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 Characterization of the ALMA Phasing System at 345 GHz

The development of the Atacama Large Millimeter/submillimeter Array (ALMA) phasing system (APS) has allowed ALMA to function as an extraordinarily sensitive station for very long baseline interferometry (VLBI) at frequencies of up to 230 GHz (~1.3 mm). Efforts are now underway to extend use of the APS to 345 GHz (~0.87 mm). Here we report a characterization of APS performance at 345 GHz based on a series of tests carried out between 2015-2021, including a successful global VLBI test campaign conducted in 2018 October in collaboration with the Event Horizon Telescope (EHT).Comment: 22 pages, 11 figures, 7 tables, accepted for publication in PAS

FIRST "Winged" and X-shaped Radio Source Candidates: II. New Redshifts

We report optical spectroscopic observations of X-shaped radio sources with the Hobby-Eberly Telescope and Multiple-Mirror Telescope, focused on the sample of candidates from the FIRST survey presented in Paper I (Cheung 2007). A total of 27 redshifts were successfully obtained, 21 of which are new, including that of a newly identified candidate source of this type which is presented here. With these observations, the sample of candidates from Paper I is over 50% spectroscopically identified. Two new broad emission-lined X-shaped radio sources are revealed, while no emission lines were detected in about one third of the observed sources; a detailed study of the line properties is deferred to a future paper. Finally, to explore their relation to the Fanaroff-Riley division, the radio luminosities and host galaxy absolute magnitudes of a spectroscopically identified sample of 50 X-shaped radio galaxies are calculated to determine their placement in the Owen-Ledlow plane.Comment: emulateapj style, 10 pages, 4 figures, 2 tables; ApJS accepted with minor revision from submitted version (v1

The protein kinase DYRK1A phosphorylates the splicing factor SF3b1/SAP155 at Thr434, a novel in vivo phosphorylation site.

BACKGROUND: The U2 small nuclear ribonucleoprotein particle (snRNP) component SF3b1/SAP155 is the only spliceosomal protein known to be phosphorylated concomitant with splicing catalysis. DYRK1A is a nuclear protein kinase that has been localized to the splicing factor compartment. Here we describe the identification of DYRK1A as a protein kinase that phosphorylates SF3b1 in vitro and in cultivated cells. RESULTS: Overexpression of DYRK1A caused a markedly increased phosphorylation of SF3b1 in COS-7 cells as assessed by Western blotting with an antibody specific for phosphorylated Thr-Pro dipeptide motifs. Phosphopeptide mapping of metabolically labelled SF3b1 showed that the majority of the in vivo-phosphopeptides corresponded to sites also phosphorylated by DYRK1A in vitro. Phosphorylation with cyclin E/CDK2, a kinase previously reported to phosphorylate SF3b1, generated a completely different pattern of phosphopeptides. By mass spectrometry and mutational analysis of SF3b1, Thr434 was identified as the major phosphorylation site for DYRK1A. Overexpression of DYRK1A or the related kinase, DYRK1B, resulted in an enhanced phosphorylation of Thr434 in endogenous SF3b1 in COS-7 cells. Downregulation of DYRK1A in HEK293 cells or in HepG2 cells by RNA interference reduced the phosphorylation of Thr434 in SF3b1. CONCLUSION: The present data show that the splicing factor SF3b1 is a substrate of the protein kinase DYRK1A and suggest that DYRK1A may be involved in the regulation of pre mRNA-splicing.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Scattering in the vicinity of relativistic jets: a method for constraining jet parameters

Relativistic jets of radio loud active galactic nuclei (AGN) produce highly directed, intense beams of radiation. A fraction of this beamed radiation scatters on the thermal plasma generally surrounding an AGN. The morphology of the scattered emission can thus provide constraints on the physical properties of the jet. We present a model to study the feasibility of constraining the parameters of a jet, especially its inclination angle and bulk Lorentz factor in this way. We apply our model to the well studied jet of M87 and the surrounding diffuse gas and find that the observational limits of the surface brightness measured in the region of the putative counterjet provide the tightest constraints on the jet parameters consistent with constraints derived by other methods. We briefly discuss the applicability of our model to other sources exhibiting relativistic motionsComment: 17 pages, 15 figures, to appear in A&A, 420, 33 (2004

New in vitro interaction-parasite reduction ratio assay for early derisk in clinical development of antimalarial combinations

The development and spread of drug-resistant phenotypes substantially threaten malaria control efforts. Combination therapies have the potential to minimize the risk of resistance development but require intensive preclinical studies to determine optimal combination and dosing regimens. To support the selection of new combinations, we developed a novel in vitro-in silico combination approach to help identify the pharmacodynamic interactions of the two antimalarial drugs in a combination which can be plugged into a pharmacokinetic/pharmacodynamic model built with human monotherapy parasitological data to predict the parasitological endpoints of the combination. This makes it possible to optimally select drug combinations and doses for the clinical development of antimalarials. With this assay, we successfully predicted the endpoints of two phase 2 clinical trials in patients with the artefenomel-piperaquine and artefenomel-ferroquine drug combinations. In addition, the predictive performance of our novel in vitro model was equivalent to that of the humanized mouse model outcome. Last, our more informative in vitro combination assay provided additional insights into the pharmacodynamic drug interactions compared to the in vivo systems, e.g., a concentration-dependent change in the maximum killing effect (Emax) and the concentration producing 50% of the killing maximum effect (EC50) of piperaquine or artefenomel or a directional reduction of the EC50 of ferroquine by artefenomel and a directional reduction of Emax of ferroquine by artefenomel. Overall, this novel in vitro-in silico-based technology will significantly improve and streamline the economic development of new drug combinations for malaria and potentially also in other therapeutic areas

Properties of Interfaces in the two and three dimensional Ising Model

To investigate order-order interfaces, we perform multimagnetical Monte Carlo simulations of the $2D$ and $3D$ Ising model. Following Binder we extract the interfacial free energy from the infinite volume limit of the magnetic probability density. Stringent tests of the numerical methods are performed by reproducing with high precision exact $2D$ results. In the physically more interesting $3D$ case we estimate the amplitude $F^s_0$ of the critical interfacial tension $F^s = F^s_0 t^\mu$ to be $F^s_0 = 1.52 \pm 0.05$. This result is in good agreement with a previous MC calculation by Mon, as well as with experimental results for related amplitude ratios. In addition, we study in some details the shape of the magnetic probability density for temperatures below the Curie point.Comment: 25 pages; sorry no figures include

Search for the active ingredients from a 2-aminothiazole DMSO stock solution with antimalarial activity

Chemical decomposition of DMSO stock solutions is a common incident that can mislead biological screening campaigns. Here, we share our case study of 2-aminothiazole 1, originating from an antimalarial class that undergoes chemical decomposition in DMSO at room temperature. As previously measured biological activities observed against Plasmodium falciparum NF54 and for the target enzyme Pf IspE were not reproducible for a fresh batch, we tackled the challenge to understand where the activity originated from. Solvent- and temperature-dependent studies using HRMS and NMR spectroscopy to monitor the decomposition led to the isolation and in vitro evaluation of several fractions against Pf IspE. After four days of decomposition, we successfully isolated the oxygenated and dimerised compounds using SFC purification and correlated the observed activities to them. Due to the unstable nature of the two isolates, it is likely that they undergo further decomposition contributing to the overall instability of the compound

Orientation and size of the `Z' in `X'-shaped radio galaxies

Some X-shaped radio galaxies show a Z-symmetric morphology in the less luminous secondary lobes. Within the scenario of a merger between two galaxies, each hosting a supermassive black hole in its center, this structure has been explained before: As the smaller galaxy spirals towards the common center, it releases gas to the ISM of the larger active galaxy. The ram pressure of this streaming gas will bend the lobes of the pre-merger jet into a Z-shape. After the black holes have merged the jet propagates in a new direction that is aligned with the angular momentum of the binary black hole. In this article we deproject the pre- and post-merger jets. Taking into account the expected angles between the jet pairs and with the assumption that their directions are uncorrelated, we show that one of three possible orientations of the jets with respect to the line of sight is more likely than the others. This actually depends on the distance where the bending occurs. Another result of our deprojection is that the streaming gas bends the jet into a Z-shape in a range between about 30 and 100 kpc distance to the center of the primary galaxy. We confirm this finding by comparing our predictions for the properties of the rotational velocity field and its radius with observations and numerical simulations of merging galaxies. Thus our results support the merger scenario as explanation for X- and Z-shaped radio galaxies with the jet pointing along the former axis of orbital angular momentum of the binary.Comment: 11 pages, 6 figures, minor changes in final version. Accepted for publication in MNRA

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