bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment
Authors: Lin Kuo-Hua , Huang Ming-Yii , Cheng Wei-Chung , Wang Shu-Chi , Fang Shih-Hua , Tu Hung-Pin , Su Chia-Cheng , Hung Yung-Li , Liu Po-Len , Chen Chi-Shuo , Wang Yu-Ting , Li Chia-Yang 
Published: February 2018

AbstractShikonin is a naphthoquinone isolated from the dried root of Lithospermum erythrorhizon, an herb used in Chinese medicine. Although several studies have indicated that shikonin exhibits antitumor activity in breast cancer, the mechanism of action remains unclear. In the present study, we performed transcriptome analysis using RNA-seq and explored the mechanism of action of shikonin in regulating the growth of different types of breast cancer cells. The IC50 of shikonin on MCF-7, SKBR-3 and MDA-MB-231 cells were 10.3 μΜ, 15.0 μΜ, 15.0 μΜ respectively. Our results also demonstrated that shikonin arrests the progression of cell cycle and induces apoptosis in MDA-MB-231 cells. Using RNA-seq transcriptome analysis, we found 38 common genes that significantly express in different types of breast cancer cells under shikonin treatment. In particular, our results indicated that shikonin induces the expression of dual specificity phosphatase (DUSP)-1 and DUSP2 in both RNA and protein levels. In addition, shikonin also inhibits the phosphorylation of JNK and p38, the downstream signaling molecules of DUSP1 and DUSP2. Therefore, our results suggest that shikonin induces the expression of DUSP1 and DUSP2 which consequently switches off JNK and p38 MAPK pathways and causes cell cycle arrest and apoptosis in breast cancer cells.
Local raster image correlation spectroscopy generates high-resolution intracellular diffusion maps
Authors: Scipioni Lorenzo , Di Bona Melody , Vicidomini Giuseppe , Diaspro Alberto , Lanzanò Luca 
Published: February 2018

AbstractRaster image correlation spectroscopy (RICS) is a powerful method for measuring molecular diffusion in live cells directly from images acquired on a laser scanning microscope. However, RICS only provides single average diffusion coefficients from regions with a lateral size on the order of few micrometers, which means that its spatial resolution is mainly limited to the cellular level. Here we introduce the local RICS (L-RICS), an easy-to-use tool that generates high resolution maps of diffusion coefficients from images acquired on a laser scanning microscope. As an application we show diffusion maps of a green fluorescent protein (GFP) within the nucleus and within the nucleolus of live cells at an effective spatial resolution of 500 nm. We find not only that diffusion in the nucleolus is slowed down compared to diffusion in the nucleoplasm, but also that diffusion in the nucleolus is highly heterogeneous.
A rare missense variant in NR1H4 associates with lower cholesterol levels
Authors: Deaton Aimee M. , Sulem Patrick , Nioi Paul , Benonisdottir Stefania , Ward Lucas D. , Davidsson Olafur B. , Lao Socheata , Helgadottir Anna , Fan Fan , Jensson Brynjar O. , Norddahl Gudmundur L. , Jonasdottir Aslaug , Jonasdottir Adalbjorg , Sigurdsson Asgeir , Kristjansson Ragnar P. , Oddsson Asmundur , Arnadottir Gudny A. , Jonsson Hakon , Olafsson Isleifur , Eyjolfsson Gudmundur I. , Sigurdardottir Olof , Bjornsson Einar S. , Olafsson Sigurdur , Steingrimsdottir Thora , Rafnar Thorunn , Thorgeirsson Gudmundur , Masson Gisli , Thorleifsson Gudmar , Gudbjartsson Daniel F. , Holm Hilma , Thorsteinsdottir Unnur , Stefansson Kari 
Published: February 2018

AbstractSearching for novel sequence variants associated with cholesterol levels is of particular interest due to the causative role of non-HDL cholesterol levels in cardiovascular disease. Through whole-genome sequencing of 15,220 Icelanders and imputation of the variants identified, we discovered a rare missense variant in NR1H4 (R436H) associating with lower levels of total cholesterol (effect = −0.47 standard deviations or −0.55 mmol L−1, p = 4.21 × 10−10, N = 150,211). Importantly, NR1H4 R436H also associates with lower levels of non-HDL cholesterol and, consistent with this, protects against coronary artery disease. NR1H4 encodes FXR that regulates bile acid homeostasis, however, we do not detect a significant association between R436H and biological markers of liver function. Transcriptional profiling of hepatocytes carrying R436H shows that it is not a loss-of-function variant. Rather, we observe changes in gene expression compatible with effects on lipids. These findings highlight the role of FXR in regulation of cholesterol levels in humans.
MASCARA-2 b
Authors: Talens G. J. J. , Justesen A. B. , Albrecht S. , McCormac J. , Van Eylen V. , Otten G. P. P. L. , Murgas F. , Palle E. , Pollacco D. , Stuik R. , Spronck J. F. P. , Lesage A.-L. , Grundahl F. , Fredslund Andersen M. , Antoci V. , Snellen I. A. G. 
Published: February 2018

In this paper we present MASCARA-2 b, a hot Jupiter transiting the mV = 7.6 A2 star HD 185603. Since early 2015, MASCARA has taken more than 1.6 million flux measurements of the star, corresponding to a total of almost 3000 h of observations, revealing a periodic dimming in the flux with a depth of 1.3%. Photometric follow-up observations were performed with the NITES and IAC80 telescopes and spectroscopic measurements were obtained with the Hertzsprung SONG telescope. We find MASCARA-2 b orbits HD 185603 with a period of 3.4741119-0.000006+0.000005 days at a distance of 0.057 ± 0.006 au, has a radius of 1.83 ± 0.07 RJ and place a 99% upper limit on the mass of <17 MJ. HD 185603 is a rapidly rotating early-type star with an effective temperature of 8980-130+90 K and a mass and radius of 1.89-0.05+0.06 M⊙, 1.60 ± 0.06 R⊙, respectively. Contrary to most other hot Jupiters transiting early-type stars, the projected planet orbital axis and stellar spin axis are found to be aligned with λ = 0.6 ± 4°. The brightness of the host star and the high equilibrium temperature, 2260 ± 50 K, of MASCARA-2 b make it a suitable target for atmospheric studies from the ground and space. Of particular interest is the detection of TiO, which has recently been detected in the similarly hot planets WASP-33 b and WASP-19 b.
Accreting, highly magnetized neutron stars at the Eddington limit: a study of the 2016 outburst of SMC X-3
Authors: Koliopanos Filippos , Vasilopoulos Georgios 
Published: February 2018

Aims.We study the temporal and spectral characteristics of SMC X-3 during its recent (2016) outburst to probe accretion onto highly magnetized neutron stars (NSs) at the Eddington limit.Methods.We obtainedXMM-Newtonobservations of SMC X-3 and combined them with long-term observations bySwift. We performed a detailed analysis of the temporal and spectral behavior of the source, as well as its short- and long-term evolution. We have also constructed a simple toy-model (based on robust theoretical predictions) in order to gain insight into the complex emission pattern of SMC X-3.Results.We confirm the pulse period of the system that has been derived by previous works and note that the pulse has a complex three-peak shape. We find that the pulsed emission is dominated by hard photons, while at energies below ~1 keV, the emission does not pulsate. We furthermore find that the shape of the pulse profile and the short- and long-term evolution of the source light-curve can be explained by invoking a combination of a “fan” and a “polar” beam. The results of our temporal study are supported by our spectroscopic analysis, which reveals a two-component emission, comprised of a hard power law and a soft thermal component. We find that the latter produces the bulk of the non-pulsating emission and is most likely the result of reprocessing the primary hard emission by optically thick material that partly obscures the central source. We also detect strong emission lines from highly ionized metals. The strength of the emission lines strongly depends on the phase.Conclusions.Our findings are in agreement with previous works. The energy and temporal evolution as well as the shape of the pulse profile and the long-term spectra evolution of the source are consistent with the expected emission pattern of the accretion column in the super-critical regime, while the large reprocessing region is consistent with the analysis of previously studied X-ray pulsars observed at high accretion rates. This reprocessing region is consistent with recently proposed theoretical and observational works that suggested that highly magnetized NSs occupy a considerable fraction of ultraluminous X-ray sources.
The sPHENIX Experiment
Authors: Pérez Lara Carlos E. 
Published: February 2018

Our understanding of QCD under extreme conditions has advanced tremendously in the last 20 years with the discovery of the Quark Gluon Plasma and its characterisation in heavy ion collisions at RHIC and LHC. The sPHENIX detector planned at RHIC is designed to further study the microscopic nature of the QGP through precision measurements of jet, upsilon and open heavy flavor probes over a broad pT range. The multi-year sPHENIX physics program will commence in early 2023, using state-of-the art detector technologies to fully exploit the highest RHIC luminosities.
The experiment incorporates the 1.4 T former BaBar solenoid magnet, and will feature high precision tracking and vertexing capabilities, provided by a compact TPC, Si-strip intermediate tracker and MAPS vertex detector. This is complemented by highly granular electromagnetic and hadronic calorimetry with full azimuthal coverage.
In this document I describe the sPHENIX detector design and physics program, with particular emphasis on the comprehensive open heavy flavour program enabled by the experiment’s large coverage, high rate capability and precision vertexing.
The shaker parameters estimation, a first step to virtual testing
Authors: Martino Jonathan , Harri Kristof 
Published: February 2018

The increase in computing resources makes simulation methods more affordable. The processing speed allows real time analysis or even more rapid tests analysis offering a real tool for test prediction and design process optimization. Vibration tests are no exception to this trend.The so called 'Virtual Vibration Testing' offers solution among others to study the influence of specific loads such as optimized signals, to better anticipate the boundary conditions between the exciter and the structure under test or to study the influence of small changes in the structure under test.This article will first present a virtual vibration test modeling with a main focus on the shaker model and will afterwards present the experimental parameters determination.The classical way of modeling a shaker is to consider the shaker as a simple mechanical structure augmented by an electrical circuit that makes the shaker move. The developed model is a two degrees of freedom mechanical lumped parameters model and the electrical circuit model takes the coil impedance and the dynamic back-electromagnetic force into account. The establishment of the equations of this model, describing the dynamics of the shaker, is presented in this article and is strongly related to the internal physical quantities of the shaker. Those quantities will be reduced into global parameters which will be estimated through experiments in order to get a fully functional shaker model.An experimental modal analysis will also be carried out to extract the modal parameters of the shaker and to combine them with the electrical measurements.Finally this article will conclude with an experimental validation of the model.
Using EHR Data to Detect Prescribing Errors in Rapidly Discontinued Medication Orders
Authors: Burlison Jonathan , McDaniel Robert , Baker Donald , Hasan Murad , Robertson Jennifer , Howard Scott , Hoffman James 
Published: February 2018

Background Previous research developed a new method for locating prescribing errors in rapidly discontinued electronic medication orders. Although effective, the prospective design of that research hinders its feasibility for regular use.
Objectives Our objectives were to assess a method to retrospectively detect prescribing errors, to characterize the identified errors, and to identify potential improvement opportunities.
Methods Electronically submitted medication orders from 28 randomly selected days that were discontinued within 120 minutes of submission were reviewed and categorized as most likely errors, nonerrors, or not enough information to determine status. Identified errors were evaluated by amount of time elapsed from original submission to discontinuation, error type, staff position, and potential clinical significance. Pearson's chi-square test was used to compare rates of errors across prescriber types.
Results In all, 147 errors were identified in 305 medication orders. The method was most effective for orders that were discontinued within 90 minutes. Duplicate orders were most common; physicians in training had the highest error rate (p < 0.001), and 24 errors were potentially clinically significant. None of the errors were voluntarily reported.
Conclusion It is possible to identify prescribing errors in rapidly discontinued medication orders by using retrospective methods that do not require interrupting prescribers to discuss order details. Future research could validate our methods in different clinical settings. Regular use of this measure could help determine the causes of prescribing errors, track performance, and identify and evaluate interventions to improve prescribing systems and processes.
Neurofasziale Integration
Authors: Pfeifer Patrick 
Published: February 2018

ZusammenfassungLassen sich spezielle Dysfunktionen der Extremitäten oder der Wirbelsäule gezielt als Filtertest nutzen, um dahinter liegende viszerale
Störungen aufzuspüren und effizient zu behandeln? Wie hängen fasziale Restriktionen mit somatoviszeralen Störungen und mit dem autonomen
Nervensystem zusammen? Diese und weitere spannende Fragen beantwortet die Neurofasziale Integration, die Kenntnisse aus Embryologie,
Osteopathie und Faszienforschung vereint.
A case of a rectal stricture related to ischemic proctitis following rupture of an aortic aneurysm
Authors: Iida Tomoya , Ohkubo Yosuke , Kubo Toshiyuki , Yamashita Kentaro , Onodera Kei , Yamamoto Eiichiro , Nosho Katsuhiko , Ito Toshiro , Yamano Hiroo , Nakase Hiroshi 
Published: February 2018

Abstract
Background and study aims Ischemic proctitis is a rare disease and comprises 2 % to 5 % of cases of ischemic colitis, because the rectum has abundant blood supply and rich collaterals. Herein, we report a case of a 73-year-old male patient with a pronounced rectal stricture caused by ischemic proctitis resulting from an abdominal aortic rupture and treated by endoscopic balloon dilation therapy. To date, only 3 cases of rectal stricture related to ischemic proctitis including our case have been reported, and this is the first case of rectal stricture related to ischemic proctitis, which was successfully treated by endoscopic balloon dilation.
Novel experimental and software methods for image reconstruction and localization in capsule endoscopy
Authors: Koulaouzidis Anastasios , Iakovidis Dimitris , Yung Diana , Mazomenos Evangelos , Bianchi Federico , Karagyris Alexandros , Dimas George , Stoyanov Danail , Thorlacius Henrik , Toth Ervin , Ciuti Gastone 
Published: February 2018

Abstract
Background and study aims Capsule endoscopy (CE) is invaluable for minimally invasive endoscopy of the gastrointestinal tract; however, several technological limitations remain including lack of reliable lesion localization. We present an approach to 3D reconstruction and localization using visual information from 2D CE images.
Patients and methods Colored thumbtacks were secured in rows to the internal wall of a LifeLike bowel model. A PillCam SB3 was calibrated and navigated linearly through the lumen by a high-precision robotic arm. The motion estimation algorithm used data (light falling on the object, fraction of reflected light and surface geometry) from 2D CE images in the video sequence to achieve 3D reconstruction of the bowel model at various frames. The ORB-SLAM technique was used for 3D reconstruction and CE localization within the reconstructed model. This algorithm compared pairs of points between images for reconstruction and localization.
Results As the capsule moved through the model bowel 42 to 66 video frames were obtained per pass. Mean absolute error in the estimated distance travelled by the CE was 4.1 ± 3.9 cm. Our algorithm was able to reconstruct the cylindrical shape of the model bowel with details of the attached thumbtacks. ORB-SLAM successfully reconstructed the bowel wall from simultaneous frames of the CE video. The “track” in the reconstruction corresponded well with the linear forwards-backwards movement of the capsule through the model lumen.
Conclusion The reconstruction methods, detailed above, were able to achieve good quality reconstruction of the bowel model and localization of the capsule trajectory using information from the CE video and images alone.
Überblick über die kongenitale stationäre Nachtblindheit mit überwiegend normalem Fundus
Authors: Zeitz Christina , Friedburg Christoph , Preising Markus , Lorenz Birgit 
Published: February 2018

ZusammenfassungKongenitale stationäre Nachtblindheit (Englisch: congenital stationary night blindness, CSNB) bezeichnet eine klinisch und genetisch unterscheidbare Gruppe von nicht progressiven Netzhauterkrankungen, die kaum Fundusauffälligkeiten zeigt. Die Vererbung kann autosomal-dominant (adCSNB), autosomal-rezessiv (arCSNB) oder X-chromosomal (XLCSNB) sein. Weitere klinische Merkmale können Myopie, Hyperopie, Strabismus, Nystagmus und reduzierter Visus sein. Mittels Elektroretinografie kann eine Riggs- und eine Schubert-Bornschein-Form unterschieden werden. Während die Riggs-Form eine Fehlfunktion der Stäbchen selbst aufweist, zeigen Patienten mit der weitaus häufigeren Schubert-Bornschein-Form eine Signalübertragungsstörung zwischen den Photorezeptoren und nachgeschalteten Bipolarzellen. Die Schubert-Bornschein-Form der CSNB lässt sich anhand des Elektroretinogramms (ERG) noch weiter in eine inkomplette (Englisch: incomplete, icCSNB) und komplette Form (Englisch: complete, cCSNB) einteilen. Während es sich bei der cCSNB um eine Fehlfunktion des ON-Signalwegs handelt, sind bei der icCSNB sowohl der ON- als auch der OFF-Signalweg und damit meist auch die Sehschärfe betroffen. Mittels klassischer Kopplungsanalyse, Kandidatengenanalyse und seit Neuerem Hochdurchsatzsequenzierung konnten bisher Mutationen in 13 verschiedenen Genen mit dieser Erkrankung assoziiert werden. Durch Studien an Zelllinien oder Tiermodellen konnte gezeigt werden, dass der Phänotyp der Patienten mit der Expression, Proteinlokalisation und Funktion der entsprechenden Moleküle korreliert: Gene, die bei Patienten mit der Riggs-Form der CSNB mutiert sind, haben eine bedeutende Rolle in der Phototransduktionskaskade der Stäbchen. Gene, die bei Patienten mit der icCSNB mutiert sind, kodieren für Proteine, die für die Freisetzung des Neurotransmitters Glutamat am synaptischen Spalt der Photorezeptoren verantwortlich sind. Gene, die bei Patienten mit der cCSNB mutiert sind, kodieren für Proteine, die für die Aufnahme des Glutamats und Weiterleitung des Signals an den ON-Bipolarzellen verantwortlich sind. Erste Therapieversuche im Tiermodell zeigen, dass die CSNB mittels eines gentherapeutischen Ansatzes geheilt werden könnte. Die CSNB betreffende Studien sind einerseits wichtig für eine genaue Diagnose für den Patienten, andererseits helfen sie bei der Entschlüsselung der Moleküle, die für die Signalübertragung zwischen Photorezeptoren und Bipolarzellen eine Rolle spielen, ein bislang wenig erforschtes Gebiet.
Mast cells promote small bowel cancer in a tumor stage-specific and cytokine-dependent manner
Authors: Saadalla Abdulrahman M. , Osman Abu , Gurish Michael F. , Dennis Kristen L. , Blatner Nichole R. , Pezeshki Abdulmohammad , McNagny Kelly M. , Cheroutre Hilde , Gounari Fotini , Khazaie Khashayarsha 
Published: February 2018

SignificanceWe show that distinct subsets of mast cells (MCs) expand with sequential oncogenic events in small bowel cancer. Mucosal mast cells (MMCs) previously detected early duringTrichinella spiralisinfection expand in adenomatous polyps in an IL-10–dependent manner. Connective tissue mast cells (CTMCs), earlier shown to expand during the resolution of inflammation following clearance ofT. spiralis,are independent of IL-10 and associate with the transition of polyps to adenocarcinoma. IL-33 upregulates the CTMC lineage-specific protease murine mast cell protease 6 (mMCP6). Ablation of mMCP6 attenuates tumor growth. Thus, tissue sentinel cells respond to oncogenic events and cellular transformation in effect to help promote cancer. Delineating the types of MCs present at various stages of disease offers actionable cellular targets for therapeutic intervention in disease progression.
Reconceptualizing crisis
Authors: De Rycker Antoon 
Published: February 2018

Abstract
As a major socially significant phenomenon, crisis has been variously understood as an event, a moment of history, a turning point, a problem, a set of challenges, a paradox and so on. Drawing on third-generation practice theory and a range of case studies, the present study explores the possibility of reconceptualizing crisis as a social practice, i.e. as ‘doing crisis’. In addition, it considers whether a social practice approach can inform the analysis of crisis-related media practices and discourses. It is argued that a crisis-as-practice perspective is possible and also directly relevant to media discourse analysis, and that it can offer new and fresh insights.
Language-specificity in motion expression
Authors: Choi Soonja 
Published: February 2018

Abstract
This chapter examines the development of motion expression in two Korean children (1;11 to 4;2), compared to children acquiring French and English (from Hickmann et al. 2009). Korean is a verb-framed language (like French but unlike English which is satellite-framed; cf. Talmy 1985, 2000), and offers the following devices for motion expression: Serial verb constructions (SVC) in which Manner and Path verbs can co-occur within a single clause, and Manner adverbs including mimetics. Analyses show that from two years on, Korean children use SVCs and start producing Manner adverbs (particularly mimetics). As a result, they express more motion information and their motion expression is therefore semantically denser than in French (but less dense than in English). These findings support the view that language-specific features influence children’s motion expression from an early stage.
Development of discourse competence
Authors: Watorek Marzena 
Published: February 2018

Abstract
This paper examines the development of discourse competence through the oral production of two text types: spatial descriptions and film retellings, collected from French children (aged 4, 7, and 10) and a control group of adult French speakers. Results suggest that for young children the construction of a static spatial description is intrinsically more complex and poses more difficulties compared to the production of narratives. The construction of a description of a multidimensional configuration implies a heavier cognitive load than the construction of a narrative based on a chronological – inherently linear – event structure. Based on the analysis of reference to entities, we identify phenomena reflecting specific difficulties for children when performing a descriptive vs. a narrative task.