MODISTools - downloading and processing MODIS remotely sensed data in R

Remotely sensed data – available at medium to high resolution across global spatial and temporal scales – are a valuable resource for ecologists. In particular, products from NASA's MODerate-resolution Imaging Spectroradiometer (MODIS), providing twice-daily global coverage, have been widely used for ecological applications. We present MODISTools, an R package designed to improve the accessing, downloading, and processing of remotely sensed MODIS data. MODISTools automates the process of data downloading and processing from any number of locations, time periods, and MODIS products. This automation reduces the risk of human error, and the researcher effort required compared to manual per-location downloads. The package will be particularly useful for ecological studies that include multiple sites, such as meta-analyses, observation networks, and globally distributed experiments. We give examples of the simple, reproducible workflow that MODISTools provides and of the checks that are carried out in the process. The end product is in a format that is amenable to statistical modeling. We analyzed the relationship between species richness across multiple higher taxa observed at 526 sites in temperate forests and vegetation indices, measures of aboveground net primary productivity. We downloaded MODIS derived vegetation index time series for each location where the species richness had been sampled, and summarized the data into three measures: maximum time-series value, temporal mean, and temporal variability. On average, species richness covaried positively with our vegetation index measures. Different higher taxa show different positive relationships with vegetation indices. Models had high R2 values, suggesting higher taxon identity and a gradient of vegetation index together explain most of the variation in species richness in our data. MODISTools can be used on Windows, Mac, and Linux platforms, and is available from CRAN and GitHub (https://github.com/seantuck12/MODISTools)

Star Clusters in the Nearby Late-Type Galaxy NGC 1311

Ultraviolet, optical and near infrared images of the nearby (D ~ 5.5 Mpc) SBm galaxy NGC 1311, obtained with the Hubble Space Telescope, reveal a small population of 13 candidate star clusters. We identify candidate star clusters based on a combination of their luminosity, extent and spectral energy distribution. The masses of the cluster candidates range from ~1000 up to ~100000 Solar masses, and show a strong positive trend of larger mass with increasing with cluster age. Such a trend follows from the fading and dissolution of old, low-mass clusters, and the lack of any young super star clusters of the sort often formed in strong starbursts. The cluster age distribution is consistent with a bursting mode of cluster formation, with active episodes of age ~10 Myr, ~100 Myr and ~1 Gyr. The ranges of age and mass we probe are consistent with those of the star clusters found in quiescent Local Group dwarf galaxies.Comment: 21 pages, 11 figures, accepted by A

A modified passive-dynamic ankle-foot orthosis:can it prevent amputation and arthrodesis in patients with ankle-foot trauma?

Introduction High-energy lower extremity trauma (HELET) may cause severe damage within the foot-ankle complex. Occasionally, arthrodesis or amputation are the only remaining options to increase activity levels. The modified passive dynamic ankle-foot orthosis (PDAFO) may prove to be a nonsurgical alternative. This study evaluated the effect of a modified PDAFO with a 6-week training program on pain and performance in patients after HELET. Materials and methods A retrospective cohort study was conducted on seventeen patients who considered an arthrodesis or an amputation after HELET. In an attempt to avoid surgery, the modified PDAFO with a 6-week training program was provided. Pain scores was measured with the Numeric Rating Scale and administered at the start of testing, immediately after the two performance tests and at the end of the day of testing. Performance was evaluated with the 6-min walk test (6MWT) and the Comprehensive high-level activity mobility predictor (CHAMP). Results A significant pain reduction was achieved after the treatment procedure. At the start of the test days (p = 0.002), after the 6MWT (p = 0.001), after the CHAMP (p < 0.001) and at the end of the day (p < 0.001). In addition, a significant improvement on performance was observed in the 6MWT (p < 0.001) and the CHAMP (p = 0.01). None of the patients considered a surgical intervention anymore. Conclusions Patients after HELET show a decrease in pain and an improvement in performance after a 6-week training program with modified PD-AFO. The results suggest that the modified PDAFO is an effective alternative for a surgical approach

Patient-reported health outcomes in long-term lung transplantation survivors

During the last three decades lung transplantation (LTx) has become a proven modality for increasing both survival and health-related quality of life (HRQoL) in patients with various end-stage lung diseases. Most previous studies have reported improved HRQoL shortly after LTx. With regard to long-term effects on HRQoL, however, the evidence is less solid. This prospective cohort study was started with 828 patients who were on the waiting list for LTx. Then, in a longitudinal follow-up, 370 post-LTx patients were evaluated annually for up to 15 years. For all wait-listed and follow-up patients, the following four HRQoL instruments were administered: State-Trait Anxiety Inventory, Zung Self-rating Depression Scale, Nottingham Health Profile, and a visual analogue scale. Cross-sectional and generalized estimating equation (GEE) analysis for repeated measures were performed to assess changes in HRQoL during follow-up. After LTx, patients showed improvement in all HRQoL domains except pain, which remained steady throughout the long-term follow-up. The level of anxiety and depressive symptoms decreased significantly and remained constant. In conclusion, this study showed that HRQoL improves after LTx and tends to remain relatively constant for the entire life span

Study protocol of the TIRED study:A randomised controlled trial comparing either graded exercise therapy for severe fatigue or cognitive behaviour therapy with usual care in patients with incurable cancer

Background: Fatigue is a common and debilitating symptom for patients with incurable cancer receiving systemic treatment with palliative intent. There is evidence that non-pharmacological interventions such as graded exercise therapy (GET) or cognitive behaviour therapy (CBT) reduce cancer-related fatigue in disease-free cancer patients and in patients receiving treatment with curative intent. These interventions may also result in a reduction of fatigue in patients receiving treatment with palliative intent, by improving physical fitness (GET) or changing fatigue-related cognitions and behaviour (CBT). The primary aim of our study is to assess the efficacy of GET or CBT compared to usual care (UC) in reducing fatigue in patients with incurable cancer. Methods: The TIRED study is a multicentre three-armed randomised controlled trial (RCT) for incurable cancer patients receiving systemic treatment with palliative intent. Participants will be randomised to GET, CBT, or UC. In addition to UC, the GET group will participate in a 12-week supervised exercise programme. The CBT group will receive a 12-week CBT intervention in addition to UC. Primary and secondary outcome measures will be assessed at baseline, post-intervention (14 weeks), and at follow-up assessments (18 and 26 weeks post-randomisation). The primary outcome measure is fatigue severity (Checklist Individual Strength subscale fatigue severity). Secondary outcome measures are fatigue (EORTC-QLQ-C30 subscale fatigue), functional impairments (Sickness Impact Profile total score, EORTC-QLQ-C30 subscale emotional functioning, subscale physical functioning) and quality of life (EORTC-QLQ-C30 subscale QoL). Outcomes at 14 weeks (primary endpoint) of either treatment arm will be compared to those of UC participants. In addition, outcomes at 18 and 26 weeks (follow-up assessments) of either treatment arm will be compared to those of UC participants. Discussion: To our knowledge, the TIRED study is the first RCT investigating the efficacy of GET and CBT on reducing fatigue during treatment with palliative intent in incurable cancer patients. The results of this study will provide information about the possibility and efficacy of GET and CBT for severely fatigued incurable cancer patients

The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure

The road to the red sequence: A detailed view of the formation of a massive galaxy at z~2

(Abridged) We present here a detailed analysis of the star formation history (SFH) of FW4871, a massive galaxy at z=1.893+-0.002. We compare rest-frame optical and NUV slitless grism spectra from the Hubble Space Telescope with a large set of composite stellar populations to constrain the underlying star formation history. Even though the morphology features prominent tidal tails, indicative of a recent merger, there is no sign of on-going star formation within an aperture encircling one effective radius, which corresponds to a physical extent of 2.6 kpc. A model assuming truncation of an otherwise constant SFH gives a formation epoch zF~10, with a truncation after 2.7 Gyr, giving a mass-weighted age of 1.5 Gyr and a stellar mass of 0.8-3E11Msun, implying star formation rates of 30-110 Msun/yr. A more complex model including a recent burst of star formation places the age of the youngest component at 145 Myr, with a mass contribution lower than 20%, and a maximum amount of dust reddening of E(B-V)<0.4 mag (95% confidence levels). This low level of dust reddening is consistent with the low emission observed at 24 micron, corresponding to rest-frame 8 micron, where PAH emission should contribute significantly if a strong formation episode were present. The colour profile of FW4871 does not suggest a significant radial trend in the properties of the stellar populations out to 3Re. We suggest that the recent merger that formed FW4871 is responsible for the quenching of its star formation.Comment: 11 pages, 8 figures, 4 tables. In press (Astronomical Journal

FIGS -- Faint Infrared Grism Survey: Description and Data Reduction

The Faint Infrared Grism Survey (FIGS) is a deep Hubble Space Telescope (HST) WFC3/IR (Wide Field Camera 3 Infrared) slitless spectroscopic survey of four deep fields. Two fields are located in the Great Observatories Origins Deep Survey-North (GOODS-N) area and two fields are located in the Great Observatories Origins Deep Survey-South (GOODS-S) area. One of the southern fields selected is the Hubble Ultra Deep Field. Each of these four fields were observed using the WFC3/G102 grism (0.8$\mu m$-1.15$\mu m$ continuous coverage) with a total exposure time of 40 orbits (~ 100 kilo-seconds) per field. This reaches a 3 sigma continuum depth of ~26 AB magnitudes and probes emission lines to $\approx 10^{-17}\ erg\ s^{-1} \ cm^{-2}$. This paper details the four FIGS fields and the overall observational strategy of the project. A detailed description of the Simulation Based Extraction (SBE) method used to extract and combine over 10000 spectra of over 2000 distinct sources brighter than m_F105W=26.5 mag is provided. High fidelity simulations of the observations is shown to significantly improve the background subtraction process, the spectral contamination estimates, and the final flux calibration. This allows for the combination of multiple spectra to produce a final high quality, deep, 1D-spectra for each object in the survey.Comment: 21 Pages. 17 Figures. To appear in Ap

Identification of a Novel Genomic Island Associated with vanD-Type Vancomycin Resistance in Six Dutch Vancomycin-Resistant Enterococcus faecium Isolates

Genomic comparison of the first six Dutch vanD-type vancomycin-resistant Enterococcus faecium (VRE) isolates with four vanD gene clusters from other enterococcal species and anaerobic gut commensals revealed that the vanD gene cluster was located on a genomic island of variable size. Phylogenetic inferences revealed that the Dutch VRE isolates were genetically not closely related and that genetic variation of the vanD-containing genomic island was not species specific, suggesting that this island is transferred horizontally between enterococci and anaerobic gut commensals.Peer reviewe