The MYStIX wide-field near-infrared data: Optimal photometry in crowded fields

We present JHK infrared data from the UK InfraRed Telescope (UKIRT) for a subset of the regions of the Massive Young Star-Forming Complex Study in Infrared and X-ray (MYStIX) survey. Some of the data were obtained specifically for the MYStIX project, and some as part of the UKIRT Infrared Deep Sky Survey's Galactic Plane Survey. In most of these fields, crowding is a significant issue for aperture photometry, and so we have re-extracted the photometry from the processed images using an optimal extraction technique, and we describe how we adapt the optimal technique to mitigate the effects of crowding. © 2013. The American Astronomical Society. All rights reserved.The MYStIX project is supported at Penn State by NASA grant NNX09AC74G, NSF grant AST-0908038, and the Chandra ACIS Team contract SV4-74018 (G. Garmire & L. Townsley, Principal Investigators), issued by the Chandra X-ray Center, which is operated by the Smithsonian Astrophysical Observatory for and on behalf of NASA under contract NAS8-03060. This research made use of data products from the Chandra Data Archive

Thermal conductivity measurements of proton-heated warm dense aluminum.

Thermal conductivity is one of the most crucial physical properties of matter when it comes to understanding heat transport, hydrodynamic evolution, and energy balance in systems ranging from astrophysical objects to fusion plasmas. In the warm dense matter regime, experimental data are very scarce so that many theoretical models remain untested. Here we present the first thermal conductivity measurements of aluminum at 0.5-2.7 g/cc and 2-10 eV, using a recently developed platform of differential heating. A temperature gradient is induced in a Au/Al dual-layer target by proton heating, and subsequent heat flow from the hotter Au to the Al rear surface is detected by two simultaneous time-resolved diagnostics. A systematic data set allows for constraining both thermal conductivity and equation-of-state models. Simulations using Purgatorio model or Sesame S27314 for Al thermal conductivity and LEOS for Au/Al release equation-of-state show good agreement with data after 15 ps. Discrepancy still exists at early time 0-15 ps, likely due to non-equilibrium conditions

The MYStIX infrared-excess source catalog

The Massive Young Star-Forming Complex Study in Infrared and X-rays (MYStIX) project provides a comparative study of 20 Galactic massive star-forming complexes (d = 0.4-3.6 kpc). Probable stellar members in each target complex are identified using X-ray and/or infrared data via two pathways: (1) X-ray detections of young/massive stars with coronal activity/strong winds or (2) infrared excess (IRE) selection of young stellar objects (YSOs) with circumstellar disks and/or protostellar envelopes. We present the methodology for the second pathway using Spitzer/IRAC, 2MASS, and UKIRT imaging and photometry. Although IRE selection of YSOs is well-trodden territory, MYStIX presents unique challenges. The target complexes range from relatively nearby clouds in uncrowded fields located toward the outer Galaxy (e.g., NGC 2264, the Flame Nebula) to more distant, massive complexes situated along complicated, inner Galaxy sightlines (e.g., NGC 6357, M17). We combine IR spectral energy distribution (SED) fitting with IR color cuts and spatial clustering analysis to identify IRE sources and isolate probable YSO members in each MYStIX target field from the myriad types of contaminating sources that can resemble YSOs: extragalactic sources, evolved stars, nebular knots, and even unassociated foreground/background YSOs. Applying our methodology consistently across 18 of the target complexes, we produce the MYStIX IRE Source (MIRES) Catalog comprising 20,719 sources, including 8686 probable stellar members of the MYStIX target complexes. We also classify the SEDs of 9365 IR counterparts to MYStIX X-ray sources to assist the first pathway, the identification of X-ray-detected stellar members. The MIRES Catalog provides a foundation for follow-up studies of diverse phenomena related to massive star cluster formation, including protostellar outflows, circumstellar disks, and sequential star formation triggered by massive star feedback processes. © 2013. The American Astronomical Society. All rights reserved.M.S.P. was supported by an NSF Astronomy and Astrophysics Postdoctoral Fellowship under award AST-0901646 during the main analysis phase of this project. The MIRES Catalog is based on observations from the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory (California Institute of Technology) under contract with NASA. This publication makes use of data products from the Two Micron All-Sky Survey, which is a joint project of the University of Massachusetts and the Infrared Processing and Analysis Center/California Institute of Technology, funded by NASA and the NSF. This work is based in part on data obtained as part of the United Kingdom Infrared Telescope (UKIRT) Infrared Deep Sky Survey and in part by data obtained in UKIRT Director's Discretionary Time. UKIRT is operated by the Joint Astronomy Centre on behalf of the Science and Technology Facilities Council of the U.K. The MYStIX project is supported at Penn State by NASA grant NNX09AC74G, NSF grant AST-0908038, and the Chandra ACIS Team contract SV4-74018 (PIs: G. Garmire and L. Townsley), issued by the Chandra X-ray Center, which is operated by the Smithsonian Astrophysical Observatory for and on behalf of NASA under contract NAS8-03060

Identifying young stars in massive star-forming regions for the MYStIX project

The Massive Young star-forming Complex Study in Infrared and X-rays (MYStIX) project requires samples of young stars that are likely members of 20 nearby Galactic massive star-forming regions. Membership is inferred from statistical classification of X-ray sources, from detection of a robust infrared excess that is best explained by circumstellar dust in a disk or infalling envelope and from published spectral types that are unlikely to be found among field stars. We present the MYStIX membership lists here, and describe in detail the statistical classification of X-ray sources via a "Naive Bayes Classifier." These membership lists provide the empirical foundation for later MYStIX science studies. © 2013. The American Astronomical Society. All rights reserved.We appreciate the significant time our anonymous referee devoted to this long paper and the useful suggestions offered. The MYStIX project is supported at Penn State by NASA grant NNX09AC74G, NSF grant AST-0908038, and the Chandra ACIS Team contract SV4-74018 (G. Garmire & L. Townsley, Principal Investigators), issued by the Chandra X-ray Center, which is operated by the Smithsonian Astrophysical Observatory for and on behalf of NASA under contract NAS8-03060. M. S. Povich was supported by an NSF Astronomy and Astrophysics Postdoctoral Fellowship under award AST-0901646. We thank Steve Majewski and Remy Indebetouw for access to results from the Spitzer Vela-Carina survey. This research made use of data products from the Chandra Data Archive and the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory (California Institute of Technology) under a contract with NASA. This research used data products from the United Kingdom Infrared Telescope (UKIRT), which is operated by the Joint Astronomy Centre on behalf of the Science and Technology Facilities Council of the U.K.; some UKIRT data were obtained as part of the UKIRT Infrared Deep Sky Survey (Lawrence et al. 2007) and some were obtained via UKIRT director's discretionary time. This research used data products from the Two Micron All Sky Survey, which is a joint project of the University of Massachusetts and the Infrared Processing and Analysis Center/California Institute of Technology, funded by the National Aeronautics and Space Administration and the National Science Foundation. The HAWK-I near-infrared observations were collected with the High Acuity Wide-field K-band Imager instrument on the ESO 8 m Very Large Telescope at Paranal Observatory, Chile, under ESO programme 60.A-9284(K). This research has also made use of NASA's Astrophysics Data System Bibliographic Services, the SIMBAD database operated at the Centre de Données Astronomique de Strasbourg, and SAOImage DS9 software developed by Smithsonian Astrophysical Observatory

A circadian based inflammatory response – implications for respiratory disease and treatment

Circadian clocks regulate the daily timing of many of our physiological, metabolic and biochemical functions. The immune system also displays circadian oscillations in immune cell count, synthesis and cytokine release, clock gene expression in cells and organs of the immune system as well as clock-controlled genes that regulate immune function. Circadian disruption leads to dysregulation of immune responses and inflammation which can further disrupt circadian rhythms. The response of organisms to immune challenges, such as allergic reactions also vary depending on time of the day, which can lead to detrimental responses particularly during the rest and early active periods. This review evaluates what is currently known in terms of circadian biology of immune response and the cross-talk between circadian and immune system. We discuss the circadian pattern of three respiratory-related inflammatory diseases, chronic obstructive pulmonary disease, allergic rhinitis and asthma. Increasing our knowledge on circadian patterns of immune responses and developing chronotherapeutic studies in inflammatory diseases with strong circadian patterns will lead to preventive measures as well as improved therapies focussing on the circadian rhythms of symptoms and the daily variation of the patients’ responses to medication

Bioassay-guided isolation and identification of antimicrobial compounds from thyme essential oil by means of overpressured layer chromatography, bioautography and GC-MS

A simple method is described for efficient isolation of compounds having an antibacterial effect. Two thyme (Thymus vulgaris) essential oils, obtained from the market, were chosen as prospective materials likely to feature several bioactive components when examined by thin layer chromatography coupled with direct bioautography as a screening method. The newly developed infusion overpressured layer chromatographic separation method coupled with direct bioautography assured that only the active components were isolated by means of overrun overpressured layer chromatography with online detection and fractionation. Each of the 5 collected fractions represented one of the five antimicrobial essential oil components designated at the screening. The purity and the activity of the fractions were confirmed with chromatography coupled various detection methods (UV, vanillin-sulphuric acid reagent, direct bioautography). The antibacterial components were identified with GC-MS as thymol, carvacrol, linalool, diethylphthalate, and alpha-terpineol. The oil component diethyl-phthalate is an artificial compound, used as plasticizer or detergent bases in the industry. Our results support that exploiting its flexibility and the possible hyphenations, overpressured layer chromatography is especially attractive for isolation of antimicrobial components from various matrixes

EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

Ontology of core data mining entities

In this article, we present OntoDM-core, an ontology of core data mining entities. OntoDM-core defines themost essential datamining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. The ontology has been thoroughly assessed following the practices in ontology engineering, is fully interoperable with many domain resources and is easy to extend

Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony.

: Plasmodium parasites, the causative agents of malaria, have evolved a unique cell division cycle in the clinically relevant asexual blood stage of infection(1). DNA replication commences approximately halfway through the intracellular development following invasion and parasite growth. The schizont stage is associated with multiple rounds of DNA replication and nuclear division without cytokinesis, resulting in a multinucleated cell. Nuclei divide asynchronously through schizogony, with only the final round of DNA replication and segregation being synchronous and coordinated with daughter cell assembly(2,3). However, the control mechanisms for this divergent mode of replication are unknown. Here, we show that the Plasmodium-specific kinase PfCRK4 is a key cell-cycle regulator that orchestrates multiple rounds of DNA replication throughout schizogony in Plasmodium falciparum. PfCRK4 depletion led to a complete block in nuclear division and profoundly inhibited DNA replication. Quantitative phosphoproteomic profiling identified a set of PfCRK4-regulated phosphoproteins with greatest functional similarity to CDK2 substrates, particularly proteins involved in the origin of replication firing. PfCRK4 was required for initial and subsequent rounds of DNA replication during schizogony and, in addition, was essential for development in the mosquito vector. Our results identified an essential S-phase promoting factor of the unconventional P. falciparum cell cycle. PfCRK4 is required for both a prolonged period of the intraerythrocytic stage of Plasmodium infection, as well as for transmission, revealing a broad window for PfCRK4-targeted chemotherapeutics.<br/

A phase I trial to assess the pharmacology of the new oestrogen receptor antagonist fulvestrant on the endometrium in healthy postmenopausal volunteers

While tamoxifen use is associated with clear benefits in the treatment of hormone-sensitive breast cancer, it also exhibits partial oestrogen agonist activity that is associated with adverse events, including endometrial cancer. Fulvestrant (‘Faslodex’) is a new oestrogen receptor antagonist that downregulates the oestrogen receptor and has no known agonist effect. This single-centre, double-blind, randomised, parallel-group trial was conducted to determine the direct effects of fulvestrant on the female endometrium when given alone and in combination with the oestrogen, ethinyloestradiol. Following a 14-day, pretrial screening period, 30 eligible postmenopausal volunteers were randomised to receive fulvestrant 250 mg, fulvestrant 125 mg or matched placebo administered as a single intramuscular injection. Two weeks postinjection, volunteers received 2-weeks concurrent exposure to ethinyloestradiol 20 μg day−1. Endometrial thickness was measured before and after the 14-day screening period with further measurements predose (to confirm a return to baseline) and on days 14, 28 and 42 post-treatment with fulvestrant. Pharmacokinetic and safety assessments were performed throughout the trial. Fulvestrant at a dose of 250 mg significantly (P=0.0001) inhibited the oestrogen-stimulated thickening of the endometrium compared with placebo. Neither the 125 mg nor 250 mg doses of fulvestrant demonstrated oestrogenic effects on the endometrium over the initial 14-day assessment period. Fulvestrant was well tolerated and reduced the incidence of ethinyloestradiol-related side effects. At the same dose level that is being evaluated in clinical trials of postmenopausal women with advanced breast cancer, fulvestrant (250 mg) is an antioestrogen with no evidence of agonist activity in the endometrium of healthy postmenopausal women