DiFX2: A more flexible, efficient, robust and powerful software correlator

Software correlation, where a correlation algorithm written in a high-level language such as C++ is run on commodity computer hardware, has become increasingly attractive for small to medium sized and/or bandwidth constrained radio interferometers. In particular, many long baseline arrays (which typically have fewer than 20 elements and are restricted in observing bandwidth by costly recording hardware and media) have utilized software correlators for rapid, cost-effective correlator upgrades to allow compatibility with new, wider bandwidth recording systems and improve correlator flexibility. The DiFX correlator, made publicly available in 2007, has been a popular choice in such upgrades and is now used for production correlation by a number of observatories and research groups worldwide. Here we describe the evolution in the capabilities of the DiFX correlator over the past three years, including a number of new capabilities, substantial performance improvements, and a large amount of supporting infrastructure to ease use of the code. New capabilities include the ability to correlate a large number of phase centers in a single correlation pass, the extraction of phase calibration tones, correlation of disparate but overlapping sub-bands, the production of rapidly sampled filterbank and kurtosis data at minimal cost, and many more. The latest version of the code is at least 15% faster than the original, and in certain situations many times this value. Finally, we also present detailed test results validating the correctness of the new code.Comment: 28 pages, 9 figures, accepted for publication in PAS

A multi-scale multi-frequency deconvolution algorithm for synthesis imaging in radio interferometry

Aims : We describe MS-MFS, a multi-scale multi-frequency deconvolution algorithm for wide-band synthesis-imaging, and present imaging results that illustrate the capabilities of the algorithm and the conditions under which it is feasible and gives accurate results. Methods : The MS-MFS algorithm models the wide-band sky-brightness distribution as a linear combination of spatial and spectral basis functions, and performs image-reconstruction by combining a linear-least-squares approach with iterative $\chi^2$ minimization. This method extends and combines the ideas used in the MS-CLEAN and MF-CLEAN algorithms for multi-scale and multi-frequency deconvolution respectively, and can be used in conjunction with existing wide-field imaging algorithms. We also discuss a simpler hybrid of spectral-line and continuum imaging methods and point out situations where it may suffice. Results : We show via simulations and application to multi-frequency VLA data and wideband EVLA data, that it is possible to reconstruct both spatial and spectral structure of compact and extended emission at the continuum sensitivity level and at the angular resolution allowed by the highest sampled frequency.Comment: 17 pages, 11 figure

Rare Presentation of Rosai-Dorfman Disease in Soft Tissue: Diagnostic Findings and Surgical Treatment.

Introduction and Importance. Rosai-Dorfman disease (RDD) is a rare, benign type II histiocytosis characterized by the infiltration of S100+ histiocytes and emperipolesis. The disease may present in the lymph nodes (nodal RDD), in extranodal sites, or in both nodal and extranodal sites. Among those patients who present exclusively in extranodal sites, only a minority of cases present in the soft tissue. Case Presentation. An 18-year-old female presented to orthopedic oncology clinic with a chief complaint of a mass located in her lower back. The patient underwent excision of the lumbosacral mass. Pathologic review demonstrated emperipolesis of lymphocytes and plasma cells within enlarged, eosinophilic histiocytes in a background of lymphoplasmacytic infiltration and collagenous stroma. Immunohistochemical staining demonstrated S100+ and CD163+ histiocytes, consistent with diagnosis of soft tissue RDD. Clinical Discussion. Histologically, RDD is generally characterized by emperipolesis-the presence of intact lymphocytes within the histiocyte cytoplasm-and a mixed infiltrate of S100+ histiocytes, mononuclear cells, plasma cells, and lymphocytes. Although soft tissue RDD may histologically resemble nodal RDD, soft tissue RDD also demonstrates some notable histologic differences including the lack of nodal architecture, the presence of increased fibrosis and collagen deposition, and generally fewer RDD cells. Conclusion. This case presentation demonstrates one few reports of isolated soft tissue RDD within the lumbosacral region without associated lymphadenopathy or skin changes and highlights the heterogeneity that still exists in the treatment paradigm of extranodal RDD

On the Calibration of Full-polarization 86GHz Global VLBI Observations

We report the development of a semi-automatic pipeline for the calibration of 86 GHz full-polarization observations performed with the Global Millimeter-VLBI array (GMVA) and describe the calibration strategy followed in the data reduction. Our calibration pipeline involves non-standard procedures, since VLBI polarimetry at frequencies above 43 GHz is not yet well established. We also present, for the first time, a full-polarization global-VLBI image at 86 GHz (source 3C 345), as an example of the final product of our calibration pipeline, and discuss the effect of instrumental limitations on the fidelity of the polarization images. Our calibration strategy is not exclusive for the GMVA, and could be applied on other VLBI arrays at millimeter wavelengths. The use of this pipeline will allow GMVA observers to get fully-calibrated datasets shortly after the data correlation.Comment: 10 pages, 10 figures. Accepted for publication in A&

Single-particle-sensitive imaging of freely propagating ultracold atoms

We present a novel imaging system for ultracold quantum gases in expansion. After release from a confining potential, atoms fall through a sheet of resonant excitation laser light and the emitted fluorescence photons are imaged onto an amplified CCD camera using a high numerical aperture optical system. The imaging system reaches an extraordinary dynamic range, not attainable with conventional absorption imaging. We demonstrate single-atom detection for dilute atomic clouds with high efficiency where at the same time dense Bose-Einstein condensates can be imaged without saturation or distortion. The spatial resolution can reach the sampling limit as given by the 8 \mu m pixel size in object space. Pulsed operation of the detector allows for slice images, a first step toward a 3D tomography of the measured object. The scheme can easily be implemented for any atomic species and all optical components are situated outside the vacuum system. As a first application we perform thermometry on rubidium Bose-Einstein condensates created on an atom chip.Comment: 24 pages, 10 figures. v2: as publishe

Differential var Gene Expression in Children with Malaria and Antidromic Effects on Host Gene Expression

Among 62 children with mild malaria, cerebral malaria, or severe malarial anemia, we analyzed the transcription of different var gene types. There was no difference in parasitemia level or body temperature between groups. However, a significantly different expression pattern was observed in children with cerebral malaria, compared with that in patients in the other 2 groups: children with cerebral malaria had lower expression of the upsA subtype but higher expression of the upsB and upsC subtypes. Furthermore, expression of human genes responsive to tumor necrosis factor and hypoxia correlated with distinct ups type

Zooming towards the Event Horizon - mm-VLBI today and tomorrow

Global VLBI imaging at millimeter and sub-millimeter wavelength overcomes the opacity barrier of synchrotron self-absorption in AGN and opens the direct view into sub-pc scale regions not accessible before. Since AGN variability is more pronounced at short millimeter wavelength, mm-VLBI can reveal structural changes in very early stages after outbursts. When combined with observations at longer wavelength, global 3mm and 1mm VLBI adds very detailed information. This helps to determine fundamental physical properties at the jet base, and in the vicinity of super-massive black holes at the center of AGN. Here we present new results from multi-frequency mm-VLBI imaging of OJ287 during a major outburst. We also report on a successful 1.3mm VLBI experiment with the APEX telescope in Chile. This observation sets a new record in angular resolution. It also opens the path towards future mm-VLBI with ALMA, which aims at the mapping of the black hole event horizon in nearby galaxies, and the study of the roots of jets in AGN.Comment: 6 pages, to appear in 11th European VLBI Network Symposium, ed. P. Charlot et al., Bordeaux (France), October 9-12, 201

Ensemble modeling highlights importance of understanding parasite-host behavior in preclinical antimalarial drug development

Emerging drug resistance and high-attrition rates in early and late stage drug development necessitate accelerated development of antimalarial compounds. However, systematic and meaningful translation of drug efficacy and host-parasite dynamics between preclinical testing stages is missing. We developed an ensemble of mathematical within-host parasite growth and antimalarial action models, fitted to extensive data from four antimalarials with different modes of action, to assess host-parasite interactions in two preclinical drug testing systems of murine parasite P. berghei in mice, and human parasite P. falciparum in immune-deficient mice. We find properties of the host-parasite system, namely resource availability, parasite maturation and virulence, drive P. berghei dynamics and drug efficacy, whereas experimental constraints primarily influence P. falciparum infection and drug efficacy. Furthermore, uninvestigated parasite behavior such as dormancy influences parasite recrudescence following non-curative treatment and requires further investigation. Taken together, host-parasite interactions should be considered for meaningful translation of pharmacodynamic properties between murine systems and for predicting human efficacious treatment

Akzeptanz, Rollendifferenzierung und geschlechtsspezifisches Verhalten in Dyaden bei Botanischen Bestimmungsübungen: Ein Vergleich zweier Medien

Die vorliegende Studie beschreibt geschlechts- und medienspezifische Effekte bei der Bestimmung von Pflanzen. Das Ziel bestand darin, explorativ zu untersuchen, welche Auswirkungen die Arbeit mit einer Online-Lernumgebung im Gegensatz zu bisherigen Bestimmungsbüchern auf die Prozesse in gemischt-geschlechtlichen Dyaden hat. Hierzu wurden vorrangig die Anzahlen medien- und pflanzenbezogener Aktionen der Probanden untersucht. Generell zeigt die Studie, dass keine schwerwiegenden geschlechtsspezifischen Effekte zu erwarten sind. Allerdings muss bei der Implementierung der Lernumgebung darauf geachtet werden, dass keine Rollendifferenzierung derart entsteht, dass innerhalb der Lerndyaden ein Proband den Computer bedient und der andere die Pflanze untersucht. Die Einstellung der Probanden gegenüber der neuen Lernumgebung war positiv, so dass von Seiten der Studenten keine Akzeptanzprobleme bezüglich der Implementierung in die Kurse zu erwarten sind

Overexpression of a Prefoldin β subunit gene reduces biomass recalcitrance in the bioenergy crop Populus.

Prefoldin (PFD) is a group II chaperonin that is ubiquitously present in the eukaryotic kingdom. Six subunits (PFD1-6) form a jellyfish-like heterohexameric PFD complex and function in protein folding and cytoskeleton organization. However, little is known about its function in plant cell wall-related processes. Here, we report the functional characterization of a PFD gene from Populus deltoides, designated as PdPFD2.2. There are two copies of PFD2 in Populus, and PdPFD2.2 was ubiquitously expressed with high transcript abundance in the cambial region. PdPFD2.2 can physically interact with DELLA protein RGA1_8g, and its subcellular localization is affected by the interaction. In P. deltoides transgenic plants overexpressing PdPFD2.2, the lignin syringyl/guaiacyl ratio was increased, but cellulose content and crystallinity index were unchanged. In addition, the total released sugar (glucose and xylose) amounts were increased by 7.6% and 6.1%, respectively, in two transgenic lines. Transcriptomic and metabolomic analyses revealed that secondary metabolic pathways, including lignin and flavonoid biosynthesis, were affected by overexpressing PdPFD2.2. A total of eight hub transcription factors (TFs) were identified based on TF binding sites of differentially expressed genes in Populus transgenic plants overexpressing PdPFD2.2. In addition, several known cell wall-related TFs, such as MYB3, MYB4, MYB7, TT8 and XND1, were affected by overexpression of PdPFD2.2. These results suggest that overexpression of PdPFD2.2 can reduce biomass recalcitrance and PdPFD2.2 is a promising target for genetic engineering to improve feedstock characteristics to enhance biofuel conversion and reduce the cost of lignocellulosic biofuel production