bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Systematic Review of the Diagnostic and Prognostic Value of Urinary Protein Biomarkers in Urothelial Bladder Cancer
Authors: D’Costa Jamie J. , Goldsmith James C. , Wilson Jayne S. , Bryan Richard T. , Ward Douglas G. 
Published: July 2016

For over 80 years, cystoscopy has remained the gold-standard for detecting tumours of the urinary bladder. Since bladder tumours have a tendency to recur and progress, many patients are subjected to repeated cystoscopies during long-term surveillance, with the procedure being both unpleasant for the patient and expensive for healthcare providers. The identification and validation of bladder tumour specific molecular markers in urine could enable tumour detection and reduce reliance on cystoscopy, and numerous classes of biomarkers have been studied. Proteins represent the most intensively studied class of biomolecule in this setting. As an aid to researchers searching for better urinary biomarkers, we report a comprehensive systematic review of the literature and a searchable database of proteins that have been investigated to date. Our objective was to classify these proteins as: 1) those with robustly characterised sensitivity and specificity for bladder cancer detection; 2) those that show potential but further investigation is required; 3) those unlikely to warrant further investigation; and 4) those investigated as prognostic markers. This work should help to prioritise certain biomarkers for rigorous validation, whilst preventing wasted effort on proteins that have shown no association whatsoever with the disease, or only modest biomarker performance despite large-scale efforts at validation.
The relationship between hemorheological parameters and mortality in critically ill patients with and without sepsis
Authors: Totsimon Kinga , Biro Katalin , Szabo Zsofia Eszter , Toth Kalman , Kenyeres Peter , Marton Zsolt 
Published: July 2016

PURPOSE: The prognostic scoring systems for mortality of intensive care patients estimate clinical outcome using several physiological and biochemical parameters. In altered hemodynamic conditions of critically ill patients, hemorheological variables may play a significant role in appropriate tissue perfusion. We investigated if hemorheological parameters are altered in critical status and if they could be markers of mortality. METHODS: 112 patients (67.8 ± 12 years, 58 males, 54 females) treated in intensive care unit with different non-surgical diseases were investigated. Routine laboratory parameters and prognostic scores were determined and hemorheological variables (hematocrit, plasma and whole blood viscosity, red blood cell aggregation and deformability) were measured on the 1st and the 2nd day after admission. RESULTS: ICU scores predicted 35.2–41.3% mortality rate, real mortality in intensive care unit was 37.5%, while 30-day mortality was 46.6%. Whole blood viscosity (WBV) and red blood cell (RBC) deformability were lower, red blood cell aggregation was higher in septic than in nonseptic patients ( p < 0.05). In septic patients calcium was increased, osmolality was decreased, while in nonseptic patients WBV and RBC aggregation were higher in nonsurvivors compared to survivors ( p < 0.05). Worsening of RBC deformability from day 1 to day 2 predicted higher mortality ( p < 0.05). CONCLUSION: Calcium and osmolality level were associated with outcome in sepsis. Whole blood viscosity, red blood cell aggregation and change in red blood cell deformability could predict mortality in nonseptic patients and they may add prognostic information over the ICU scores. Further investigations are needed to evaluate the benefit of our findings in clinical practice.
Choosing an Advanced Therapy in Parkinson’s Disease; is it an Evidence-Based Decision in Current Practice?
Authors: Nijhuis Frouke A.P. , van Heek Jolien , Bloem Bastiaan R. , Post Bart , Faber Marjan J. 
Published: July 2016

Background: In advanced Parkinson’s disease (PD), neurologists and patients face a complex decision for an advanced therapy. When choosing a treatment, the best available evidence should be combined with the professional’s expertise and the patient’s preferences. Objective: The objective of this study was to explore current decision-making in advanced PD. Methods: We conducted focus group discussions and individual interviews with patients ( N = 20) who had received deep brain stimulation, Levodopa-Carbidopa intestinal gel, or subcutaneous apomorphine infusion, and with their caregivers ( N = 16). Furthermore, we conducted semi-structured interviews with neurologists ( N = 7) and PD nurse specialists ( N = 3) to include the perspectives of all key players in this decision-making process. Data were analyzed by two researchers using a qualitative thematic analysis approach. Results: Four themes representing current experiences with the decision-making process were identified: 1) information and information needs, 2) factors influencing treatment choice and individual decision strategies, 3) decision-making roles, and 4) barriers and facilitators to shared decision-making (SDM). Patient preferences were taken into account, however patients were not always provided with adequate information. The professional’s expertise influenced the decision-making process in both positive and negative ways. Although professionals and patients considered SDM essential for the decision of an advanced treatment, they mentioned several barriers for the implementation in current practice. Conclusions: In this study we found several factors explaining why in current practice, evidence-based decision-making in advanced PD is not optimal. An important first step would be to develop objective information on all treatment options.
Transaminases and gamma glutamyl transpeptidase for detecting nonalcoholic steatohepatitis and fibrosis in nonalcoholic fatty liver disease
Authors: Alam Shahinul , Gupta Utpal Das , Kabir Jahangir , Noor-E-Alam Sheikh Mohammad , Chowdhury Ziaur Rahman , Alam A.K.M. Khorshed 
Published: July 2016

Background: Nonalcoholic steatohepatitis (NASH) and advanced fibrosis are the spectrum of nonalcoholic fatty liver disease (NAFLD) that may progress to cirrhosis.Objective: We aimed to determine the detecting capacity of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and gamma glutamyl transpeptidase (GGT) for NASH and significant fibrosis.Methods: Demographic and laboratory data of 502 sonologically diagnosed NAFLD patients were retrospectively analysed. Area under receiver operating characteristics curve (AUROC) was performed for NASH and fibrosis score ?2 (significant fibrosis) with ALT, AST and GGT of 233 biopsied patients.Results: Of 502 patients ALT, AST and GGT was elevated in 252 (50.1 %), 184 (36.7%) and 138 (27.4%) respectively. There was no difference in histological activity and fibrosis score between normal and elevated ALT and AST. Forty two (40.2%) NASH and 23(20.2%) significant fibrosis had normal ALT level. GGT was differed in NASH and Non NASH (p< .005) and between significant fibrosis (p< .01) and insignificant fbrosis. To detect NASH AUROC curve ofGGT was 67.5%, whereas of ALT and AST was 55.2% and 55.7%. For significant fibrosis AUROC curve of ALT, AST and GGT was 44, 50 and 68.4 % respectively. GGT level of39.5 U/L could detect NASH with a 63% sensitivity and 65% specificity irrespective of sex. GGT 40.5U/L had 60% sensitivity and 59 % specificity to detect significant fibrosis. For fibrosis ?2 AUROC curve was 75.4% in male.Conclusion: No optimal ALT and AST level could detect NASH and fibrosis. GGT level of 40 U/L had a better detecting capacity for NASH and fibrosis especially in male.
MAKING PLANET NINE: A SCATTERED GIANT IN THE OUTER SOLAR SYSTEM
Authors: Bromley Benjamin C. , Kenyon Scott J. 
Published: July 2016

ABSTRACT
Correlations in the orbits of several minor planets in the outer solar system suggest the presence of a remote, massive Planet Nine. With at least 10 times the mass of the Earth and a perihelion well beyond 100 au, Planet Nine poses a challenge to planet formation theory. Here we expand on a scenario in which the planet formed closer to the Sun and was gravitationally scattered by Jupiter or Saturn onto a very eccentric orbit in an extended gaseous disk. Dynamical friction with the gas then allowed the planet to settle in the outer solar system. We explore this possibility with a set of numerical simulations. Depending on how the gas disk evolves, scattered super-Earths or small gas giants settle on a range of orbits, with perihelion distances as large as 300 au. Massive disks that clear from the inside out on million-year timescales yield orbits that allow a super-Earth or gas giant to shepherd the minor planets as observed. A massive planet can achieve a similar orbit in a persistent, low-mass disk over the lifetime of the solar system.
KEPLER ECLIPSING BINARIES WITH DELTA SCUTI/GAMMA DORADUS PULSATING COMPONENTS. I. KIC 9851944
Authors: Guo Zhao , Gies Douglas R. , Matson Rachel A. , Hernández Antonio García 
Published: July 2016

ABSTRACT
KIC 9851944 is a short-period (P = 2.16 days) eclipsing binary in the Kepler field of view. By combining the analysis of Kepler photometry and phase-resolved spectra from Kitt Peak National Observatory and Lowell Observatory, we determine the atmospheric and physical parameters of both stars. The two components have very different radii (2.27 R
⊙, 3.19 R
⊙) but close masses (1.76 M
⊙, 1.79 M
⊙) and effective temperatures (7026, 6902 K), indicating different evolutionary stages. The hotter primary is still on the main sequence (MS), while the cooler and larger secondary star has evolved to the post-MS, burning hydrogen in a shell. A comparison with coeval evolutionary models shows that it requires solar metallicity and a higher mass ratio to fit the radii and temperatures of both stars simultaneously. Both components show δ Scuti-type pulsations, which we interpret as p-modes and p and g mixed modes. After a close examination of the evolution of δ Scuti pulsational frequencies, we make a comparison of the observed frequencies with those calculated from MESA/GYRE.
THE REVERBERATION LAG IN THE LOW-MASS X-RAY BINARY H1743-322
Authors: Marco Barbara De , Ponti Gabriele 
Published: July 2016

ABSTRACT
The evolution of the inner accretion flow of a black hole X-ray binary during an outburst is still a matter of active research. X-ray reverberation lags are powerful tools for constraining disk–corona geometry. We present a study of X-ray lags in the black hole transient H1743-322. We compared the results obtained from analysis of all the publicly available XMM-Newton observations. These observations were carried out during two different outbursts that occurred in 2008 and 2014. During all the observations the source was caught in the hard state and at similar luminosities (

). We detected a soft X-ray lag of ∼60 ms, most likely due to thermal reverberation. We did not detect any significant change of the lag amplitude among the different observations, indicating a similar disk–corona geometry at the same luminosity in the hard state. On the other hand, we observe significant differences between the reverberation lag detected in H1743-322 and in GX 339-4 (at similar luminosities in the hard state), which might indicate variations of the geometry from source to source.
APERTURE EFFECTS ON THE OXYGEN ABUNDANCE DETERMINATIONS FROM CALIFA DATA
Authors: Iglesias-Páramo J. , Vílchez J. M. , Rosales-Ortega F. F. , Sánchez S. F. , Puertas S. Duarte , Petropoulou V. , Paz A. Gil de , Galbany L. , Mollá M. , Catalán-Torrecilla C. , Morales A. Castillo , Mast D. , Husemann B. , García-Benito R. , Mendoza M. A. , Kehrig C. , Pérez-Montero E. , Papaderos P. , Gomes J. M. , Walcher C. J. , Delgado R. M. González , Marino R. A. , López-Sánchez Á. R. , Ziegler B. , Flores H. , Alves J. 
Published: July 2016

ABSTRACT
This paper aims to provide aperture corrections for emission lines in a sample of spiral galaxies from the Calar Alto Legacy Integral Field Area Survey (CALIFA) database. In particular, we explore the behavior of the log([O iii] λ5007/Hβ)/([N ii] λ6583/Hα) (O3N2) and log[N ii] λ6583/Hα (N2) flux ratios since they are closely connected to different empirical calibrations of the oxygen abundances in star-forming galaxies. We compute the median growth curves of Hα, Hα/Hβ, O3N2, and N2 up to 2.5R
50 and 1.5 disk

. These distances cover most of the optical spatial extent of the CALIFA galaxies. The growth curves simulate the effect of observing galaxies through apertures of varying radii. We split these growth curves by morphological types and stellar masses to check if there is any dependence on these properties. The median growth curve of the Hα flux shows a monotonous increase with radius with no strong dependence on galaxy inclination, morphological type, and stellar mass. The median growth curve of the Hα/Hβ ratio monotonically decreases from the center toward larger radii, showing for small apertures a maximum value of ≈10% larger than the integrated one. It does not show any dependence on inclination, morphological type, and stellar mass. The median growth curve of N2 shows a similar behavior, decreasing from the center toward larger radii. No strong dependence is seen on the inclination, morphological type, and stellar mass. Finally, the median growth curve of O3N2 increases monotonically with radius, and it does not show dependence on the inclination. However, at small radii it shows systematically higher values for galaxies of earlier morphological types and for high stellar mass galaxies. Applying our aperture corrections to a sample of galaxies from the SDSS survey at 0.02 ≤ z ≤ 0.3 shows that the average difference between fiber-based and aperture-corrected oxygen abundances, for different galaxy stellar mass and redshift ranges, reaches typically to ≈11%, depending on the abundance calibration used. This average difference is found to be systematically biased, though still within the typical uncertainties of oxygen abundances derived from empirical calibrations. Caution must be exercised when using observations of galaxies for small radii (e.g., below 0.5

) given the high dispersion shown around the median growth curves. Thus, the application of these median aperture corrections to derive abundances for individual galaxies is not recommended when their fluxes come from radii much smaller than either R
50 or

.
FOREGROUND BIAS FROM PARAMETRIC MODELS OF FAR-IR DUST EMISSION
Authors: Kogut A. , Fixsen D. J. 
Published: July 2016

ABSTRACT
We use simple toy models of far-IR dust emission to estimate the accuracy to which the polarization of the cosmic microwave background can be recovered using multi-frequency fits, if the parametric form chosen for the fitted dust model differs from the actual dust emission. Commonly used approximations to the far-IR dust spectrum yield CMB residuals comparable to or larger than the sensitivities expected for the next generation of CMB missions, despite fitting the combined CMB + foreground emission to precision 0.1% or better. The Rayleigh–Jeans approximation to the dust spectrum biases the fitted dust spectral index by

and the inflationary B-mode amplitude by

. Fitting the dust to a modified blackbody at a single temperature biases the best-fit CMB by

if the true dust spectrum contains multiple temperature components. A 13-parameter model fitting two temperature components reduces this bias by an order of magnitude if the true dust spectrum is in fact a simple superposition of emission at different temperatures, but fails at the level

for dust whose spectral index varies with frequency. Restricting the observing frequencies to a narrow region near the foreground minimum reduces these biases for some dust spectra but can increase the bias for others. Data at THz frequencies surrounding the peak of the dust emission can mitigate these biases while providing a direct determination of the dust temperature profile.
A NEW METHOD FOR FINDING POINT SOURCES IN HIGH-ENERGY NEUTRINO DATA
Authors: Fang Ke , Miller M. Coleman 
Published: July 2016

ABSTRACT
The IceCube collaboration has reported the first detection of high-energy astrophysical neutrinos, including ∼50 high-energy starting events, but no individual sources have been identified. It is therefore important to develop the most sensitive and efficient possible algorithms to identify the point sources of these neutrinos. The most popular current method works by exploring a dense grid of possible directions to individual sources, and identifying the single direction with the maximum probability of having produced multiple detected neutrinos. This method has numerous strengths, but it is computationally intensive and because it focuses on the single best location for a point source, additional point sources are not included in the evidence. We propose a new maximum likelihood method that uses the angular separations between all pairs of neutrinos in the data. Unlike existing autocorrelation methods for this type of analysis, which also use angular separations between neutrino pairs, our method incorporates information about the point-spread function and can identify individual point sources. We find that if the angular resolution is a few degrees or better, then this approach reduces both false positive and false negative errors compared to the current method, and is also more computationally efficient up to, potentially, hundreds of thousands of detected neutrinos.
SYNTHESIS OF FORMAMIDE AND RELATED ORGANIC SPECIES IN THE INTERSTELLAR MEDIUM VIA CHEMICAL DYNAMICS SIMULATIONS
Authors: Spezia Riccardo , Jeanvoine Yannick , Hase William L. , Song Kihyung , Largo Antonio 
Published: July 2016

ABSTRACT
We show, by means of direct dynamics simulations, how it is possible to define possible reactants and mechanisms leading to the formation of formamide in the interstellar medium. In particular, different ion–molecule reactions in the gas phase were considered: NH3OH+, NH2OH

, H2COH+, and NH4
+ for the ions and NH2OH, H2CO, and NH3 for the partner neutrals. These calculations were combined with high level ab initio calculations to investigate possible further evolution of the products observed. In particular, for formamide, we propose that the NH2OH

+ H2CO reaction can produce an isomer, NH2OCH

, that, after dissociative recombination, can produce neutral formamide, which was observed in space. The direct dynamics do not pre-impose any reaction pathways and in other reactions, we did not observe the formation of formamide or any possible precursor. On the other hand, we obtained other interesting reactions, like the formation of NH2CH

. Finally, some radiative association processes are proposed. All of the results obtained are discussed in light of the species observed in radioastronomy.
ALMA IMAGING AND GRAVITATIONAL LENS MODELS OF SOUTH POLE TELESCOPE—SELECTED DUSTY, STAR-FORMING GALAXIES AT HIGH REDSHIFTS
Authors: Spilker J. S. , Marrone D. P. , Aravena M. , Béthermin M. , Bothwell M. S. , Carlstrom J. E. , Chapman S. C. , Crawford T. M. , Breuck C. de , Fassnacht C. D. , Gonzalez A. H. , Greve T. R. , Hezaveh Y. , Litke K. , Ma J. , Malkan M. , Rotermund K. M. , Strandet M. , Vieira J. D. , Weiss A. , Welikala N. 
Published: July 2016

ABSTRACT
The South Pole Telescope has discovered 100 gravitationally lensed, high-redshift, dusty, star-forming galaxies (DSFGs). We present 0.″5 resolution 870

Atacama Large Millimeter/submillimeter Array imaging of a sample of 47 DSFGs spanning

, and construct gravitational lens models of these sources. Our visibility-based lens modeling incorporates several sources of residual interferometric calibration uncertainty, allowing us to properly account for noise in the observations. At least 70% of the sources are strongly lensed by foreground galaxies (

), with a median magnification of

, extending to

. We compare the intrinsic size distribution of the strongly lensed sources to a similar number of unlensed DSFGs and find no significant differences in spite of a bias between the magnification and intrinsic source size. This may indicate that the true size distribution of DSFGs is relatively narrow. We use the source sizes to constrain the wavelength at which the dust optical depth is unity and find this wavelength to be correlated with the dust temperature. This correlation leads to discrepancies in dust mass estimates of a factor of two compared to estimates using a single value for this wavelength. We investigate the relationship between the [C ii] line and the far-infrared luminosity and find that the same correlation between the [C ii]/

ratio and

found for low-redshift star-forming galaxies applies to high-redshift galaxies and extends at least two orders of magnitude higher in

. This lends further credence to the claim that the compactness of the IR-emitting region is the controlling parameter in establishing the “[C ii] deficit.”
KECK/MOSFIRE SPECTROSCOPY OF z = 7–8 GALAXIES: Lyα EMISSION FROM A GALAXY AT z = 7.66
Authors: Song Mimi , Finkelstein Steven L. , Livermore Rachael C. , Capak Peter L. , Dickinson Mark , Fontana Adriano 
Published: July 2016

ABSTRACT
We report the results from some of the deepest Keck/Multi-Object Spectrometer For Infra-Red Exploration data yet obtained for candidate z ≳ 7 galaxies. Our data show one significant line detection with 6.5σ significance in our combined 10 hr of integration which is independently detected on more than one night, thus ruling out the possibility that the detection is spurious. The asymmetric line profile and non-detection in the optical bands strongly imply that the detected line is Lyα emission from a galaxy at z(Lyα) = 7.6637 ± 0.0011, making it the fourth spectroscopically confirmed galaxy via Lyα at z > 7.5. This galaxy is bright in the rest-frame ultraviolet (UV; M
UV ∼ −21.2) with a moderately blue UV slope (

), and exhibits a rest-frame Lyα equivalent width of EW(Lyα)

Å. The non-detection of the 11 other z ∼ 7–8 galaxies in our long 10 hr integration, reaching a median 5σ sensitivity of 28 Å in the rest-frame EW(Lyα), implies a 1.3σ deviation from the null hypothesis of a non-evolving distribution in the rest-frame EW(Lyα) between 3 < z < 6 and z = 7–8. Our results are consistent with previous studies finding a decline in Lyα emission at z > 6.5, which may signal the evolving neutral fraction in the intergalactic medium at the end of the reionization epoch, although our weak evidence suggests the need for a larger statistical sample to allow for a more robust conclusion.