS will enable kilo-pixel spectro-imaging focal planes, enhancing sub-millimeter astrophysics and cosmology. Particular applications include cluster astrophysics, cosmic microwave background (CMB) science, and line intensity mapping. This article details the development, design and bench-marking of radio frequency (RF) on-chip architecture of SOFTS for Ka and W-bands.

Probing the role of magnetic fields in star-forming filaments: NIKA2-Pol commissioning results toward OMC-1

Dust polarization observations are a powerful, practical tool to probe the geometry (and to some extent, the strength) of magnetic fields in starforming regions. In particular, Planck polarization data have revealed the importance of magnetic fields on large scales in molecular clouds. However, due to insufficient resolution, Planck observations are unable to constrain the B-field geometry on prestellar and protostellar scales. The high angular resolution of 11.7 arcsec provided by NIKA2-Pol 1.15 mm polarimetric imaging, corresponding to 0.02 pc at the distance of the Orion molecular cloud (OMC), makes it possible to advance our understanding of the B-field morphology in star-forming filaments and dense cores (IRAM 30m large program B-FUN). The commissioning of the NIKA2-Pol instrument has led to several challenging issues, in particular, the instrumental polarization or intensity-to-polarization “leakage” effect. In the present paper, we illustrate how this effect can be corrected for, leading to reliable exploitable data in a structured, extended source such as OMC-1. We present a statistical comparison between NIKA2-Pol and SCUBA2-Pol2 results in the OMC-1 region. We also present tentative evidence of local pinching of the B-field lines near Orion-KL, in the form of a new small-scale hourglass pattern, in addition to the larger-scale hourglass already seen by other instruments such as Pol2.

Multi-probe analysis of the galaxy cluster CL J1226.9+3332: Hydrostatic mass and hydrostatic-to-lensing bias

We present a multi-probe analysis of the well-known galaxy cluster CL J1226.9+3332 as a proof of concept for multi-wavelength studies within the framework of the NIKA2 Sunyaev-Zel’dovich Large Program (LPSZ). CL J1226.9+3332 is a massive and high redshift (z = 0.888) cluster that has already been observed at several wavelengths. A joint analysis of the thermal SZ (tSZ) effect at millimeter wavelength with the NIKA2 camera and in X-ray with the XMM-Newton satellite permits the reconstruction of the cluster’s thermodynamical properties and mass assuming hydrostatic equilibrium. We test the robustness of our mass estimates against different definitions of the data analysis transfer function. Using convergence maps reconstructed from the data of the CLASH program we obtain estimates of the lensing mass, which we compare to the estimated hydrostatic mass. This allows us to measure the hydrostatic-to-lensing mass bias and the associated systematic effects related to the NIKA2 measurement. We obtain M500HSE = (7:65 ± 1:03) × 1014M⊙ and M500lens = (7:35 ± 0:65) × 1014M⊙, which implies a HSE-to-lensing bias consistent with 0 within 20%.

Exploring the millimetre emission in nearby galaxies: Analysis of the edge-on galaxy NGC 891

New observations of the edge-on galaxy NGC 891, at 1.15 and 2mm obtained with the IRAM 30-m telescope and the NIKA2 camera, within the framework of the IMEGIN (Interpreting the Millimetre Emission of Galaxies with IRAM and NIKA2) Large Program, are presented in this work. By using multiwavelength maps (from the mid-IR to the cm wavelengths) we perform SED fitting in order to extract the physical properties of the galaxy on both global and local (~kpc) scales. For the interpretation of the observations we make use of a state-of-the-art SED fitting code, HerBIE (HiERarchical Bayesian Inference for dust Emission). The observations indicate a galaxy morphology, at mm wavelengths, similar to that of the cold dust emission traced by submm observations and to that of the molecular gas. The contribution of the radio emission at the NIKA2 bands is very small (negligible at 1.15 mm and ~ 10% at 2 mm) while it dominates the total energy budget at longer wavelengths (beyond 5 mm). On local scales, the distribution of the free-free emission resembles that of the dust thermal emission while the distribution of the synchrotron emission shows a deficiency along the major axis of the disc of the galaxy.

The NIKA2 Sunyaev-Zeldovich Large Program: Precise galaxy cluster physics for an accurate cluster-based cosmology

The NIKA2 Guaranteed-Time SZ Large Program (LPSZ) is dedicated to the high-angular resolution SZ mapping of a representative sample of 45 SZ-selected galaxy clusters drawn from the catalogues of the Planck satellite, or of the Atacama Cosmology Telescope. The LPSZ sample spans a mass range from 3 to 11 × 1014M⊙ and a redshift range from 0:5 to 0:9, extending to higher redshift and lower mass the previous samples dedicated to the cluster mass calibration and universal properties estimation. The main goals of the LPSZ are the measurement of the average radial profile of the ICM pressure up to R500 by combining NIKA2 with Planck or ACT data, and the estimation of the scaling law between the SZ observable and the mass using NIKA2, XMM-Newton and Planck/ACT data. Furthermore, combining LPSZ data with existing or forthcoming public data in lensing, optical/NIR or radio domains, we will build a consistent picture of the cluster physics and further gain knowledge on the mass estimate as a function of the cluster morphology and dynamical state.

We give an overview of the LPSZ, present recent results and discuss the future implication for cosmology with galaxy clusters.

Searching for high-z DSFGs with NIKA2 and NOEMA

As the possible progenitors of passive galaxies at z=2-3, dusty starforming galaxies (DSFGs) at z>4 provide a unique perspective to study the formation, assembly, and early quenching of massive galaxies in the early Universe. The extreme obscuration in optical-IR makes (sub)mm spectral scans the most universal and unbiased way to confirm/exclude the high-z nature of candidate dusty star-forming galaxies. We present here the status of the NIKA2 Cosmological Legacy Survey (N2CLS), which is the deepest wide-area singledish survey in the millimeter searching for high-z DSFGs. We also introduce a joint-analysis method to effciently search for the spectroscopic redshift of high-z DSFGs with noisy spectra and photometric data and present its success in identifying the redshift of DSFGs found in NIKA2 science verification data.

Galactic star formation with NIKA2 (GASTON): Filament convergence and its link to star formation

In the past decade filaments have been recognised as a major structural element of the interstellar medium, the densest of these filaments hosting the formation of most stars. In some star-forming molecular clouds converging networks of filaments, also known as hub filament systems, can be found. These hubs are believed to be preferentially associated to massive star formation. As of today, there are no metrics that allow the systematic quantification of a filament network convergence. Here, we used the IRAM 30m NIKA2 observations of the Galactic plane from the GASTON large programme to systematically identify filaments and produce a filament convergence parameter map. We use such a map to show that: i. hub filaments represent a small fraction of the global filament population; ii. hubs host, in proportion, more massive and more luminous compact sources that non-hubs; iii. hub-hosting clumps are more evolved that non-hubs; iv. no discontinuities are observed in the properties of compact sources as a function of convergence parameter. We propose that the rapid global collapse of clumps is responsible for (re)organising filament networks into hubs and, in parallel, enhancing the mass growth of compact sources.

PSZ2 G091: A massive double cluster at z ~ 0.822 observed by the NIKA2 camera

PSZ2 G091.83+26.11 is a massive galaxy cluster with M500 = 7:43 × 1014M⊙ at z = 0:822. This object exhibits a complex morphology with a clear bimodality observed in X-rays. However, it was detected and analysed in the Planck sample as a single, spherical cluster following a universal profile [1]. This model can lead to miscalculations of thermodynamical quantities, like the pressure profile. As future multiwavelength cluster experiments will detect more and more objects at higher redshifts (where we expect the fraction of merging objects to be higher), it is crucial to quantify this systematic effect. In this work, we use high-resolution observations of PSZ2 G091.83+26.11 by the NIKA2 camera to integrate the morphological characteristics of the cluster in our modelling. This is achieved by fitting a two-halo model to the SZ image and then by reconstruction of the resulting projected pressure profile. We then compare these results with the spherical assumption.

Galactic Star Formation with NIKA2 (GASTON): Evidence of mass accretion onto dense clumps

High-mass stars (m* ≳ 8 M⊙) play a crucial role in the evolution of galaxies, and so it is imperative that we understand how they are formed. We have used the New IRAM KIDs Array 2 (NIKA2) camera on the Institut de Radio Astronomie Millimétrique (IRAM) 30-m telescope to conduct high-sensitivity continuum mapping of ~ 2 deg2 of the Galactic plane (GP) as part of the Galactic Star Formation with NIKA2 (GASTON) large program. We have identified a total of 1467 clumps within our deep 1.15 mm continuum maps and, by using overlapping continuum, molecular line, and maser parallax data, we have determined their distances and physical properties. By placing them upon an approximate evolutionary sequence based upon 8 μm Spitzer imaging, we find evidence that the most massive dense clumps accrete material from their surrounding environment during their early evolution, before dispersing as star formation advances, supporting clump-fed models of high-mass star formation.

Overdensity of SubMillimiter Galaxies in the GJ526 Field mapped with the NIKA2 Camera

Using the NIKA2 dual band millimeter camera installed on the IRAM30m telescope, we have mapped a relatively large field (~ 70 arcmin2) in the direction of the star GJ526 to investigate the nature of the sources found with the MAMBO camera at 1.2 mm ten years earlier. We have found that they must be dust-obscured galaxies (SMGs) in the background beyond the star. The new NIKA2 map at 1.15 mm reveals additional sources and, in fact, an overdensity of SMGs predominantly distributed along a filament-like structure in projection on the sky across the whole observed field. We speculate this might be a cosmic filament at high redshift as revealed in cosmological hydrodynamical simulations. Measurement of spectroscopic redshifts of the SMGs in the candidate filament is required now for a definitive confirmation of the nature of the structure.

Crab nebula at 260 GHz with the NIKA2 polarimeter: Implications for the polarization angle calibration of future CMB experiments

The quest for primordial gravitational waves enclosed in the Cosmic Microwave Background (CMB) polarization B-modes signal motivates the development of a new generation of high sensitive experiments (e.g. CMBS4, LiteBIRD), thus allowing to probe the inflationary epoch in the early Universe. However, this will be only possible by ensuring a high control of the instrumental systematic effects and an accurate absolute calibration of the polarization angle.

The Crab nebula is known to be a polarization calibrator on the sky for CMB experiments. Already used for the Planck satellite it exhibits a high polarized signal at microwave wavelengths. In this work we present Crab polarization observations obtained, in the 260 GHz frequency band, with the NIKA2 instrument. Furthermore, we discuss the accuracy needed on such a measurement to improve the constraints on the absolute angle calibration for CMB experiments.

The LPSZ-CLASH galaxy cluster sample: Combining lensing and hydrostatic mass estimates

Starting from the clusters included in the NIKA sample and in the NIKA2 Sunyaev-Zel’dovich Large Program (LPSZ) we have selected a sample of six common objects with the Cluster Lensing And Supernova survey with Hubble (CLASH) lensing data. For the LPSZ clusters we have at our disposal both high-angular resolution observations of the thermal SZ with NIKA and NIKA2 and X-ray observations with XMM-Newton from which hydrostatic mass estimates can be derived. In addition, the CLASH dataset includes lensing convergence maps that can be converted into lensing estimates of the total mass of the cluster. One-dimensional mass profiles are used to derive integrated mass estimates accounting for systematic effects (data processing, modeling, etc.). Two-dimensional analysis of the maps can reveal substructures in the cluster and, therefore, inform us about the dynamical state of each system. Moreover, we are able to study the hydrostatic mass to lensing mass bias, across different morphology and a range of redshift clusters to give more insight on the hydrostatic mass bias. The analysis presented in this proceeding follows the study discussed in [20].

Mapping the intracluster medium temperature in the era of NIKA2 and MUSTANG-2

We present preliminary results from an on-going program that aims at mapping the intracluster medium (ICM) temperature of high redshift galaxy clusters from the MaDCoWS sample using a joint analysis of shallow X-ray data obtained by Chandra and high angular resolution Sunyaev-Zel’dovich (SZ) observations realized with the NIKA2 and MUSTANG-2 cameras. We also present preliminary results from an on-going Open Time program within the NIKA2 collaboration that aims at mapping the ICM temperature of a galaxy cluster at z = 0.45 from the resolved detection of the relativistic corrections to the SZ spectrum. These studies demonstrate how high angular resolution SZ observations will play a major role in the coming decade to push the investigation of ICM dynamics and non-gravitational processes to high redshift before the next generation X-ray observatories come into play.

Dust Emission in Galaxies at Millimeter Wavelengths: Cooling of star forming regions in NGC6946

Interstellar dust plays an important role in the formation of molecular gas and the heating and cooling of the interstellar medium. The spatial distribution of the mm-wavelength dust emission from galaxies is largely unexplored. The NIKA2 Guaranteed Time Project IMEGIN (Interpreting the Millimeter Emission of Galaxies with IRAM and NIKA2) has recently mapped the mm emission in the grand design spiral galaxy NGC6946. By subtracting the contributions from the free-free, synchrotron, and CO line emission, we map the distribution of the pure dust emission at 1:15mm and 2mm. Separating the arm/interarm regions, we find a dominant 2mm emission from interarms indicating the significant role of the general interstellar radiation field in heating the cold dust. Finally, we present maps of the dust mass, temperature, and emissivity index using the Bayesian MCMC modeling of the spectral energy distribution in NGC6946.

GASTON: Galactic Star Formation with NIKA2 A new population of cold massive sources discovered

Understanding where and when the mass of stars is determined is one of the fundamental, mostly unsolved, questions in astronomy. Here, we present the first results of GASTON, the Galactic Star Formation with NIKA2 large programme on the IRAM 30m telescope, that aims to identify new populations of low-brightness sources to tackle the question of stellar mass determination across all masses. In this paper, we focus on the high-mass star formation part of the project, for which we map a ~ 2 deg2 region of the Galactic plane around l = 24° in both 1.2 mm and 2.0 mm continuum. Half-way through the project, we reach a sensitivity of 3.7 mJy/beam at 1.2mm. Even though larger than our target sensitivity of 2 mJy, the current sensitivity already allows the identification of a new population of cold, compact sources that remained undetected in any (sub-)mm Galactic plane survey so far. In fact, about 25% of the ~ 1600 compact sources identified in the 1.2mm GASTON image are new detections. We present a preliminary analysis of the physical properties of the GASTON sources as a function of their evolutionary stage, arguing for a potential evolution of the mass distribution of these sources with time.

Cluster cosmology with the NIKA2 SZ Large Program

The main limiting factor of cosmological analyses based on thermal Sunyaev-Zel’dovich (SZ) cluster statistics comes from the bias and systematic uncertainties that affect the estimates of the mass of galaxy clusters. High-angular resolution SZ observations at high redshift are needed to study a potential redshift or morphology dependence of both the mean pressure profile and of the mass-observable scaling relation used in SZ cosmological analyses. The NIKA2 camera is a new generation continuum instrument installed at the IRAM 30-m telescope. With a large field of view, a high angular resolution and a high-sensitivity, the NIKA2 camera has unique SZ mapping capabilities. In this paper, we present the NIKA2 SZ large program, aiming at observing a large sample of clusters at redshifts between 0.5 and 0.9, and the characterization of the first cluster oberved with NIKA2.

Mapping the gas thermodynamic properties of the massive cluster merger MOO J1142+1527 at z = 1.2

We present the results of the analysis of the very massive cluster MOO J1142+1527 at a redshift z = 1.2 based on high angular resolution NIKA2 Sunyaev-Zel’dovich (SZ) andChandraX-ray data. This multi-wavelength analysis enables us to estimate the shape of the temperature profile with unprecedented precision at this redshift and to obtain a map of the gas entropy distribution averaged along the line of sight. The comparison between the cluster morphological properties observed in the NIKA2 andChandramaps together with the analysis of the entropy map allows us to conclude that MOOJ1142+1527 is an on-going merger hosting a cool-core at the position of the X-ray peak. This work demonstrates how the addition of spatially-resolved SZ observations to low signal-to-noise X-ray data can bring valuable insights on the intracluster medium thermodynamic properties atz>1.

Observing with NIKA2Pol from the IRAM 30m telescope : Early results on the commissioning phase

The NIKA2 polarization channel at 260 GHz (1.15 mm) has been proposed primarily to observe galactic star-forming regions and probe the critical scales between 0.01-0.05 pc at which magnetic field lines may channel the matter of interstellar filaments into growing dense cores. The NIKA2 polarime-ter consists of a room temperature continuously rotating multi-mesh HWP and a cold polarizer that separates the two orthogonal polarizations onto two 260 GHz KIDs arrays. We describe in this paper the preliminary results obtained during the most recent commissioning campaign performed in December 2018. We concentrate here on the analysis of the extended sources, while the observation of compact sources is presented in a companion paper [12]. We present preliminary NIKA2 polarization maps of the Crab nebula. We find that the integrated polarization intensity flux measured by NIKA2 is consistent with expectations. In terms of polarization angle, we are still limited by systematic uncertainties that will be further investigated in the forthcoming commissioning campaigns.

Preliminary results on the instrumental polarization of NIKA2-Pol at the IRAM 30m telescope

Clarifying the role of magnetic fields in the star formation process is crucial. Observations have already shown that magnetic fields play an important role in the early stages of star formation. The high spatial resolution (∼0.01 to 0.05 pc) provided by NIKA2-Pol 1.2 mm imaging polarimetry of nearby clouds will help us clarify the geometry of the B-field within dense cores and molecular filaments as part of the IRAM 30m large program B-FUN. There are numerous challenging issues in the validation of NIKA2-Pol such as the calibration of instrumental polarization. The commissioning phase of NIKA2-Pol is underway and is helping us characterize the intensity-to-polarization “leakage” pattern of the instrument. We present a preliminary analysis of the leakage pattern and its dependence with elevation. We also present the current leakage correction made possible by the NIKA2 pipeline in polarization mode based on the NIKA2-Pol commissioning data taken in December 2018. Based on reduced Stokes I, Q, U data we find that the leakage pattern of NIKA2-Pol depends on elevation and is sensitive to the focus of the telescope.

Debris disks around stars in the NIKA2 era

The new NIKA2 camera at the IRAM 30m radiotelescope was used to observe three known debris disks in order to constrain the SED of their dust emission in the millimeter wavelength domain. We have found that the spectral index between the two NIKA2 bands (1mm and 2mm) is consistent with the Rayleigh-Jeans regime (λ-2), unlike the steeper spectra (λ-3) measured in the submillimeter-wavelength domain for two of the three disks - around the stars Vega and HD107146. We provide a succesful proof of concept to model this spectral inversion in using two populations of dust grains, those smaller and those larger than a grain radius a0 of 0.5mm. This is obtained in breaking the slope of the size distribution and the functional form of the absorption coefficient of the standard model. The third disk - around the star HR8799 - does not exhibit this spectral inversion but is also the youngest.

NIKA2 mapping and cross-instrument SED extraction of extended sources with Scanamorphos

The steps taken to tailor to NIKA2 observations the Scanamorphos algorithm (initially developed to subtract low-frequency noise from Herschel on-the-fly observations) are described, focussing on the consequences of the different instrument architecture and observation strategy. The method, making the most extensive use of the redundancy built in the multi-scan coverage with large arrays of a given region of the sky, is applicable to extended sources, while the pipeline is so far optimized for compact sources. An example of application is given. A related tool to build consistent broadband SEDs from 60 microns to 2 mm, combining Herschel and NIKA2 data, has also been developed. Its main task is to process the data least affected by low-frequency noise and coverage limitations (i.e. the Herschel data) through the same transfer function as the NIKA2 data, simulating the same scan geometry and applying the same noise and atmospheric signal as extracted from the 1mm and 2mm data.

The NIKA polarimeter on science targets: Crab nebula observations at 150 GHz and dual-band polarization images of Orion Molecular Cloud OMC-1

We present here the polarization system of the NIKA camera and give a summary of the main results obtained and performed studies on Orion and the Crab nebula. The polarization system was equipped with a room temperature continuously rotating multi-mesh half wave plate and a grid polarizer facing the NIKA cryostat window. NIKA even though less sensitive than NIKA2 had polarization capability in both 1 and 2 millimiter bands. NIKA polarization observations demonstrated the ability of such a technology in detecting the polarization of different targets, compact and extended sources like the Crab nebula and Orion Molecular Cloud region OMC-1. These measurements together with the developed techniques to deal with systematics, opened the way to the current observations of NIKA2 in polarization that will provide important advances in the studies of galactic and extra-galactic emission and magnetic fields.

NIKA: a mm camera for Sunyaev-Zel’dovich science in clusters of galaxies

Clusters of galaxies, the largest bound objects in the Universe, constitute a cosmological probe of choice, which is sensitive to both dark matter and dark energy. Within this framework, the Sunyaev-Zel’dovich (SZ) effect has opened a new window for the detection of clusters of galaxies and for the characterization of their physical properties such as mass, pressure and temperature. NIKA, a KID-based dual band camera installed at the IRAM 30-m telescope, was particularly well adapted in terms of frequency, angular resolution, field-of-view and sensitivity, for the mapping of the thermal and kinetic SZ effect in high-redshift clusters. In this paper, we present the NIKA cluster sample and a review of the main results obtained via the measurement of the SZ effect on those clusters: reconstruction of the cluster radial pressure profile, mass, temperature and velocity.

A low-mass galaxy cluster as a test-case study for the NIKA2 SZ Large Program

High-resolution mapping of the hot gas in galaxy clusters is a key tool for cluster-based cosmological analyses. Taking advantage of the NIKA2 millimeter camera operated at the IRAM 30-m telescope, the NIKA2 SZ Large Program seeks to get a high-resolution follow-up of 45 galaxy clusters covering a wide mass range at high redshift in order to re-calibrate some of the tools needed for the cosmological exploitation of SZ surveys. We present the second cluster analysis of this program, targeting one of the faintest sources of the sample in order to tackle the difficulties in data reduction for such faint, low-SNR clusters. In this study, the main challenge is the precise estimation of the contamination by sub-millimetric point sources, which greatly affects the tSZ map of the cluster. We account for this contamination by performing a joint fit of the SZ signal and of the flux density of the compact sources. A prior knowledge of these fluxes is given by the adjustment of the SED of each source using data from both NIKA2 and the Herschel satellite. The first results are very promising and demonstrate the possibility to estimate thermodynamic properties with NIKA2, even in a compact cluster heavily contaminated by point sources.

Association between methylenetetrahydrofolate reductase polymorphisms and non-syndromic cleft lip with or without palate susceptibility: an updated systematic review and meta-analysis

Methylenetetrahydrofolate reductase (MTHFR) polymorphisms are thought to be involved in the development of cleft lip with or without cleft palate (NSCL/P), but published results are contradictory. We therefore designed an updated meta-analysis to pool eligible studies and to evaluate further the possible relations between MTHFR polymorphisms (c.677C>T and c.1298A>C) and susceptibility to NSCL/P. A comprehensive search based on PubMed, Medline, Web of Science, and Embase databases was made up to February 2018. Twenty-three case-control and 10 case-parent trio studies (including 1149 cases and 1161 controls) were retrieved. Odds ratio (OR) with 95% CI were used to estimate the pooled strength of association under different genetic models. The Q test and I² test were used to estimate heterogeneity among studies, the quality of which was assessed using the Newcastle-Ottawa scale. In the MTHFR c.677C>T polymorphism group, there were significant overall results for the recessive (OR 1.231, 95%CI 1.092 to 1.387) and homozygote (OR 1.252, 95%CI 1.078 to 1.456) models. Subgroup analysis by subjects and ethnicity identified only associations in European mothers for the recessive model and the homozygote model. For the c.1298A>C group, there were no significant results for either European or Asian patients for all genetic models. The MTHFR c.677C>T polymorphism might increase susceptibility to NSCL/P in European mothers, but was negatively associated in Asian patients, and the MTHFR c.1298A>C polymorphism is not involved in the development of NSCL/P in either European or Asian patients.

[Investigation on endometrium from menstrual blood as a source of non-invasive tissue]

Objective: To investigate the feasibility of a non-invasive sampling method by collecting menstrual blood and obtaining endometrium for further research in menstruation-related diseases. Methods: On the second day of menstruation, menstrual blood was collected with menstrual cups for 4 hours, and the menstrual endometrium was filtered through a metal screen for weighing, cryopreserved, immunohistochemical staining and cell culture. Results: The collection process was painless and non-invasive. In the control group, the menstrual volume was (9.1±0.7) ml, and the endometrial tissue weight was (91.0±14.7) g. In the endometriosis group, the menstrual volume was (9.6±1.9) ml (P=0.022), and the endometrial tissue weight was (134.7±43.9) g (P=0.057). Endometrial cell culture was successful in all patients and should not be contaminated. The growth curve was a finite cell line type. The expression of cytokeratin 19 and vimentin in menstrual endometrium and cells were positive. Conclusions: By collecting menstrual blood and filtering endometrial tissue, it is an ideal non-invasive sampling method. In combination with advanced experimental technology, menstrual endometrium make further researches of endometriosis, endometrial lesions or other menstruation-related diseases possible.

Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function

The emerging avian-origin H7N9 influenza A virus, which causes mild to lethal human respiratory disease, continues to circulate in China, posing a great threat to public health. Influenza NS1 protein plays a key role in counteracting host innate immune responses, allowing the virus to efficiently replicate in the host. In this study, we compared NS1 amino acid sequences of H7N9 influenza A virus with those of other strains, and determined NS1 protein variability within the H7N9 virus and then evaluated the impact of amino acid substitutions on ability of the NS1 proteins to inhibit host innate immunity. Interestingly, the amino acid residue S212 was identified to have a profound effect on the primary function of NS1, since S212P substitution disabled H7N9 NS1 in suppressing the host RIG-I-dependent interferon response, as well as the ability to promote the virus replication. In addition, we identified another amino acid residue, I178, serving as a key site to keep NS1 protein high steady-state levels. When the isoleucine was replaced by valine at 178 site (I178V mutation), NS1 of H7N9 underwent rapid degradation through proteasome pathway. Furthermore, we observed that P212S and V178I mutation in NS1 of PR8 virus enhanced virulence and promoted the virus replication in vivo. Together, these results indicate that residues I178 and S212 within H7N9 NS1 protein are critical for stability and functioning of the NS1 protein respectively, and may contribute to the enhanced pathogenicity of H7N9 influenza virus.

Protein expression in dairy cows with and without subclinical hypocalcaemia

AIM

To determine differences in plasma proteomic profiles between healthy cows and those with subclinical hypocalcaemia within 12 hours after calving, and thereby explore the underlying biological mechanism of subclinical hypocalcaemia in dairy cows.

METHODS

Plasma samples were collected within 6 hours of calving from Holstein cows on a farm in Heilongjiang, China; 32 with subclinical hypocalcaemia (plasma calcium concentration 1.38-2.00 mmol/L and no clinical signs) and 59 control cows (plasma calcium concentration 2.10-2.8 mmol/L). Plasma samples were applied to weak cationic exchange protein chips for protein profiling by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS), and the data were analysed using the PBS-IIC system. The amplitude of peaks for the two groups were compared using the Wilcoxon sum-rank test, and the mass-to-charge ratio of the peaks that differed was used to identify peptide fragments using the Swiss-Prot protein database.

RESULTS

Seven peaks were identified in the subclinical hypocalcaemia group that differed from those of the control group (p<0.001), that represented six unique proteins. Expression of serum albumin, fibrinogen alpha chain, amyloid beta A4 proteins and neurosecretory protein VGF were increased, and expression of apolipoprotein A-II and serum amyloid A proteins were decreased in the subclinical hypocalcaemic cows compared with control cows.

CONCLUSION

Use of SELDI-TOF-MS technology can effectively identify differences in plasma protein expression patterns in cows with subclinical hypocalcaemia. Neurosecretory protein VGF and amyloid beta A4 protein might represent useful biomarkers for diagnosis of subclinical hypocalcaemia.

Ultrafine particles generated from coloring with scented markers in the presence of ozone

High concentrations of ultrafine particles (UFPs) have been previously reported during school art activities. This is possibly due to secondary organic aerosols (SOAs) formed from reactions between ozone and volatile organic compounds emitted from art products. Four brands of markers, three scented and one unscented, were tested inside a stainless steel chamber at eight different ozone concentrations between 0 and 300 ppb. Out of the 32 tested markers, only the lemon- and orange-scented markers from one brand reacted with ozone to form UFPs. Limonene, pinene, and several other terpenes were identified as ingredients of ink in SOA-forming markers. Coloring with one lemon-scented marker for 1 min without ozone generated on average approximately 26 ± 4 ppb of limonene inside the chamber. At 150 ppb ozone, using one lemon marker for 1 min formed on average 7.7 × 10(10) particles. The particle size distribution indicated an initial mode of 15 nm which grew to 40 nm. At 50 ppb ozone and below, no significant SOA formation occurred. The number of particles formed is moderately correlated with the mass of ink used (R(2)  = 0.68). Based on these data, scented markers are not likely a strong source of SOA under normal indoor ozone levels.

Outcomes and patterns of secondary relapse in platinum-sensitive ovarian cancer: implications for tertiary cytoreductive surgery

AIM

To evaluate the outcomes and patterns of patients with secondary relapsed ovarian cancer.

METHODS

A retrospective study was conducted. The cases comprised 83 patients who underwent tertiary cytoreductive surgery (TCS) followed by chemotherapy, whereas the controls consisted of 76 patients who received chemotherapy alone.

RESULTS

The median survival was 20 months in 159 patients. Patients with microscopic residual disease after TCS had a median survival of 32.9 months compared with 14.6 months in those with macroscopic residual disease [hazard ratio (HR), 2.82; P = 0.001) and 15.0 months in patients with chemotherapy alone (HR, 2.23; P = 0.001). When stratified by a progression-free interval (PFI) after secondary cytoreduction (SCR), TCS showed no benefit in patients with a PFI ≤12 months or a PFI >12 months compared with those with chemotherapy alone. TCS improved survival in patients with recurrent disease in the pelvis compared with those with recurrent disease in the middle or upper abdomen, with a median survival of 34.9 months and 14.6 months, respectively (HR, 2.94; P = 0.010). However, TCS was not a survival determinant by multivariate analysis. A multivariate analysis identified a PFI after SCR (≤12 mos vs. >12 mos; HR, 2.34; 95% CI, 1.29-4.24; P = 0.005), mesenteric lymph node metastasis at SCR (yes vs. no; HR, 4.18; 95% CI, 1.93-9.03; P < 0.001) and treatment arms at secondary relapse (chemotherapy alone vs. TCS; HR, 1.56; 95% CI, 1.03-2.38; P = 0.037) as independent predictors of survival.

CONCLUSIONS

Limited survival benefit from tertiary cytoreductive surgery was observed in patients with platinum-sensitive secondary relapsed ovarian cancer.

Adoptive immunotherapy of intracranial tumors by systemic transfer of tumor-draining lymph node cells (Review)

T lymphocytes, reactive against tumor antigens, mediate the regression of established tumors upon adoptive transfer. We have developed an effective therapy for experimental brain tumors by systemic intravenous transfer of ex vivo activated T cells derived from tumor-draining lymph nodes. Both CD4 and CD8 T cells are required to mediate tumor regression which is exquisitely specific and confers immunologic memory. Several factors influencing the efficacy of adoptive immunotherapy for brain tumors are markedly different than for optimal treatment of tumors at other visceral sites. A similarly designed phase I clinical trial has been initiated for the treatment of malignant astrocytomas.

The multi-hit hypothesis of primary biliary cirrhosis: polyinosinic-polycytidylic acid (poly I:C) and murine autoimmune cholangitis

A void in understanding primary biliary cirrhosis (PBC) is the absence of appropriate animal models. Our laboratory has studied a murine model of autoimmune cholangitis induced following immunization with 2-octynoic acid (2OA), an antigen identified following extensive quantitative structural activity relationship (QSAR) analysis, using human autoantibodies and three-dimensional analysis of the mitochondrial autoantigen, the E2 subunit of the pyruvate dehydrogenase complex (PDC-E2). Mice immunized with 2OA coupled to bovine serum albumin (BSA) develop anti-mitochondrial antibodies (AMAs) of the identical specificity as humans with PBC, and in addition develop inflammatory portal cell infiltrates in liver. However, the natural history of disease is less severe than in humans and does not include fibrosis. Data from human and autoimmune murine models suggest that environmental and/or infectious agents can exacerbate autoimmune reactions, and a model of PBC has been described in which polyinosinic-polycytidylic acid (poly I:C), a viral RNA mimetic and Toll-like receptor 3 (TLR-3) agonist induces low-titre AMAs and in mild portal infiltrates. We took advantage of our established model to determine whether immunization with 2OA-BSA coupled with poly I:C alters the disease process. Indeed, the addition of poly I:C produces a profound exacerbation of autoimmune cholangitis, including a significant increase in CD8(+) infiltrating T cells, as well as a marked increase of proinflammatory cytokines. In addition, mice have evidence of fibrosis. These findings lend support to the concept that besides breakdown of self-tolerance, there is a requirement of a second 'hit' during the breakdown process that leads to disease which more faithfully mimics human PBC.

Expression of tumor invasion factors determines systemic engraftment and induction of humoral hypercalcemia in a mouse model of adult T-cell leukemia

Infection with human T-cell leukemia virus type 1 (HTLV-1) leads sometimes to the development of adult T-cell lymphoma/leukemia (ATL), which is invariably fatal and often associated with humoral hypercalcemia of malignancy. The transformation of infected CD4 T cells and the pathogenesis of leukemia have been studied with great limitation in tissue culture and patients. To better understand the pathogenesis and perform preclinical drug studies, animal models of ATL are urgently needed. In mice, inoculation of HTLV-1 cell lines mostly leads to development of localized lymphomas. To develop an ATL animal model with leukemic spread of ATL cells, mouse strains with different well-defined immune deficiencies were inoculated intraperitoneally with different HTLV-1-infected cell lines (ACH.2, C8166, MT-2, MET-1). Inoculation of MET-1 cells into NOD/SCID mice provided the best model system for slowly developing T-cell leukemia with multiple organ involvement. In leukemic mice, an increase in serum calcium levels correlated with expression of receptor activator of nuclear factor kappa-light-chain-enhancer of activated B cells ligand on leukemic cells and secretion of parathyroid hormone-related protein and interleukin-6. In contrast to the other cell lines that did not spread systemically, MET-1 expressed both the adhesion molecules CD11a (LFA-1alpha) and CD49d (VLA-4alpha) and produced or induced expression of matrix metalloproteinases 1, 2, 3, and 9, thus underlining the importance of these molecules in the spread of adult T-cell leukemia cells. The MET-1/NOD/SCID model will be useful for developing interventions against invasion and spread of leukemic cells and subsequent humoral hypercalcemia of malignancy.

Expression of recombinant rat Neurotrophin-3 in Chinese hamster ovary cells

The CHO cell line stably producing recombinant rat NT-3 was established. The insertion of rNT-3 cDNA into transferred cell gonome was analyzed with Southern blot. The expressed protein was identified by Dot ELISA (enzyme-linked immunosorbent assay) and Western blot. Western blot showed a clear specific band of about 14 ku for NT-3. The mean level of rNT-3 in four NT-3cDNA/CHO cell lines was about 2 100 ng/10(6) cells/48 h determined by EIA. The conditioned-medium (CM) of NT-3cDNA/CHO cells could promote the fiber outgrowth of the dissociated dorsal root ganglion of 8-day-old chick embryos, which shows a dose-response relationship. A half-maximal concentration of the biological activity (EC50) of the recombinant protein was approximately 16.7 ng/mL. The MoAb 3W3 of NT-3 could neutralize the biological activity of the rNT-3.

Transcriptional regulation of parathyroid hormone-related protein promoter P2 by NF-kappaB in adult T-cell leukemia/lymphoma

Parathyroid hormone-related protein (PTHrP) plays a primary role in the development of humoral hypercalcemia of malignancy (HHM) that occurs in the majority of patients with adult T-cell leukemia/lymphoma (ATLL) due to human T-cell lymphotropic virus type-1 (HTLV-1) infection. We previously showed that ATLL cells constitutively express high levels of PTHrP via activation of promoters P2 and P3, resulting in HHM. In this study, we characterized a nuclear factor-kappaB (NF-kappaB) binding site in the P2 promoter of human PTHrP. Using electrophoretic mobility shift assays, we detected a specific complex in Tax-expressing human T cells composed of p50/c-Rel, and two distinct complexes in ATLL cells consisting of p50/p50 homodimers and a second unidentified protein(s). Chromatin immunoprecipitation assays confirmed in vivo binding of p50 and c-Rel on the PTHrP P2 promoter. Using transient co-transfection with NF-kappaB expression plasmids and PTHrP P2 luciferase reporter-plasmid, we showed that NF-kappaB p50/p50 alone and p50/c-Rel or p50/Bcl-3 cooperatively upregulated the PTHrP P2 promoter. Furthermore, inhibition of NF-kappaB activity by Bay 11-7082 reduced PTHrP P2 promoter-initiated transcripts in HTLV-1-infected T cells. In summary, the data demonstrated that transcriptional regulation of PTHrP in ATLL cells can be controlled by NF-kappaB activation and also suggest a Tax-independent mechanism of activation of PTHrP in ATLL.

Therapeutic vaccine generated by electrofusion of dendritic cells and tumour cells

Immunotherapy with fusion of dendritic cells (DCs) and tumour cells potentially confers the advantages of DC antigen-presenting functionality and a continuous source of unaltered tumour antigens. However, fusion using chemical or viral fusogens has been inefficient. We have recently developed a high throughput electrofusion technique with which very efficient fusion rates (15-54%) were observed in over 300 experiments, using a variety of murine and human tumour cell lines. The fused cells display a mature DC phenotype and express tumour-associated antigens. In two pre-clinical animal models (B16 melanoma transduced with the LacZ gene and the MCA 205 fibrosarcoma), a single vaccination of mice bearing tumours established in the lung, brain and skin resulted in tumour regression and prolongation of life. However, therapeutic efficacy required the administration of adjuvants such as IL-12 and OX-40R mAbs. Effective immunotherapy also required the delivery of fusion cells directly into lymphoid organs (spleen or lymph nodes). Using five defined human T cell lines derived from melanoma patients, allogeneic DCs of HLA-A2, HLA-DR4 and HLA-DR7 haplotypes fused with MART-1, gp100, tyrosinase and TRP-2 expressing 888 mel melanoma cells were analysed for their ability to stimulate specific cytokine (IFN-gamma and GM-CSF) secretion. DC-888 mel hybrids presented all tumour-associated epitopes to both CD4 and CD8 T cell lines in the context of MHC class II and I molecules, respectively. The therapeutic efficacy of a DC-tumour fusion vaccine is now being evaluated for the treatment of metastatic melanoma.

Adoptive immunotherapy of CNS malignancies

Although many patients with malignant brain tumors can be rendered free of bulk disease by current surgery and radiotherapy techniques, complete tumor eradication is extremely difficult to achieve, raising interest for T-cell adoptive immunotherapy. Conclusive experimental data generated by many investigators coupled with clinical experience have debunked many of the theoretical 'obstacles' to immunotherapy in the CNS. First, there does not appear to be a significant vascular barrier in brain tumors to prevent trafficking of systemically administered activated T cells. Moreover, T cells stimulated in the periphery by DC vaccination are able to mediate regression of established intracranial tumors. Second, brain tumor patients are able to mount an immune response against autologous tumor. Not surprisingly, patient factors such as tumor burden, corticosteroid use, advanced age, or recent chemotherapy can inhibit the immune response to tumor. Directing this type of therapy to patients without these factors may improve the likelihood of response. Third, therapeutic immune responses occurring within the CNS against tumors derived from CNS tissue have not been associated with clinical signs of autoimmune reactions against normal brain tissue. The general toxicity associated with the systemic adoptive transfer of ex vivo activated LN cells is very low. Toxicity of activated T cells delivered locally into the tumor resection cavity likewise is low and transient. Current phase II clinical trials of AI are in progress to determine the response rate for patients with newly diagnosed malignant gliomas. Future developments to characterize shared brain tumor antigens and develop more effective strategies for vaccination may lead to a more effective and broadly applicable therapy for CNS malignancies.

T-cell adoptive therapy of tumors: mechanisms of improved therapeutic performance

The T cells of many cancer patients are naturally sensitized to tumor-associated antigens (Ag), or they can readily be sensitized with vaccine maneuvers. In melanoma patients, the adoptive transfer of such T cells can often be causally linked to the objective regression of established tumors. So far, few patients have shown sustained clinical benefit from such therapy, but preclinical mouse studies have now clearly delineated the hurdles that must be overcome to render T-cell-based antitumor therapy effective. Contrary to earlier expectations, it is now established that remarkably potent CD4+ and CD8+ pre-effector T cells are naturally sensitized even in mice bearing progressive, weakly immunogenic tumors. However, such T cells often display signal transduction impairments as a consequence of the tumor environment, which limit their acquisition of optimal effector function. Extracorporealization and culture of these tumor-sensitized T cells with appropriate activation stimuli not only restores normal signal transduction, but also confers resolute effector activity that can often sustain tumor rejection upon reinfusion. In mouse studies, the L-selectin(low) fraction of T cells in tumor-draining lymph nodes (TDLN) constitutes the potent pre-effector population and comprises both CD4+ and helper-independent CD8+ T cells. Appropriate in vitro activation confers an apparently unrestricted trafficking capacity to this fraction, and even the ability to proliferate within the tumor bed, leading to unprecedented tumor rejection at anatomic sites (e.g., subcutaneous and intracranial) that were historically refractory to such treatment. Such results underscore the surprising capacity of appropriately activated effector T cells to withstand the immunosuppressive, tolerogenic, and apoptotic influences of the typical tumor environment. Given the increasingly appreciated and critical communications between T cells and host Ag-presenting cells (APC), which cross-present tumor Ag, it is likely that dendritic cell-based vaccine maneuvers that promote sensitization of T1-committed L-selectin(low) antitumor T cells will play an increasingly important role in adoptive therapy strategies.

An integrated computational pipeline and database to support whole-genome sequence annotation

We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome annotation. The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture.