bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantification and Characterization of UVB-Induced Mitochondrial Fragmentation in Normal Primary Human Keratinocytes
Authors: Jugé Romain , Breugnot Josselin , Da Silva Célia , Bordes Sylvie , Closs Brigitte , Aouacheria Abdel
Published: October 2016

UV irradiation is a major environmental factor causing skin dryness, aging and cancer. UVB in particular triggers cumulative DNA damage, oxidative stress and mitochondrial dysfunction. The objective of our study was to provide both qualitative and quantitative analysis of how mitochondria respond to UVB irradiation in normal human epidermal keratinocytes (NHEK) of healthy donors, with the rationale that monitoring mitochondrial shape will give an indication of cell population fitness and enable the screening of bioactive agents with UVB-protective properties. Our results show that NHEK undergo dose-dependent mitochondrial fragmentation after exposure to UVB. In order to obtain a quantitative measure of this phenomenon, we implemented a novel tool for automated quantification of mitochondrial morphology in live cells based on confocal microscopy and computational calculations of mitochondrial shape descriptors. This method was used to substantiate the effects on mitochondrial morphology of UVB irradiation and of knocking-down the mitochondrial fission-mediating GTPase Dynamin-related protein 1 (DRP1). Our data further indicate that all the major mitochondrial dynamic proteins are expressed in NHEK but that their level changes were stronger after mitochondrial uncoupler treatment than following UVB irradiation or DRP1 knock-down. Our system and procedures might be of interest for the identification of cosmetic or dermatologic UVB-protective agents.
Influence of molecular designs on polaronic and vibrational transitions in a conjugated push-pull copolymer
Authors: Cobet Christoph , Gasiorowski Jacek , Menon Reghu , Hingerl Kurt , Schlager Stefanie , White Matthew S. , Neugebauer Helmut , Sariciftci N. Serdar , Stadler Philipp
Published: October 2016

Electron-phonon interactions of free charge-carriers in doped pi-conjugated polymers are conceptually described by 1-dimensional (1D) delocalization. Thereby, polaronic transitions fit the 1D-Froehlich model in quasi-confined chains. However, recent developments in conjugated polymers have diversified the backbones to become elaborate heterocylcic macromolecules. Their complexity makes it difficult to investigate the electron-phonon coupling. In this work we resolve the electron-phonon interactions in the ground and doped state in a complex push-pull polymer. We focus on the polaronic transitions using in-situ spectroscopy to work out the differences between single-unit and push-pull systems to obtain the desired structural- electronic correlations in the doped state. We apply the classic 1D-Froehlich model to generate optical model fits. Interestingly, we find the 1D-approach in push-pull polarons in agreement to the model, pointing at the strong 1D-character and plain electronic structure of the push-pull structure. In contrast, polarons in the single-unit polymer emerge to a multi- dimensional problem difficult to resolve due to their anisotropy. Thus, we report an enhancement of the 1D-character by the push-pull concept in the doped state - an important view in light of the main purpose of push-pull polymers for photovoltaic devices.
mTOR independent regulation of macroautophagy by Leucine Rich Repeat Kinase 2 via Beclin-1
Authors: Manzoni Claudia , Mamais Adamantios , Roosen Dorien A. , Dihanich Sybille , Soutar Marc P. M. , Plun-Favreau Helene , Bandopadhyay Rina , Hardy John , Tooze Sharon A. , Cookson Mark R. , Lewis Patrick A.
Published: October 2016

Leucine rich repeat kinase 2 is a complex enzyme with both kinase and GTPase activities, closely linked to the pathogenesis of several human disorders including Parkinson’s disease, Crohn’s disease, leprosy and cancer. LRRK2 has been implicated in numerous cellular processes; however its physiological function remains unclear. Recent reports suggest that LRRK2 can act to regulate the cellular catabolic process of macroautophagy, although the precise mechanism whereby this occurs has not been identified. To investigate the signalling events through which LRRK2 acts to influence macroautophagy, the mammalian target of rapamycin (mTOR)/Unc-51-like kinase 1 (ULK1) and Beclin-1/phosphatidylinositol 3-kinase (PI3K) pathways were evaluated in astrocytic cell models in the presence and absence of LRRK2 kinase inhibitors. Chemical inhibition of LRRK2 kinase activity resulted in the stimulation of macroautophagy in a non-canonical fashion, independent of mTOR and ULK1, but dependent upon the activation of Beclin 1-containing class III PI3-kinase.
Measuring milk fat content by random laser emission
Authors: Abegão Luis M. G. , Pagani Alessandra A. C. , Zílio Sérgio C. , Alencar Márcio A. R. C. , Rodrigues José J.
Published: October 2016

The luminescence spectra of milk containing rhodamine 6G are shown to exhibit typical signatures of random lasing when excited with 532 nm laser pulses. Experiments carried out on whole and skim forms of two commercial brands of UHT milk, with fat volume concentrations ranging from 0 to 4%, presented lasing threshold values dependent on the fat concentration, suggesting that a random laser technique can be developed to monitor such important parameter.
Islet-like organoids derived from human pluripotent stem cells efficiently function in the glucose responsiveness in vitro and in vivo
Authors: Kim Youngjin , Kim Hyeongseok , Ko Ung Hyun , Oh Youjin , Lim Ajin , Sohn Jong-Woo , Shin Jennifer H. , Kim Hail , Han Yong-Mahn
Published: October 2016

Insulin secretion is elaborately modulated in pancreatic ß cells within islets of three-dimensional (3D) structures. Using human pluripotent stem cells (hPSCs) to develop islet-like structures with insulin-producing ß cells for the treatment of diabetes is challenging. Here, we report that pancreatic islet-like clusters derived from hESCs are functionally capable of glucose-responsive insulin secretion as well as therapeutic effects. Pancreatic hormone-expressing endocrine cells (ECs) were differentiated from hESCs using a step-wise protocol. The hESC-derived ECs expressed pancreatic endocrine hormones, such as insulin, somatostatin, and pancreatic polypeptide. Notably, dissociated ECs autonomously aggregated to form islet-like, 3D structures of consistent sizes (100–150 μm in diameter). These EC clusters (ECCs) enhanced insulin secretion in response to glucose stimulus and potassium channel inhibition in vitro. Furthermore, ß cell-deficient mice transplanted with ECCs survived for more than 40 d while retaining a normal blood glucose level to some extent. The expression of pancreatic endocrine hormones was observed in tissues transplanted with ECCs. In addition, ECCs could be generated from human induced pluripotent stem cells. These results suggest that hPSC-derived, islet-like clusters may be alternative therapeutic cell sources for treating diabetes.
Protein N-glycosylation and N-glycan trimming are required for postembryonic development of the pest beetle Tribolium castaneum
Authors: Walski Tomasz , Van Damme Els J. M. , Smargiasso Nicolas , Christiaens Olivier , De Pauw Edwin , Smagghe Guy
Published: October 2016

In holometabolous insects the transition from larva to adult requires a complete body reorganization and relies on N-glycosylated proteins. N-glycosylation is an important posttranslational modification that influences protein activity but its impact on the metamorphosis has not been studied yet. Here we used the red flour beetle, Tribolium castaneum, to perform a first comprehensive study on the involvement of the protein N-glycosylation pathway in metamorphosis. The transcript levels for genes encoding N-glycan processing enzymes increased during later developmental stages and, in turn, transition from larva to adult coincided with an enrichment of more extensively modified paucimannose glycans, including fucosylated ones. Blockage of N-glycan attachment resulted in larval mortality, while RNAi of α-glucosidases involved in early N-glycan trimming and quality control disrupted the larva to pupa transition. Additionally, simultaneous knockdown of multiple genes responsible for N-glycan processing towards paucimannose structures revealed their novel roles in pupal appendage formation and adult eclosion. Our findings revealed that, next to hormonal control, insect post-embryonic development and metamorphosis depend on protein N-glycan attachment and efficient N-glycan processing. Consequently, disruption of these processes could be an effective new approach for insect control.
In Vivo Near Infrared Virtual Intraoperative Surgical Photoacoustic Optical Coherence Tomography
Authors: Lee Donghyun , Lee Changho , Kim Sehui , Zhou Qifa , Kim Jeehyun , Kim Chulhong
Published: October 2016

Since its first implementation in otolaryngological surgery nearly a century ago, the surgical microscope has improved the accuracy and the safety of microsurgeries. However, the microscope shows only a magnified surface view of the surgical region. To overcome this limitation, either optical coherence tomography (OCT) or photoacoustic microscopy (PAM) has been independently combined with conventional surgical microscope. Herein, we present a near-infrared virtual intraoperative photoacoustic optical coherence tomography (NIR-VISPAOCT) system that combines both PAM and OCT with a conventional surgical microscope. Using optical scattering and absorption, the NIR-VISPAOCT system simultaneously provides surgeons with real-time comprehensive biological information such as tumor margins, tissue structure, and a magnified view of the region of interest. Moreover, by utilizing a miniaturized beam projector, it can back-project 2D cross-sectional PAM and OCT images onto the microscopic view plane. In this way, both microscopic and cross-sectional PAM and OCT images are concurrently displayed on the ocular lens of the microscope. To verify the usability of the NIR-VISPAOCT system, we demonstrate simulated surgeries, including in vivo image-guided melanoma resection surgery and in vivo needle injection of carbon particles into a mouse thigh. The proposed NIR-VISPAOCT system has potential applications in neurosurgery, ophthalmological surgery, and other microsurgeries.
A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation
Authors: Limozin Laurent , Bongrand Pierre , Robert Philippe
Published: October 2016

Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation.
Flexoelectric effect in an in-plane switching (IPS) liquid crystal cell for low-power consumption display devices
Authors: Kim Min Su , Bos Philip J. , Kim Dong-Woo , Yang Deng-Ke , Lee Joong Hee , Lee Seung Hee
Published: October 2016

Technology of displaying static images in portable displays, advertising panels and price tags pursues significant reduction in power consumption and in product cost. Driving at a low-frequency electric field in fringe-field switching (FFS) mode can be one of the efficient ways to save powers of the recent portable devices, but a serious drop of image-quality, so-called image-flickering, has been found in terms of the coupling of elastic deformation to not only quadratic dielectric effect but linear flexoelectric effect. Despite of the urgent requirement of solving the issue, understanding of such a phenomenon is yet vague. Here, we thoroughly analyze and firstly report the flexoelectric effect in in-plane switching (IPS) liquid crystal cell. The effect takes place on the area above electrodes due to splay and bend deformations of nematic liquid crystal along oblique electric fields, so that the obvious spatial shift of the optical transmittance is experimentally observed and is clearly demonstrated based on the relation between direction of flexoelectric polarization and electric field polarity. In addition, we report that the IPS mode has inherent characteristics to solve the image-flickering issue in the low-power consumption display in terms of the physical property of liquid crystal material and the electrode structure.
No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis
Authors: Loley Christina , Alver Maris , Assimes Themistocles L. , Bjonnes Andrew , Goel Anuj , Gustafsson Stefan , Hernesniemi Jussi , Hopewell Jemma C. , Kanoni Stavroula , Kleber Marcus E. , Lau King Wai , Lu Yingchang , Lyytikäinen Leo-Pekka , Nelson Christopher P. , Nikpay Majid , Qu Liming , Salfati Elias , Scholz Markus , Tukiainen Taru , Willenborg Christina , Won Hong-Hee , Zeng Lingyao , Zhang Weihua , Anand Sonia S. , Beutner Frank , Bottinger Erwin P. , Clarke Robert , Dedoussis George , Do Ron , Esko Tõnu , Eskola Markku , Farrall Martin , Gauguier Dominique , Giedraitis Vilmantas , Granger Christopher B. , Hall Alistair S. , Hamsten Anders , Hazen Stanley L. , Huang Jie , Kähönen Mika , Kyriakou Theodosios , Laaksonen Reijo , Lind Lars , Lindgren Cecilia , Magnusson Patrik K. E. , Marouli Eirini , Mihailov Evelin , Morris Andrew P. , Nikus Kjell , Pedersen Nancy , Rallidis Loukianos , Salomaa Veikko , Shah Svati H. , Stewart Alexandre F. R. , Thompson John R. , Zalloua Pierre A. , Chambers John C. , Collins Rory , Ingelsson Erik , Iribarren Carlos , Karhunen Pekka J. , Kooner Jaspal S. , Lehtimäki Terho , Loos Ruth J. F. , März Winfried , McPherson Ruth , Metspalu Andres , Reilly Muredach P. , Ripatti Samuli , Sanghera Dharambir K. , Thiery Joachim , Watkins Hugh , Deloukas Panos , Kathiresan Sekar , Samani Nilesh J. , Schunkert Heribert , Erdmann Jeanette , König Inke R.
Published: October 2016

In recent years, genome-wide association studies have identified 58 independent risk loci for coronary artery disease (CAD) on the autosome. However, due to the sex-specific data structure of the X chromosome, it has been excluded from most of these analyses. While females have 2 copies of chromosome X, males have only one. Also, one of the female X chromosomes may be inactivated. Therefore, special test statistics and quality control procedures are required. Thus, little is known about the role of X-chromosomal variants in CAD. To fill this gap, we conducted a comprehensive X-chromosome-wide meta-analysis including more than 43,000 CAD cases and 58,000 controls from 35 international study cohorts. For quality control, sex-specific filters were used to adequately take the special structure of X-chromosomal data into account. For single study analyses, several logistic regression models were calculated allowing for inactivation of one female X-chromosome, adjusting for sex and investigating interactions between sex and genetic variants. Then, meta-analyses including all 35 studies were conducted using random effects models. None of the investigated models revealed genome-wide significant associations for any variant. Although we analyzed the largest-to-date sample, currently available methods were not able to detect any associations of X-chromosomal variants with CAD.
Role of Mir-155 in Controlling HIF-1α Level and Promoting Endothelial Cell Maturation
Authors: Yang Deguang , Wang Jinhong , Xiao Meng , Zhou Tao , Shi Xu
Published: October 2016

Stem-cell-based therapy for cardiovascular disease, especially ischemic heart disease (IHD), is a promising approach to facilitating neovascularization through the migration of stem cells to the ischemic site and their subsequent differentiation into endothelial cells (ECs). Hypoxia is a chief feature of IHD and the stem cell niche. However, whether hypoxia promotes stem cell differentiation into ECs or causes them to retain their stemness is controversial. Here, the differentiation of pluripotent stem cells (iPSCs) into endothelial cells (ECs) was induced under hypoxia. Though the angiogenic capability and angiogenesis-related autocrine/paracrine factors of the ECs were improved under hypoxia, the level of hypoxia inducible factor 1α (HIF-1α) was nonetheless found to be restricted along with the EC differentiation. The down-regulation of HIF-1α was found to have been caused by VEGF-induced microRNA-155 (miR-155). Moreover, miR-155 was also found to enhance the angiogenic capability of induced ECs by targeting E2F2 transcription factor. Hence, miR-155 not only contributes to controlling HIF-1α expression under hypoxia but also promotes angiogenesis, which is a key feature of mature ECs. Revealing the real role of hypoxia and clarifying the function of miR-155 in EC differentiation may facilitate improvement of angiogenic gene- and stem-cell-based therapies for ischemic heart disease.
Emerging fields in fingermark (meta)detection – a critical review
Authors: Bécue Andy
Published: October 2016

Nanoparticles, chemical imaging and immunodetection applied to fingermarks are critically reviewed in this paper. For each topic, forensic and analytical considerations are assessed in regards with two main purposes: detection and metadetection. Expectations in terms of research are also proposed.
The combined action of methanolysis and heterogeneous photocatalysis in the decomposition of chemical warfare agents
Authors: Petrea Nicoleta , Petre Răzvan , Epure Gabriel , Şomoghi Vasile , Tănase Liviu C. , Teodorescu Cristian M. , Neaţu Ştefan
Published: October 2016

The combination of methanolysis and photocatalysis can be used for the decomposition of CWA. Herein, we present such a catalytic system, which is able to perform efficient nerve agent decomposition in just 1 minute.
Oligo(aryl-triazole)s CH⋯Cl−interactions guide chloride efficient and selective transmembrane transport
Authors: Chen Sujun , Zhang Sitong , Bao Chunyan , Wang Chenxi , Lin Qiuning , Zhu Linyong
Published: October 2016

Using specific C–H⋯Cl−interactions, oligo(aryl-triazole) based transporters realized efficient/selective Cl−transmembrane transport by adjusting their molecular lipophilicity and anion affinity.
Control of morphology and defect density in zinc oxide for improved dye-sensitized solar cells
Authors: Kim Seul Ah , Abbas Muhammad Awais , Lee Lanlee , Kang Byungwuk , Kim Hahkjoon , Bang Jin Ho
Published: October 2016

The surface characteristics of the ZnO photoelectrode in dye-sensitized solar cells are elucidated by in-depth electrochemical analyses including open-circuit voltage decay measurements and electrochemical impedance spectroscopy.
1-(3,5-Dinitro-1H-pyrazol-4-yl)-3-nitro-1H-1,2,4-triazol-5-amine (HCPT) and its energetic salts: highly thermally stable energetic materials with high-performance
Authors: Li Chuan , Zhang Man , Chen Qishan , Li Yingying , Gao Huiqi , Fu Wei , Zhou Zhiming
Published: October 2016

A new C–N linked heterocoupled energetic compound and its energetic salts have been prepared as heat-resistant energetic materials.
Carbohydrate receptors combining both a macrocyclic building block and flexible side arms as recognition units: binding properties of compounds with CH2OH groups as side arms
Authors: Amrhein Felix , Lippe Jan , Mazik Monika
Published: October 2016

The potential of compounds combining both a macrocyclic building block and two hydroxyl-bearing side arms to act as carbohydrate receptors was studied.
Revisiting the mechanistic origins of Thiele's ester dimerization: probing the reliability of predictive models for cycloadditions
Authors: Chen Jun , Wulff Jeremy E.
Published: October 2016

In considering the full range of outcomes for the Thiele ester synthesis, we find that radical stabilization arguments are more effective than frontier molecular orbital methods at predicting the outcome of the Diels–Alder dimerization.
Shape-memory and self-healing polyurethanes based on cyclic poly(ε-caprolactone)
Authors: Chen Wei , Zhou Yanyan , Li Ying , Sun Jun , Pan Xiangqiang , Yu Qian , Zhou Nianchen , Zhang Zhengbiao , Zhu Xiulin
Published: October 2016

This work provides an unprecedented example for the exploration of the cyclic topology effects on the shape memory performance of bulk polyurethane materials, providing a novel angle to elucidate the structure–property relationship of polymeric materials.
Macrocyclization of N,N′-propylenebis(3-formyl-5-tert-butylsalicylaldimine): a ratiometric fluorescence chemodosimeter for ZnII
Authors: Das Sudhanshu , Adhikary Jaydeep , Chakraborty Prateeti , Chakraborty Tonmoy , Das Debasis
Published: October 2016

Side off compartmental ligandN,N′-propylenebis(3-formyl-5-tert-butylsalicylaldimine) is used as a ratiometric fluorescence chemodosimeter for the selective detection of ZnIIions.
One-pot synthesis of CuFeO2 nanoparticles capped with glycerol and proteomic analysis of their nanocytotoxicity against fungi
Authors: Abdelhamid Hani Nasser , Kumaran Sekar , Wu Hui-Fen
Published: October 2016

One-pot synthesis of cuprous ferrite (CuFeO2) nanoparticles modified with glycerol (glycerol@CuFeO2 NPs) using oligol and reducing agent was reported.
Compatibility studies between an amphiphilic pH-sensitive polymer and hydrophobic drug using multiscale simulations
Authors: Wang Yan , Ren Jia Wei , Zhang Can Yang , Chan He Meng , Wu Zhi Min , Guo Xin Dong
Published: October 2016

Dissipative particle dynamics simulations are integrated to investigate the morphologies of drug-loaded micelles and the drug distributions inside the micelles at different pH conditions.
Hematite decorated multi-walled carbon nanotubes (α-Fe2O3/MWCNTs) as sorbents for Cu(ii) and Cr(vi): comparison of hybrid sorbent performance to its nanomaterial building blocks
Authors: Verdugo Edgard M. , Xie Yang , Baltrusaitis Jonas , Cwiertny David M.
Published: October 2016

Hybrid nanostructured sorbents were fabricatedviathe deposition and growth of hematite nanoparticles on carbon nanotubes, and fundamental aspects of their performance toward common heavy metal pollutants were evaluated.
Selective colonization mechanism of Shewanella putrefaciens in dyeing wastewater outlets
Authors: Xu Jiajie , He Weina , Li Yanyan , Zhang DiJun , Zhou Jun , Zhang Chundan , Li Ye , Wang Rixin , Su Xiurong
Published: October 2016

The responses ofS. putrefaciensto dyeing wastewater have been investigated using differential proteomics, metabolomics, and real-time fluorescent quantitative PCR techniques.
Negatively charged gold nanoparticles as a dexamethasone carrier: stability in biological media and bioactivity assessment in vitro
Authors: Rossi A. , Donati S. , Fontana L. , Porcaro F. , Battocchio C. , Proietti E. , Venditti I. , Bracci L. , Fratoddi I.
Published: October 2016

AuNP and AuNP/DXM stability and drug release kinetics in different biological media.
Influence of a reagents addition strategy on the Fenton oxidation of rhodamine B: control of the competitive reaction of ·OH
Authors: Zhou Wei , Zhao Haiqian , Gao Jihui , Meng Xiaoxiao , Wu Shaohua , Qin Yukun
Published: October 2016

Microlevel competitive reactions of ·OH could be regulated by applying a macrolevel addition strategy of the Fenton reagents.
Combined pretreatment of lignocellulosic biomass by solid base (calcined Na2SiO3) and ionic liquid for enhanced enzymatic saccharification
Authors: Sun Xiyan , Sun Xitong , Zhang Fan
Published: October 2016

Combined pretreatment of lignocellulose by [BMIm]Cl and solid base Na2SiO3 enhances the enzymatic hydrolysis of willow and soybean straw.
Characterization of the laccase-mediated oligomerization of 4-hydroxybenzoic acid
Authors: Slagman Sjoerd , Escorihuela Jorge , Zuilhof Han , Franssen Maurice C. R.
Published: October 2016

The curious (lac)case of four dimers – how minor 4-hydroxybenzoic acid dimers can be of major importance.
The synthesis and electrical properties of hybrid gel electrolytes derived from Keggin-type heteropoly acids and 3-(pyridin-1-ium-1-yl)propane-1-sulfonate (PyPs)
Authors: Narayanan Sumaletha , Tong Xia , Thangadurai Venkataraman
Published: October 2016

Cyclic voltammetry of PyPs–H3PWMo at room temperature between −4 and +4 V vs. Ag/AgCl at a 10 mV s−1 scan rate and comparison of electrical conductivity of PyPs–H3PWMo with other known promising proton conductors.
Multicomponent synthesis of hydrazino depsipeptides
Authors: Suć Josipa , Barić Danijela , Jerić Ivanka
Published: October 2016

Hydrazino depsipeptides, a new class of backbone extended peptidomimetics were prepared by the Passerini reaction of α-hydrazino acids, carbonyl compounds and isocyanides.
Fe3O4@P(DVB/MAA)/Pd composite microspheres: preparation and catalytic degradation performance
Authors: Zhang Baoliang , Wang Jiqi , Chen Junjie , Li Hengyang , Wang Hai , Zhang Hepeng
Published: October 2016

Fe3O4@P(DVB/MAA)/Pd composite microspheres were synthesized with a combination of coating and loading processes using Fe3O4 nanoparticles as a core.
Angular-dependent magnetism in Co(001) single-crystal nanowires: capturing the vortex nucleation fields
Authors: Montazer A. H. , Ramazani A. , Almasi Kashi M. , Zavašnik J.
Published: October 2016

The analytical predictions on angular dependence of vortex nucleation field are realized in a weakly interacting Co(001) single-crystal nanowire system.
Adipose inflammation at the heart of vascular disease
Authors: Autieri Michael V.
Published: October 2016

Visceral adipose tissue is a primary site of chronic inflammation in obesity and may contribute to systemic inflammation and development of atherosclerotic vascular disease. Few studies identify molecular mechanisms and secretory pathways which mediate this process. In this edition of Clinical Science, Kwok et al. utilize a transgenic mouse in which dominant-negative c-Jun NH2 terminal kinase (dnJNK) expression is restricted to adipose tissue to implicate JNK-driven expression of adipocyte fatty acid binding protein (A-FABP) in visceral adipose tissue as a key secretory pathway to exacerbate development of atherosclerosis in ApoE-/- mice. They further demonstrate that ApoE-/- mice transplanted with visceral adipose tissue in which JNK has been inactivated display less systemic inflammation and develop significantly less atherosclerosis compared with control mice. Together, the findings of the present study reinforce our understanding of visceral adipose tissue as a secretory organ and the importance of the JNK/A-FABP pathway in mediating adipose vascular cross-talk and exacerbation of atherosclerosis.
Longitudinal Effects on Early Adolescent Language: A Twin Study
Authors: Harlaar Nicole , DeThorne Laura Segebart , Smith Jamie Mahurin , Betancourt Mariana Aparicio , Petrill Stephen A.
Published: October 2016

Purpose

We evaluated genetic and environmental contributions to individual differences in language skills during early adolescence, measured by both language sampling and standardized tests, and examined the extent to which these genetic and environmental effects are stable across time.

Method

We used structural equation modeling on latent factors to estimate additive genetic, shared environmental, and nonshared environmental effects on variance in standardized language skills (i.e., Formal Language) and productive language-sample measures (i.e., Productive Language) in a sample of 527 twins across 3 time points (mean ages 10–12 years).

Results

Individual differences in the Formal Language factor were influenced primarily by genetic factors at each age, whereas individual differences in the Productive Language factor were primarily due to nonshared environmental influences. For the Formal Language factor, the stability of genetic effects was high across all 3 time points. For the Productive Language factor, nonshared environmental effects showed low but statistically significant stability across adjacent time points.

Conclusions

The etiology of language outcomes may differ substantially depending on assessment context. In addition, the potential mechanisms for nonshared environmental influences on language development warrant further investigation.

Supplemental Material

https://doi.org/10.23641/asha.14963922
Response measurement by laser Doppler vibrometry in vibration qualification tests with non-Gaussian random excitation
Authors: Troncossi M. , Di Sante R. , Rivola A.
Published: October 2016

In the field of vibration qualification testing, random excitations are typically imposed on the tested system in terms of a power spectral density (PSD) profile. This is the one of the most popular ways to control the shaker or slip table for durability tests. However, these excitations (and the corresponding system responses) exhibit a Gaussian probability distribution, whereas not all real-life excitations are Gaussian, causing the response to be also non-Gaussian. In order to introduce non-Gaussian peaks, a further parameter, i.e., kurtosis, has to be controlled in addition to the PSD. However, depending on the specimen behaviour and input signal characteristics, the use of non-Gaussian excitations with high kurtosis and a given PSD does not automatically imply a non-Gaussian stress response. For an experimental investigation of these coupled features, suitable measurement methods need to be developed in order to estimate the stress amplitude response at critical failure locations and consequently evaluate the input signals most representative for real-life, non-Gaussian excitations. In this paper, a simple test rig with a notched cantilevered specimen was developed to measure the response and examine the kurtosis values in the case of stationary Gaussian, stationary non-Gaussian, and burst non-Gaussian excitation signals. The laser Doppler vibrometry technique was used in this type of test for the first time, in order to estimate the specimen stress amplitude response as proportional to the differential displacement measured at the notch section ends. A method based on the use of measurements using accelerometers to correct for the occasional signal dropouts occurring during the experiment is described. The results demonstrate the ability of the test procedure to evaluate the output signal features and therefore to select the most appropriate input signal for the fatigue test.
Experimental and computational study of shielding effectiveness of polycarbonate carbon nanocomposites
Authors: Karimi Pouyan , Ostoja-Starzewski Martin , Jasiuk Iwona
Published: October 2016

The electrical and electromagnetic interference shielding effectiveness (EMI SE) properties of composites with a polycarbonate matrix and varying amounts of three different types of carbon fillers (carbon black, carbon nanotubes, and graphene nanoplatelets) are analyzed experimentally and theoretically over the 8.5–12 GHz frequency range. A finite element model is also used to study the EMI shielding mechanisms. The theoretical study predicts that the carbon fillers' concentration, sample thickness, incident angle, polarization type, and frequency are the main parameters that have effect on shielding effectiveness of a sample that is confirmed by the experimental and simulation results. Permittivity and related alternating current (AC) conductivity measurements in the above mentioned frequency range are presented for these three types of composites, providing an appropriate way to design a shield. Experimental, theoretical and simulation results indicate that both permittivity and conductivity have significant effects on the SE. It is found that the electrical conductivity, which itself needs a percolating (connected) path, is not the only criterion for shielding and that the connectivity of fillers (and, hence, higher conductivity) does not necessarily lead to a higher SE.
Thermal stability of nonmagnetic Cd and In impurities in Fe3O4
Authors: Sato W. , Ida T. , Komatsuda S. , Fujisawa T. , Takenaka S. , Ohkubo Y.
Published: October 2016

Magnetite (Fe3O4) was doped with radioactive 111mCd and 111In ions as impurities, and their residence sites and thermal stability were investigated by means of time-differential perturbed angular correlation (TDPAC) spectroscopy. Well-defined TDPAC spectra unequivocally show their sites: Cd ions are stably located only in the tetrahedral A site in all the temperature range of the present observation (77 K–873 K); In ions also specifically occupy the A site at low temperature, but at high temperature part of them select the B site in a reversible fashion. The energy difference between the A and B sites for the accommodation of In was experimentally determined to be 0.119 (9) eV by assuming a Boltzmann distribution for the populations of the 111In probe in the respective sites. The element-dependent thermal stabilities observed for Cd and In were well corroborated by density functional theory calculations. The successful observation of thermally activated site-to-site displacement of impurity In ions in Fe3O4 is reported.
Influence of static magnetic field strength on the temperature resolution of a magnetic nanoparticle thermometer
Authors: Zhong Jing , Dieckhoff Jan , Schilling Meinhard , Ludwig Frank
Published: October 2016

This paper investigates the influence of dc magnetic field strength on the resolution of a magnetic nanoparticle (MNP) thermometer, which employs the fundamental f0 and 2f0 harmonics of the MNP magnetization induced by ac and superimposed dc magnetic fields. In ac and parallel dc magnetic fields, the strength of dc magnetic field modulates the harmonics of the MNP magnetization, which affects their temperature sensitivities and measurement signal-to-noise ratios (SNRs). A temperature-adjustable fluxgate-based magnetic particle spectrometer was used to measure the spectra of the MNP magnetization at different temperatures. To determine the temperature, the amplitudes of the measured f0 and 2f0 harmonics were modeled based on the static Langevin function. AC susceptibility measurements on a MNP sample demonstrate the applicability of the static Langevin function for the description of the MNP magnetization spectra at a low frequency ac magnetic field without taking into account the MNP dynamics. Our simulations and experiments show that with increasing dc magnetic field from 0.2 mT to 2.0 mT, both the amplitude of the 2f0 harmonic and the temperature sensitivity of the amplitude ratio of the 2f0 to f0 harmonics increase by a factor of about 10 in an ac magnetic field with a frequency of 70 Hz and an amplitude of 1 mT. Concomitantly, the SNR of the 2f0 harmonic significantly increases by about 20 dB. Consequently, the temperature resolution of the MNP thermometer is improved from 1.97 K to 0.26 K.
Modeling of the refractive index and composition of luminescent nanometric chlorinated-silicon nitride films with embedded Si-quantum dots
Authors: Rodríguez-Gómez A. , Escobar-Alarcón L. , Serna R. , Cabello F. , Haro-Poniatowski E. , García-Valenzuela A. , Alonso J. C.
Published: October 2016

The refractive index of nanometric (<100 nm) chlorinated-silicon nitride films with embedded silicon quantum dots, prepared by remote plasma enhanced chemical vapor deposition was investigated by spectroscopic ellipsometry. The complex refractive indexes and thicknesses of the films were obtained from the ellipsometric measurements using the Cauchy model. The chemical composition of the bulk of the films, including the hydrogen, chlorine, and oxygen content, was measured by elastic forward analysis (EFA) and X-ray photoelectron spectroscopy (XPS). The EFA and XPS results indicate that the films are composed of nearly stoichiometric silicon nitride (Si3N4) with different amounts of hydrogen, chlorine, and oxygen, and that their top surface is oxidized. Based on the composition results the refractive index of the films was fitted using the effective medium approximation considering the system: Si substrate + Si3N4 + Si + voids + top ultrathin oxidized surface layer.
Dwell time effects on high coercivity CoFe2O4 thin films deposited by the solution processing
Authors: Tang Xianwu , Jin Linghua , Chen Fangchu , Wei Renhuai , Yang Jie , Dai Jianming , Song Wenhai , Zhu Xuebin , Sun Yuping
Published: October 2016

High room temperature coercivity CoFe2O4 (CFO) thin films are desirable in view of many applications, which is seldom achieved over 3 kOe in solution deposited CFO thin films. Herein, grain growth kinetic is investigated in the solution derived CFO thin films with coercivity larger than 4 kOe, showing a relaxation mechanism. The coercivity and magnetization increase initially and then decrease with increasing dwell time. The high coercivity is originated mainly from the critical grain size and the growth strain induced by the small crystallites and poorly developed grains. The results will provide a route to fabricate larger-area CFO thin films with high coercivity on silicon wafers by low-cost solution processing.
Radiative recombination mechanisms in polar and non-polar InGaN/GaN quantum well LED structures
Authors: Badcock T. J. , Ali M. , Zhu T. , Pristovsek M. , Oliver R. A. , Shields A. J.
Published: October 2016

We study the photoluminescence internal quantum efficiency (IQE) and recombination dynamics in a pair of polar and non-polar InGaN/GaN quantum well (QW) light-emitting diode (LED) structures as a function of excess carrier density and temperature. In the polar LED at 293 K, the variation of radiative and non-radiative lifetimes is well described by a modified ABC type model which accounts for the background carrier concentration in the QWs due to unintentional doping. As the temperature is reduced, the sensitivity of the radiative lifetime to excess carrier density becomes progressively weaker. We attribute this behaviour to the reduced mobility of the localised electrons and holes at low temperatures, resulting in a more monomolecular like radiative process. Thus we propose that in polar QWs, the degree of carrier localisation determines the sensitivity of the radiative lifetime to the excess carrier density. In the non-polar LED, the radiative lifetime is independent of excitation density at room temperature, consistent with a wholly excitonic recombination mechanism. These findings have significance for the interpretation of LED efficiency data within the context of the ABC recombination model.
Expert Game experiment predicts emergence of trust in professional communication networks
Authors: Bendtsen Kristian Moss , Uekermann Florian , Haerter Jan O.
Published: October 2016

Significance

Social capital can be seen as the economic benefit obtained from preferential treatment between members of a group and has drawn attention because of its ability to increase productivity in modern organizations. However, little is known about how trust dynamically forms between individuals in a competitive environment. We propose the Expert Game played by a group of humans. By constraining available communication capacity, individuals must work under time constraints and gain access to a desired expert by means of communication. Monetary rewards are only given for successful completion of the task. As the game is repeated, our experiments and simulations show how humans develop preference toward others and how social capital is produced. We thereby quantify economic utility of trust.
Backtracked and paused transcription initiation intermediate of
Escherichia coli
RNA polymerase
Authors: Lerner Eitan , Chung SangYoon , Allen Benjamin L. , Wang Shuang , Lee Jookyung , Lu Shijia W. , Grimaud Logan W. , Ingargiola Antonino , Michalet Xavier , Alhadid Yazan , Borukhov Sergei , Strick Terence R. , Taatjes Dylan J. , Weiss Shimon
Published: October 2016

Significance

Transcription initiation by RNA polymerase (RNAP) is a highly regulated rate-limiting step in many genes and involves numerous intermediate states that remain incompletely understood. Here, we report the characterization of a previously hypothesized slow initiation pathway involving RNAP backtracking and pausing. This backtracked and paused state is observed when all nucleoside triphosphates (NTPs) are present at physiologically relevant concentrations, but becomes more prevalent with unbalanced NTP levels, which may occur in vivo under conditions of metabolic stress. Pausing and backtracking in initiation may play an important role in regulating RNAP transcription. Moreover, similar RNA backtracked states may contribute to promoter-proximal pausing among eukaryotic RNA polymerase II enzymes.
Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array
Authors: Stranges P. Benjamin , Palla Mirkó , Kalachikov Sergey , Nivala Jeff , Dorwart Michael , Trans Andrew , Kumar Shiv , Porel Mintu , Chien Minchen , Tao Chuanjuan , Morozova Irina , Li Zengmin , Shi Shundi , Aberra Aman , Arnold Cleoma , Yang Alexander , Aguirre Anne , Harada Eric T. , Korenblum Daniel , Pollard James , Bhat Ashwini , Gremyachinskiy Dmitriy , Bibillo Arek , Chen Roger , Davis Randy , Russo James J. , Fuller Carl W. , Roever Stefan , Ju Jingyue , Church George M.
Published: October 2016

Significance

DNA sequencing has been dramatically expanding its scope in basic life science research and clinical medicine. Recently, a set of polymer-tagged nucleotides were shown to be viable substrates for replication and electronically detectable in a nanopore. Here, we describe the design and characterization of a DNA polymerase–nanopore protein construct on an integrated chip. This system incorporates all four tagged nucleotides and distinguishes single–tagged-nucleotide addition in real time. Coupling protein catalysis and nanopore-based detection to an electrode array could provide the foundation of a highly scalable, single-molecule, electronic DNA-sequencing platform.
miR-30 functions as an oncomiR in gastric cancer cells through regulation of P53-mediated mitochondrial apoptotic pathway
Authors: Wang Jianjun , Jiao Yang , Cui Lunmeng , Jiang Lili
Published: October 2016

The present study was designed to investigate the role of miR-30 in the development of Gastric cancer (GC). miR-30 expression was increased in GC tissues and cell lines. Downregulation of miR-30 inhibited cell proliferation and promoted apoptosis in HGC-27 cells. Upregulation of miR-30 enhanced the proliferation and inhibited apoptosis. P53 expression was decreased in GC tissues. P53 expression was correlated with miR-30 expression. Downregulation of miR-30 increased P53 expression. Knockdown of P53 inhibited miR-30-inhibitor-induced suppression of cell proliferation and increase of apoptosis. Downregulation of miR-30 increased ROS generation which was inhibited by shP53. miR-30 inhibitors induced a decrease in mitochondrial oxygen consumption, cytoplasmic release of cytochrome c, and activation of Caspase 3 and 9, activating mitochondrial apoptotic pathway. Downregulation of P53 and N-acetyl-cysteine suppressed miR-30 inhibitors-activated mitochondrial dysfunction and apoptotic events. In conclusion, we identified that miR-30 functioned as a potential oncomiR through P53/ROS-mediated regulation of mitochondrial apoptotic pathway.
RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications
Authors: Alkan Ferhat , Erten Cesim
Published: October 2016

Motivation

Analysis of protein–protein interaction (PPI) networks provides invaluable insight into several systems biology problems. High-throughput experimental techniques together with computational methods provide large-scale PPI networks. However, a major issue with these networks is their erroneous nature; they contain false-positive interactions and usually many more false-negatives. Recently, several computational methods have been proposed for network reconstruction based on topology, where given an input PPI network the goal is to reconstruct the network by identifying false-positives/-negatives as correctly as possible.

Results

We observe that the existing topology-based network reconstruction algorithms suffer several shortcomings. An important issue is regarding the scalability of their computational requirements, especially in terms of execution times, with the network sizes. They have only been tested on small-scale networks thus far and when applied on large-scale networks of popular PPI databases, the executions require unreasonable amounts of time, or may even crash without producing any output for some instances even after several months of execution. We provide an algorithm, RedNemo, for the topology-based network reconstruction problem. It provides more accurate networks than the alternatives as far as biological qualities measured in terms of most metrics based on gene ontology annotations. The recovery of a high-confidence network modified via random edge removals and rewirings is also better with RedNemo than with the alternatives under most of the experimented removal/rewiring ratios. Furthermore, through extensive tests on databases of varying sizes, we show that RedNemo achieves these results with much better running time performances.

Availability and Implementation

Supplementary material including source code, useful scripts, experimental data and the results are available at http://webprs.khas.edu.tr/~cesim/RedNemo.tar.gz

Supplementary information

Supplementary data are available at Bioinformatics online.
Leveraging modern DNA assembly techniques for rapid, markerless genome modification
Authors: Tikh Ilya B , Samuelson James C
Published: October 2016

The ability to alter the genomic material of a prokaryotic cell is necessary for experiments designed to define the biology of the organism. In addition, the production of biomolecules may be significantly improved by application of engineered prokaryotic host cells. Furthermore, in the age of synthetic biology, speed and efficiency are key factors when choosing a method for genome alteration. To address these needs, we have developed a method for modification of the Escherichia coli genome named FAST-GE for Fast Assembly-mediated Scarless Targeted Genome Editing. Traditional cloning steps such as plasmid transformation, propagation and isolation were eliminated. Instead, we developed a DNA assembly-based approach for generating scarless strain modifications, which may include point mutations, deletions and gene replacements, within 48 h after the receipt of polymerase chain reaction primers. The protocol uses established, but optimized, genome modification components such as I-SceI endonuclease to improve recombination efficiency and SacB as a counter-selection mechanism. All DNA-encoded components are assembled into a single allele-exchange vector named pDEL. We were able to rapidly modify the genomes of both E. coli B and K-12 strains with high efficiency. In principle, the method may be applied to other prokaryotic organisms capable of circular dsDNA uptake and homologous recombination.