bluuebunny/crossref_metadata_2025_split huggingface dataset:
Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography
Authors: Lee Dan Bi , Kim Jong-Min , Seok Jong Hyeon , Lee Ji-Hye , Jo Jae Deok , Mun Ji Young , Conrad Chelsie , Coe Jesse , Nelson Garrett , Hogue Brenda , White Thomas A. , Zatsepin Nadia , Weierstall Uwe , Barty Anton , Chapman Henry , Fromme Petra , Spence John , Chung Mi Sook , Oh Chang-Hyun , Kim Kyung Hyun 
Published: February 2018

AbstractTime-resolved serial femtosecond crystallography with X-ray free electron laser (XFEL) holds the potential to view fast reactions occurring at near-physiological temperature. However, production and characterization of homogeneous micron-sized protein crystals at high density remain a bottleneck, due to the lack of the necessary equipments in ordinary laboratories. We describe here supersaturation-controlled microcrystallization and visualization and analysis tools that can be easily used in any laboratory. The microcrystallization conditions of the influenza virus hemagglutinin were initially obtained with low reproducibility, which was improved by employing a rapid evaporation of hanging drops. Supersaturation-controlled microcrystallization was then developed in a vapor diffusion mode, where supersaturation was induced by evaporation in hanging drops sequentially for durations ranging from 30 sec to 3 min, depending on the protein. It was applied successfully to the microcrystal formation of lysozyme, ferritin and hemagglutinin with high density. Moreover, visualization and analysis tools were developed to characterize the microcrystals observed by light microscopy. The size and density distributions of microcrystals analyzed by the tools were found to be consistent with the results of manual analysis, further validated by high-resolution microscopic analyses. Our supersaturation-controlled microcrystallization and visualization and analysis tools will provide universal access to successful XFEL studies.
Sahel rainfall strength and onset improvements due to more realistic Atlantic cold tongue development in a climate model
Authors: Steinig S. , Harlaß J. , Park W. , Latif M. 
Published: February 2018

AbstractThe simulation of Sahel rainfall and its onset during the West African Monsoon (WAM) remains a challenge for current state-of-the-art climate models due to their persistent biases, especially in the tropical Atlantic region. Here we show that improved representation of Atlantic Cold Tongue (ACT) development is essential for a more realistic seasonal evolution of the WAM, which is due to a further inland migration of the precipitation maximum. The observed marked relationship between ACT development and Sahel rainfall onset only can be reproduced by a climate model, the Kiel Climate Model (KCM), when sufficiently high resolution in its atmospheric component is employed, enabling enhanced equatorial Atlantic interannual sea surface temperature variability in the ACT region relative to versions with coarser atmospheric resolution. The ACT/Sahel rainfall relationship in the model critically depends on the correct seasonal phase-locking of the interannual variability rather than on its magnitude. We compare the KCM results with those obtained from climate models participating in the Coupled Model Intercomparison Project phase 5 (CMIP5).
Measurement of nuclear reaction cross sections by using Cherenkov radiation toward high-precision proton therapy
Authors: Masuda Takamitsu , Kataoka Jun , Arimoto Makoto , Takabe Miho , Nishio Teiji , Matsushita Keiichiro , Miyake Tasuku , Yamamoto Seiichi , Inaniwa Taku , Toshito Toshiyuki 
Published: February 2018

AbstractMonitoring the in vivo dose distribution in proton therapy is desirable for the accurate irradiation of a tumor. Although positron emission tomography (PET) is widely used for confirmation, the obtained distribution of positron emitters produced by the protons does not trace the dose distribution due to the different physical processes. To estimate the accurate dose from the PET image, the cross sections of nuclear reactions that produce positron emitters are important yet far from being sufficient. In this study, we measured the cross sections of 16O(p,x)15O, 16O(p,x)13N, and 16O(p,x)11C with a wide-energy range (approximately 5–70 MeV) by observing the temporal evolution of the Cherenkov radiation emitted from positrons generated via β+ decay along the proton path. Furthermore, we implemented the new cross sectional data into a conventional Monte Carlo (MC) simulation, so that a direct comparison was possible with the PET measurement. We confirmed that our MC results showed good agreement with the experimental data, both in terms of the spatial distributions and temporal evolutions. Although this is the first attempt at using the Cherenkov radiation in the measurements of nuclear cross sections, the obtained results suggest the method is convenient and widely applicable for high precision proton therapy.
EphB2 receptor tyrosine kinase promotes hepatic fibrogenesis in mice via activation of hepatic stellate cells
Authors: Mimche Patrice N. , Lee Choon M. , Mimche Sylvie M. , Thapa Manoj , Grakoui Arash , Henkemeyer Mark , Lamb Tracey J. 
Published: February 2018

AbstractHepatic fibrosis is the result of an excessive wound-healing response subsequent to chronic liver injury. A feature of liver fibrogenesis is the secretion and deposition of extracellular matrix proteins by activated hepatic stellate cells (HSCs). Here we report that upregulation of EphB2 is a prominent feature of two mouse models of hepatic fibrosis and also observed in humans with liver cirrhosis. EphB2 is upregulated and activated in mouse HSCs following chronic carbon tetrachloride (CCl4) exposure. Moreover, we show that EphB2 deficiency attenuates liver fibrosis and inflammation and this is correlated with an overall reduction in pro-fibrotic markers, inflammatory chemokines and cytokines. In an in vitro system of HSCs activation we observed an impaired proliferation and sub-optimal differentiation into fibrogenic myofibroblasts of HSCs isolated from EphB2−/− mice compared to HSCs isolated from wild type mice. This supports the hypothesis that EphB2 promotes liver fibrosis partly via activation of HSCs. Cellular apoptosis which is generally observed during the regression of liver fibrogenesis was increased in liver specimens of CCl4-treated EphB2−/− mice compared to littermate controls. This data is suggestive of an active repair/regeneration system in the absence of EphB2. Altogether, our data validate this novel pro-fibrotic function of EphB2 receptor tyrosine kinase.
CD63, MHC class 1, and CD47 identify subsets of extracellular vesicles containing distinct populations of noncoding RNAs
Authors: Kaur Sukhbir , Elkahloun Abdel G. , Arakelyan Anush , Young Lynn , Myers Timothy G. , Otaizo-Carrasquero Francisco , Wu Weiwei , Margolis Leonid , Roberts David D. 
Published: February 2018

AbstractExtracellular vesicles (EVs) mediate the intercellular transfer of RNAs, which alter gene expression in target cells. EV heterogeneity has limited progress towards defining their physiological functions and utility as disease-specific biomarkers. CD63 and MHC1 are widely used as markers to purify EVs. CD47 is also present on EVs and alters their effects on target cells, suggesting that specific surface markers define functionally distinct EVs. This hypothesis was addressed by comparing Jurkat T cell EVs captured using CD47, CD63, and MHC1 antibodies. These EV subsets have similar sizes but divergent RNA contents. Apart from differences in numbers of nonannotated transcripts, CD63+, MHC1+, and CD47+EVs have similar overall contents of most noncoding RNA classes, but the relative enrichment of specific RNAs differs. The enrichment of micro-RNAs is highly divergent, and some including miR320a are selectively concentrated in CD47+EVs. Small nucleolar RNAs including SNORD116@ and SNHG10 are also selectively enriched in CD47+EVs, whereas no small nuclear RNAs are enriched in CD47+EVs. Conversely, MHC1+EVs are selectively enriched in a subset of tRNAs including TRE-CTC and TRR-CCG. This heterogeneity in RNA composition suggests multiple sorting mechanisms that direct specific RNAs into subsets of EVs that express specific surface markers.
Breastfeeding moderates FTO related adiposity: a birth cohort study with 30 years of follow-up
Authors: Horta Bernardo Lessa , Victora Cesar G. , França Giovanny V. A. , Hartwig Fernando P. , Ong Ken K. , Rolfe Emanuella de Lucia. , Magalhães Elma I. S. , Lima Natalia P. , Barros Fernando C. 
Published: February 2018

AbstractThis study assessed the association of breastfeeding with body composition at 30 years, among subjects who have been prospectively followed since birth in a southern Brazilian city. We also evaluated whether breastfeeding moderated the association between the rs9939609 variant in theFTOgene and adiposity. At 30 years, total and predominant breastfeeding were positively associated with lean mass index and inversely with visceral fat thickness. Among subjects breastfed for <1 month, all outcomes showed monotonically increasing values with additional copies of the A allele in theFTOgenotype (rs9939609). Associations among subjects breastfed for one month or longer tended to be in the same direction but showed lower magnitude and were less consistent; for all outcomes. Interactions had p values ≤ 0.05 for body mass index, fat mass index and waist circumference. Even among young adults, breastfeeding moderates the association between theFTOvariant rs9939609 and body composition.
Generation and characterization of a IgG monoclonal antibody specific for GM3 (NeuGc) ganglioside by immunizing β3Gn-T5 knockout mice
Authors: He Dongwei , Fan Xiaoyan , Liu Boyi , Tian Yiqing , Zhang Xiangmei , Kang Lin , Tai Yan , Liu Shuzhen , Wang Qian , Li Qingxia , Cai Jianhui 
Published: February 2018

AbstractA murine monoclonal antibody (MAb-1) specific for GM3 has been generated by immunizing β3Gn-T5 knockout mice with purified GM3 ganglioside. The binding specificity of MAb-1 (IgG3 subclass) was established by an enzyme-linked immunosorbent assay (ELISA) and FACS and the antibody showed high binding specificity with GM3. Cell viability assay showed that MAb-1 significantly suppressed cell growth. Immunohistochemistry analysis revealed that MAb-1 was strongly expressed in human ovarian cancer tissues, whereas it was hardly expressed in normal tissues. Finally, antibody-dependent cellular cytotoxicity (ADCC) activities were determined by measuring lactate dehydrogenase (LDH) releasing assay and the results showed high ADCC activities in two representative ovarian cancer cell lines (OVHM and ID8). All of these data indicate that MAb-1 may be potentially used as a therapeutic antibody against ovarian cancers in clinical trials.
Broad-spectrum neutralization of avian influenza viruses by sialylated human milk oligosaccharides: in vivo assessment of 3′-sialyllactose against H9N2 in chickens
Authors: Pandey Ramesh Prasad , Kim Dae Hee , Woo Jinsuk , Song Jaeyoung , Jang Sang Ho , Kim Joon Bae , Cheong Kwang Myun , Oh Jin Sik , Sohng Jae Kyung 
Published: February 2018

AbstractTwo sialylated human milk oligosaccharides (SHMOs) 3′-sialyllactose (3′-SL) and 6′-sialyllactose (6′-SL) were accessed for their possible antiviral activity against six different subtypes of thirteen avian influenza (AI) viruses in vitro. 3′-SL exhibited promising antiviral activity against almost all subtypes of tested AI viruses in hemagglutination inhibition assay, whereas 6′-SL showed activity against few selected H1N1, H1N2, and H3N2 subtype strains. 3′-SL has minimum inhibitory concentration values of 15.62 mM or less in more than half of the viruses examined. 3′-SL also showed effective inactivation of H9N2 Korea isolate (A/Chicken/Korea/MS96/1996) at 12.5 mM concentration in Madin Darby Canine Kidney (MDCK) cell line. Thus, 3′-SL was further studied for in vivo study against H9N2 virus in pathogen free chicken experiment models. In vivo study exhibited improved clinical symptoms on H9N2 infected chickens when treated with 3′-SL. Moreover, treating chickens with 3′-SL resulted in complete elimination of H9N2 viruses within 24 h of virus infection (0.8 HAU of H9N2). Indirect ELISA assay confirmed complete wash-out of H9N2 viruses from the colon after neutralization by 3′-SL without entering the blood stream. These in vivo results open up possible applications of 3′-SL for the prevention of AI virus infections in birds by a simple cleansing mechanism.
Nitrogen-doped mesoporous SiC materials with catalytically active cobalt nanoparticles for the efficient and selective hydrogenation of nitroarenes
Authors: Eckardt Mirco , Zaheer Muhammad , Kempe Rhett 
Published: February 2018

AbstractMesoporous nitrogen-doped silicon carbide catalysts with integrated cobalt nanoparticles (Co@N-SiC) were synthesized by the thermal decomposition of a microphase-separated block copolymer of polycarbosilane and polyethylene. The catalysts are highly active, reusable and offer selective hydrogenation of the nitro group in the presence of hydrogenation-sensitive functional groups.
Plasma homocysteine concentrations and risk of intracerebral hemorrhage: a systematic review and meta-analysis
Authors: Zhou Zhike , Liang Yifan , Qu Huiling , Zhao Mei , Guo Feng , Zhao Chuansheng , Teng Weiyu 
Published: February 2018

AbstractIntracerebral hemorrhage (ICH) has the highest mortality rate in all strokes. However, controversy still exists concerning the association between plasma homocysteine (Hcy) and ICH. A systematic review and meta-analysis was conducted using Pubmed, Embase, and Web of Science up to April 18, 2017. Standard mean difference (SMD) for mean differences of plasma Hcy levels with 95% confidence intervals (CI) was calculated. Seven studies including 667 ICH patients and 1821 ischemic stroke patients were identified for meta-analysis. Our results showed that Hcy levels in ICH patients were significantly higher than those in healthy controls (SMD = 0.59, 95% CI = 0.51–0.68, P < 0.001); no statistic differences were found in the comparisons of Hcy levels between ICH and ischemic stroke (SMD = −0.03, 95% CI = −0.13–0.06, P > 0.05); further subgroup analysis of ethnicity (Asians: SMD = 0.57, 95% CI = 0.48–0.66, P < 0.001; Caucasians: SMD = 0.77, 95% CI = 0.51–1.02, P < 0.001) and sample size (small samples: SMD = 0.55, 95% CI = 0.30–0.80, P < 0.001; large samples size: SMD = 0.60, 95% CI = 0.51–0.69, P < 0.001) in relation to Hcy levels between ICH and healthy controls did not change these results. In conclusion, Hcy level may be an aggravating factor in atherosclerosis, which is positively associated with high risk of ICH. Race-specific differences between Asians and Caucasians have no impact on the risk of ICH.
Machine learning of correlated dihedral potentials for atomistic molecular force fields
Authors: Friederich Pascal , Konrad Manuel , Strunk Timo , Wenzel Wolfgang 
Published: February 2018

AbstractComputer simulation increasingly complements experimental efforts to describe nanoscale structure formation. Molecular mechanics simulations and related computational methods fundamentally rely on the accuracy of classical atomistic force fields for the evaluation of inter- and intramolecular energies. One indispensable component of such force fields, in particular for large organic molecules, is the accuracy of molecule-specific dihedral potentials which are the key determinants of molecular flexibility. We show in this work that non-local correlations of dihedral potentials play a decisive role in the description of the total molecular energy—an effect which is neglected in most state-of-the-art dihedral force fields. We furthermore present an efficient machine learning approach to compute intramolecular conformational energies. We demonstrate with the example of α-NPD, a molecule frequently used in organic electronics, that this approach outperforms traditional force fields by decreasing the mean absolute deviations by one order of magnitude to values smaller than 0.37 kcal/mol (16.0 meV) per dihedral angle.
Collaboration and competition: ethics in toxicology
Authors: Walker Emma S. , Roberts Ruth A. 
Published: February 2018

Abstract
From animal research through adverse events in clinical trials to health scares around food contamination, toxicology has frequently been a focus of scientific and societal concern. As these concerns shift with each new drug, new technology or public health scare, how can toxicology stay current, relevant and ethical? Two of the biggest ethical challenges in pharmaceutical toxicology are the use of animals in testing and the high safety-related attrition rates in new drug development. Both of these require progress in the discipline that will only be driven by research funding. Yet, very little is invested in these two fields compared with investment in new efficacy models, new disease targets and new technologies. How can this be addressed? Here, we explore current paradigms in toxicology that may have the potential for perceived or actual unethical ramifications. We discuss the underpinnings of such practices and make recommendations for change around peer review, resourcing, transparency and data sharing. These ideas build on the analysis presented in the 2004 Paton Prize lecture (Purchase, 2004) where issues around conflict of interest (COI), collaboration and competition in the context of ethical behaviours were highlighted. These areas are clearly relevant to many aspects of scientific research but here we focus on toxicology and specifically toxicology in the pharmaceutical industry.
A Meta-Analysis: Acoustic Measurement of Roughness and Breathiness
Authors: v. Latoszek Ben Barsties , Maryn Youri , Gerrits Ellen , De Bodt Marc 
Published: February 2018

Purpose

Over the last 5 decades, many acoustic measures have been created to measure roughness and breathiness. The aim of this study is to present a meta-analysis of correlation coefficients (
r
) between auditory-perceptual judgment of roughness and breathiness and various acoustic measures in both sustained vowels and continuous speech.

Method

Scientific literature reporting perceptual–acoustic correlations on roughness and breathiness were sought in 28 databases. Weighted average correlation coefficients (
r
w
) were calculated when multiple
r
-values were available for a specific acoustic marker. An
r
w
≥ .60 was the threshold for an acoustic measure to be considered acceptable.

Results

From 103 studies of roughness and 107 studies of breathiness that were investigated, only 33 studies and 34 studies, respectively, met the inclusion criteria of the meta-analysis on sustained vowels. Eighty-six acoustic measures were identified for roughness and 85 acoustic measures for breathiness on sustained vowels, in which 43 and 39 measures, respectively, yielded multiple
r
-values. Finally, only 14 measures for roughness and 12 measures for breathiness produced
r
w
≥ .60. On continuous speech, 4 measures for roughness and 21 measures for breathiness were identified, yielding 3 and 6 measures, respectively, with multiple
r
-values in which only 1 and 2, respectively, had
r
w
≥ .60.

Conclusion
This meta-analysis showed that only a few acoustic parameters were determined as the best estimators for roughness and breathiness.
Low‐power‐delay‐product radix‐4 8*8 Booth multiplier in CMOS
Authors: Xue H. , Patel R. , Boppana N.V.V.K. , Ren S. 
Published: February 2018

The quest continues for microelectronic implementations with higher throughput and reduced power consumption, particularly for digital signal processing, graphic processing unit and CPU portable applications. This Letter focuses on the digital multiplier circuit, which is a key component in determining the power‐delay‐product for numerous battery powered applications. A proposed radix‐4 8 × 8 Booth multiplier is implemented using four stages with a unique optimised stage‐1 architecture. Instead of using adder/subtractor in stage‐1, it is replaced with a novel binary‐to‐2's complement converter and a 2:1 MUX to reduce the delay and power consumption by 7.08 and 49.46%, respectively, compared to the other stages. The proposed design is implemented using CMOS 90 nm technology with 1.2 V supply to demonstrate performance.
New insights into the outflows from R Aquarii
Authors: Liimets T. , Corradi R. L. M. , Jones D. , Verro K. , Santander-García M. , Kolka I. , Sidonio M. , Kankare E. , Kankare J. , Pursimo T. , Wilson P. A. 
Published: February 2018

Context. The source R Aquarii is a symbiotic binary surrounded by a large and complex nebula with a prominent curved jet. It is one of the closest known symbiotic systems, and therefore offers a unique opportunity to study the central regions of these systems and the formation and evolution of astrophysical jets.
Aims. We aim to study the evolution of the central jet and outer nebula of R Aqr, taking advantage of a long term monitoring campaign of optical imaging, as well as of high-resolution integral field spectroscopy.
Methods. Narrow-band images acquired over a period of more than 21 yr were compared in order to study the expansion and evolution of all components of the R Aqr nebula. The magnification method was used to derive the kinematic ages of the features that appear to expand radially. Integral field spectroscopy of the [O III] 5007 Å emission is used to study the velocity structure of the central regions of the jet.
Results. New extended features, further out than the previously known hourglass nebula, are detected. The kinematic distance to R Aqr is calculated to be 178 pc using the expansion of the large hourglass nebula. This nebula of R Aqr is found to be roughly 650 yr old, while the inner regions have ages ranging from 125 to 290 yr. The outer nebula is found to be well described by a ballistic expansion, while for most components of the jet strong deviations from such behaviour are found. We find that the northern jet is mostly red-shifted while its southern part is blue-shifted, apparently at odds with findings from previous studies but almost certainly a consequence of the complex nature of the jet and variations in ionisation and illumination between observations.