bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive comparison between APOGEE and LAMOST
Authors: Anguiano B. , Majewski S. R. , Allende-Prieto C. , Meszaros S. , Jönsson H. , García-Hernández D. A. , Beaton R. L. , Stringfellow G. S. , Cunha K. , Smith V. V. 
Published: September 2018

Context. In the era of massive spectroscopy surveys, automated stellar parameter pipelines and their validation are extremely important for an efficient scientific exploitation of the spectra.
Aims. We undertake a critical and comprehensive comparison of the radial velocities and the main stellar atmosphere parameters for stars in common between the latest data releases from the Apache Point Observatory Galaxy Evolution Experiment (APOGEE) and the Large sky Area Multi-Object Spectroscopic Telescope (LAMOST) surveys.
Methods. APOGEE is a high-resolution (R = 22 500) spectroscopic survey with high signal-to-noise ratio that is part of the Sloan Digital Sky Survey (SDSS). The latest data release, SDSS DR14, comprises APOGEE spectra for 263 444 stars, together with main stellar parameters and individual abundances for up to 20 chemical species. LAMOST is a low-resolution (R = 1800) optical spectroscopic survey also in the Northern Hemisphere, where 4000 fibers can be allocated simultaneously. LAMOST DR3 contains 3 177 995 stars.
Results. A total of 42 420 dwarfs and giants stars are in common between the APOGEE DR14 – LAMOST DR3 stellar catalogs. A comparison between APOGEE and LAMOST RVs shows a clear offset of 4.54 ± 0.03 km s−1, with a dispersion of 5.8 km s−1, in the sense that APOGEE radial velocities are higher. We observe a small offset in the effective temperatures of about 13 K, with a scatter of 155 K. A small offset in [Fe/H] of about 0.06 dex together with a scatter of 0.13 dex is also observed. We note that the largest offset between the surveys occurs in the surface gravities. Using only surface gravities in calibrated red giants from APOGEE DR14, with which there are 24 074 stars in common, a deviation of 0.14 dex is found with substantial scatter (0.25 dex). There are 17 482 red giant stars in common between APOGEE DR14 and those in LAMOST tied to APOGEE DR12 via the code called the Cannon. There is generally good agreement between the two data-sets. However, we find that the differences in the stellar parameters depend on effective temperature. For metal-rich stars, a different trend for the [Fe/H] discrepancies is found. Surprisingly, we see no correlation between the internal APOGEE DR14 – DR12 differences in Teff and those in DR14 – LAMOST tied to DR12, where a correlation should be expected since LAMOST has been calibrated to APOGEE DR12. We find no correlation either between the [Fe/H] discrepancies, suggesting that LAMOST/Cannon is not well coupled to the APOGEE DR12 stellar parameter scale. An [Fe/H] dependence between the stellar parameters in APOGEE DR12 and those in DR14 is reported. We find a weak correlation in the differences between APOGEE DR14 – DR12 and LAMOST on DR12 surface gravity for stars hotter than 4800 K and in the log g range between 2.0 and 2.8 dex. We do not observe an [Fe/H] dependency in the gravity discrepancies.
Shadows and asymmetries in the T Tauri disk HD 143006: evidence for a misaligned inner disk
Authors: Benisty M. , Juhász A. , Facchini S. , Pinilla P. , de Boer J. , Pérez L. M. , Keppler M. , Muro-Arena G. , Villenave M. , Andrews S. , Dominik C. , Dullemond C. P. , Gallenne A. , Garufi A. , Ginski C. , Isella A. 
Published: September 2018

Context. While planet formation is thought to occur early in the history of a protoplanetary disk, the presence of planets embedded in disks, or of other processes driving disk evolution, might be traced from their imprints on the disk structure.
Aims. We study the morphology of the disk around the T Tauri star HD 143006, located in the ~5–11 Myr-old Upper Sco region, and we look for signatures of the mechanisms driving its evolution.
Methods. We observed HD 143006 in polarized scattered light with VLT/SPHERE at near-infrared (J-band, 1.2 μm) wavelengths, reaching an angular resolution of ~0.037′′ (~6 au). We obtained two datasets, one with a 145 mas diameter coronagraph, and the other without, enabling us to probe the disk structure down to an angular separation of ~0.06′′ (~10 au).
Results. In our observations, the disk of HD 143006 is clearly resolved up to ~0.5′′ and shows a clear large-scale asymmetry with the eastern side brighter than the western side. We detect a number of additional features, including two gaps and a ring. The ring shows an overbrightness at a position angle (PA) of ~140°, extending over a range in position angle of ~60°, and two narrow dark regions. The two narrow dark lanes and the overall large-scale asymmetry are indicative of shadowing effects, likely due to a misaligned inner disk. We demonstrate the remarkable resemblance between the scattered light image of HD 143006 and a model prediction of a warped disk due to an inclined binary companion. The warped disk model, based on the hydrodynamic simulations combined with three-dimensional radiative transfer calculations, reproduces all major morphological features. However, it does not account for the observed overbrightness at PA ~ 140°.
Conclusions. Shadows have been detected in several protoplanetary disks, suggesting that misalignment in disks is not uncommon. However, the origin of the misalignment is not clear. As-yet-undetected stellar or massive planetary companions could be responsible for them, and naturally account for the presence of depleted inner cavities.
The Influence of Oxygen Saturation on the Relationship Between Hemoglobin Mass and VO2max
Authors: Goodrich Jesse , Ryan Benjamin , Byrnes William 
Published: September 2018

AbstractHemoglobin mass (tHb) is a key determinant of maximal oxygen uptake (VO2max). We examined whether oxyhemoglobin desaturation (ΔSaO2) at VO2max modifies the relationship between tHb and VO2max at moderate altitude (1,625 m). Seventeen female and 16 male competitive, endurance-trained moderate-altitude residents performed two tHb assessments and two graded exercise tests on a cycle ergometer to determine VO2max and ΔSaO2. In males and females respectively, VO2max (ml·kg−1·min−1) ranged from 62.5–83.0 and 44.5–67.3; tHb (g·kg−1) ranged from 12.1–17.5 and 9.1–13.0; and SaO2 at VO2max (%) ranged from 81.7–94.0 and 85.7–95.0. tHb was related to VO2max when expressed in absolute terms and after correcting for body mass (r=0.94 and 0.86, respectively); correcting by ΔSaO2 did not improve these relationships (r=0.93 and 0.83). Additionally, there was a negative relationship between tHb and SaO2 at VO2max (r=–0.57). In conclusion, across a range of endurance athletes at moderate altitude, the relationship between tHb and VO2max was found to be similar to that observed at sea level. However, correcting tHb by ΔSaO2 did not explain additional variability in VO2max despite significant variability in ΔSaO2; this raises the possibility that tHb and exercise-induced ΔSaO2 are not independent in endurance athletes.
Evaluation of a Center of Research Excellence in Polycystic Ovary Syndrome as a Large-Scale Collaborative Research Translation Initiative, Including Evaluating Translation of Guideline Impact
Authors: Kozica-Olenski Samantha , Teede Helena , Garad Rhonda 
Published: September 2018

AbstractResearch translation and evaluation are often underconsidered in research design and implementation thus limiting research benefit to the end user. In this article, we first describe a best practice approach to evaluation, for a center of research excellence in polycystic ovary syndrome. Within this, we outline a comprehensive research translation program with inbuilt evaluation of the first International Evidence-based Guideline for the Assessment and Management of Polycystic Ovary Syndrome (2018). We seek to provide a real-world example of comprehensive approaches to evaluation and research translation.
Validation of the Predictive Model of the European Society of Cardiology for Early Mortality in Acute Pulmonary Embolism
Authors: Cugno Massimo , Depetri Federica , Gnocchi Laura , Porro Fernando , Bucciarelli Paolo 
Published: September 2018

Background Acute pulmonary embolism (PE) is burdened by high mortality, especially within 30 days from the diagnosis. The development and the validation of predictive models for the risk of early mortality allow to differentiate patients who can undergo home treatment from those who need admission into intensive care units.
Methods To validate the prognostic model for early mortality after PE diagnosis proposed by the European Society of Cardiology (ESC) in 2014, we analyzed data of a cohort of 272 consecutive patients with acute PE, observed in our hospital during a 10-year period. Moreover, we evaluated the additional contribution of D-dimer, measured at PE diagnosis, in improving the prognostic ability of the model. All cases of PE were objectively diagnosed by angiography chest CT scan or perfusion lung scan.
Results The overall mortality rate within 30 days from PE diagnosis was 10% (95% confidence interval [CI]: 6.4–13.5%). According to the ESC prognostic model, the risk of death increased 3.23 times in the intermediate-low-risk category, 5.55 times in the intermediate-high-risk category, and 23.78 times in the high-risk category, as compared with the low-risk category. The receiver operating characteristic analysis showed a good discriminatory power of the model (area under the curve [AUC] = 0.77 [95% CI: 0.67–0.87]), which further increased when D-dimer was added (AUC = 0.85 [95% CI: 0.73–0.96]).
Conclusion This study represents a good validation of the ESC predictive model whose performance can be further improved by adding D-dimer plasma levels measured at PE diagnosis.
Comparing Cementing Techniques in Total Knee Arthroplasty: An In Vitro Study
Authors: Wetzels Thomas , van Erp Joost , Brouwer Reinoud W. , Bulstra Sjoerd K. , van Raay Jos J. A. M. 
Published: September 2018

AbstractAseptic loosening remains to be a major reason for revision in total knee arthroplasty. Cement penetration of 2 to 5 mm increases the interface strength and consequently decreases the likelihood of loosening. But despite this overall accepted optimal cement penetration, there is still a wide variety of cementing techniques used in total knee arthroplasty. The purpose of this study was to evaluate two cementing techniques on the tibial and femoral sides, with regard to cement penetration. Five paired cadaveric knees were used. A total knee arthroplasty was placed according to standard practice, with a setup that mimics the clinical practice. On the tibial side, we compared the application of cement to the bone surface alone, to the application of cement to both the bone surface and the component. On the femoral side, we compared the application of cement to the posterior condyles of the component and to the anterior and distal parts of the bone surface, to the application of cement to the component alone. After the cement had cured, the arthroplasty was removed and the bone was examined to determine the cement penetration using digital software. When applying cement to both the tibial bone surface and the tibial component, the cement penetration increased compared with applying cement to the tibial bone surface alone (3.46 vs. 2.66 mm, p = 0.007). With regard to the distal femoral cuts, the cement penetration did not vary when applied to either the bone or the component (2.81 vs. 2.91 mm). But applying it to the anterior bone surface did seem preferable, when compared with only applying it to the component. The average cement penetration did not differ, but applying the cement to the bone did enlarge the total length of the cement distribution (2.48 vs. 0.96 mm, p = 0.011). Almost no cement was detected on the posterior surface of the femoral cut. We concluded that applying cement to both the tibial bone surface and the component improves cement penetration.
Cytotoxicity analysis of staphylococcal bi-component β-pore forming toxins using the CHO cells expressing human lymphocyte receptor CCR5
Authors: Peng Zhao , Shibata Nao , Tada Hideaki , Kaneko Jun 
Published: September 2018

ABSTRACT
CCR5-mediated cytotoxicity of staphylococcal bi-component toxins was investigated using human CCR5-expressing CHO cells. Cytotoxicity of rim domain loop-exchange mutants between LukE and Hlg2 indicated that loop-4 of LukE is essential for cytotoxicity in combination with LukD. Interestingly, Hlg2 showed LukF-dependent CCR5-mediated cytotoxicity, suggesting that the F-components of toxins also play a role in the cell-specific cytotoxicity.
EURAMET supplementary comparison of ambient dose equivalent H*(10) in 137Cs and ISO Narrow Beam Series N-60 x-ray beams at low dose rates
Authors: Hupe Oliver , Díaz stor Armando Cornejo 
Published: September 2018

Comparison measurements among national standards laboratories are required to demonstrate their equivalence in the realization and transfer of the quantity ambient dose equivalent, H*(10), for photon radiation by these laboratories.
The first comparison of the radiation protection quantity H*(10) with focus on the special needs for calibration of area dosemeters, low dose rates and large fields, started in January 2013 and was completed in December 2014. The comparison was piloted by the PTB as EURAMET project No. 1132 known also as EURAMET.RI(I)-S11.
The operation and results of the comparison are reported here. The transfer instrument was a secondary standard ionization chamber for H*(10) with a volume of 10000 cm3. The response of this transfer instrument in various photon reference fields (N-60 and 1 mSv/h, S-Cs and 10 μSv/h, S-Cs and 1 mSv/h, radiation quality according to ISO 4037-1:1996 [1]) was compared.
Measurements were made by the fourteen participants from the following countries: Germany, Austria, Greece, Norway, Sweden, Finland, Portugal, Spain, Czech Republic, Romania, the Netherlands, Slovenia, Italy and by one international organization. The results obtained by almost all of the participants are consistent with the stated uncertainties.
KEY WORDS FOR SEARCH
Dosimetry, comparison, ambient dose equivalent, ISO narrow beam, EURAMET, CIPM MRA, BIPM KCDB

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
A cost-effective technique for generating preservable biomass smoke extract and measuring its effect on cell receptor expression in human bronchial epithelial cells
Authors: Rajendra K C , Zosky Graeme R , Shukla Shakti D , O’Toole Ronan F 
Published: September 2018

Abstract
Nearly half of the world’s population uses biomass fuel for the purposes of cooking and heating. Smoke derived from biomass increases the risk of the development of lung diseases, including pneumonia, chronic obstructive pulmonary disease, airway tract infections, and lung cancer. Despite the evidence linking biomass smoke exposure to pulmonary disease, only a small number of experimental studies have been conducted on the impact of biomass smoke on airway epithelial cells. This is in part due to the lack of a standard and easily accessible procedure for the preparation of biomass smoke. Here, we describe a cost-effective and reproducible method for the generation of different smoke extracts, in particular, cow dung smoke extract (CDSE) and wood smoke extract (WSE) for use in a range of biological applications. We examined the effect of the biomass smoke extracts on human bronchial epithelial cell expression of a known responder to cigarette smoke exposure (CSE), the platelet-activating factor receptor (PAFR). Similar to the treatment with CSE, we observed a dose-dependent increase in PAFR expression on human airway epithelial cells that were exposed to CDSE and WSE. This method provides biomass smoke in a re-usable form for cell and molecular bioscience studies on the pathogenesis of chronic lung disease.
Ximmer: a system for improving accuracy and consistency of CNV calling from exome data
Authors: Sadedin Simon P , Ellis Justine A , Masters Seth L , Oshlack Alicia 
Published: September 2018

Abstract

Background
While exome and targeted next-generation DNA sequencing are primarily used for detecting single nucleotide changes and small indels, detection of copy number variants (CNVs) can provide highly valuable additional information from the data. Although there are dozens of exome CNV detection methods available, these are often difficult to use, and accuracy varies unpredictably between and within datasets.

Findings
We present Ximmer, a tool that supports an end-to-end process for evaluating, tuning, and running analysis methods for detection of CNVs in germline samples. Ximmer includes a simulation framework, implementations of several commonly used CNV detection methods, and a visualization and curation tool that together enable interactive exploration and quality control of CNV results. Using Ximmer, we comprehensively evaluate CNV detection on four datasets using five different detection methods. We show that application of Ximmer can improve accuracy and aid in quality control of CNV detection results. In addition, Ximmer can be used to run analyses and explore CNV results in exome data.

Conclusions
Ximmer offers a comprehensive tool and method for applying and improving accuracy of CNV detection methods for exome data.
Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration
Authors: Gao Guangqi , Xu Meng , Bai Chunling , Yang Yulan , Li Guangpeng , Xu Junyang , Wei Zhuying , Min Jiumeng , Su Guanghua , Zhou Xianqiang , Guo Jun , Hao Yu , Zhang Guiping , Yang Xukui , Xu Xiaomin , Widelitz Randall B , Chuong Cheng-Ming , Zhang Chi , Yin Jun , Zuo Yongchun 
Published: September 2018

Abstract

Background
As one of the most recognizable characteristics in birds, plumage color has a high impact on understanding the evolution and mechanisms of coloration. Feather and skin are ideal tissues to explore the genomics and complexity of color patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst's pheasant (Chrysolophus amherstiae), exhibit brilliant colors in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage coloration mechanisms in birds.

Results
We sequenced and assembled a genome of golden pheasant with high coverage and annotated 15,552 protein-coding genes. The genome of Lady Amherst's pheasant is sequenced with low coverage. Based on the feather pigment identification, a series of genomic and transcriptomic comparisons were conducted to investigate the complex features of plumage coloration. By identifying the lineage-specific sequence variations in Chrysolophus and golden pheasant against different backgrounds, we found that four melanogenesis biosynthesis genes and some lipid-related genes might be candidate genomic factors for the evolution of melanin and carotenoid pigmentation, respectively. In addition, a study among 47 birds showed some candidate genes related to carotenoid coloration in a broad range of birds. The transcriptome data further reveal important regulators of the two colorations, particularly one splicing transcript of the microphthalmia-associated transcription factor gene for pheomelanin synthesis.

Conclusions
Analysis of the golden pheasant and its sister pheasant genomes, as well as comparison with other avian genomes, are helpful to reveal the underlying regulation of their plumage coloration. The present study provides important genomic information and insights for further studies of avian plumage evolution and diversity.
Project Tycho 2.0: a repository to improve the integration and reuse of data for global population health
Authors: van Panhuis Willem G , Cross Anne , Burke Donald S 
Published: September 2018

Abstract

Objective
In 2013, we released Project Tycho, an open-access database comprising 3.6 million counts of infectious disease cases and deaths reported for over a century by public health surveillance in the United States. Our objective is to describe how Project Tycho version 1 (v1) data has been used to create new knowledge and technology and to present improvements made in the newly released version 2.0 (v2).

Materials and Methods
We analyzed our user database and conducted online searches to analyze the use of Project Tycho v1 data. For v2, we added new US data and dengue data for other countries, and grouped data into 360 datasets, each with a digital object identifier and rich metadata. In addition, we used standard vocabularies to encode data where possible, improving compliance with FAIR (findable, accessible, interoperable, reusable) guiding principles for data management.

Results
Since release, 3174 people have registered to use Project Tycho data, leading to 18 new peer-reviewed papers and 27 other creative works, such as conference papers, student theses, and software applications. Project Tycho v2 comprises 5.7 million counts of infectious diseases in the United States and of dengue-related conditions in 98 additional countries.

Discussion
Project Tycho v2 contributes to improving FAIR compliance of global health data, but more work is needed to develop community-accepted standard representations for global health data.

Conclusion
FAIR principles are a valuable guide for improving the integration and reuse of data in global health to improve disease control and save lives.
High skilled migration through the lens of policy
Authors: Parsons Christopher R , Rojon Sebastien , Rose Lena , Samanani Farhan 
Published: September 2018

Abstract
High skilled migrants and the policies designed to attract and select such individuals are widely championed. In formulating and evaluating such policies, however, policy makers and academics alike face significant challenges, since, from the perspective of policy, what it means to be high skilled remains a fluid concept. The resulting ambiguity stymies meaningful international comparisons of the mobility of skills, undermines the design and evaluation of immigration policies and hinders the measurement of human capital. In this paper, we adopt an inductive approach to examine how high skilled migrants are classified based upon states’ unilateral immigration policies, thereby highlighting the difficulties of comparing high skilled policies across countries. We further elucidate the challenges in measuring the outcomes of high skilled migration policies that arise due to differing national priorities in recording high skilled migrants. We conclude by making a number of policy recommendations, which if enacted, would bring clarity to scholars and policy makers alike in terms of being able to meaningfully compare the composition, and assess the efficacy of, high skilled migration policies across countries. In doing so we introduce three datasets comprising: harmonised high skill migration flow data, skilled occupational concordances and high skilled unilateral and bilateral migration policy data, which undergird our analysis and that can be built upon in years to come.