bluuebunny/crossref_metadata_2025 huggingface dataset:
Intravoxel incoherent motion diffusion‐weighted imaging for characterizing focal hepatic lesions: Correlation with lesion enhancement
Authors: Choi In Young , Lee Seung Soo , Sung Yu Sub , Cheong Hyunhee , Lee Hoyoung , Byun Jae Ho , Kim So Yeon , Lee So Jung , Shin Yong Moon , Lee Moon‐gyu
Published: September 2016

Purpose

To evaluate the value of intravoxel incoherent motion (IVIM) parameters for characterizing focal hepatic lesions, and to assess the correlation between IVIM parameters and arterial nodule enhancement.

Materials and Methods

We retrospectively evaluated 161 lesions (91 hepatocellular carcinomas [HCCs], 27 intrahepatic cholangiocarcinomas [IHCCs], 20 hemangiomas, 9 combined hepatocellular‐cholangiocarcinomas, 9 metastases, and 5 other tumors) in 161 patients (105 men and 56 women; mean age, 56.4 years). Diffusion‐weighted imaging was performed using nine b‐values (0–900 s/mm2) at 1.5T. Apparent diffusion coefficient (ADC), molecular diffusion coefficient (Dslow), perfusion fraction (f), and perfusion‐related diffusion coefficient (Dfast) were compared among the hepatic lesions using analysis of variance (ANOVA). Receiver‐operating‐characteristic analysis was performed to assess diagnostic performance. The enhancement fraction (EF) and the relative enhancement (RE) of the hepatic lesions on arterial phase gadoxetic acid‐enhanced images were correlated with the IVIM parameters using Spearman's test.

Results

For the differentiation of hemangiomas from malignant tumors, Dslow showed the largest area under the curve (0.933) among all parameters. Although ADC did not show any difference among malignant lesions (P ≥ 0.28), HCCs showed a significantly lower Dslow than IHCC (P < 0.001) and a higher f than did IHCC (P < 0.001) and metastasis (P = 0.027); f had a significant positive correlation with EF (r = 0.420, P < 0.001) and RE (r = 0.264, P = 0.001).

Conclusion

IVIM parameters are more helpful in characterizing malignant hepatic lesions than ADC; f may reflect the extent and degree of hepatic nodule enhancement in the arterial phase, and may allow for differentiation of HCC from IHCC and metastasis.

Level of Evidence: 3

J. MAGN. RESON. IMAGING 2017;45:1589–1598
Cerebrospinal fluid dynamics at the lumbosacral level in patients with spinal stenosis: A pilot study
Authors: Chun Se‐Woong , Lee Hack‐Jin , Nam Koong‐Ho , Sohn Chul‐Ho , Kim Kwang Dong , Jeong Eun‐Jin , Chung Sun G. , Kim Keewon , Kim Dong‐Joo
Published: September 2016

Spinal stenosis is a common degenerative condition. However, how neurogenic claudication develops has not been clearly elucidated. Moreover, cerebrospinal fluid physiology at the lumbosacral level has not received adequate attention. This study was conducted to compare cerebrospinal fluid hydrodynamics at the lumbosacral spinal level between patients with spinal stenosis and healthy controls. Twelve subjects (four patients and eight healthy controls; 25–77 years old; seven males) underwent phase‐contrast magnetic resonance imaging to quantify cerebrospinal fluid dynamics. The cerebrospinal fluid flow velocities were measured at the L2 and S1 levels. All subjects were evaluated at rest and after walking (to provoke neurogenic claudication in the patients). The caudal peak flow velocity in the sacral spine (−0.25 ± 0.28 cm/s) was attenuated compared to that in the lumbar spine (−0.93 ± 0.46 cm/s) in both patients and controls. The lumbar caudal peak flow velocity was slower in patients (−0.65 ± 0.22 cm/s) than controls (−1.07 ± 0.49 cm/s) and this difference became more pronounced after walking (−0.66 ± 0.37 cm/s in patients, −1.35 ± 0.52 cm/s in controls; p = 0.028). The sacral cerebrospinal fluid flow after walking was barely detectable in patients (caudal peak flow velocity: −0.09 ± 0.03 cm/s). Cerebrospinal fluid dynamics in the lumbosacral spine were more attenuated in patients with spinal stenosis than healthy controls. After walking, the patients experiencing claudication did not exhibit an increase in the cerebrospinal fluid flow rate as the controls did. Altered cerebrospinal fluid dynamics may partially explain the pathophysiology of spinal stenosis. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:104–112, 2017.
Clinicopathologic features and prognosis of primary gastrointestinal stromal tumor patients under 35 years of age: A 10‐year retrospective study
Authors: Zhang Peng , Deng Rui , Liu Ke , Shuai Xiao‐Ming , Bai Jie , Chang Wei‐Long , Gao Jin‐Bo , Cai Kai‐Lin , Wang Guo‐Bin , Tao Kai‐Xiong
Published: September 2016

Objectives

To investigate gastrointestinal stromal tumor (GIST) clinicopathologic characteristics in young adults.

Methods

Clinicopathologic data from GIST patients under 35 years diagnosed at our hospital from January 2005 to December 2014 were retrospectively collected.

Results

Thirty‐one (5.3%, 31/585) patients were included; 17 (54.8%) were female. The most common presentation and primary tumor site were gastrointestinal bleeding (n = 18, 58.1%) and the small intestine (n = 13, 41.9%), respectively. Fifteen (48.4%) GISTs were classified as having a high relapse risk; two (6.4%), intermediate; nine (29.0%), low; and five (16.1%), very low. All patients underwent tumor resection. With a median follow‐up of 51 months for 20 (64.5%) patients, 12 (60%) were given imatinib methylate as adjuvant therapy. One (5%) patient died of peritoneal GIST dissemination, four (20%) developed abdominal recurrences, two (10%) had hepatic metastasis, and thirteen (65%) were disease free. The 5‐year disease‐free survival rate was 51.2%.

Conclusions

GISTs rarely occur in young adults. The most common location is the small intestine. A slight female predominance was observed in the current study. Adjuvant therapy longer than the recommended duration may be beneficial for GISTs with a high relapse risk. Combined targeted therapy and surgery is appropriate for recurrent and metastatic GISTs in select patients. J. Surg. Oncol. 2016;114:977–981. © 2016 Wiley Periodicals, Inc.
Simulation of continuum electrical conduction and Joule heating using DEM domains
Authors: Hubert C. , André D. , Dubar L. , Iordanoff I. , Charles J.L.
Published: September 2016

This paper proposes an original method to simulate the electrical conduction in continuums with the Discrete Element Method (DEM). The proposed method is based on the graphs theory applied to electrical resistance network, where the resistance between two discrete elements is estimated through the notion of ‘transmission surface’ to assume the discrete domain as a continuous medium. In addition to the electrical conduction, the Joule heating of a DEM domain has also been developed to take full advantage of the electrical conduction. The proposed method has been implemented in the free DEM software named ‘GranOO’.

The numerical results were compared against analytical approaches when applicable, or against Finite Element Method if the geometries become more complex or in case of dynamic loadings. The results are found satisfactory with errors around 3% for the electrical conduction and Joule heating of reasonably complex domains and loading cases. When it comes to more complex domains, such as electrical constriction, whilst the results remain close to those obtained with reference solutions (around 6%), they highlight the importance of taking care about the domains discretization.

Finally, the proposed method is applied to detect cracks onset on a cylindrical rod torsion test to show how to take advantage of the proposed work. Copyright © 2016 John Wiley & Sons, Ltd.
MicroRNA‐463‐3p/ABCG4: A new axis in glucose‐stimulated insulin secretion
Authors: Hou Xuwei , Wu Wei , Yin Bo , Liu Xuefeng , Ren Fu
Published: September 2016

Objective

Glucose‐stimulated insulin secretion (GSIS) is known to be essential in the control of metabolic fuel homeostasis, though the molecular mechanisms involved remain unclear.

Methods

MicroRNA (miRNA)−463‐3p and ATP‐binding cassette A4 (ABCG4) expression was analyzed by real‐time PCR, and the potential role of miRNA‐463‐3p or ABCG4 was evaluated by overexpressing or silencing such miRNA or genes.

Results

The miRNA‐463‐3p inhibited GSIS without affecting cell viability. Further, mechanistic studies demonstrated that ABCG4 was a direct target of microRNA‐463‐3p and, to this effect, that ABCG4 played an important role in GSIS. The targeting was relevant in pancreatic islet β‐cells, where GSIS through the miRNA‐463‐3p/ABCG4 axis was observed. Interestingly, in type 2 diabetes human pancreatic islets, expression of miRNA‐463‐3p and insulin was upregulated and ABCG4 downregulated compared with nondiabetic controls, and their expression levels were closely correlated.

Conclusions

The findings collectively establish a link between GSIS and the miRNA‐463‐3p/ABCG4 axis and represent a promising target for future diabetes mellitus treatments.
Inner surface modification of halloysite nanotubes and its influence on morphology and thermal properties of polystyrene/polyamide‐11 blends
Authors: Sahnoune Mohamed , Taguet Aurélie , Otazaghine Belkacem , Kaci Mustapha , Lopez‐Cuesta José‐Marie
Published: September 2016

The asymmetry of halloysite surface chemistry was used to perform a selective modification of its inner surface via grafting of a synthesized styrene/(methacryloyloxy)methyl phosphonic acid copolymer. Fourier transform infrared spectroscopy, thermogravimetric analysis (TGA) and pyrolysis gas chromatography/mass spectrometry were used to evidence and quantify the grafting. Then, raw and hybrid nanoparticles were incorporated in polystyrene (PS)/polyamide‐11 (PA11) blends (80/20 and 60/40 wt%). Scanning electron micrographs showed differences in localization of the halloysite nanotubes (HNTs), since raw halloysite is concentrated in the PA11 phase while modified halloysite is also located at the PS/PA11 interface, leading to a better interfacial adhesion between PS and PA11. An inhibiting effect of modified halloysite on PA11 coalescence was evidenced by measuring the particle size distribution of the extracted nodules. Moreover, the presence of modified halloysite at the interface shows an improvement in terms of thermal stability as observed by TGA, but with no significant effects on PA11 crystallization behaviour as shown by differential scanning calorimetry results. Rheological measurements were carried out to study the influence of the surface modification of halloysite on the blend morphology. A gel‐like behaviour was observed for the (60/40 wt%) HNTs reinforced composition that was enhanced in the case of 10% functionalized halloysite. © 2016 Society of Chemical Industry
Depletion of the Fragile X Mental Retardation Protein in Embryonic Stem Cells Alters the Kinetics of Neurogenesis
Authors: Khalfallah Olfa , Jarjat Marielle , Davidovic Laetitia , Nottet Nicolas , Cestèle Sandrine , Mantegazza Massimo , Bardoni Barbara
Published: September 2016

Fragile X syndrome (FXS) is the most common form of inherited intellectual disability and a leading cause of autism. FXS is due to the silencing of the Fragile X Mental Retardation Protein (FMRP), an RNA binding protein mainly involved in translational control, dendritic spine morphology and synaptic plasticity. Despite extensive studies, there is currently no cure for FXS. With the purpose to decipher the initial molecular events leading to this pathology, we developed a stem-cell-based disease model by knocking-down the expression of Fmr1 in mouse embryonic stem cells (ESCs). Repressing FMRP in ESCs increased the expression of amyloid precursor protein (APP) and Ascl1. When inducing neuronal differentiation, βIII-tubulin, p27kip1, NeuN, and NeuroD1 were upregulated, leading to an accelerated neuronal differentiation that was partially compensated at later stages. Interestingly, we observed that neurogenesis is also accelerated in the embryonic brain of Fmr1-knockout mice, indicating that our cellular model recapitulates the molecular alterations present in vivo. Importantly, we rescued the main phenotype of the Fmr1 knockdown cell line, not only by reintroducing FMRP but also by pharmacologically targeting APP processing, showing the role of this protein in the pathophysiology of FXS during the earliest steps of neurogenesis. Our work allows to define an early therapeutic window but also to identify more effective molecules for treating this disorder.
Concise Review: Lessons from Naïve Human Pluripotent Cells
Authors: Ware Carol B.
Published: September 2016

The naïve state of pluripotency is actively being explored by a number of labs. There is some controversy in the field as to the true identity of naïve human pluripotent cells as they are not exact mirrors of the mouse. The various reports published, although in basic agreement, present discrepancies in the characterization of the various lines, which likely reflect the etiology of these lines. The primary lesson learned from these contributions is that a human naïve state reflecting the preimplantation human is likely to exist. The essential factors that will universally maintain the naïve state in human cells in vitro are not yet fully understood. These first need to be identified in order to describe the definitive characteristics of this state. Comparisons of naïve and primed human pluripotent cells have also highlighted consistencies between states and broadened our understanding of embryonic metabolism, epigenetic change required for development, embryonic DNA repair strategies and embryonic expression dynamics.
Phytosterol Esterification is Markedly Decreased in Preterm Infants Receiving Routine Parenteral Nutrition
Authors: Savini Sara , Correani Alessio , Pupillo Daniele , D'Ascenzo Rita , Biagetti Chiara , Pompilio Adriana , Simonato Manuela , Verlato Giovanna , Cogo Paola , Taus Marina , Nicolai Albano , Carnielli Virgilio Paolo
Published: September 2016

Several studies reported the association between total plasma phytosterol concentrations and the parenteral nutrition‐associated cholestasis (PNAC). To date, no data are available on phytosterol esterification in animals and in humans during parenteral nutrition (PN). We measured free and esterified sterols (cholesterol, campesterol, stigmasterol, and sitosterol) plasma concentrations during PN in 16 preterm infants (500–1249 g of birth weight; Preterm‐PN), in 11 term infants (Term‐PN) and in 12 adults (Adult‐PN). Gas chromatography–mass spectrometry was used for measurements. Plasma concentrations of free cholesterol (Free‐CHO), free phytosterols (Free‐PHY) and esterified phytosterols (Ester‐PHY) were not different among the three PN groups. Esterified cholesterol (Ester‐CHO) was statistically lower in Preterm‐PN than Adult‐PN. Preterm‐PN had significantly higher Free‐CHO/Ester‐CHO and Free‐PHY/Ester‐PHY ratios than Adult‐PN (Free‐CHO/Ester‐CHO: 1.1 ± 0.7 vs. 0.6 ± 0.2; Free‐PHY/Ester‐PHY: 4.1 ± 2.6 vs. 1.3 ± 0.8; *P < 0.05). Free‐CHO/Ester‐CHO and Free‐PHY/Ester‐PHY ratios of Term‐PN (Free‐CHO/Ester‐CHO: 1.1 ± 0.4; Free‐PHY/Ester‐PHY: 2.9 ± 1.7) were not different from either Preterm‐PN or from Adult‐PN. Plasma Free‐CHO/Ester‐CHO and Free‐PHY/Ester‐PHY were unchanged after 24 h on fat‐free PN both in Preterm‐PN and in Adult‐PN. Free‐PHY/Ester‐PHY did not correlate with phytosterol intake in Preterm‐PN. Free‐PHY/Ester‐PHY of Preterm‐PN was positively correlated with the Free‐CHO/Ester‐CHO and negatively correlated with gestational age and birth weight. In conclusion, PHY were esterified to a lesser extent than CHO in all study groups; the esterification was markedly decreased in Preterm‐PN compared to Adult‐PN. The clinical consequences of these findings warrant further investigations.
Go beyond just paying: Effects of payment method on level of construal
Authors: Chen Rong , Xu Xiaobing , Shen Hao
Published: September 2016

Does paying by credit card induce consumers to think more abstractly than paying in cash? In a series of five studies, we show that priming people with a concept of a credit card as the payment method could lead them to construe information more abstractly than priming them with a concept of cash as the payment method. We distinguish between two processes that might account for the above effect, examine the factors that moderate this effect, and demonstrate the marketing implications of our findings.
Sexual Satisfaction and the Importance of Sexual Health to Quality of Life Throughout the Life Course of U.S. Adults
Authors: Flynn Kathryn E. , Lin Li , Bruner Deborah Watkins , Cyranowski Jill M. , Hahn Elizabeth A. , Jeffery Diana D. , Reese Jennifer Barsky , Reeve Bryce B. , Shelby Rebecca A. , Weinfurt Kevin P.
Published: September 2016

Introduction

Discussions about sexual health are uncommon in clinical encounters, despite the sexual dysfunction associated with many common health conditions. Understanding of the importance of sexual health and sexual satisfaction in U.S. adults is limited.

Aim

To provide epidemiologic data on the importance of sexual health for quality of life and people's satisfaction with their sex lives and to examine how each is associated with demographic and health factors.

Methods

Data are from a cross-sectional self-report questionnaire from a sample of 3,515 English-speaking U.S. adults recruited from an online panel that uses address-based probability sampling.

Main Outcome Measures

We report ratings of importance of sexual health to quality of life (single item with five-point response) and the Patient-Reported Outcomes Measurement Information System Satisfaction With Sex Life score (five items, each with five-point responses, scores centered on the U.S. mean).

Results

High importance of sexual health to quality of life was reported by 62.2% of men (95% CI = 59.4–65.0) and 42.8% of women (95% CI = 39.6–46.1, P < .001). Importance of sexual health varied by sex, age, sexual activity status, and general self-rated health. For the 55% of men and 45% of women who reported sexual activity in the previous 30 days, satisfaction with sex life differed by sex, age, race-ethnicity (among men only), and health. Men and women in excellent health had significantly higher satisfaction than participants in fair or poor health. Women with hypertension reported significantly lower satisfaction (especially younger women), as did men with depression or anxiety (especially younger men).

Conclusion

In this large study of U.S. adults' ratings of the importance of sexual health and satisfaction with sex life, sexual health was a highly important aspect of quality of life for many participants, including participants in poor health. Moreover, participants in poorer health reported lower sexual satisfaction. Accordingly, sexual health should be a routine part of clinicians' assessments of their patients. Health care systems that state a commitment to improving patients' overall health must have resources in place to address sexual concerns. These resources should be available for all patients across the lifespan.
Revising theSchizoparmaceae:Coniellaand its synonymsPilidiellaandSchizoparme
Authors: Alvarez L.V. , Groenewald J.Z. , Crous P.W.
Published: September 2016

The asexual generaConiella(1918) andPilidiella(1927), including their sexual morphs inSchizoparme(1923), have a cosmopolitan distribution and are associated with foliar, fruit, leaf, stem and root diseases on a wide variety of hosts. Species of these genera sometimes occur as secondary invaders of plant tissues infected by other organisms or that are injured by other causes. Several studies published over the last few decades had conflicting ideas as to whetherConiella,PilidiellaandSchizoparmeshould be regarded as synonymous or as separate genera. The present study aims to resolve the generic classification of these genera through phylogenetic analyses of the concatenated alignment of partial LSU nrDNA,rpb2, ITS nrDNA andtef1sequence data of 117 isolates, combined with their morphology. Results revealed that all strains cluster in a single well-supported clade. Conidial colour, traditionally the distinguishing character betweenConiellaandPilidiella, evolved multiple times throughout the clade, and is not a good character at generic level inSchizoparmaceae. The three genera should therefore be regarded as synonymous, with the older nameConiellahaving priority. Furthermore, this study delineated 13 new species, and new combinations were proposed for a further 15 species.
The performance of single and multi-collector ICP-MS instruments for fast and reliable34S/32S isotope ratio measurements
Authors: Hanousek Ondrej , Brunner Marion , Pröfrock Daniel , Irrgeher Johanna , Prohaska Thomas
Published: September 2016

The performance and validation characteristics of different single collector inductively coupled plasma mass spectrometers based on different technical principles (ICP-SFMS, ICP-QMS in reaction and collision modes, and ICP-MS/MS) were evaluated in comparison to the performance of MC ICP-MS for fast and reliable S isotope ratio measurements.
Single addition of an allylamine monomer enables access to end-functionalized RAFT polymers for native chemical ligation
Authors: Isahak Naatasha , Gody Guillaume , Malins Lara R. , Mitchell Nicholas J. , Payne Richard J. , Perrier Sébastien
Published: September 2016

A novel method for the introduction of a single protected amine-functional monomer at the chain end of RAFT polymers has been developed to enable native chemical ligation with peptide thioesters.
The reductive aromatization of tridecacyclene
Authors: Sumy Daniel P. , Finke Aaron D. , Whalley Adam C.
Published: September 2016

X-ray analysis of the dipotassium adduct of tridecacyclene reveals significant evidence of increased aromatic character despite its tub-like shape.
Guanidiniocarbonyl pyrrole (GCP) conjugated PAMAM-G2, a highly efficient vector for gene delivery: the importance of DNA condensation
Authors: Samanta Krishnananda , Jana Poulami , Bäcker Sandra , Knauer Shirley , Schmuck Carsten
Published: September 2016

A novel hybrid compound1efficiently shuttles genetic material into HeLa cells at concentrations as low as 0.6 μM, whereas the parent compound PAMAM-G2 is ineffective even at 200 μM.
A hexameric [MnIII18Na6] wheel based on [MnIII3O]7+ sub-units
Authors: Manoli Maria , Inglis Ross , Piligkos Stergios , Yanhua Lan , Wernsdorfer Wolfgang , Brechin Euan K. , Tasiopoulos Anastasios J.
Published: September 2016

A nano-sized hexameric [MnIII3Na]6 molecular aggregate is reported which is the second largest oxime-based Mn cluster known to date, the largest member of the family of molecular oligomers based on [Mn3] triangles, and the only one with a wheel-like metal topology.
Comparative study of singlet oxygen production by photosensitiser dyes encapsulated in silicone: towards rational design of anti-microbial surfaces
Authors: Noimark Sacha , Salvadori Enrico , Gómez-Bombarelli Rafael , MacRobert Alexander J. , Parkin Ivan P. , Kay Christopher W. M.
Published: September 2016

Theoretical and experimental toolbox for the rational design of light-activated antimicrobial surfaces.
Competition between quasi-planar and cage-like structures in the B29−cluster: photoelectron spectroscopy and ab initio calculations
Authors: Li Hai-Ru , Jian Tian , Li Wei-Li , Miao Chang-Qing , Wang Ying-Jin , Chen Qiang , Luo Xue-Mei , Wang Kang , Zhai Hua-Jin , Li Si-Dian , Wang Lai-Sheng
Published: September 2016

B29−and B29clusters have competitive stingray-shapedversusseashell-like structures. The anion favors the former conformation slightly, whereas the neutral ion is dominated by the latter.
Probing the potential of halogen-free superhalogen anions as effective electrolytes of Li-ion batteries: a theoretical prospect from combined ab initio and DFT studies
Authors: Sun Yin-Yin , Li Jin-Feng , Zhou Fu-Qiang , Li Jian-Li , Yin Bing
Published: September 2016

The potential of superhalogens as efficient components of electrolytes in Li-ion batteries is verified from ab initio and DFT studies.
Dipeptide concave nanospheres based on interfacially controlled self-assembly: from crescent to solid
Authors: Wang Juan , Shen Guizhi , Ma Kai , Jiao Tifeng , Liu Kai , Yan Xuehai
Published: September 2016

Concave nanospheres based on the self-assembly of simple dipeptides not only provide alternatives for modeling the interactions between biomacromolecules, but also present a range of applications for purification and separation, and delivery of active species.
Benzothiazole–pyrimidine-based BODIPY analogues: promising luminophores with fluorescence sensing and imaging ability and asymmetrization-induced solid-state emission
Authors: Wang Xiaoqing , Liu Qingsong , Qi Fen , Li Lin , Yu Hai-Dong , Liu Zhipeng , Huang Wei
Published: September 2016

A series of boron difluoride dyes were demonstrated to possess intense emission both in solution and solid-state. Their fluorogenic sensing and imaging abilities were also investigated.
Highly water-soluble three-redox state organic dyes as bifunctional analytes
Authors: Carretero-González Javier , Castillo-Martínez Elizabeth , Armand Michel
Published: September 2016

Common organic dyes show three stable redox states, offering an alternative to questionable vanadium for the implementation of redox-flow batteries.
Methylammonium lead iodide grain boundaries exhibit depth-dependent electrical properties
Authors: MacDonald Gordon A. , Yang Mengjin , Berweger Samuel , Killgore Jason P. , Kabos Pavel , Berry Joseph J. , Zhu Kai , DelRio Frank W.
Published: September 2016

In this communication, the nanoscale through-film and lateral photo-response and conductivity of large-grained methylammonium lead iodide (MAPbI3) thin films are studied.
Hydroxysafflor yellow A inhibits IL-1β-induced release of IL-6, IL-8, and MMP-1 via suppression of ERK, NF-κB and AP-1 signaling in SW982 human synovial cells
Authors: Cheng Bin-Feng , Gao Yao-Xin , Lian Jun-Jiang , Guo Dan-Dan , Wang Lei , Wang Mian , Yang Hai-Jie , Feng Zhi-Wei
Published: September 2016

Hydroxysafflor yellow A reduces IL-6, IL-8, and MMP-1 releaseviainhibiting ERK, NF-κB and AP-1 signaling in SW982 cells.
Zeolite and zeotype-catalysed transformations of biofuranic compounds
Authors: Li Hu , Yang Song , Riisager Anders , Pandey Ashok , Sangwan Rajender S. , Saravanamurugan Shunmugavel , Luque Rafael
Published: September 2016

Lignocellulosic biomass is an important renewable resource that could substitute fossil feedstocks as a raw material for high value chemicals production.
Brushed polyethylene glycol and phosphorylcholine for grafting nanoparticles against protein binding
Authors: Wang Bo , Blin Thomas , Käkinen Aleksandr , Ge Xinwei , Pilkington Emily H. , Quinn John F. , Whittaker Michael R. , Davis Thomas P. , Ke Pu Chun , Ding Feng
Published: September 2016

To provide a molecular insight for guiding polymer coating in surface science and nanotechnology, we examined the structural and stealth properties of brushed PEG- and phosphorylcholine-grafted iron oxide nanoparticles.
Exfoliation of graphite into graphene in aqueous solution: an application as graphene/TiO2 nanocomposite to improve visible light photocatalytic activity
Authors: Giovannetti R. , Rommozzi E. , Zannotti M. , D'Amato C. A. , Ferraro S. , Cespi M. , Bonacucina G. , Minicucci M. , Di Cicco A.
Published: September 2016

Graphene dispersion (GR) was prepared by liquid-phase sonication of graphite and evaluated by XRD, DLS and UV-Vis analysis. It was used to prepare PP@mgGR–TiO2, showing positive effects on ARS photodegradation under visible light irradiation.
Synthesis and application of core–shell magnetic metal–organic framework composites Fe3O4/IRMOF-3
Authors: Li Weigang , Li Gang , Liu Dan
Published: September 2016

A core–shell structured magnetic MOF composite, Fe3O4/IRMOF-3, was synthesized by a novel method and applied as a catalyst in the Knoevenagel condensation reaction.
Effervescence-assisted dispersive liquid–liquid microextraction based on the solidification of a floating ionic liquid with a special collection method for the rapid determination of benzoylurea insecticides in water samples
Authors: Hu Lu , Qian Heng , Yang Xiaoling , Li Songqing , Zhang Sanbing , Lu Runhua , Zhou Wenfeng , Gao Haixiang
Published: September 2016

Dispersion liquid–liquid microextraction based on the solidification of a floating ionic liquid.
Improving the performance of solid-state quantum dot-sensitized solar cells based on TiO2/CuInS2photoelectrodes with annealing treatment
Authors: Yang Lin , Ma Yunping , Liu Jihong , Mai Yaohua
Published: September 2016

CuInS2were prepared over TiO2films, and are exploited as sensitizer in solid-state QDSSCs with spiro-OMeTAD as hole conductor.
Highly efficient, stable and controllable multi-core, rattle-type Ag@SiO2 catalyst for the reduction of 4-nitrophenol
Authors: Hou Jie , Yu Bo , Liu Er-gang , Dong Wei-bing , Lu Ping-chao , Wang Zhao , Yang Victor C. , Gong Jun-bo
Published: September 2016

Multi-core, rattle-type Ag@silica nanoparticles with different silver loadings were prepared via selective etching methods.
Enhanced activity of α-Fe2O3 for photocatalytic NO removal
Authors: Balbuena J. , Cruz-Yusta M. , Cuevas A. L. , López-Escalante M. C. , Martín F. , Pastor A. , Sánchez L.
Published: September 2016

Unique electrospun α-Fe2O3 fibers of singular nano-architecture were obtained exhibiting a highly enhanced NO conversion photocatalytic efficiency
An efficient method for tylosin removal from an aqueous solution by goethite modified straw mass
Authors: Yin Yongyuan , Guo Xuetao , Yang Chen , Gao Liangmin , Hu Youbiao
Published: September 2016

Renewable agricultural residues are produced in large quantities as waste, and their storage and management create environmental problems.
Transition-metal-free synthesis of oxazoles: valuable structural fragments in drug discovery
Authors: Ibrar Aliya , Khan Imtiaz , Abbas Naeem , Farooq Umar , Khan Ajmal
Published: September 2016

This review article encapsulates the recent developments in the metal-free approaches used to construct oxazole moiety.
Functionalization of side chain terminals with fused aromatic rings in carbazole–diketopyrrolopyrrole based conjugated polymers for improved charge transport properties
Authors: Sun Ying , Huang Qizan , Zhang Xueqin , Ding Xiaojing , Han Pei , Lin Baoping , Yang Hong , Guo Lingxiang
Published: September 2016

Through functionalization of the side chain terminal with fused aromatic rings, the charge transport properties of carbazole–diketopyrrolopyrrole based polymers were improved.
pH/temperature-sensitive hydrogel-based molecularly imprinted polymers (hydroMIPs) for drug delivery by frontal polymerization
Authors: Wang Xiao-Lin , Yao Hong-Fei , Li Xiu-Yuan , Wang Xu , Huang Yan-Ping , Liu Zhao-Sheng
Published: September 2016

Frontal polymerization was successfully utilized, for the first time, to obtain pH/temperature-sensitive hydrogel-based molecularly imprinted polymers (hydroMIPs).
Ag(i)-based high-energy metal organic frameworks (HE-MOFs) incorporating coordinated moieties in channels: synthesis, structure and physicochemical properties
Authors: Song Xiaxia , Zhang Sheng , Zhao Guowei , Zhang Wendou , Chen Dongpo , Yang Qi , Wei Qing , Xie Gang , Yang Desuo , Chen Sanping , Gao Shengli
Published: September 2016

A new Ag(i)-based HE-MOFs exhibited a compact 3D structure with channels containing coordinated NO3− and CH3COO− ions. The superior density, thermostability, insensitiveness and detonation properties indicated it can be used as potential explosive.
Improved ceramifiable properties of EVA composites with whitened and capsulized red phosphorus (WCRP)
Authors: Xinhao Gong , Yucai Shen , Tingwei Wang
Published: September 2016

Phase separation between SGFs and phosphates promotes formation of cristobalite at high temperature, which leads to improvements in ceramifiable properties.
Large-scale synthesis of high-quality graphene sheets by an improved alternating current arc-discharge method
Authors: Wu Xiaohui , Liu Yang , Yang Hao , Shi Zujin
Published: September 2016

N2 favors the formation of curved graphene by doping N atoms into the graphitic lattice. By introducing H2, which can effectively reduce formation of dangling bonds and closed structure, the mixed buffer gas yields products of intact structures with low heteroatom content.
Synthesis and application of colloidal beta-cyclodextrin-decorated silver nanoparticles for rapid determination of malachite green in environmental water using surface-enhanced Raman spectroscopy
Authors: Jia Fei , Yang Xudong , Li Zhenyu
Published: September 2016

A series of AgNPs were synthesized by silver mirror reaction in the presence of CDs. Combined with SERS, a rapid method for the determination of MG was established successfully.
Highly efficient and thermally stable fullerene-free organic solar cells based on a small molecule donor and acceptor
Authors: Badgujar Sachin , Song Chang Eun , Oh Sora , Shin Won Suk , Moon Sang-Jin , Lee Jong-Cheol , Jung In Hwan , Lee Sang Kyu
Published: September 2016

We studied fullerene-free organic solar cells using rhodanine-terminated BDT3TR and O-IDTBR.
Enhancing the photovoltaic performance of planar heterojunction perovskite solar cells by doping the perovskite layer with alkali metal ions
Authors: Chang Jingjing , Lin Zhenhua , Zhu Hai , Isikgor Furkan Halis , Xu Qing-Hua , Zhang Chunfu , Hao Yue , Ouyang Jianyong
Published: September 2016

Doping the perovskite layer with a small amount of alkali metal ions can enhance the photovoltaic efficiency of perovskite solar cells.
Ruthenium phenanthroimidazole complexes for near infrared light-emitting electrochemical cells
Authors: Bideh Babak Nemati , Roldán-Carmona Cristina , Shahroosvand Hashem , Nazeeruddin Mohammad Khaja
Published: September 2016

By adding different electron donor moieties to the ancillary ligand in ruthenium(ii) phenanthroimidazole complexes, we successfully designed near infrared light emitting complexes suitable for light emitting electrochemical cells (LECs).
Improved i.p. drug delivery with bioadhesive nanoparticles
Authors: Deng Yang , Yang Fan , Cocco Emiliano , Song Eric , Zhang Junwei , Cui Jiajia , Mohideen Muneeb , Bellone Stefania , Santin Alessandro D. , Saltzman W. Mark
Published: September 2016

Significance

Resistance to platinum-based chemotherapies and paclitaxel is common in recurrence of both high-grade ovarian and endometrial cancers. Paclitaxel resistance has been correlated with overexpression of class III β-tubulin, the preferential target of the epothilones, microtubule-stabilizing agents. Epothilone B (EB) is manifold more effective than paclitaxel, but clinical use is limited by side effects. To reduce side effects, we encapsulated EB into bioadhesive nanoparticles (BNPs), reasoning that bioadhesive nanoparticles loaded with epothilone B (EB/BNPs) would interact with abdominal tissues and gradually release EB in proximity of peritoneal cancer implants, thus maintaining EB concentration at the site of action and limiting systemic exposure and toxicity. Our experiments show the higher therapeutic activity and limited toxicity of EB/BNPs compared with nonadhesive nanoparticles loaded with EB or carrier-free EB.
Inferring interaction partners from protein sequences
Authors: Bitbol Anne-Florence , Dwyer Robert S. , Colwell Lucy J. , Wingreen Ned S.
Published: September 2016

Significance

Specific protein−protein interactions play crucial roles in the stability of multiprotein complexes and in signal transduction. Thus, mapping these interactions is key to a systems-level understanding of cells. Systematic experimental identification of protein interaction partners is still challenging. However, a large and rapidly growing amount of sequence data is now available. Is it possible to identify which proteins interact just from their sequences? We propose an approach based on sequence covariation, building on methods used with success to predict the three-dimensional structures of proteins from sequences alone. Our method identifies specific interaction partners with high accuracy among the members of several ubiquitous prokaryotic protein families, and provides a way to predict protein−protein interactions directly from sequence data.
Oriented collagen fibers direct tumor cell intravasation
Authors: Han Weijing , Chen Shaohua , Yuan Wei , Fan Qihui , Tian Jianxiang , Wang Xiaochen , Chen Longqing , Zhang Xixiang , Wei Weili , Liu Ruchuan , Qu Junle , Jiao Yang , Austin Robert H. , Liu Liyu
Published: September 2016

Significance

Intravasation is an early stage of metastasis that involves metastatic cells moving from the tumor into the extracellular matrix (ECM), breakthrough of the basement membrane, and entry into blood vessels. We found that the oriented fibers greatly enhance and facilitate the metastatic cell intravasation process during metastasis. We suggest that a possible “tissue treatment” therapy could be considered, in which the ECM fiber structure orientation in the tumor microenvironment might be altered to minimize the intravasation rate of metastatic cells.
Rational design of a Kv1.3 channel-blocking antibody as a selective immunosuppressant
Authors: Wang Rongsheng E. , Wang Ying , Zhang Yuhan , Gabrelow Chase , Zhang Yong , Chi Victor , Fu Qiangwei , Luo Xiaozhou , Wang Danling , Joseph Sean , Johnson Kristen , Chatterjee Arnab K. , Wright Timothy M. , Nguyen-Tran Vân T. B. , Teijaro John , Theofilopoulos Argyrios N. , Schultz Peter G. , Wang Feng
Published: September 2016

Significance

There is considerable interest in developing immunosuppressants that can specifically target effector memory T cells which are key to the pathogenesis of many inflammatory disorders. The potassium channel Kv1.3 has been found to play an important role in TEMactivation, but not in naive and central memory T cells. It has proven challenging to generate small molecules or antibodies that potently and selectively block Kv1.3 function. We generated antibody fusions by grafting potent Kv1.3 blocking peptides into complementary-determining regions (CDRs) of humanized antibodies, and among those, identified a candidate with high in vitro potency, excellent physiochemical and pharmacologic properties, and in vivo efficacy in a rat model. These novel toxin-antibody fusions have therapeutic potential for a variety of TEM-mediated inflammatory diseases.
O
-fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of
Toxoplasma gondii
Authors: Bandini Giulia , Haserick John R. , Motari Edwin , Ouologuem Dinkorma T. , Lourido Sebastian , Roos David S. , Costello Catherine E. , Robbins Phillips W. , Samuelson John
Published: September 2016

Significance

We describe here the discovery that assemblies of
O
-fucosylated proteins localize to the nuclear membrane of
Toxoplasma gondii
, particularly in proximity to the nuclear pore complexes (NPCs).
O
-fucose is added to Ser and Thr residues found in some of the Phe-Gly (FG) domain-containing proteins that characterize the NPC channel as well as in Ser-rich sequences in many proteins predicted to have roles in transcription, mRNA processing, and cell signaling.
O
-fucosylation of nucleocytosolic proteins has not been described previously in any eukaryote and appears to be unique to
T
.
gondii
and closely related apicomplexans.
A generative model for the behavior of RNA polymerase
Authors: Azofeifa Joseph G , Dowell Robin D
Published: September 2016

Motivation

Transcription by RNA polymerase is a highly dynamic process involving multiple distinct points of regulation. Nascent transcription assays are a relatively new set of high throughput techniques that measure the location of actively engaged RNA polymerase genome wide. Hence, nascent transcription is a rich source of information on the regulation of RNA polymerase activity. To fully dissect this data requires the development of stochastic models that can both deconvolve the stages of polymerase activity and identify significant changes in activity between experiments.

Results

We present a generative, probabilistic model of RNA polymerase that fully describes loading, initiation, elongation and termination. We fit this model genome wide and profile the enzymatic activity of RNA polymerase across various loci and following experimental perturbation. We observe striking correlation of predicted loading events and regulatory chromatin marks. We provide principled statistics that compute probabilities reminiscent of traveler’s and divergent ratios. We finish with a systematic comparison of RNA Polymerase activity at promoter versus non-promoter associated loci.

Availability and Implementation

Transcription Fit (Tfit) is a freely available, open source software package written in C/C ++ that requires GNU compilers 4.7.3 or greater. Tfit is available from GitHub (https://github.com/azofeifa/Tfit).

Supplementary information

Supplementary data are available at Bioinformatics online.
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization
Authors: Vachaspati Pranjal , Warnow Tandy
Published: September 2016

Motivation

The estimation of phylogenetic trees is a major part of many biological dataset analyses, but maximum likelihood approaches are NP-hard and Bayesian MCMC methods do not scale well to even moderate-sized datasets. Supertree methods, which are used to construct trees from trees computed on subsets, are critically important tools for enabling the statistical estimation of phylogenies for large and potentially heterogeneous datasets. Supertree estimation is itself NP-hard, and no current supertree method has sufficient accuracy and scalability to provide good accuracy on the large datasets that supertree methods were designed for, containing thousands of species and many subset trees.

Results

We present FastRFS, a new method based on a dynamic programming method we have developed to find an exact solution to the Robinson-Foulds Supertree problem within a constrained search space. FastRFS has excellent accuracy in terms of criterion scores and topological accuracy of the resultant trees, substantially improving on competing methods on a large collection of biological and simulated data. In addition, FastRFS is extremely fast, finishing in minutes on even very large datasets, and in under an hour on a biological dataset with 2228 species.

Availability and Implementation

FastRFS is available on github at https://github.com/pranjalv123/FastRFS

Supplementary information

Supplementary data are available at Bioinformatics online.
FoldAtlas: a repository for genome-wide RNA structure probing data
Authors: Norris Matthew , Kwok Chun Kit , Cheema Jitender , Hartley Matthew , Morris Richard J , Aviran Sharon , Ding Yiliang
Published: September 2016

Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work.

Availability and Implementation

The FoldAtlas website can be accessed at www.foldatlas.com. Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985.

Supplementary information

Supplementary data are available at Bioinformatics online.
The challenge of measuring magnetic fields in strongly pulsating stars: the case of HD 96446
Authors: Järvinen S. P. , Hubrig S. , Ilyin I. , Schöller M. , Briquet M.
Published: September 2016

Among the early B-type stars, He-rich Bp stars exhibit the strongest large-scale organized magnetic fields with a predominant dipole contribution. The presence of β Cep-like pulsations in the typical magnetic early Bp-type star HD 96446 was announced a few years ago, but the analysis of the magnetic field geometry was hampered by the absence of a reliable rotation period and a sophisticated procedure for accounting for the impact of pulsations on the magnetic field measurements. Using new spectropolarimetric observations and a recently determined rotation period based on an extensive spectroscopic time series, we investigate the magnetic field model parameters of this star under more detailed considerations of the pulsation behaviour of line profiles.
KIC 2831097 – a 2-yr-orbital-period RR Lyrae binary candidate
Authors: Sódor Á. , Skarka M. , Liška J. , Bognár Zs.
Published: September 2016

We report the discovery of a new Kepler first-overtone RR Lyrae pulsator, KIC 2831097. The pulsation shows large, 0.1-d amplitude, systematic phase variations that can be interpreted as light traveltime effect caused by orbital motion in a binary system, superimposed on a linear pulsation-period decrease. The assumed eccentric (e = 0.47) orbit with the period of ≈2 yr is the shortest among the non-eclipsing RR Lyrae binary candidates. The binary model gives the lowest estimate for the mass of the companion of 8.4 M⊙, that places it among black hole candidates. Beside the first-overtone pulsation, numerous additional non-radial pulsation frequencies were also identified. We detected an ≈47-d Blazhko-like irregular light-curve modulation.
X-ray observations of a subhalo associated with the NGC 4839 group infalling toward the Coma cluster
Authors: Sasaki Toru , Matsushita Kyoko , Sato Kosuke , Okabe Nobuhiro
Published: September 2016

We report on Suzaku X-ray observations of the dark subhalo associated with the merging group of NGC 4839 in the Coma cluster. The X-ray image exhibits an elongated tail toward the southwest. The X-ray peak shifts approximately 1′ away from the weak-lensing mass center toward the opposite direction of the Coma cluster center. We investigated the temperature, normalization, pressure, and entropy distributions around the subhalo. Excluding the X-ray tail, the temperature beyond the truncation radius is 8–10 keV, which is twice as high as that of the subhalo and the X-ray tail. The pressure is nearly uniform, excluding the southern part of the subhalo at two times of the truncation radius. We computed the gas mass within the truncation radius and the X-ray tail. While the gas fraction within the truncation radius is about five times smaller than that of regular groups, the gas mass in the subhalo and the X-ray tail to weak-lensing mass ratio is consistent with that of regular groups. Assuming an infall velocity of 2000 km s−1, the ram pressure is 1.4 times greater than the gravitational force per unit area. Assuming the Kelvin–Helmholtz instabilities, the total lost mass is approximately 3 × 1011 M⊙. If this gas had originally been within the truncation radius, the gas mass fraction of the subhalo would have been comparable with those of regular groups before infalling to the Coma cluster.