bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential inhibition of metabolite amyloid formation by generic fibrillation-modifying polyphenols
Authors: Shaham-Niv Shira , Rehak Pavel , Zaguri Dor , Levin Aviad , Adler-Abramovich Lihi , Vuković Lela , Král Petr , Gazit Ehud 
Published: April 2018

AbstractThe formation of ordered amyloid fibrils by proteins and polypeptides is associated with human disorders. A recent extension of the amyloidogenic building block family includes several small metabolites, which form assemblies with structural and functional similarities to well-established amyloids. Here we investigate whether generic amyloid polyphenolic inhibitors can also restrict the formation of metabolite fibrils. We reveal that epigallocatechin gallate and tannic acid inhibit amyloid-like fibrillation of adenine, phenylalanine, and tyrosine. Moreover, the compounds reduce the cytotoxicity triggered by these assemblies. In contrast, acetylsalicylic acid, used as a control does not have an inhibitory effect. The compounds’ differential effects at various time points is consistent with molecular dynamics simulations, providing information about the inhibition mechanisms and inhibitors’ key interactions with the monomeric and subsequent crystalline fibril states. Taken together, we provide additional evidence for the fundamental similarities between protein- and metabolite-based amyloids, the inhibition process and dynamics of association.
A prototypic small molecule database for bronchoalveolar lavage-based metabolomics
Authors: Walmsley Scott , Cruickshank-Quinn Charmion , Quinn Kevin , Zhang Xing , Petrache Irina , Bowler Russell P. , Reisdorph Richard , Reisdorph Nichole 
Published: April 2018

AbstractThe analysis of bronchoalveolar lavage fluid (BALF) using mass spectrometry-based metabolomics can provide insight into lung diseases, such as asthma. However, the important step of compound identification is hindered by the lack of a small molecule database that is specific for BALF. Here we describe prototypic, small molecule databases derived from human BALF samples (n=117). Human BALF was extracted into lipid and aqueous fractions and analyzed using liquid chromatography mass spectrometry. Following filtering to reduce contaminants and artifacts, the resulting BALF databases (BALF-DBs) contain 11,736 lipid and 658 aqueous compounds. Over 10% of these were found in 100% of samples. Testing the BALF-DBs using nested test sets produced a 99% match rate for lipids and 47% match rate for aqueous molecules. Searching an independent dataset resulted in 45% matching to the lipid BALF-DB compared to<25% when general databases are searched. The BALF-DBs are available for download from MetaboLights. Overall, the BALF-DBs can reduce false positives and improve confidence in compound identification compared to when general databases are used.
Unifying cancer and normal RNA sequencing data from different sources
Authors: Wang Qingguo , Armenia Joshua , Zhang Chao , Penson Alexander V. , Reznik Ed , Zhang Liguo , Minet Thais , Ochoa Angelica , Gross Benjamin E. , Iacobuzio-Donahue Christine A. , Betel Doron , Taylor Barry S. , Gao Jianjiong , Schultz Nikolaus 
Published: April 2018

AbstractDriven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing. Here, we developed a pipeline that processes and unifies RNA-seq data from different studies, which includes uniform realignment, gene expression quantification, and batch effect removal. We find that uniform alignment and quantification is not sufficient when combining RNA-seq data from different sources and that the removal of other batch effects is essential to facilitate data comparison. We have processed data from GTEx and TCGA and successfully corrected for study-specific biases, enabling comparative analysis between TCGA and GTEx. The normalized datasets are available for download on figshare.
Curated compendium of human transcriptional biomarker data
Authors: Golightly Nathan P. , Bell Avery , Bischoff Anna I. , Hollingsworth Parker D. , Piccolo Stephen R. 
Published: April 2018

AbstractOne important use of genome-wide transcriptional profiles is to identify relationships between transcription levels and patient outcomes. These translational insights can guide the development of biomarkers for clinical application. Data from thousands of translational-biomarker studies have been deposited in public repositories, enabling reuse. However, data-reuse efforts require considerable time and expertise because transcriptional data are generated using heterogeneous profiling technologies, preprocessed using diverse normalization procedures, and annotated in non-standard ways. To address this problem, we curated 45 publicly available, translational-biomarker datasets from a variety of human diseases. To increase the data's utility, we reprocessed the raw expression data using a uniform computational pipeline, addressed quality-control problems, mapped the clinical annotations to a controlled vocabulary, and prepared consistently structured, analysis-ready data files. These data, along with scripts we used to prepare the data, are available in a public repository. We believe these data will be particularly useful to researchers seeking to perform benchmarking studies—for example, to compare and optimize machine-learning algorithms' ability to predict biomedical outcomes.
The low-mass pre-main sequence population of Scorpius OB1
Authors: Damiani Francesco 
Published: April 2018

Context. The low-mass members of OB associations, expected to be a major component of their total population, are in most cases poorly studied because of the difficulty of selecting these faint stars in crowded sky regions. Our knowledge of many OB associations relies on only a relatively small number of massive members.
Aims. We study here the Sco OB1 association, with the aim of a better characterization of its properties, such as global size and shape, member clusters and their morphology, age and formation history, and total mass.
Methods. We use deep optical and near-infrared (NIR) photometry from the VPHAS+ and VVV surveys, over a wide area (2.6° × 2.6°), complemented by Spitzer infrared (IR) data, and Chandra and XMM-Newton X-ray data. A new technique is developed to find clusters of pre-main sequence M-type stars using suitable color-color diagrams, complementing existing selection techniques using narrow-band Hα photometry or NIR and ultraviolet (UV) excesses, and X-ray data.
Results. We find a large population of approximately 4000 candidate low-mass Sco OB1 members whose spatial properties correlate well with those of Hα-emission, NIR-excess, UV-excess, and X-ray detected members, and unresolved X-ray emission. The low-mass population is spread among several interconnected subgroups: they coincide with the HII regions G345.45+1.50 and IC4628, and the rich clusters NGC 6231 and Trumpler 24, with an additional subcluster intermediate between these two. The total mass of Sco OB1 is estimated to be ~ 8500 M⊙. Indication of a sequence of star-formation events is found, from South (NGC 6231) to North (G345.45+1.50). We suggest that the diluted appearance of Trumpler 24 indicates that the cluster is now dissolving into the field, and that tidal stripping by NGC 6231 nearby contributes to the process.
The first direct double neutron star merger detection: Implications for cosmic nucleosynthesis
Authors: Rosswog S. , Sollerman J. , Feindt U. , Goobar A. , Korobkin O. , Wollaeger R. , Fremling C. , Kasliwal M. M. 
Published: April 2018

Context. The astrophysical r-process site where about half of the elements, heavier than iron are produced, has been a puzzle for several decades. Here we discuss the role of one of the leading ideas – neutron star mergers (NSMs) – in the light of the first direct detection of such an event in both gravitational (GW) and electromagnetic (EM) waves.
Aims. Our aim is to understand the implications of the first GW/EM observations of a NSM for cosmic nucleosynthesis.
Methods. We analyse bolometric and NIR lightcurves of the first detected double NSM and compare them to nuclear reaction network-based macronova models.
Results. The slope of the bolometric lightcurve is consistent with the radioactive decay of neutron star ejecta with Ye ≲ 0.3 (but not larger), which provides strong evidence for an r-process origin of the electromagnetic emission. This rules out in particular “nickel winds” as major source of the emission. We find that the NIR lightcurves can be well fitted either with or without lanthanide-rich ejecta. Our limits on the ejecta mass together with estimated rates directly confirm earlier purely theoretical or indirect observational conclusions that double neutron star mergers are indeed a major site of cosmic nucleosynthesis. If the ejecta mass was typical, NSMs can easily produce all of the estimated Galactic r-process matter, and – depending on the real rate – potentially even more. This could be a hint that the event ejected a particularly large amount of mass, maybe due to a substantial difference between the component masses. This would be compatible with the mass limits obtained from the GW-observation.
Conclusions. The recent observations suggests that NSMs are responsible for a broad range of r-process nuclei and that they are at least a major, but likely the dominant r-process site in the Universe.
Unveiling the remarkable photodissociation region of Messier 8
Authors: Tiwari M. , Menten K. M. , Wyrowski F. , Pérez-Beaupuits J. P. , Wiesemeyer H. , Güsten R. , Klein B. , Henkel C. 
Published: April 2018

Aims. Messier 8 (M8) is one of the brightest HII regions in the sky. We collected an extensive dataset comprising multiple sub- millimeter spectral lines from neutral and ionized carbon and from CO. Based on this dataset, we aim to understand the morphology of M8 and that of its associated photodissociation region (PDR) and to carry out a quantitative analysis of the physical conditions of these regions such as kinetic temperatures and volume densities.
Methods. We used the Stratospheric Observatory For Infrared Astronomy (SOFIA), the Atacama Pathfinder Experiment (APEX) 12 m, and the Institut de Radioastronomie Millimétrique (IRAM) 30 m telescopes to perform a comprehensive imaging survey of the emission from the fine structure lines of [C II] and [C I] and multiple rotational transitions of carbon monoxide (CO) isotopologs within 1.3 × 1.3 pc around the dominant Herschel 36 (Her 36) system, which is composed of at least three massive stars. To further explore the morphology of the region, we compared archival infrared, optical, and radio images of the nebula with our newly obtained fine structure line and CO data, and in particular with the velocity information these data provide. We performed a quantitative analysis, using both LTE and non-LTE methods to determine the abundances of some of the observed species, kinetic temperatures, and volume densities.
Results. Bright CO, [C II] and [C I] emission have been found toward the HII region and the PDR in M8. Our analysis places the bulk of the molecular material in the background of the nebulosity illuminated by the bright stellar systems Her 36 and 9 Sagitarii. Since the emission from all observed atomic and molecular tracers peaks at or close to the position of Her 36, we conclude that the star is still physically close to its natal dense cloud core and heats it. A veil of warm gas moves away from Her 36 toward the Sun and its associated dust contributes to the foreground extinction in the region. One of the most prominent star forming regions in M8, the Hourglass Nebula, is particularly bright due to cracks in this veil close to Her 36. We obtain H2 densities ranging from ~104–106 cm–3 and kinetic temperatures of 100–150 K in the bright PDR caused by Her 36 using radiative transfer modeling of various transitions of CO isotopologs.
Influence of stellar structure, evolution, and rotation on the tidal damping of exoplanetary spin-orbit angles
Authors: Damiani C. , Mathis S. 
Published: April 2018

Context. It is debated whether close-in giant planets can form in-situ and if not, which mechanisms are responsible for their migration. One of the observable tests for migration theories is the current value of the obliquity, that is, the angle between the stellar equatorial plane and the orbital plane. However, after the main migration mechanism has ended, the obliquity and the semi-major axis keep on evolving due to the combined effects of tides and magnetic braking. The observed correlation between effective temperature and measured projected obliquity in well-characterised systems has been taken as evidence of such mechanisms being at play.
Aims. Our aim is to produce an improved model for the tidal evolution of the obliquity, including all the components of the dynamical tide for circular misaligned systems. This model is developed to take into account the strong variations in structure and rotation of stars during their evolution, and their consequences for the efficiency of tidal dissipation.
Methods. Our model uses an analytical formulation for the frequency-averaged dissipation in convective layers for each mode, depending only on global stellar parameters and rotation. It also includes the effect of magnetic braking in the framework of a double zone stellar model.
Results. For the orbital configurations of typical hot Jupiters, the obliquity is generally damped on a much shorter timescale than the semi-major axis. The final outcome of tidal evolution is also very sensitive to the initial conditions, with Jupiter-mass planets being either quickly destroyed or put on more distant orbits, depending on the initial ratio of planetary orbital momentum to stellar spin momentum. However, we find that everything else being the same, the evolution of the obliquity around low-mass stars with a thin convective zone is not slower than around those with a thicker convective zone. On the contrary, we find that more massive stars, which remain faster rotators throughout their main-sequence, produce more efficient dissipation.
J1342+0928 supports the timeline in theRh=ctcosmology
Authors: Melia Fulvio 
Published: April 2018

Aims.The discovery of quasar J1342+0928 (z= 7.54) reinforces the time compression problem associated with the premature formation of structure in Λ cold dark matter (ΛCDM). Adopting thePlanckparameters, we see this quasar barely 690 Myr after the big bang, no more than several hundred Myr after the transition from Pop III to Pop II star formation. Yet conventional astrophysics would tell us that a 10M⊙seed, created by a Pop II/III supernova, should have taken at least 820 Myr to grow via Eddington-limited accretion. This failure by ΛCDM constitutes one of its most serious challenges, requiring exotic “fixes”, such as anomalously high accretion rates, or the creation of enormously massive (~ 105M⊙) seeds, neither of which is ever seen in the local Universe, or anywhere else for that matter. Indeed, to emphasize this point, J1342+0928 is seen to be accreting at about the Eddington rate, negating any attempt at explaining its unusually high mass due to such exotic means. In this paper, we aim to demonstrate that the discovery of this quasar instead strongly confirms the cosmological timeline predicted by theRh=ctUniverse.Methods.We assume conventional Eddington-limited accretion and the time versus redshift relation in this model to calculate when a seed needed to start growing as a function of its mass in order to reach the observed mass of J1342+0928 atz= 7.54.Results.Contrary to the tension created in the standard model by the appearance of this massive quasar so early in its history, we find that in theRh=ctcosmology, a 10M⊙seed atz~ 15 (the start of the Epoch of Reionization att~ 878 Myr) would have easily grown into an 8 × 108M⊙black hole atz= 7.54 (t~ 1.65 Gyr) via conventional Eddington-limited accretion.
Organische Angststörung bei posteriorer kortikaler Atrophie
Authors: Linsmayer Denise , Kindler Christoph , Anheier Wiebke , Reiff Julia , Suppa Per , Braus Dieter 
Published: April 2018

ZusammenfassungWir berichten von einer 54-jährigen Patientin, die über eine seit einem Jahr erfolglos behandelte, progrediente Angstsymptomatik mit rezidivierenden Sehstörungen mit room-tilt-illusions sowie subjektiven Gesichtsfeldeinschränkungen klagte und sich bei uns zur Einholung einer Zweitmeinung vorstellte. Sie berichtete außerdem über Störungen der Konzentration und Aufmerksamkeit sowie über Schwierigkeiten beim Schreiben, einhergehend mit verändertem Schriftbild und Häufung grammatikalischer Fehler. Anhand des Falles werden die relevanten anamnestischen und klinischen Angaben, die neuropsychologischen und bildmorphologischen Befunde sowie differenzialdiagnostische Überlegungen bei Verdacht auf posteriore kortikale Atrophie, eine seltenere neurodegenerative Erkrankung mit psychischen Symptomen, dargestellt.
Treatment of a Paediatric Distal Femoral Malunion Deformity
Authors: Pavarotti Greta , Boudrieau Randy 
Published: April 2018

Objective The aim of this article was to describe the surgical re-alignment technique and stabilization of a distal femoral deformity in a 6-week-old, male, Foxhound.
Methods A healing metaphyseal fracture, resulting in a valgus deformity with internal rotation, was observed just proximal to the distal femoral physis. The deformity was treated by an opening wedge osteotomy with lateral translation and external rotation of the distal epiphysis using a guide-wire technique; a corticocancellous allograft bridged the defect, which was stabilized with a 2.0-mm locking Y-plate designed for human phalangeal fractures.
Results Successful deformity correction was obtained with subsequent healing of the osteotomy and maintained longitudinal bone growth. Sciatic neurapraxia developed as a result of a migrating adjunct pin (9 days post-operatively), which was removed. At long-term follow-up (4 years), a 12% shortening of the femur did result in addition to an asymptomatic grade 2 medial patellar luxation (MPL). The cause of the MPL was not evident; the owners declined treatment and the dog continued to function as an active hunting dog.
Clinical Significance Prior to ossification of the epiphyses in very young animals, which precludes effective radiographic pre-planning, the guide-wire technique can be utilized as the primary tool for performing angular deformity correction. Adequate fixation and stabilization can be obtained with small human specialty locking plates.
Free versus Pedicled Perforator Flaps for Lower Extremity Reconstruction: A Multicenter Comparison of Institutional Practices and Outcomes
Authors: Koh Keith , Goh Terence , Song Christopher , Suh Hyun , Rovito Peter , Hong Joon-Pio , Hallock Geoffrey 
Published: April 2018

Background Of all body regions, lower extremity wounds have been and remain the greatest challenge. Perforator free flaps have been accepted as a reasonable option to solve this dilemma but require the complexity of microsurgery. As a consequence, the possibility that pedicled perforator flaps could supplant even perforator free flaps has recently gained intense enthusiasm.
Methods A retrospective investigation was undertaken to compare the validity for the use of perforator flaps of all types at three dissimilar institutions, that is, a university, a regional center, and a community hospital. All flaps performed in the 5-year period, 2011 to 2015, were included to allow at least 1-year follow-up before data analysis. A total of 433 free perforator flaps and 52 pedicled perforator flaps had been performed specifically for the lower extremity.
Results Patient demographics, wound etiology, and comorbidities were similar for all institutions. Free flaps were more commonly needed after trauma and for chronic ulcers. Pedicled flaps were more likely an option after tumor excision. Large defects or those involving the foot were better served by free flaps. Overall success for free perforator flaps was 90.1% and for pedicled perforator flaps was 92.3%, with no significant difference noted (p = 0.606) between institutions. Peripheral vascular disease was the only significant comorbidity risk factor for both free and pedicled flap failure.
Conclusion Perforator flaps in general have become a reasonable solution for soft tissue defects of the lower extremity. Following careful consideration of the etiology, dimensions, location, patient comorbidities, and presence of adequate perforators, a pedicled or free perforator flap could potentially be successful. Pedicled perforator flaps, if adequate healthy soft tissues remain adjacent to the defect, forecast a continuance of the evolution in seeking simplicity yet reliability by the best flap possible for soft tissue closure of the lower limb wound.
Cerebral Proliferative Angiopathy: Case Report
Authors: Gatto Luana , Brisson Rodrigo , Demartini Zeferino , Koppe Gelson , Rocha Carlos 
Published: April 2018

AbstractProliferative angiopathy (PA) is a rare cerebral vascular disease in which anomalous vessels continually recruit additional feeder arteries, amid a functional brain parenchyma. We report the case of a young woman with progressive history of headache, motor deficit, seizures and drowsiness. She received a misdiagnosis of brain arteriovenous malformation (AVM) and evolved with dysarthria and cognitive decline after an unsuccessful embolization performed at another institution. We opted for conservative treatment with periodic control by imaging tests. Proliferative angiopathy differs in natural history, prognosis, histopathology and treatment of the usual AVMs. Endovascular procedures aggravate the neurological deficits, which are usually progressive and tend to worsen over time.
The Association Between Self-Rated Fitness and Cardiorespiratory Fitness in Adults
Authors: Jensen Karina , Rosthøj Susanne , Linneberg Allan , Aadahl Mette 
Published: April 2018

AbstractTo assess criterion validity of a single item question on self-rated physical fitness against objectively measured cardiorespiratory fitness. From the Health2008 study 749 men and women between 30 and 60 years of age rated their fitness as excellent, very good, good, fair or poor. Cardiorespiratory fitness was estimated with the watt-max test. Agreement between self-rated and objectively measured physical fitness was assessed by Cohen’s weighted kappa coefficient. Correlation was determined by Goodman & Kruskal’s gamma correlation coefficient. All analyses were stratified according to gender. Data from 323 men and 426 women were analysed. There was a slight agreement between self-rated and objectively measured fitness in men (weighted kappa: 0.18, [95%CI: 0.13;0.23]) and a fair agreement in women (weighted kappa: 0.27, [95%CI: 0.22;0.32]). In both genders, self-rated fitness was positively correlated with objectively measured fitness (moderate correlation; gamma correlation coefficient for men: 0.63 [95%CI: 0.54;0.72] and women: 0.67 [95%CI: 0.59;0.75]). There was a slight to fair agreement and moderate, positive correlations between self-rated physical fitness and watt-max estimated cardiorespiratory fitness. Hence, a single-item question on physical fitness may be a cost-effective method of assessing fitness in large population studies, but is not valid for individual assessments.