bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small stepping motion of processive dynein revealed by load-free high-speed single-particle tracking
Authors: Ando Jun , Shima Tomohiro , Kanazawa Riko , Shimo-Kon Rieko , Nakamura Akihiko , Yamamoto Mayuko , Kon Takahide , Iino Ryota 
Published: January 2020

AbstractCytoplasmic dynein is a dimeric motor protein which processively moves along microtubule. Its motor domain (head) hydrolyzes ATP and induces conformational changes of linker, stalk, and microtubule binding domain (MTBD) to trigger stepping motion. Here we applied scattering imaging of gold nanoparticle (AuNP) to visualize load-free stepping motion of processive dynein. We observed artificially-dimerized chimeric dynein, which has the head, linker, and stalk from Dictyostelium discoideum cytoplasmic dynein and the MTBD from human axonemal dynein, whose structure has been well-studied by cryo-electron microscopy. One head of a dimer was labeled with 30 nm AuNP, and stepping motions were observed with 100 μs time resolution and sub-nanometer localization precision at physiologically-relevant 1 mM ATP. We found 8 nm forward and backward steps and 5 nm side steps, consistent with on- and off-axes pitches of binding cleft between αβ-tubulin dimers on the microtubule. Probability of the forward step was 1.8 times higher than that of the backward step, and similar to those of the side steps. One-head bound states were not clearly observed, and the steps were limited by a single rate constant. Our results indicate dynein mainly moves with biased small stepping motion in which only backward steps are slightly suppressed.
First annulus formation in the European anchovy; a two-stage approach for robust validation
Authors: Basilone Gualtiero , Barra Marco , Ferreri Rosalia , Mangano Salvatore , Pulizzi Maurizio , Giacalone Giovanni , Fontana Ignazio , Aronica Salvatore , Gargano Antonella , Rumolo Paola , Genovese Simona , Bonanno Angelo 
Published: January 2020

AbstractThe age determination in fast-growing short-living species, such as European anchovy (Engraulis encrasicolus), has been widely recognized as a difficult task and bias introduced by readers leads to bias in reconstructing the population age structure. In this context, it is worth to note that age structure of fish population represents key information in fishery ecology and for stock assessment models. The uncertainty in estimating the age of the European anchovy by otolith reading is linked to the number of false-growth increments (checks) laid down before the annulus formation. While direct validation methods (e.g. mark-recapture, rearing, radiochemical dating) are difficult to implement specially for this short living species, the use of different indirect methods, supported by a coherent statistical approach, represents a robust and easier validation tool. A statistical modeling approach has been here adopted to assess the coherence of two well-known methods, namely Edge Analysis and Marginal Increment Analysis, in order to validate the first annulus formation in European anchovy. Both methodologies in two different yearly cycles converged toward the same result, thus confirming the annulus identification for the first year class. In addition, the completion dates of the checks and the first annulus were computed in order to gain a better insight into otolith growth dynamic. According to the species spawning period, the completion date of the first annulus falls in the summer period, while the first and second checks completion dates were mostly found in summer and winter respectively. General additive models using marginal increments as dependent variable showed a significant effect of the month, highlighting the presence of only one clear minimum in July/August, as well as specific relationships with condition factor and gonadosomatic index. Modeling the otolith edge morphology, the probability to find a hyaline band displayed in both years a similar shape, characterized by a minimum in July/August and higher values between November and January. The obtained results evidenced temporally coherent patterns providing a better insight in the otolith growth dynamic as well as a more robust validation of the first annulus formation in the European anchovy.
Static intra-access pressure ratio and cardiovascular events in patients undergoing haemodialysis
Authors: Jeon Hee Jung , Oh Jieun , Lee Young-Ki , Cho Ajin , Yoon Jong Woo , Kim Hyunsuk , Shin Dong Ho 
Published: January 2020

AbstractStatic intra-access pressure ratio (SIAPR) measurement, using haemodialysis machine transducers, is the vascular access surveillance method in patients undergoing haemodialysis. However, little is known about the relationship between the SIAPR and arterial stiffness, and the clinical usefulness of the SIAPR in predicting cardiovascular events. A total of 209 patients undergoing maintenance haemodialysis were evaluated. The SIAPRs ranged from 0.01 to 0.52 (median: 0.23). When the patients were divided into two groups according to their median of SIAPR, the incidence of previous cardiovascular disease, E/E′ ratio, and brachial-ankle pulse wave velocity were significantly higher in the patients with SIAPRs of ≤0.23 than in those with SIAPRs of >0.23. Conversely, patients with worse comorbid status had a lower SIAPR than patients without it. In the Kaplan-Meier analysis, the cumulative incidence of cardiovascular events was significantly higher in the patients with SIAPRs of ≤0.23 than in those with SIAPRs of >0.23 (P < 0.001). In the multiple Cox regression analysis, an increase in the SIAPR was associated with a reduced risk for cardiovascular events [hazard ratio: 0.36, 95% confidence interval: 0.21–0.60, P = 0.001]. Therefore, a low SIAPR related with arterial stiffness was a predictor for cardiovascular events.
Identifying unreliable predictions in clinical risk models
Authors: Myers Paul D. , Ng Kenney , Severson Kristen , Kartoun Uri , Dai Wangzhi , Huang Wei , Anderson Frederick A. , Stultz Collin M. 
Published: January 2020

AbstractThe ability to identify patients who are likely to have an adverse outcome is an essential component of good clinical care. Therefore, predictive risk stratification models play an important role in clinical decision making. Determining whether a given predictive model is suitable for clinical use usually involves evaluating the model’s performance on large patient datasets using standard statistical measures of success (e.g., accuracy, discriminatory ability). However, as these metrics correspond to averages over patients who have a range of different characteristics, it is difficult to discern whether an individual prediction on a given patient should be trusted using these measures alone. In this paper, we introduce a new method for identifying patient subgroups where a predictive model is expected to be poor, thereby highlighting when a given prediction is misleading and should not be trusted. The resulting “unreliability score” can be computed for any clinical risk model and is suitable in the setting of large class imbalance, a situation often encountered in healthcare settings. Using data from more than 40,000 patients in the Global Registry of Acute Coronary Events (GRACE), we demonstrate that patients with high unreliability scores form a subgroup in which the predictive model has both decreased accuracy and decreased discriminatory ability.
Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice
Authors: Ali Zahir , Shami Ashwag , Sedeek Khalid , Kamel Radwa , Alhabsi Abdulrahman , Tehseen Muhammad , Hassan Norhan , Butt Haroon , Kababji Ahad , Hamdan Samir M. , Mahfouz Magdy M. 
Published: January 2020

AbstractPrecise genome editing by systems such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) requires high-efficiency homology-directed repair (HDR). Different technologies have been developed to improve HDR but with limited success. Here, we generated a fusion between the Cas9 endonuclease and the Agrobacterium VirD2 relaxase (Cas9-VirD2). This chimeric protein combines the functions of Cas9, which produces targeted and specific DNA double-strand breaks (DSBs), and the VirD2 relaxase, which brings the repair template in close proximity to the DSBs, to facilitate HDR. We successfully employed our Cas9-VirD2 system for precise ACETOLACTATE SYNTHASE (OsALS) allele modification to generate herbicide-resistant rice (Oryza sativa) plants, CAROTENOID CLEAVAGE DIOXYGENASE-7 (OsCCD7) to engineer plant architecture, and generate in-frame fusions with the HA epitope at HISTONE DEACETYLASE (OsHDT) locus. The Cas9-VirD2 system expands our ability to improve agriculturally important traits in crops and opens new possibilities for precision genome engineering across diverse eukaryotic species.
Sub-molecular structural relaxation at a physisorbed interface with monolayer organic single-crystal semiconductors
Authors: Yamamura Akifumi , Fujii Hiromasa , Ogasawara Hirohito , Nordlund Dennis , Takahashi Osamu , Kishi Yuutaro , Ishii Hiroyuki , Kobayashi Nobuhiko , Niitsu Naoyuki , Blülle Balthasar , Okamoto Toshihiro , Wakabayashi Yusuke , Watanabe Shun , Takeya Jun 
Published: January 2020

AbstractArranging molecules into highly symmetric, topological crystal structures has been recognized as the best approach to functionalize electronic properties in molecular crystals, where the constituent molecules have been assumed to be rigid in shape. Here, in striking contrast, we demonstrate that the molecules in a monolayer organic crystal can undergo a significant deformation in proximity to the substrate, which is reflected by an asymmetry in the electron density profile. X-ray reflectivity and X-ray absorption spectroscopies in conjunction with density-functional theory calculations reveal that the highly planarized π-core are deformed into a bent shape, while the bulk lattice parameters are maintained. The molecular shape change is found to be perfectly suppressed in a bilayer single crystal, which leads to a 40% increase in mobility in the bilayer crystal. Our finding of a unique, sub-molecular scale shape change in monolayer single crystals can offer possibilities for functionalizing electrical properties via nano-scale physisorption.
Down-regulation of the insulin signaling pathway by SHC may correlate with congenital heart disease in Chinese populations
Authors: Luo Zhiling , Xu Longjiang , Lu Jiang , Shen Yan , Tang Yongyan , Wang Xiuyun , Wu Yilin , Sun Hao , Guo Tao 
Published: January 2020

Abstract
Background/Aims: Congenital heart disease (CHD) is one of the most common and severe congenital defects. The incidence of fetal cardiac malformation is increased in the context of maternal gestational diabetes mellitus (GDM). Therefore, we wanted to determine whether abnormalities in the insulin signaling pathway are associated with the occurrence of nonsyndromic CHD (ns-CHD). Methods: We used digital gene expression profiling (DGE) of right atrial myocardial tissue samples from eight ns-CHD patients and four controls. The genes potentially associated with CHD were validated by real-time fluorescence quantitative PCR analysis of right atrial myocardial tissues from 37 patients and 10 controls and the H9C2 cell line. Results: The results showed that the insulin signaling pathway, which is mediated by the SHC gene family, was inhibited in the ns-CHD patients. The expression levels of five genes (PTPRF, SHC4, MAP2K2, MKNK2, and ELK1) in the pathway were significantly down-regulated in the patients’ atrial tissues (P&lt;0.05 for all). In vitro, the H9C2 cells cultured in high glucose (33 mmol/l) expressed less SHC4, MAP2K2, and Elk-1 than those cultured in low glucose (25 mmol/l). Furthermore, the high glucose concentration down-regulated the 25 genes associated with blood vessel development based on Gene Ontology (GO) term enrichment analyses of RNA-seq data. Conclusion: We considered that changes in the insulin signaling pathway mediated by SHC might be involved in the heart development process. This mechanism might account for the increase in the incidence of fetal cardiac malformations in the context of GDM.
PIC: a data reduction algorithm for integral field spectrographs
Authors: Berdeu Anthony , Soulez Ferréol , Denis Loïc , Langlois Maud , Thiébaut Éric 
Published: January 2020

Context.The improvement of large size detectors permitted the development of integral field spectrographs (IFSs) in astronomy. Spectral information for each spatial element of a two-dimensional field of view is obtained thanks to integral field units that spread the spectra on the 2D grid of the sensor.Aims.Here we aim to solve the inherent issues raised by standard data-reduction algorithms based on direct mapping of the 2D + λdata cube: the spectral cross-talk due to the overlap of neighbouring spectra, the spatial correlations of the noise due to the re-interpolation of the cube on a Cartesian grid, and the artefacts due to the influence of defective pixels.Methods.The proposed method, Projection, Interpolation, and Convolution (PIC), is based on an “inverse-problems” approach. By accounting for the overlap of neighbouring spectra as well as the spatial extension in a spectrum of a given wavelength, the model inversion reduces the spectral cross-talk while deconvolving the spectral dispersion. Considered as missing data, defective pixels undetected during the calibration are discarded on-the-fly via a robust penalisation of the data fidelity term.Results.The calibration of the proposed model is presented for the Spectro-Polarimetric High-contrast Exoplanet REsearch instrument (SPHERE). This calibration was applied to extended objects as well as coronagraphic acquisitions dedicated to exoplanet detection or disc imaging. Artefacts due to badly corrected defective pixels or artificial background structures observed in the cube reduced by the SPHERE data reduction pipeline are suppressed while the reconstructed spectra are sharper. This reduces the false detections by the standard exoplanet detection algorithms.Conclusions.These results show the pertinence of the inverse-problems approach to reduce the raw data produced by IFSs and to compensate for some of their imperfections. Our modelling forms an initial building block necessary to develop methods that can reconstruct and/or detect sources directly from the raw data.
Successful application of PSF-R techniques to the case of the globular cluster NGC 6121 (M 4)
Authors: Massari D. , Marasco A. , Beltramo-Martin O. , Milli J. , Fiorentino G. , Tolstoy E. , Kerber F. 
Published: January 2020

Context. Precise photometric and astrometric measurements on astronomical images require an accurate knowledge of the point spread function (PSF). When the PSF cannot be modelled directly from the image, PSF-reconstruction techniques become the only viable solution. So far, however, their performance on real observations has rarely been quantified.
Aims. In this Letter, we test the performance of a novel hybrid technique, called PRIME, on Adaptive Optics-assisted SPHERE/ZIMPOL observations of the Galactic globular cluster NGC 6121.
Methods. PRIME couples PSF-reconstruction techniques, based on control-loop data and direct image fitting performed on the only bright point-like source available in the field of view of the ZIMPOL exposures, with the aim of building the PSF model.
Results. By exploiting this model, the magnitudes and positions of the stars in the field can be measured with an unprecedented precision, which surpasses that obtained by more standard methods by at least a factor of four for on-axis stars and by up to a factor of two on fainter, off-axis stars.
Conclusions. Our results demonstrate the power of PRIME in recovering precise magnitudes and positions when the information directly coming from astronomical images is limited to only a few point-like sources and, thus, paving the way for a proper analysis of future Extremely Large Telescope observations of sparse stellar fields or individual extragalactic objects.
Die Keratoplastik in Deutschland: systematische Auswertung der Krankenhausqualitätsberichte der Jahre 2006 bis 2017
Authors: Daniel Moritz Claudius , Böhringer Daniel , Lapp Thabo , Maier Philip Christian , Reinhard Thomas , Lang Stefan J. 
Published: January 2020

Zusammenfassung
Hintergrund Die Keratoplastik zählt weltweit zu den am häufigsten durchgeführten Gewebetransplantationen. Traditionell entfiel die überwiegende Mehrheit der Eingriffe auf die perforierende Keratoplastik. Mit deren Weiterentwicklung in den vergangenen 15 Jahren gewann jedoch insbesondere die posteriore lamellierende Keratoplastik zur Behandlung der Fuchs-Endotheldystrophie sowie der bullösen Keratopathie zunehmend an Bedeutung. Basierend auf informellen Umfrageergebnissen wurde postuliert, dass sich auch in Deutschland ein Trend hin zur posterioren lamellierenden Keratoplastik abzeichnet.
Ziel der Arbeit Anhand der Qualitätsberichte der Krankenhäuser sollte geprüft werden, ob der Anteil der lamellierenden Keratoplastik in Deutschland im Zeitraum 2006 bis 2017 zugenommen hat. Zudem sollte die Zahl der HLA-kompatibel (HLA: humanes Leukozytenantigen) durchgeführten Keratoplastiken ermittelt werden.
Material und Methoden Die Operationszahlen der perforierend/lamellierend bzw. HLA-kompatibel durchgeführten Keratoplastiken wurden anhand der OPS-Ziffern aus den Krankenhausqualitätsberichten der Jahre 2006 bis einschließlich 2017 extrahiert. Die deskriptive statistische Auswertung erfolgte mit dem Softwarepaket R (www.r-project.org).
Ergebnisse Von 2006 bis 2017 wurden deutschlandweit insgesamt 43 021 Keratoplastiken durchgeführt. Die Zahl der durchgeführten Keratoplastiken stieg von 2849 im Jahr 2006 auf 8231 im Jahr 2017. Die absolute Zahl perforierender Keratoplastiken blieb insgesamt konstant. Der relative Anteil lamellierender Keratoplastiken stieg von 6,5% (2006) auf 61,4% (2017) an. Die Zahl der HLA-kompatibel durchgeführten Keratoplastiken lag stets unter 20% und war ab 2010 rückläufig (2010: 19,7%; 2017: 9,8%).
Diskussion Die posteriore lamellierende Keratoplastik hat auch in Deutschland stark an Stellenwert gewonnen und seit 2014 die perforierende Keratoplastik als häufigste Form der Keratoplastik abgelöst. Die perforierende Keratoplastik, deren absolute Zahl über den gesamten Untersuchungszeitraum insgesamt konstant blieb, hat jedoch nach wie vor einen hohen Stellenwert bei der Behandlung von vorwiegend stromalen oder durchgreifenden Hornhautdefekten. Der Anteil HLA-kompatibler Keratoplastiken hat vermutlich insbesondere vor dem Hintergrund fehlender eindeutiger Nachweise einer Verringerung der Abstoßungsraten in Standardsituationen in den letzten Jahren weiter abgenommen.
Development of the Composition of the Biopolymer Base for Nasal Gel
Authors: Bakhrushina Elena , Demina Natalya , Krasnyuk Ivan , Moiseeva Anna 
Published: January 2020

AbstractIn many cases the nasal cavity is the gateway for the infection; it necessitates the development of a drug for nasal administration with antiviral, adsorptive and protective properties. Gels were chosen as an optimal dosage form. The study is aimed at studying the properties of biopolymer gelling agents and determining the composition of the future dosage form.
Materials and methods Gel samples with 3, 4 and 5% concentrations were prepared using the following gelling agents: sodium alginate Protanal CR8223, Protanal CR8133, Manucol LKХ (FMC BioPolymer) and xanthan gum GrinstedXanthan (DuPontDanisco), Xanthural 180 (CP Kelco). Adsorption and osmotic activity, bioadhesion and thermostability of the samples were determined.
Results Basing on the totality of the obtained results, 3 compositions prospective for the dosage form development were selected: xanthan gums (particle size 180pm) from various manufacturers: Grinsted Xanthan 3 and 4% concentrations, Xanthural 180 5% concentration. These compositions possess high adsorption activity (25.06; 21.35; 20.6 g respectively), optimal osmotic activity (155, 171, 100%) and have significant bioadhesion (28.4421; 22.7237; 30.2835 N) that allows the drug to stay in the nasal cavity for a long period of time. All selected compositions demonstrated good high-temperature stability.
Conclusion The obtained data shows prospects of applying the samples for the development of nasal gel with an immunobiological substance.
Aqueous Root Extract from Ononis spinosa Exerts Anti-adhesive Activity against Uropathogenic Escherichia coli
Authors: Deipenbrock Melanie , Sendker Jandirk , Hensel Andreas 
Published: January 2020

AbstractExtracts from Ononis spinosa are traditionally used for urinary tract infections due to diuretic and anti-inflammatory activity. A potential influence on the virulence of uropathogenic Escherichia coli has not been investigated until now. The following study aimed to investigate the influence of an aqueous O. spinosa extract on uropathogenic E. coli and uropathogenic E. coli host cell interaction. A hot water extract from the roots of O. spinosa (O. spinosa extract) was characterized by LC-qTOF-MS. The influence of O. spinosa extract on the proliferation of uropathogenic E. coli UTI89 and on cell viability against human T24 bladder cells was investigated. Anti-adhesive activity of O. spinosa extract was assessed by flow cytometry, evaluating the adhesion of fluorescent-labelled UTI89 to T24 bladder cells. Internalization of uropathogenic E. coli into T24 cells was monitored by an invasion assay. O. spinosa extract was characterized by the presence of isoflavones, isoflavanones, licoagrosides, pterocarpans, tartaric acid derivatives, and saponines. O. spinosa extract had no influence on the proliferation of uropathogenic E. coli (125 – 1000 µg/mL) and did not influence the cell viability of T24 cells. Bacterial adhesion to T24 cells was significantly (p > 0.001) inhibited by O. spinosa extract in a concentration-dependent manner (125 – 1000 µg/mL) during coincubation. Preincubation of uropathogenic E. coli or T24 cells with O. spinosa extract reduced bacterial adhesion, but to a lower extent than during coincubation. Consequently, the reduced bacterial adhesion also leads to a reduced internalization of uropathogenic E. coli uropathogenic E. coli into the host cell. O. spinosa extract does not interact with FimH-mediated uropathogenic E. coli adhesion to host cells. From these data, the traditional use of O. spinosa extracts for urinary tract infections seems to be rationalized.
Assertion, presumption and presupposition
Authors: Brosig Benjamin , Yap Foong Ha , Ahrens Kathleen 
Published: January 2020

AbstractIn this paper, we analyze the clitic YUM (< ‘thing’) in Khalkha Mongolian which, in different syntactic contexts, reinforces assertiveness or expresses different shades of presumption or presupposition. The former holds for declaratives where the presence of YUM conveys the speaker’s strong subjective commitment. In question clauses, YUM is used to indicate the speaker’s subjective and often strong guess, sometimes to the point that the speaker presupposes that the proposition actually obtains. In subordinate clauses, YUM may fulfill the same function or serve as a structurally necessary nominalizer for adjectival predicates without introducing any semantic opposition. In declaratives marked as immediately perceived, YUM conveys inference via assumptive reasoning. We thus analyze YUM as a marker of subjective speaker conviction that within the Khalkha Mongolian declarative system is opposed to both simple factuality and overt evidential marking.