bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging endogenous macrophage iron deposits reveals a metabolic biomarker of polarized tumor macrophage infiltration and response to CSF1R breast cancer immunotherapy
Authors: Leftin Avigdor , Ben-Chetrit Nir , Joyce Johanna A. , Koutcher Jason A. 
Published: January 2019

AbstractIron deposits are a phenotypic trait of tumor-associated macrophages (TAMs). Histological iron imaging and contrast-agent free magnetic resonance imaging (MRI) can detect these deposits, but their presence in human cancer, and correlation with immunotherapeutic response is largely untested. Here, primarily using these iron imaging approaches, we evaluated the spatial distribution of polarized macrophage populations containing high endogenous levels of iron in preclinical murine models and human breast cancer, and used them as metabolic biomarkers to correlate TAM infiltration with response to immunotherapy in preclinical trials. Macrophage-targeted inhibition of the colony stimulating factor 1 receptor (CSF1R) by immunotherapy was confirmed to inhibit macrophage accumulation and slow mammary tumor growth in mouse models while also reducing hemosiderin iron-laden TAM accumulation as measured by both iron histology and in vivo iron MRI (FeMRI). Spatial profiling of TAM iron deposit infiltration defined regions of maximal accumulation and response to the CSF1R inhibitor, and revealed differences between microenvironments of human cancer according to levels of polarized macrophage iron accumulation in stromal margins. We therefore demonstrate that iron deposition serves as an endogenous metabolic imaging biomarker of TAM infiltration in breast cancer that has high translational potential for evaluation of immunotherapeutic response.
Frequency conversion of microwave signal without direct bias current using nanoscale magnetic tunnel junctions
Authors: Algarin J. M. , Ramaswamy B. , Weinberg I. N. , Chen Y. J. , Krivorotov I. N. , Katine J. A. , Shapiro B. , Waks E. 
Published: January 2019

AbstractFrequency conversion forms an integral block of the electronic circuits used in various applications including energy harvesting, communications and signal processing. These frequency conversion units however require external power sources and occupy a large device footprint making it difficult to be integrated in micro-circuits. Here we demonstrate that nanoscale magnetic tunnel junctions can act as frequency converters without an external power supply or DC bias source. The device directly mixes an external microwave signal with the internal spin precession oscillations to create new frequencies tunable by an external magnetic field in a single device with a small device footprint. We observe up-conversion and down-conversion of the input signal for excitation frequencies between 2 GHz and 6 GHz. We also show that the device acts as a zero-bias rectifier that can generate voltages exceeding 12 mV when the excitation frequency matches the natural oscillations mode of the device.
Crabp2 Promotes Metastasis of Lung Cancer Cells via HuR and Integrin β1/FAK/ERK Signaling
Authors: Wu Jun-I , Lin Yi-Pei , Tseng Chien-Wei , Chen Hui-Jane , Wang Lu-Hai 
Published: January 2019

AbstractIncreased Crabp2 levels have been found in various types of cancer, and are associated with poor patients’ survival. Although Crabp2 is found to be overexpressed in lung cancer, its role in metastasis of lung cancer is unclear. In this study, Crabp2 was overexpressed in high-metastatic C10F4 than low-metastatic lung cancer cells. Analysis of clinical samples revealed that high CRABP2 levels were correlated with lymph node metastases, poor overall survival, and increased recurrence. Knockdown of Crabp2 decreased migration, invasion, anoikis resistance, andin vivometastasis. Crabp2 was co-immunoprecipitated with HuR, and overexpression of Crabp2 increased HuR levels, which promoted integrin β1/FAK/ERK signaling. Inhibition of HuR or integrin β1/FAK/ERK signaling reversed the promoting effect of Crabp2 in migration, invasion, and anoikis resistance. Knockdown of Crabp2 further inhibited the growth of cancer cells as compared with that by gemcitabine or irinotecan alone. The expression of Crabp2 in human lung tumors was correlated with stress marker CHOP. In conclusion, our findings have identified the promoting role of Crabp2 in anoikis resistance and metastasis. CRABP2 may serve as a prognostic marker and targeting CRABP2 may be exploited as a modality to reduce metastasis.
Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats
Authors: Stanisavljević Suzana , Čepić Aleksa , Bojić Svetlana , Veljović Katarina , Mihajlović Sanja , Đedović Neda , Jevtić Bojan , Momčilović Miljana , Lazarević Milica , Mostarica Stojković Marija , Miljković Đorđe , Golić Nataša 
Published: January 2019

AbstractGut microbiota dysbiosis has been considered the essential element in the pathogenesis of multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE). Antibiotics were administered orally to Dark Agouti (DA) rats early in their life with the aim of perturbing gut microbiota and investigating the effects of such intervention on the course of EAE. As a result, the diversity of the gut microbiota was reduced under the influence of antibiotics. Mainly, Firmicutes and Actinobacteria were replaced by Proteobacteria and Bacteroidetes, while decreased proportions of Clostridia and Bacilli classes were accompanied by an increase in Gamma-Proteobacteria in antibiotic-treated animals. Interestingly, a notable decrease in the Helicobacteraceae, Spirochaetaceae and Turicibacteriaceae was scored in antibiotic-treated groups. Also, levels of short chain fatty acids were reduced in the faeces of antibiotic-treated rats. Consequently, aggravation of EAE, paralleled with stronger immune response in lymph nodes draining the site of immunization, and increased inflammation within the CNS, were observed in antibiotic-treated DA rats. Thus, the alteration of gut microbiota leads to an escalation of CNS-directed autoimmunity in DA rats. The results of this study indicate that antibiotic use in early life may have subsequent unfavourable effects on the regulation of the immune system.
New insights into the coordination between the polymerization and 3′-5′ exonuclease activities in ϕ29 DNA polymerase
Authors: del Prado Alicia , Rodríguez Irene , Lázaro José María , Moreno-Morcillo María , de Vega Miguel , Salas Margarita 
Published: January 2019

AbstractBacteriophage ϕ29 DNA polymerase has two activities: DNA polymerization and 3′-5′ exonucleolysis governed by catalytic sites present in two structurally distant domains. These domains must work together to allow the correct replication of the template and to prevent the accumulation of errors in the newly synthesized DNA strand. ϕ29 DNA polymerase is endowed with a high processivity and strand displacement capacity together with a high fidelity. Previous studies of its crystallographic structure suggested possible interactions of residues of the exonuclease domain like the Gln180 with the fingers subdomain, or water mediated and direct hydrogen bond by the polar groups of residues Tyr101 and Thr189 that could stabilize DNA binding. To analyse their functional importance for the exonuclease activity of ϕ29 DNA polymerase we engineered mutations to encode amino acid substitutions. Our results confirm that both residues, Tyr101 and Thr189 are involved in the 3′-5′ exonuclease activity and in binding the dsDNA. In addition, Tyr101 is playing a role in processivity and Thr189 is an important determinant in the fidelity of the DNA polymerase. On the other hand, the biochemical characterization of the mutant derivatives of residue Gln180 showed how the mutations introduced enhanced the 3′-5′ exonuclease activity of the enzyme. A potential structural conformation prone to degrade the substrate is discussed.
X-ray structure of Fasciola hepatica Sigma class glutathione transferase 1 reveals a disulfide bond to support stability in gastro-intestinal environment
Authors: Line Kirsty , Isupov Michail N. , LaCourse E. James , Cutress David J. , Morphew Russell M. , Brophy Peter M. , Littlechild Jennifer A. 
Published: January 2019

AbstractSigma class GST (Prostaglandin D synthase), FhGST-S1, is present in the excretory–secretory products (ES) of the liver fluke parasite Fasciola hepatica as cargo of extracellular vesicles (EVs) released by the parasite. FhGST-S1 has a well characterised role in the modulation of the immune response; a key fluke intercession that allows for establishment and development within their hosts. We have resolved the three-dimensional structure of FhGST-S1 in complex with its co-factor glutathione, in complex with a glutathione-cysteine adduct, and in a glutathione disulfide complex in order to initiate a research pipeline to mechanistically understand how FhGST-S1 functions within the host environment and to rationally design selective inhibitors. The overall fold of FhGST-S1 shows high structural similarity to other Sigma class GSTs. However, a unique interdomain disulfide bond was found in the FhGST-S1 which could stabilise the structure within the host gastro-intestinal environment. The position of the two domains of the protein with respect to each other is seen to be crucial in the formation of the active site cleft of the enzyme. The interdomain disulfide bond raises the possibility of oxidative regulation of the active site of this GST protein.
Epidemiology, Patterns of treatment, and Mortality of Pediatric Trauma Patients in Japan
Authors: Aoki Makoto , Abe Toshikazu , Saitoh Daizoh , Oshima Kiyohiro 
Published: January 2019

AbstractLimited information exists regarding the epidemiology, patterns of treatment, and mortality of pediatric trauma patients in Japan. To evaluate the characteristics and mortality of pediatric trauma patients in Japan, especially in traffic accidents. This was a retrospective cohort study between 2004 and 2015 from a nationwide trauma registry in Japan. Pediatric trauma patients divided into four age groups: <1 years; 1 ≤ 5 years; 6 ≤ 10 years; and 11 ≤ 15 years. Data on patients’ demographics, trauma mechanism and severity, treatments and in-hospital mortality were analyzed between the groups. There were 15,441 pediatric trauma patients during the study period. Among 15,441 pediatric patients, 779 belonged to the <1 year age group, 3,933 to the 1 ≤ 5 years age group, 5,545 to the 6 ≤ 10 age group, and 5,184 to the 11 ≤ 15 years age group. Male injuries (69%) were more frequent than female injuries. Head injuries (44%) were the most frequent and severe. Traffic accidents were the leading cause of trauma (44%). Overall in-hospital mortality was 3.9% and emergency department mortality was 1.4%. In-hospital mortality was 5.3%, 4.7%, 3.0% and 4.0% for the <1 year, 1 ≤ 5 years, 6 ≤ 10 years, and 11 ≤ 15 years age groups respectively. A total of 57% of all trauma deaths were before or upon arrival at hospital. Traffic accidents for the <1 year age group was the highest category of mortality (15%). The overall in-hospital mortality of Japanese pediatric trauma patients was 3.9% based on the nationwide trauma registry of Japan. The main cause of severe trauma was traffic accidents, especially in patients <1 year of age whose mortality was 15%.
Integration of facial features under memory load
Authors: Ölander K. , Muukkonen I. , Saarela T. P. , Salmela V. R. 
Published: January 2019

AbstractSimple visual items and complex real-world objects are stored into visual working memory as a collection of independent features, not as whole or integrated objects. Storing faces into memory might differ, however, since previous studies have reported perceptual and memory advantage for whole faces compared to other objects. We investigated whether facial features can be integrated in a statistically optimal fashion and whether memory maintenance disrupts this integration. The observers adjusted a probe – either a whole face or isolated features (eyes or mouth region) – to match the identity of a target while viewing both stimuli simultaneously or after a 1.5 second retention period. Precision was better for the whole face compared to the isolated features. Perceptual precision was higher than memory precision, as expected, and memory precision further declined as the number of memorized items was increased from one to four. Interestingly, the whole-face precision was better predicted by models assuming injection of memory noise followed by integration of features than by models assuming integration of features followed by the memory noise. The results suggest equally weighted or optimal integration of facial features and indicate that feature information is preserved in visual working memory while remembering faces.
Using host species traits to understand the Wolbachia infection distribution across terrestrial beetles
Authors: Kajtoch Łukasz , Kolasa Michał , Kubisz Daniel , Gutowski Jerzy M. , Ścibior Radosław , Mazur Miłosz A. , Holecová Milada 
Published: January 2019

AbstractKnowledge of Wolbachia prevalence with respect to its hosts is restricted mainly to taxonomic/phylogenetic context. In contrast, relations between infection and most host’s ecological and biological traits are poorly understood. This study aimed to elaborate on relations between bacteria and its beetle hosts in taxonomic and the ecological contexts. In particular, the goal is to verify which ecological and biological traits of beetles could cause them to be prone to be infected. Verification of Wolbachia infection status across 297 beetle taxa showed that approximately 27% of taxa are infected by supergroups A and B. Only minor support for coevolution between bacteria and its beetle hosts was observed in some genera of beetles, but in general coevolution between beetles and Wolbachia was rejected. Some traits of beetles were found to be unrelated to Wolbachia prevalence (type of range and thermal preferences); some traits were related with ambiguous effects (habitats, distribution, mobility and body size); some were substantially related (reproduction mode and trophy). The aforementioned summary does not show obvious patterns of Wolbachia prevalence and diversity in relation to host taxonomy, biology, and ecology. As both Wolbachia and Coleoptera are diverse groups, this lack of clear patterns is probably a reflection of nature, which is characterised by highly diversified and probably unstable relations.
Ambient Aqueous-Phase Synthesis of Copper Nanoparticles and Nanopastes with Low-Temperature Sintering and Ultra-High Bonding Abilities
Authors: Kamikoriyama Yoichi , Imamura Hiroshi , Muramatsu Atsushi , Kanie Kiyoshi 
Published: January 2019

AbstractCopper nanoparticles (NPs) with an average particle diameter of 50–60 nm were successfully obtained by reducing an aqueous solution of a copper(II)-nitrilotriacetic acid complex with an aqueous hydrazine solution at room temperature under an air atmosphere. Copper NP-based nanopastes were printed onto a glass substrate using a metal screen mask and pressureless sintered under a nitrogen atmosphere at 200 °C for 30 min. The electrical resistivity of the resulting copper electrode was 16 μΩ · cm. For a metal-to-metal bonding test, copper nanopaste was printed on an oxygen-free copper plate, another oxygen-free copper plate was placed on top, and the bonding strength between the copper plates when pressureless sintered under a nitrogen atmosphere at 200 °C for 30 min was 39 MPa. TEM observations confirmed that highly crystalline metal bonding occurred between the copper NPs and the copper plate to introduce the ultrahigh strength. The developed copper NPs could provide promising advances as nanopastes for sustainable fabrication of copper electrodes and die attachment materials for the production of next-generation power semiconductors.
Mechanism of substrate-induced anisotropic growth of monolayer WS2 by kinetic Monte Carlo simulations
Authors: Wu Lixiang , Yang Weihuang , Wang Gaofeng 
Published: January 2019

AbstractControlled anisotropic growth of two-dimensional materials provides an approach for the synthesis of large single crystals and nanoribbons, which are promising for applications as low-dimensional semiconductors and in next-generation optoelectronic devices. In particular, the anisotropic growth of transition metal dichalcogenides induced by the substrate is of great interest due to its operability. To date, however, their substrate-induced anisotropic growth is typically driven by the optimization of experimental parameters without uncovering the fundamental mechanism. Here, the anisotropic growth of monolayer tungsten disulfide on an ST-X quartz substrate is achieved by chemical vapor deposition, and the mechanism of substrate-induced anisotropic growth is examined by kinetic Monte Carlo simulations. Results show that, besides the variation of substrate adsorption, the chalcogen to metal (C/M) ratio is a major contributor to the large growth anisotropy and the polarization of undergrowth and overgrowth; either perfect isotropy or high anisotropy can be expected when the C/M ratio equals 2.0 by properly controlling the linear relationship between gas flux and temperature.
Qresp, a tool for curating, discovering and exploring reproducible scientific papers
Authors: Govoni Marco , Munakami Milson , Tanikanti Aditya , Skone Jonathan H. , Runesha Hakizumwami B. , Giberti Federico , de Pablo Juan , Galli Giulia 
Published: January 2019

AbstractWe propose a strategy and present a simple tool to facilitate scientific data reproducibility by making available, in a distributed manner, all data and procedures presented in scientific papers, together with metadata to render them searchable and discoverable. In particular, we describe a graphical user interface (GUI), Qresp, to curate papers (i.e. generate metadata) and to explore curated papers and automatically access the data presented in scientific publications.
Representation of Hearing Loss and Hearing Aids in the U.S. Newspaper Media: Cross-Sectional Analysis of Secondary Data
Authors: Manchaiah Vinaya , Ratinaud Pierre , Beukes Eldré W. 
Published: January 2019

Purpose
News media plays an important role in formulating people's knowledge and opinions about various aspects of life, including health. The current study explored how hearing loss and hearing aids are represented in the U.S. newspaper media.

Method
A cross-sectional study design was selected to analyze publicly available newspaper media data. The data sets were generated from the database, the U.S. Major Dailies by ProQuest, by searching key words for newspapers published during 1990–2017. Cluster analysis (i.e., text pattern analysis) and chi-square tests were performed using Iramuteq software.

Results

The hearing loss data set had 1,527 texts (i.e., articles). The cluster analysis resulted in 7 clusters, which were named as (1)
causes and consequences
(26.1%), (2)
early identification and diagnosis
(9%), (3)
health promotion and prevention
(22.1%), (4)
recreational noise exposure
(10.4%), (5)
prevalence
(14.3%), (6)
research and development
(12.4%), and (7)
cognitive hearing science
(5.6%). The hearing aids data set had 2,667 texts. The cluster analysis resulted in 8 clusters, which were named as (1)
signal processing
(20.2%), (2)
insurance
(8.9%), (3)
prevalence
(12.4%), (4)
research and development
(5.4%), (5)
activities and relation
(16.2%), (6)
features to address background noise
(13.8%), (7)
innovation
(12%), and (8)
wireless and connectivity
(11.1%). Time series analysis of clusters in both “hearing loss” and “hearing aids” data sets indicated changes in the pattern of information presented in the newspaper media during 1990–2016 (e.g., Cluster 7 focuses on cognitive hearing science in a hearing loss data set emerging only since the year 2012 and growing rapidly).

Conclusions
The text pattern analysis showed that the U.S. newspaper media focuses on a range of issues when considering hearing loss and hearing aids and that patterns or trends change over time. The study results can be helpful for hearing health care professionals to understand what presuppositions society in general may have as the media has the ability to influence societal perception and opinions.
Gaia GraL: Gaia DR2 Gravitational Lens Systems
Authors: Delchambre L. , Krone-Martins A. , Wertz O. , Ducourant C. , Galluccio L. , Klüter J. , Mignard F. , Teixeira R. , Djorgovski S. G. , Stern D. , Graham M. J. , Surdej J. , Bastian U. , Wambsganss J. , Le Campion J.-F. , Slezak E. 
Published: January 2019

Aims. In this work, we aim to provide a reliable list of gravitational lens candidates based on a search performed over the entire Gaia Data Release 2 (Gaia DR2). We also aim to show that the astrometric and photometric information coming from the Gaia satellite yield sufficient insights for supervised learning methods to automatically identify strong gravitational lens candidates with an efficiency that is comparable to methods based on image processing.
Methods. We simulated 106 623 188 lens systems composed of more than two images, based on a regular grid of parameters characterizing a non-singular isothermal ellipsoid lens model in the presence of an external shear. These simulations are used as an input for training and testing our supervised learning models consisting of extremely randomized trees (ERTs). These trees are finally used to assign to each of the 2 129 659 clusters of celestial objects extracted from the Gaia DR2 a discriminant value that reflects the ability of our simulations to match the observed relative positions and fluxes from each cluster. Once complemented with additional constraints, these discriminant values allow us to identify strong gravitational lens candidates out of the list of clusters.
Results. We report the discovery of 15 new quadruply-imaged lens candidates with angular separations of less than 6″ and assess the performance of our approach by recovering 12 of the 13 known quadruply-imaged systems with all their components detected in Gaia DR2 with a misclassification rate of fortuitous clusters of stars as lens systems that is below 1%. Similarly, the identification capability of our method regarding quadruply-imaged systems where three images are detected in Gaia DR2 is assessed by recovering 10 of the 13 known quadruply-imaged systems having one of their constituting images discarded. The associated misclassification rate varies between 5.83% and 20%, depending on the image we decided to remove.