bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurements of the size and correlations between ions using an electrolytic point contact
Authors: Rigo Eveline , Dong Zhuxin , Park Jae Hyun , Kennedy Eamonn , Hokmabadi Mohammad , Almonte-Garcia Lisa , Ding Li , Aluru Narayana , Timp Gregory 
Published: May 2019

AbstractThe size of an ion affects everything from the structure of water to life itself. In this report, to gauge their size, ions dissolved in water are forced electrically through a sub-nanometer-diameter pore spanning a thin membrane and the current is measured. The measurements reveal an ion-selective conductance that vanishes in pores <0.24 nm in diameter—the size of a water molecule—indicating that permeating ions have a grossly distorted hydration shell. Analysis of the current noise power spectral density exposes a threshold, below which the noise is independent of current, and beyond which it increases quadratically. This dependence proves that the spectral density, which is uncorrelated below threshold, becomes correlated above it. The onset of correlations for Li+, Mg2+, Na+ and K+-ions extrapolates to pore diameters of 0.13 ± 0.11 nm, 0.16 ± 0.11 nm, 0.22 ± 0.11 nm and 0.25 ± 0.11 nm, respectively—consonant with diameters at which the conductance vanishes and consistent with ions moving through the sub-nanopore with distorted hydration shells in a correlated way.
SETER/PR: a robust 18-gene predictor for sensitivity to endocrine therapy for metastatic breast cancer
Authors: Sinn Bruno V. , Fu Chunxiao , Lau Rosanna , Litton Jennifer , Tsai Tsung-Heng , Murthy Rashmi , Tam Alda , Andreopoulou Eleni , Gong Yun , Murthy Ravi , Gould Rebekah , Zhang Ya , King Tari A. , Viale Agnes , Andrade Victor , Giri Dilip , Salgado Roberto , Laios Ioanna , Sotiriou Christos , Marginean Esmeralda C. , Kwiatkowski Danielle N. , Layman Rachel M. , Booser Daniel , Hatzis Christos , Vicente Valero V. , Fraser Symmans W. 
Published: May 2019

AbstractThere is a clinical need to predict sensitivity of metastatic hormone receptor-positive and HER2-negative (HR+/HER2−) breast cancer to endocrine therapy, and targeted RNA sequencing (RNAseq) offers diagnostic potential to measure both transcriptional activity and functional mutation. We developed the SETER/PR index to measure gene expression microarray probe sets that were correlated with hormone receptors (ESR1 and PGR) and robust to preanalytical and analytical influences. We tested SETER/PR index in biopsies of metastastic HR+/HER2− breast cancer against the treatment outcomes in 140 patients. Then we customized the SETER/PR assay to measure 18 informative, 10 reference transcripts, and sequence the ligand-binding domain (LBD) of ESR1 using droplet-based targeted RNAseq, and tested that in residual RNA from 53 patients. Higher SETER/PR index in metastatic samples predicted longer PFS and OS when patients received endocrine therapy as next treatment, even after adjustment for clinical-pathologic risk factors (PFS: HR 0.534, 95% CI 0.299 to 0.955, p = 0.035; OS: HR 0.315, 95% CI 0.157 to 0.631, p = 0.001). Mutated ESR1 LBD was detected in 8/53 (15%) of metastases, involving 1−98% of ESR1 transcripts (all had high SETER/PR index). A signature based on probe sets with good preanalytical and analytical performance facilitated our customization of an accurate targeted RNAseq assay to measure both phenotype and genotype of ER-related transcription. Elevated SETER/PR was associated with prolonged sensitivity to endocrine therapy in patients with metastatic HR+/HER2− breast cancer, especially in the absence of mutated ESR1 transcript.
In-situ detection based on the biofilm hydrophilicity for environmental biofilm formation
Authors: Tanaka Nobuyuki , Kogo Takeshi , Hirai Nobumitsu , Ogawa Akiko , Kanematsu Hideyuki , Takahara Junko , Awazu Akane , Fujita Nobuko , Haruzono Yoshihide , Ichida Shunji , Tanaka Yo 
Published: May 2019

AbstractA biofilm has a unique structure composed of microorganisms, extracellular polymeric substances (EPSs), etc., and it is layered on a substrate in water. In material science, it is important to detect the biofilm formed on a surface to prevent biofouling. EPSs, the major component of the biofilm, mainly consist of polysaccharides, proteins, nucleic acids, and lipids. Because these biomolecules have a variety of hydrophilicities or hydrophobicities, the substrate covered with the biofilm shows different wettability from the initial state. To detect the biofilm formation, this study employed a liquid-squeezing-based wettability assessment method with a simple wettability index: the liquid-squeezed diameter of a smaller value indicates higher wettability. The method is based on the liquid-squeezing behaviour of a liquid that covers sample surfaces when an air-jet is applied. To form the biofilm, polystyrene surfaces were immersed and incubated in a water-circulated bioreactor that had collected microorganisms in ambient air. After the 14-d incubation, good formation of the biofilm on the surfaces was confirmed by staining with crystal violet. Although the contact angles of captive bubbles on the surfaces with the biofilm were unmeasurable, the liquid-squeezing method could distinguish between hydrophilic and hydrophobic initial surfaces with and without biofilm formation using the diameter of the liquid-squeezed area. The surface wettability is expected to be a promising property for in-situ detection of biofilm formation on a macroscopic scale.
Quantifying ultrasonic mouse vocalizations using acoustic analysis in a supervised statistical machine learning framework
Authors: Vogel Adam P. , Tsanas Athanasios , Scattoni Maria Luisa 
Published: May 2019

AbstractExamination of rodent vocalizations in experimental conditions can yield valuable insights into how disease manifests and progresses over time. It can also be used as an index of social interest, motivation, emotional development or motor function depending on the animal model under investigation. Most mouse communication is produced in ultrasonic frequencies beyond human hearing. These ultrasonic vocalizations (USV) are typically described and evaluated using expert defined classification of the spectrographic appearance or simplistic acoustic metrics resulting in nine call types. In this study, we aimed to replicate the standard expert-defined call types of communicative vocal behavior in mice by using acoustic analysis to characterize USVs and a principled supervised learning setup. We used four feature selection algorithms to select parsimonious subsets with maximum predictive accuracy, which are then presented into support vector machines (SVM) and random forests (RF). We assessed the resulting models using 10-fold cross-validation with 100 repetitions for statistical confidence and found that a parsimonious subset of 8 acoustic measures presented to RF led to 85% correct out-of-sample classification, replicating the experts’ labels. Acoustic measures can be used by labs to describe USVs and compare data between groups, and provide insight into vocal-behavioral patterns of mice by automating the process on matching the experts’ call types.
Red muscle activity in bluegill sunfish Lepomis macrochirus during forward accelerations
Authors: Schwalbe Margot A. B. , Boden Alexandra L. , Wise Tyler N. , Tytell Eric D. 
Published: May 2019

AbstractFishes generate force to swim by activating muscles on either side of their flexible bodies. To accelerate, they must produce higher muscle forces, which leads to higher reaction forces back on their bodies from the environment. If their bodies are too flexible, the forces during acceleration could not be transmitted effectively to the environment, but fish can potentially use their muscles to increase the effective stiffness of their body. Here, we quantified red muscle activity during acceleration and steady swimming, looking for patterns that would be consistent with the hypothesis of body stiffening. We used high-speed video, electromyographic recordings, and a new digital inertial measurement unit to quantify body kinematics, red muscle activity, and 3D orientation and centre of mass acceleration during forward accelerations and steady swimming over several speeds. During acceleration, fish co-activated anterior muscle on the left and right side, and activated all muscle sooner and kept it active for a larger fraction of the tail beat cycle. These activity patterns are both known to increase effective stiffness for muscle tissue in vitro, which is consistent with our hypothesis that fish use their red muscle to stiffen their bodies during acceleration. We suggest that during impulsive movements, flexible organisms like fishes can use their muscles not only to generate propulsive power but to tune the effective mechanical properties of their bodies, increasing performance during rapid movements and maintaining flexibility for slow, steady movements.
Postmortem plasma pentraxin 3 is a useful marker of fatal acute coronary syndrome
Authors: Tojo Misa , Shintani-Ishida Kaori , Tsuboi Hajime , Nakamura Mami , Idota Nozomi , Ikegaya Hiroshi 
Published: May 2019

AbstractPentraxin 3 (PTX3) is an acute-phase protein that belongs to the pentraxin superfamily. Recently, many clinical studies have demonstrated that plasma PTX3 concentrations rapidly increase in patients with the acute coronary syndrome (ACS). The aim of this study was to evaluate the forensic utility of postmortem plasma PTX3 as a marker of fatal ACS. We compared the plasma PTX3 concentration in cadavers with suspected fatal ACS to that exhibited in control cases (e.g., asphyxia and immediate death due to a fatal injury). The ACS groups included a coronary stenosis group, which exhibited apparent coronary stenosis, but an absence of coronary thrombi, a coronary thrombi group with thrombi found in the coronary artery, and a group of myocardial rupture following an acute myocardial infarction. The plasma PTX3 concentration was significantly higher in the coronary thrombi group than the control group and other ACS groups. The postmortem plasma PTX3 concentration was higher than the clinical reference values, which appeared to be caused by a postmortem release from circulating neutrophils. In conclusion, although the clinical reference value cannot be applied to postmortem samples, the postmortem plasma PTX3 concentration may be a useful marker of death occurring immediately after the onset of fatal ACS.
Doxycycline inhibits electric field-induced migration of non-small cell lung cancer (NSCLC) cells
Authors: Chang Hui-Fang , Cheng Hung-Tien , Chen Huai-Yi , Yeung Wing Kiu , Cheng Ji-Yen 
Published: May 2019

AbstractAdenocarcinoma, large cell carcinoma and squamous cell carcinoma are the most commonly diagnosed subtypes of non-small cell lung cancers (NSCLC). Numerous lung cancer cell types have exhibited electrotaxis under direct current electric fields (dcEF). Physiological electric fields (EF) play key roles in cancer cell migration. In this study, we investigated electrotaxis of NSCLC cells, including human large cell lung carcinoma NCI-H460 and human lung squamous cell carcinoma NCI-H520 cells. Non-cancerous MRC-5 lung fibroblasts were included as a control. After dcEF stimulation, NCI-H460 and NCI-H520 cells, which both exhibit epithelial-like morphology, migrated towards the cathode, while MRC-5 cells, which have fibroblast-like morphology, migrated towards the anode. The effect of doxycycline, a common antibiotic, on electrotaxis of MRC-5, NCI-H460 and NCI-H520 cells was examined. Doxycycline enhanced the tested cells’ motility but inhibited electrotaxis in the NSCLC cells without inhibiting non-cancerous MRC-5 cells. Based on our finding, further in-vivo studies could be devised to investigate the metastasis inhibition effect of doxycycline in an organism level.
Network pharmacology-based identifcation of potential targets of the flower of Trollius chinensis Bunge acting on anti-inflammatory effectss
Authors: Liang Jing-wei , Wang Ming-yang , Olounfeh Kamara Mohamed , Zhao Nan , Wang Shan , Meng Fan-hao 
Published: May 2019

AbstractThe flower of Trollius chinensis Bunge was widely used for the treatment of inflammation-related diseases in traditional Chinese medicine (TCM). In order to clarify the anti-inflammatory mechanism of this Chinese herbs, a comprehensive network pharmacology strategy that consists of three sequential modules (pharmacophore matching, enrichment analysis and molecular docking.) was carried out. As a result, Apoptosis signal-regulating kinase 1 (ASK1), Janus kinase 1 (JAK1), c-Jun N-terminal kinases (JNKs), transforming protein p21 (HRas) and mitogen-activated protein kinase 14 (p38α) that related to the anti-inflammatory effect were filtered out. In further molecular dynamics (MD) simulation, the conformation of CID21578038 and CID20055288 were found stable in the protein ASK1 and JNKs respectively. The current investigation revealed that two effective compounds in the flower of Trollius chinensis Bunge played a crucial role in the process of inflammation by targeting ASK1 and JNKs, the comprehensive strategy can serve as a universal method to guide in illuminating the mechanism of the prescription of traditional Chinese medicine by identifying the pathways or targets.
Surface deep profile synchrotron studies of mechanically modified top-down silicon nanowires array using ultrasoft X-ray absorption near edge structure spectroscopy
Authors: Turishchev S. Yu. , Parinova E. V. , Pisliaruk A. K. , Koyuda D. A. , Yermukhamed D. , Ming T. , Ovsyannikov R. , Smirnov D. , Makarova A. , Sivakov V. 
Published: May 2019

AbstractAtomic, electronic structure and composition of top-down metal-assisted wet-chemically etched silicon nanowires were studied by synchrotron radiation based X-ray absorption near edge structure technique. Local surrounding of the silicon and oxygen atoms in silicon nanowires array was studied on as-prepared nanostructured surfaces (atop part of nanowires) and their bulk part after, first time applied, in-situ mechanical removal atop part of the formed silicon nanowires. Silicon suboxides together with disturbed silicon dioxide were found in the composition of the formed arrays that affects the electronic structure of silicon nanowires. The results obtained by us convincingly testify to the homogeneity of the phase composition of the side walls of silicon nanowires and the electronic structure in the entire length of the nanowire. The controlled formation of the silicon nanowires array may lead to smart engineering of its atomic and electronic structure that influences the exploiting strategy of metal-assisted wet-chemically etched silicon nanowires as universal matrices for different applications.
Purified human anti-Tn and anti-T antibodies specifically recognize carcinoma tissues
Authors: Zlocowski Natacha , Grupe Veronica , Garay Yohana C. , Nores Gustavo A. , Lardone Ricardo D. , Irazoqui Fernando J. 
Published: May 2019

AbstractDescribed in several epithelial cancer cells, Tn- (GalNAcα1-O-Ser/Thr) and T- (Galβ3GalNAcα1-O-Ser/Thr) antigens are examples of tumor-associated antigens. Increased expression of Tn- and T-antigens is associated with tumor invasion and metastasis, and patients with high concentration of anti-Tn and anti-T antibodies have a more benign evolution of pathology. Asialofetuin (ASF) and ovine submaxillary mucin (OSM) are two glycoproteins that expose T- and Tn-antigen, respectively. In this work, using ASF or OSM we affinity-purified anti-T and anti-Tn antibodies from normal human plasma and tested their ability to specifically recognize tumor human tissues. Whereas purified anti-T antibodies (purity degree increase of 127-fold, and 22% recovery) were mainly IgG, for purified anti-Tn antibodies (purity degree enhancement of 125-fold, and 26% yield) the IgM fraction was predominant over the IgG one. IgG2 subclass was significantly enriched in both purified antibody samples. Purified antibodies did not bind normal human tissue (0/42), although recognized malignant tissues from different origin such as colon carcinoma (11/77 by anti-Tn; 7/79 by anti-T), breast carcinoma (10/23 by anti-Tn; 7/23 by anti-T), and kidney carcinoma (45/51 by anti-Tn; 42/51 by anti-T). Our results suggest that purified human anti-Tn and anti-T antibodies have a potential as anti-tumor therapeutic agents; restoring their levels in human sera could positively affect the evolution of patients with epithelial tumor pathologies.
Increased sea ice cover alters food web structure in East Antarctica
Authors: Michel Loïc N. , Danis Bruno , Dubois Philippe , Eleaume Marc , Fournier Jérôme , Gallut Cyril , Jane Philip , Lepoint Gilles 
Published: May 2019

AbstractIn recent years, sea ice cover along coasts of East Antarctica has tended to increase. To understand ecological implications of these environmental changes, we studied benthic food web structure on the coasts of Adélie Land during an event of unusually high sea ice cover (i.e. two successive austral summers without seasonal breakup). We used integrative trophic markers (stable isotope ratios of carbon, nitrogen and sulfur) to build ecological models and explored feeding habits of macroinvertebrates. In total, 28 taxa spanning most present animal groups and functional guilds were investigated. Our results indicate that the absence of seasonal sea ice breakup deeply influenced benthic food webs. Sympagic algae dominated the diet of many key consumers, and the trophic levels of invertebrates were low, suggesting omnivore consumers did not rely much on predation and/or scavenging. Our results provide insights about how Antarctic benthic consumers, which typically live in an extremely stable environment, might adapt their feeding habits in response to sudden changes in environmental conditions and trophic resource availability. They also show that local and/or global trends of sea ice increase in Antarctica have the potential to cause drastic changes in food web structure, and therefore to impact benthic communities.
Global geographic patterns of heterospecific pollen receipt help uncover potential ecological and evolutionary impacts across plant communities worldwide
Authors: Arceo-Gómez Gerardo , Schroeder Amelia , Albor Cristopher , Ashman Tia-Lynn , Knight Tiffany M. , Bennett Joanne M. , Suarez Brian , Parra-Tabla Victor 
Published: May 2019

AbstractSpecies interactions are known to be key in driving patterns of biodiversity across the globe. Plant-plant interactions through heterospecific pollen (HP) transfer by their shared pollinators is common and has consequences for plant reproductive success and floral evolution, and thus has the potential to influence global patterns of biodiversity and plant community assembly. The literature on HP transfer is growing and it is therefore timely to review patterns and causes of among-species variation in HP receipt at a global scale, thus uncovering its potential contribution to global patterns of biodiversity. Here we analyzed published data on 245 species distributed across five continents to evaluate latitudinal and altitudinal patterns of HP receipt. We further analyzed the role of floral symmetry and evolutionary history in mediating patterns of HP receipt. Latitude and elevation affected the likelihood and intensity of HP receipt indicating that HP transfer increases in species-rich communities and in areas with high abundance of vertebrate pollinators. Floral symmetry and evolutionary history determined HP load size across plant communities worldwide. Overall, our results suggest that HP receipt may have the potential to contribute to global geographic patterns of plant diversity by imposing strong selective pressures in species-rich areas across the globe.
Deep learning and alternative learning strategies for retrospective real-world clinical data
Authors: Chen David , Liu Sijia , Kingsbury Paul , Sohn Sunghwan , Storlie Curtis B. , Habermann Elizabeth B. , Naessens James M. , Larson David W. , Liu Hongfang 
Published: May 2019

AbstractIn recent years, there is increasing enthusiasm in the healthcare research community for artificial intelligence to provide big data analytics and augment decision making. One of the prime reasons for this is the enormous impact of deep learning for utilization of complex healthcare big data. Although deep learning is a powerful analytic tool for the complex data contained in electronic health records (EHRs), there are also limitations which can make the choice of deep learning inferior in some healthcare applications. In this paper, we give a brief overview of the limitations of deep learning illustrated through case studies done over the years aiming to promote the consideration of alternative analytic strategies for healthcare.
Star-planet tidal interaction and the limits of gyrochronology
Authors: Gallet F. , Delorme P. 
Published: May 2019

Context. Age estimation techniques such as gyrochronology and magnetochronology cannot be applied to stars that have exchanged angular momentum with their close environments. This is especially true for a massive close-in planetary companion (with a period of a few days or less) that could have been strongly impacted by the rotational evolution of the host star, throughout the stellar evolution, through the star-planet tidal interaction.
Aims. In this article, we provide the community with a reliable region in which empirical techniques such as gyrochronology can be used with confidence.
Methods. We combined a stellar angular momentum evolution code with a planetary orbital evolution code to study in detail the impact of star-planet tidal interaction on the evolution of the surface rotation rate of the star.
Results. We show that the interaction of a close-in massive planet with its host star can strongly modify the surface rotation rate of this latter, in most of the cases associated with a planetary engulfment. A modification of the surface rotation period of more than 90% can survive a few hundred Myr after the event and a modification of 10% can last for a few Gyr. In such cases, a gyrochronology analysis of the star would incorrectly make it appear as rejuvenated, thus preventing us from using this method with confidence. To try overcome this issue, we proposed the proof of concept of a new age determination technique that we call the tidal-chronology method, which is based on the observed pair Prot, ⋆–Porb of a given star-planet system, where Prot, ⋆ is the stellar surface rotational period and Porb the planetary orbital period.
Conclusions. The gyrochronology technique can only be applied to isolated stars or star-planet systems outside a specific range of Prot, ⋆–Porb. This region tends to expand for increasing stellar and planetary mass. In that forbidden region, or if any planetary engulfment is suspected, gyrochronology should be used with extreme caution, while tidal-chronology could be considered. This technique does not provide a precise age for the system yet; however, it is already an extension of gyrochronology and could be helpful to determine a more precise range of possible ages for planetary systems composed of a star between 0.3 and 1.2 M⊙ and a planet more massive than 1 Mjup initially located at a few hundredths of au from the host star.