Characterizing the Youngest Herschel-detected Protostars I. Envelope Structure Revealed by CARMA Dust Continuum Observations

We present CARMA 2.9 mm dust continuum emission observations of a sample of 14 Herschel-detected Class 0 protostars in the Orion A and B molecular clouds, drawn from the PACS Bright Red Sources (PBRS) sample (Stutz et al.). These objects are characterized by very red 24 \micron\ to 70 \micron\ colors and prominent submillimeter emission, suggesting that they are very young Class 0 protostars embedded in dense envelopes. We detect all of the PBRS in 2.9 mm continuum emission and emission from 4 protostars and 1 starless core in the fields toward the PBRS; we also report 1 new PBRS source. The ratio of 2.9 mm luminosity to bolometric luminosity is higher by a factor of $\sim$5 on average, compared to other well-studied protostars in the Perseus and Ophiuchus clouds. The 2.9 mm visibility amplitudes for 6 of the 14 PBRS are very flat as a function of uv-distance, with more than 50\% of the source emission arising from radii $<$ 1500 AU. These flat visibility amplitudes are most consistent with spherically symmetric envelope density profiles with $\rho$~$\propto$~R$^{-2.5}$. Alternatively, there could be a massive unresolved structure like a disk or a high-density inner envelope departing from a smooth power-law. The large amount of mass on scales $<$ 1500 AU (implying high average central densities) leads us to suggest that that the PBRS with flat visibility amplitude profiles are the youngest PBRS and may be undergoing a brief phase of high mass infall/accretion and are possibly among the youngest Class 0 protostars. The PBRS with more rapidly declining visibility amplitudes still have large envelope masses, but could be slightly more evolved.Comment: Accepted to ApJ, 40 pages, 9 Figures, 4 Table

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown

<p>Abstract</p> <p>Background</p> <p>Methods of determining whether or not any particular HIV-1 sequence stems - completely or in part - from some unknown HIV-1 subtype are important for the design of vaccines and molecular detection systems, as well as for epidemiological monitoring. Nevertheless, a single algorithm only, the Branching Index (BI), has been developed for this task so far. Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments.</p> <p>Results</p> <p>We have developed <it>Unknown Subtype Finder </it>(USF), an algorithm based on a probabilistic model, which automatically determines which parts of an input sequence originate from a subtype yet unknown. The underlying model is based on a simple profile hidden Markov model (pHMM) for each <it>known </it>subtype and an additional pHMM for an <it>unknown </it>subtype. The emission probabilities of the latter are estimated using the emission frequencies of the known subtypes by means of a (position-wise) probabilistic model for the emergence of new subtypes. We have applied USF to SIV and HIV-1 sequences formerly classified as having emerged from an unknown subtype. Moreover, we have evaluated its performance on artificial HIV-1 recombinants and non-recombinant HIV-1 sequences. The results have been compared with the corresponding results of the BI.</p> <p>Conclusions</p> <p>Our results demonstrate that USF is suitable for detecting segments in HIV-1 sequences stemming from yet unknown subtypes. Comparing USF with the BI shows that our algorithm performs as good as the BI or better.</p

The warm and dense Galaxy - tracing the formation of dense cloud structures out to the Galactic Center

The past two decades have seen extensive surveys of the far-infrared to submillimeter continuum emission in the plane of our Galaxy. We line out prospects for the coming decade for corresponding molecular and atomic line surveys which are needed to fully understand the formation of the dense structures that give birth to clusters and stars out of the diffuse interstellar medium. We propose to work towards Galaxy wide surveys in mid-J CO lines to trace shocks from colliding clouds, Galaxy-wide surveys for atomic Carbon lines in order to get a detailed understanding of the relation of atomic and molecular gas in clouds, and to perform extensive surveys of the structure of the dense parts of molecular clouds to understand the importance of filaments/fibers over the full range of Galactic environments and to study how dense cloud cores are formed from the filaments. This work will require a large (50m) Single Dish submillimeter telescope equipped with massively multipixel spectrometer arrays, such as envisaged by the AtLAST project.Comment: Science white paper submitted to the Astro2020 Decadal Surve

HOPS 383: An Outbursting Class 0 Protostar in Orion

We report the dramatic mid-infrared brightening between 2004 and 2006 of HOPS 383, a deeply embedded protostar adjacent to NGC 1977 in Orion. By 2008, the source became a factor of 35 brighter at 24 microns with a brightness increase also apparent at 4.5 microns. The outburst is also detected in the submillimeter by comparing APEX/SABOCA to SCUBA data, and a scattered-light nebula appeared in NEWFIRM K_s imaging. The post-outburst spectral energy distribution indicates a Class 0 source with a dense envelope and a luminosity between 6 and 14 L_sun. Post-outburst time-series mid- and far-infrared photometry shows no long-term fading and variability at the 18% level between 2009 and 2012. HOPS 383 is the first outbursting Class 0 object discovered, pointing to the importance of episodic accretion at early stages in the star formation process. Its dramatic rise and lack of fading over a six-year period hint that it may be similar to FU Ori outbursts, although the luminosity appears to be significantly smaller than the canonical luminosities of such objects.Comment: Accepted by ApJ Letters, 6 pages, 4 figures; v2 has an updated email address for the lead autho

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

BACKGROUND: Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events. RESULTS: We developed a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach. Given a partition of the aligned input sequence family into known sequence subtypes, our model can jump between states corresponding to these different subtypes, depending on which subtype is locally most similar to a database sequence. Jumps between different subtypes are indicative of intersubtype recombinations. We applied our method to a large set of genome sequences from human immunodeficiency virus (HIV) and hepatitis C virus (HCV) as well as to simulated recombined genome sequences. CONCLUSION: Our results demonstrate that jumps in our jumping profile HMM often correspond to recombination breakpoints; our approach can therefore be used to detect recombinations in genomic sequences. The recombination breakpoints identified by jpHMM were found to be significantly more accurate than breakpoints defined by traditional methods based on comparing single representative sequences

Molecular outflows in the young open cluster IC348

We present a wide-field survey of the young open cluster IC348 for molecular H2 outflows. Outflow activity is only found at its south-western limit, where a new subcluster of embedded sources is in an early phase of its formation. If the IC348 cluster had been built up by such subclusters forming at different times, this could explain the large age-spread that Herbig (1998) found for the IC348 member stars. In addition to several compact groups of H2 knots, our survey reveals a large north-south oriented outflow, and we identify the newly discovered far-infrared and mm-object IC348MMS as its source. New deep images in the 1-0 S(1) line of molecular hydrogen trace the HH211 jet and counterjet as highly-collimated chains of knots, resembling the interferometric CO and SiO jets. This jet system appears rotated counter-clockwise by about 3 degrees with respect to the prominent H2 bow shocks. Furthermore, we resolve HH211-mm as a double point-like source in the mm-continuum.Comment: 10 pages, 9 figures, accepted for publication in Ap

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1

Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach proposed by Spang et al. The input data for our server is a partial or complete genome sequence from HIV-1; our tool assigns regions of the input sequence to known subtypes of HIV-1 and predicts phylogenetic breakpoints. jpHMM is available online at