bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of Lateral Pelvic Lymph‐Node Metastasis in Low Rectal Cancer by Magnetic Resonance Imaging
Authors: Ishibe Atsushi , Ota Mitsuyoshi , Watanabe Jun , Suwa Yusuke , Suzuki Shinsuke , Kanazawa Amane , Watanabe Kazuteru , Ichikawa Yasushi , Kunisaki Chikara , Endo Itaru 
Published: November 2015

AbstractObjectiveThis study was designed to evaluate the diagnostic accuracy of magnetic resonance imaging (MRI) for lateral pelvic lymph‐node metastasis.
PatientsEighty‐four patients with primary lower rectal cancer were examined by MRI and subsequently underwent radical surgery with lateral pelvic lymph‐node dissection, without preoperative treatment. Lateral lymph‐node metastases were assessed preoperatively by MRI, and the results were compared with the histopathological findings. The criterion for lateral lymph‐node metastasis was any recognizable lymph node in the pelvic wall, regardless of diameter.ResultLateral pelvic lymph‐node metastasis was diagnosed on preoperative MRI in 16 patients (19.9 %). The overall patient‐based sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of MRI were 75, 69.1, 36.4, 92.2, and 70.2 %, respectively. When a cut‐off value of 10 mm was used for diagnosis, the corresponding values were 43.8, 98.5, 87.5, 88.1, and 88.1 %, respectively. The mean diameter of metastatic nodes (14.7 mm) was significantly larger than that of negative nodes (5.7 mm; P < 0.01).ConclusionMRI is an effective technique for predicting lateral pelvic node involvement and thus may facilitate preoperative decision‐making in rectal cancer treatment. A cut‐off value of 10 mm is useful for avoiding unnecessary lateral lymph‐node dissection.
Influence of Nonionic Surfactant on Hydrolysis of Vinyl Sulfone Reactive Dye
Authors: Cai Guoqiang , Sun Liangxi , Wu Jindan , Wang Jiping 
Published: November 2015

AbstractNonionic surfactants are widely used in reactive dyeing processes, and the interaction between surfactants and reactive dyes affect the hydrolytic property of reactive dyes. In this study, reactive brilliant blue KN‐R (C.I. reactive blue 19) was employed as a model dye, and fatty alcohol polyoxyethylene ether (AEO‐9) was selected as a model nonionic surfactant. The interaction was first investigated in aqueous solutions by a UV‐spectrophotometry method, then the effect of surfactant concentration on the hydrolytic behavior of KN‐R was studied using high performance liquid chromatography method. Below the critical micelle concentration, the surfactant served as dispersant; the hydrolysis of reactive dye was accelerated. However, when the concentration of surfactant was above its critical micelle concentration, the dye was solubilized into the micellar phase, which was revealed from the changes in absorbance intensity and wavelength of the maximum absorbance. This led to slowed hydrolysis of reactive dye. These findings are useful in understanding the effect of concentration of nonionic surfactant on the hydrolysis of vinyl sulfone reactive dyes.
Fish oil supplemented for 9 months does not improve glycaemic control or insulin sensitivity in subjects with impaired glucose regulation: a parallel randomised controlled trial
Authors: Clark Louise F. , Thivierge M. C. , Kidd Claire A. , McGeoch Susan C. , Abraham Prakash , Pearson Donald W. M. , Horgan Graham W. , Holtrop Grietje , Thies Frank , Lobley Gerald E. 
Published: November 2015

AbstractThe effects of fish oil (FO) supplementation on glycaemic control are unclear, and positive effects may occur only when the phospholipid content of tissue membranes exceeds 14 % asn-3 PUFA. Subjects (n36, thirty-three completed) were paired based on metabolic parameters and allocated into a parallel double-blind randomised trial with one of each pair offered daily either 6 g of FO (3·9 gn-3 PUFA) or 6 g of maize oil (MO) for 9 months. Hyperinsulinaemic–euglycaemic–euaminoacidaemic (HIEGEAA) clamps (with [6,62H2glucose]) were performed at the start and end of the intervention. Endogenous glucose production (EGP) and whole-body protein turnover (WBPT) were each measured after an overnight fast. The primary outcome involved the effect of oil type on insulin sensitivity related to glycaemic control. The secondary outcome involved the effect of oil type on WBPT. Subjects on FO (n16) had increased erythrocyten-3 PUFA concentrations >14 %, whereas subjects on MO (n17) had unalteredn-3 PUFA concentrations at 9 %. Type of oil had no effect on fasting EGP, insulin sensitivity or total glucose disposal during the HIEGEAA clamp. In contrast, under insulin-stimulated conditions, total protein disposal (P=0·007) and endogenous WBPT (P=0·001) were both increased with FO. In an associated pilot study (n4, three completed), althoughn-3 PUFA in erythrocyte membranes increased to >14 % with the FO supplement, the enrichment in muscle membranes remained lower (8 %;P<0·001). In conclusion, long-term supplementation with FO, at amounts near the safety limits set by regulatory authorities in Europe and the USA, did not alter glycaemic control but did have an impact on WBPT.
Torque, chemistry and efficiency in molecular motors: a study of the rotary–chemical coupling in F1-ATPase
Authors: Mukherjee Shayantani , Bora Ram Prasad , Warshel Arieh 
Published: November 2015

AbstractDetailed understanding of the action of biological molecular machines must overcome the challenge of gaining a clear knowledge of the corresponding free-energy landscape. An example for this is the elucidation of the nature of converting chemical energy to torque and work in the rotary molecular motor of F1-ATPase. A major part of the challenge involves understanding the rotary–chemical coupling from a non-phenomenological structure/energy description. Here we focused on using a coarse-grained model of F1-ATPase to generate a structure-based free-energy landscape of the rotary–chemical process of the whole system. In particular, we concentrated on exploring the possible impact of the position of the catalytic dwell on the efficiency and torque generation of the molecular machine. It was found that the experimentally observed torque can be reproduced with landscapes that have different positions for the catalytic dwell on the rotary–chemical surface. Thus, although the catalysis is undeniably required for torque generation, the experimentally observed position of the catalytic dwell at 80° might not have a clear advantage for the force generation by F1-ATPase. This further implies that the rotary–chemical couplings in these biological motors are quite robust and their efficiencies do not depend explicitly on the position of the catalytic dwells. Rather, the specific positioning of the dwells with respect to the rotational angle is a characteristic arising due to the structural construct of the molecular machine and might not bear any clear connection to the thermodynamic efficiency for the system.
Chromatin-remodeling and the initiation of transcription
Authors: Lorch Yahli , Kornberg Roger D. 
Published: November 2015

AbstractThe nucleosome serves as a general gene repressor by the occlusion of regulatory and promoter DNA sequences. Repression is relieved by the SWI/SNF-RSC family of chromatin-remodeling complexes. Research reviewed here has revealed the essential features of the remodeling process.
The nature of chemical innovation: new enzymes by evolution
Authors: Arnold Frances H. 
Published: November 2015

AbstractI describe how we direct the evolution of non-natural enzyme activities, using chemical intuition and information on structure and mechanism to guide us to the most promising reaction/enzyme systems. With synthetic reagents to generate new reactive intermediates and just a few amino acid substitutions to tune the active site, a cytochrome P450 can catalyze a variety of carbene and nitrene transfer reactions. The cyclopropanation, N–H insertion, C–H amination, sulfimidation, and aziridination reactions now demonstrated are all well known in chemical catalysis but have no counterparts in nature. The new enzymes are fully genetically encoded, assemble and function inside of cells, and can be optimized for different substrates, activities, and selectivities. We are learning how to use nature's innovation mechanisms to marry some of the synthetic chemists’ favorite transformations with the exquisite selectivity and tunability of enzymes.
Verified decision procedures for MSO on words based on derivatives of regular expressions
Authors: TRAYTEL DMITRIY , NIPKOW TOBIAS 
Published: November 2015

AbstractMonadic second-order logic on finite words is a decidable yet expressive logic into which many decision problems can be encoded. Since MSO formulas correspond to regular languages, equivalence of MSO formulas can be reduced to the equivalence of some regular structures (e.g., automata). This paper presents a verified functional decision procedure for MSO formulas that is not based on automata but on regular expressions. Functional languages are ideally suited for this task: regular expressions are data types and functions on them are defined by pattern matching and recursion and are verified by structural induction. Decision procedures for regular expression equivalence have been formalized before, usually based on Brzozowski derivatives. Yet, for a straightforward embedding of MSO formulas into regular expressions, an extension of regular expressions with a projection operation is required. We prove total correctness and completeness of an equivalence checker for regular expressions extended in that way. We also define a language-preserving translation of formulas into regular expressions with respect to two different semantics of MSO. Our results have been formalized and verified in the theorem prover Isabelle. Using Isabelle's code generation facility, this yields purely functional, formally verified programs that decide equivalence of MSO formulas.
Design of dual band-notched lamp-shaped antenna with UWB characteristics
Authors: Yadav Swati , Gautam Anil Kumar , Kanaujia Binod Kumar 
Published: November 2015

To restrict electromagnetic interference at WiMAX (3.3–3.7 GHz) and wireless local area network (WLAN) (5.15–5.825 GHz) bands operating within ultra wide bandwidth (UWB) band, a novel design of lamp-shaped UWB microstrip antenna with dual band-notched characteristics is presented. The proposed antenna is composed of a lamp-shaped radiating patch with two rectangular ground planes on both the sides of the radiator with the gap of 0.57 mm. To improve impedance mismatch at middle frequencies, two triangular strips one at each of the ground plane are added; whereas a rectangular slot is etched in the radiating patch to remove impedance mismatch at higher frequencies of the UWB band. Furthermore, an L-shaped slot in the radiator and two L-shaped slots in the ground plane are used to restrict electromagnetic interference (EMI) at WiMAX and WLAN bands, respectively, without affecting the electrical performance of the UWB antenna. Effects of the key parameters on the frequency range of the notched bands are also investigated. The proposed design shows a measured impedance bandwidth of 12.5 GHz (2.7–14.4 GHz), with the two band-notched bands of 3.0–3.9 and 4.9–5.8 GHz. The antenna is suitable to be integrated within the portable UWB devices without EMI interference at WiMAX and WLAN bands.
Mahogunin regulates fusion between amphisomes/MVBs and lysosomes via ubiquitination of TSG101
Authors: Majumder P , Chakrabarti O 
Published: November 2015

AbstractAberrant metabolic forms of the prion protein (PrP), membrane-associated CtmPrP and cytosolic (cyPrP) interact with the cytosolic ubiquitin E3 ligase, Mahogunin Ring Finger-1 (MGRN1) and affect lysosomes. MGRN1 also interacts with and ubiquitinates TSG101, an ESCRT-I protein, involved in endocytosis. We report that MGRN1 modulates macroautophagy. In cultured cells, functional depletion of MGRN1 or overexpression of CtmPrP and cyPrP blocks autophagosome–lysosome fusion, alleviates the autophagic flux and its degradative competence. Concurrently, the degradation of cargo from the endo-lysosomal pathway is also affected. This is significant because catalytic inactivation of MGRN1 alleviates fusion of lysosomes with either autophagosomes (via amphisomes) or late endosomes (either direct or mediated through amphisomes), without drastically perturbing maturation of late endosomes, generation of amphisomes or lysosomal proteolytic activity. The compromised lysosomal fusion events are rescued by overexpression of TSG101 and/or its monoubiquitination in the presence of MGRN1. Thus, for the first time we elucidate that MGRN1 simultaneously modulates both autophagy and heterophagy via ubiquitin-mediated post-translational modification of TSG101.
Mutations in RASA1 and GDF2 identified in patients with clinical features of hereditary hemorrhagic telangiectasia
Authors: Hernandez Felicia , Huether Robert , Carter Lester , Johnston Tami , Thompson Jennifer , Gossage James R , Chao Elizabeth , Elliott Aaron M 
Published: November 2015

AbstractHereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant vascular disorder caused by mutations in ENG, ACVRL1 and SMAD4, which function in regulating the transforming growth factor beta and bone morphogenetic protein signaling pathways. Symptoms of HHT can be present in individuals who test negative for mutations in these three genes indicating other genes may be involved. In this study, we tested for mutations in two genes, RASA1 and GDF2, which were recently reported to be involved in vascular disorders. To determine whether RASA1 and GDF2 have phenotypic overlap with HHT and should be included in diagnostic testing, we developed a next-generation sequencing assay to detect mutations in 93 unrelated individuals who previously tested negative for mutations in ENG, ACVRL1 and SMAD4, but were clinically suspected to have HHT. Pathogenic mutations in RASA1 were identified in two samples (2.15%) and a variant of unknown significance in GDF2 was detected in one sample. All three individuals experienced epistaxis with dermal lesions described in medical records as telangiectases. These results indicate that the inclusion of RASA1 and GDF2 screening in individuals suspected to have HHT will increase the detection rate and aid clinicians in making an accurate diagnosis.
Recombinase-based conditional and reversible gene regulation via XTR alleles
Authors: Robles-Oteiza Camila , Taylor Sarah , Yates Travis , Cicchini Michelle , Lauderback Brian , Cashman Christopher R. , Burds Aurora A. , Winslow Monte M. , Jacks Tyler , Feldser David M. 
Published: November 2015

AbstractSynthetic biological tools that enable precise regulation of gene function within in vivo systems have enormous potential to discern gene function in diverse physiological settings. Here we report the development and characterization of a synthetic gene switch that, when targeted in the mouse germline, enables conditional inactivation, reports gene expression and allows inducible restoration of the targeted gene. Gene inactivation and reporter expression is achieved through Cre-mediated stable inversion of an integrated gene-trap reporter, whereas inducible gene restoration is afforded by Flp-dependent deletion of the inverted gene trap. We validate our approach by targeting the p53 and Rb genes and establishing cell line and in vivo cancer model systems, to study the impact of p53 or Rb inactivation and restoration. We term this allele system XTR, to denote each of the allelic states and the associated expression patterns of the targeted gene: eXpressed (XTR), Trapped (TR) and Restored (R).
Multipole plasmons and their disappearance in few-nanometre silver nanoparticles
Authors: Raza Søren , Kadkhodazadeh Shima , Christensen Thomas , Di Vece Marcel , Wubs Martijn , Mortensen N. Asger , Stenger Nicolas 
Published: November 2015

AbstractElectron energy-loss spectroscopy can be used for detailed spatial and spectral characterization of optical excitations in metal nanoparticles. In previous electron energy-loss experiments on silver nanoparticles with radii smaller than 20 nm, only the dipolar surface plasmon resonance was assumed to play a role. Here, applying electron energy-loss spectroscopy to individual silver nanoparticles encapsulated in silicon nitride, we observe besides the usual dipole resonance an additional surface plasmon resonance corresponding to higher angular momenta for nanoparticle radii as small as 4 nm. We study the radius and electron beam impact position dependence of both resonances separately. For particles smaller than 4 nm in radius the higher-order surface plasmon mode disappears, in agreement with generalized non-local optical response theory, while the dipole resonance blueshift exceeds our theoretical predictions. Unlike in optical spectra, multipole surface plasmons are important in electron energy-loss spectra even of ultrasmall metallic nanoparticles.
Stable ultrathin partially oxidized copper film electrode for highly efficient flexible solar cells
Authors: Zhao Guoqing , Wang Wei , Bae Tae-Sung , Lee Sang-Geul , Mun ChaeWon , Lee Sunghun , Yu Huashun , Lee Gun-Hwan , Song Myungkwan , Yun Jungheum 
Published: November 2015

AbstractAdvances in flexible optoelectronic devices have led to an increasing need for developing highly efficient, low-cost, flexible transparent conducting electrodes. Copper-based electrodes have been unattainable due to the relatively low optical transmission and poor oxidation resistance of copper. Here, we report the synthesis of a completely continuous, smooth copper ultra-thin film via limited copper oxidation with a trace amount of oxygen. The weakly oxidized copper thin film sandwiched between zinc oxide films exhibits good optoelectrical performance (an average transmittance of 83% over the visible spectral range of 400–800 nm and a sheet resistance of 9 Ω sq−1) and strong oxidation resistance. These values surpass those previously reported for copper-based electrodes; further, the record power conversion efficiency of 7.5% makes it clear that the use of an oxidized copper-based transparent electrode on a polymer substrate can provide an effective solution for the fabrication of flexible organic solar cells.
Remote control of self-assembled microswimmers
Authors: Grosjean G. , Lagubeau G. , Darras A. , Hubert M. , Lumay G. , Vandewalle N. 
Published: November 2015

AbstractPhysics governing the locomotion of microorganisms and other microsystems is dominated by viscous damping. An effective swimming strategy involves the non-reciprocal and periodic deformations of the considered body. Here, we show that a magnetocapillary-driven self-assembly, composed of three soft ferromagnetic beads, is able to swim along a liquid-air interface when powered by an external magnetic field. More importantly, we demonstrate that trajectories can be fully controlled, opening ways to explore low Reynolds number swimming. This magnetocapillary system spontaneously forms by self-assembly, allowing miniaturization and other possible applications such as cargo transport or solvent flows.
Screening and Molecular Analysis of Single Circulating Tumor Cells Using Micromagnet Array
Authors: Huang Yu-Yen , Chen Peng , Wu Chun-Hsien , Hoshino Kazunori , Sokolov Konstantin , Lane Nancy , Liu Huaying , Huebschman Michael , Frenkel Eugene , Zhang John X. J. 
Published: November 2015

AbstractImmunomagnetic assay has been developed to detect rare circulating tumor cells (CTCs), which shows clinical significance in cancer diagnosis and prognosis. The generation and fine-tuning of the magnetic field play essential roles in such assay toward effective single-cell-based analyses of target cells. However, the current assay has a limited range of field gradient, potentially leading to aggregation of cells and nanoparticles. Consequently, quenching of the fluorescence signal and mechanical damage to the cells may occur, which lower the system sensitivity and specificity. We develop a micromagnet-integrated microfluidic system for enhanced CTC detection. The ferromagnetic micromagnets, after being magnetized, generate localized magnetic field up to 8-fold stronger than that without the micromagnets and strengthen the interactions between CTCs and the magnetic field. The system is demonstrated with four cancer cell lines with over 97% capture rate, as well as with clinical samples from breast, prostate, lung and colorectal cancer patients. The system captures target CTCs from patient blood samples on a standard glass slide that can be examined using the fluorescence in-situ hybridization method for the single-cell profiling. All cells showed clear hybridization signals, indicating the efficacy of the compact system in providing retrievable cells for molecular studies.
Nano-sized precipitate stability and its controlling factors in a NiAl-strengthened ferritic alloy
Authors: Sun Zhiqian , Song Gian , Ilavsky Jan , Ghosh Gautam , Liaw Peter K. 
Published: November 2015

AbstractCoherent B2-ordered NiAl-type precipitates have been used to reinforce solid-solution body-centered-cubic iron for high-temperature application in fossil-energy power plants. In this study, we investigate the stability of nano-sized precipitates in a NiAl-strengthened ferritic alloy at 700–950 °C using ultra-small angle X-ray scattering and electron microscopies. Here we show that the coarsening kinetics of NiAl-type precipitates is in excellent agreement with the ripening model in multicomponent alloys. We further demonstrate that the interfacial energy between the matrix and NiAl-type precipitates is strongly dependent on differences in the matrix/precipitate compositions. Our results profile the ripening process in multicomponent alloys by illustrating controlling factors of interfacial energy, diffusivities and element partitioning. The study provides guidelines to design and develop high-temperature alloys with stable microstructures for long-term service.
Folic acid protects against arsenic-mediated embryo toxicity by up-regulating the expression of Dvr1
Authors: Ma Yan , Zhang Chen , Gao Xiao-Bo , Luo Hai-Yan , Chen Yang , Li Hui-hua , Ma Xu , Lu Cai-Ling 
Published: November 2015

AbstractAs a nutritional factor, folic acid can prevent cardiac and neural defects during embryo development. Our previous study showed that arsenic impairs embryo development by down-regulating Dvr1/GDF1 expression in zebrafish. Here, we investigated whether folic acid could protect against arsenic-mediated embryo toxicity. We found that folic acid supplementation increases hatching and survival rates, decreases malformation rate and ameliorates abnormal cardiac and neural development of zebrafish embryos exposed to arsenite. Both real-time PCR analysis and whole in-mount hybridization showed that folic acid significantly rescued the decrease in Dvr1 expression caused by arsenite. Subsequently, our data demonstrated that arsenite significantly decreased cell viability and GDF1 mRNA and protein levels in HEK293ET cells, while folic acid reversed these effects. Folic acid attenuated the increase in subcellular reactive oxygen species (ROS) levels and oxidative adaptor p66Shc protein expression in parallel with the changes in GDF1 expression and cell viability. P66Shc knockdown significantly inhibited the production of ROS and the down-regulation of GDF1 induced by arsenite. Our data demonstrated that folic acid supplementation protected against arsenic-mediated embryo toxicity by up-regulating the expression of Dvr1/GDF1 and folic acid enhanced the expression of GDF1 by decreasing p66Shc expression and subcellular ROS levels.