bluuebunny/crossref_metadata_2025 huggingface dataset:
Pathways on demand: automated reconstruction of human signaling networks
Authors: Ritz Anna , Poirel Christopher L , Tegge Allison N , Sharp Nicholas , Simmons Kelsey , Powell Allison , Kale Shiv D , Murali TM
Published: March 2016

Signaling pathways are a cornerstone of systems biology. Several databases store high-quality representations of these pathways that are amenable for automated analyses. Despite painstaking and manual curation, these databases remain incomplete. We present PATHLINKER, a new computational method to reconstruct the interactions in a signaling pathway of interest. PATHLINKER efficiently computes multiple short paths from the receptors to transcriptional regulators (TRs) in a pathway within a background protein interaction network. We use PATHLINKER to accurately reconstruct a comprehensive set of signaling pathways from the NetPath and KEGG databases. We show that PATHLINKER has higher precision and recall than several state-of-the-art algorithms, while also ensuring that the resulting network connects receptor proteins to TRs. PATHLINKER’s reconstruction of the Wnt pathway identified CFTR, an ABC class chloride ion channel transporter, as a novel intermediary that facilitates the signaling of Ryk to Dab2, which are known components of Wnt/β-catenin signaling. In HEK293 cells, we show that the Ryk–CFTR–Dab2 path is a novel amplifier of β-catenin signaling specifically in response to Wnt 1, 2, 3, and 3a of the 11 Wnts tested. PATHLINKER captures the structure of signaling pathways as represented in pathway databases better than existing methods. PATHLINKER’s success in reconstructing pathways from NetPath and KEGG databases point to its applicability for complementing manual curation of these databases. PATHLINKER may serve as a promising approach for prioritizing proteins and interactions for experimental study, as illustrated by its discovery of a novel pathway in Wnt/β-catenin signaling. Our supplementary website at http://bioinformatics.cs.vt.edu/~murali/supplements/2016-sys-bio-applications-pathlinker/ provides links to the PATHLINKER software, input datasets, PATHLINKER reconstructions of NetPath pathways, and links to interactive visualizations of these reconstructions on GraphSpace.
Effects of local structure of Ce3+ ions on luminescent properties of Y3Al5O12:Ce nanoparticles
Authors: He Xiaowu , Liu Xiaofang , Li Rongfeng , Yang Bai , Yu Kaili , Zeng Min , Yu Ronghai
Published: March 2016

Ce3+-doped yttrium aluminum garnet (YAG:Ce) nanocrystals were successfully synthesized via a facile sol-gel method. Multiple characterization techniques were employed to study the structure, morphology, composition and photoluminescence properties of YAG:Ce nanophosphors. The YAG:Ce0.0055 sintered at 1030 °C exhibited a typical 5d1-4f1 emission band with the maximum peak located at 525 nm, and owned a short fluorescence lifetime τ1 (~28 ns) and a long fluorescence lifetime τ2 (~94 ns). Calcination temperature and Ce3+ doping concentration have significant effects on the photoluminescence properties of the YAG:Ce nanophosphors. The emission intensity was enhanced as the calcination temperature increased from 830 to 1030 °C, but decreased dramatically with the increase of Ce3+ doping concentration from 0.55 to 5.50 at.% due to the concentration quenching. By optimizing the synthesized condition, the strongest photoluminescence emission intensity was achieved at 1030 °C with Ce3+ concentration of 0.55 at.%.
Intranasal Delivery of Recombinant AAV Containing BDNF Fused with HA2TAT: a Potential Promising Therapy Strategy for Major Depressive Disorder
Authors: Ma Xian-cang , Liu Peng , Zhang Xiao-ling , Jiang Wen-hui , Jia Min , Wang Cai-xia , Dong Ying-ying , Dang Yong-hui , Gao Cheng-ge
Published: March 2016

Depression is a disturbing psychiatric disease with unsatisfied therapy. Not all patients are sensitive to anti-depressants currently in use, side-effects are unavoidable during therapy and the cases with effectiveness are always accompanied with delayed onset of clinical efficacy. Delivering brain-derived neurotrophic factor (BDNF) to brain seems to be a promising therapy. However, a better approach to delivery is still rudimentary. The purpose of our present work is to look for a rapid-onset and long-lasting therapeutic strategy for major depressive disorder (MDD) by effectively delivering BDNF to brain. BDNF, fused with cell-penetrating peptides (TAT and HA2), was packaged in adenovirus associated virus (AAV) to construct the BDNF-HA2TAT/AAV for intranasally delivering BDNF to central nervous system (CNS) via nose-brain pathway. Intranasal administration of BDNF-HA2TAT/AAV to normal mice displayed anti-depression effect in forced swimming test when the delivery lasted relatively longer. The AAV applied to mice subjected to chronic mild stress (CMS) through intranasal administration for 10 days also alleviated depression-like behaviors. Western-blotting analysis revealed that BDNF-HA2TAT/AAV nasal administration enhanced hippocampal BDNF content. These results indicate intranasal administration of constructed BDNF-HA2TAT/AAV exerts anti-depression effect in CMS mice by increasing hippocampal BDNF, suggesting that this strategy holds a promising therapeutic potential for MDD.
RNA sequencing reveals region-specific molecular mechanisms associated with epileptogenesis in a model of classical hippocampal sclerosis
Authors: Vieira A. S. , de Matos A. H. , do Canto A. M. , Rocha C. S. , Carvalho B. S. , Pascoal V. D. B. , Norwood B. , Bauer S. , Rosenow F. , Gilioli R. , Cendes F. , Lopes-Cendes I.
Published: March 2016

We report here the first complete transcriptome analysis of the dorsal (dDG) and ventral dentate gyrus (vDG) of a rat epilepsy model presenting a hippocampal lesion with a strict resemblance to classical hippocampal sclerosis (HS). We collected the dDG and vDG by laser microdissection 15 days after electrical stimulation and performed high-throughput RNA-sequencing. There were many differentially regulated genes, some of which were specific to either of the two sub-regions in stimulated animals. Gene ontology analysis indicated an enrichment of inflammation-related processes in both sub-regions and of axonal guidance and calcium signaling processes exclusively in the vDG. There was also a differential regulation of genes encoding molecules involved in synaptic function, neural electrical activity and neuropeptides in stimulated rats. The data presented here suggests, in the time point analyzed, a remarkable interaction among several molecular components which takes place in the damaged hippocampi. Furthermore, even though similar mechanisms may function in different regions of the DG, the molecular components involved seem to be region specific.
The Lipid Bilayer Provides a Site for Cortisone Crystallization at High Cortisone Concentrations
Authors: Alsop Richard J. , Khondker Adree , Hub Jochen S. , Rheinstädter Maikel C.
Published: March 2016

Cortisone is an injected anti-inflammatory drug that can cause painful side effects known as “steroid flares” which are caused by cortisone crystallizing at the injection site. We used molecular dynamics simulations and X-ray diffraction to study the interaction of cortisone with model lipid membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) at drug concentrations from 0 mol% to 50 mol%. Cortisone was found to partition in the lipid bilayer and locate in the hydrophilic to hydrophobic interface of the membranes. Cortisone strongly affects the integrity of the membrane, as quantified by a decreased membrane thickness, increased area per lipid and decreased lipid tail order parameters. At cortisone concentrations of more than 20 mol%, signals from crystallized cortisone were observed. These crystallites are embedded in the bilayers and orient with the membranes. While the cortisone molecules align parallel to the bilayers at low concentrations, they start to penetrate the hydrophobic core at higher concentrations. Trans-membrane crystallites start to nucleate when the membrane thickness has decreased such that cortisone molecules in the different leaflets can find partners from the opposite leaflet resulting in a non-zero density of cortisone molecules in the bilayer center. We suggest that the lipid bilayer provides a site for cortisone crystallization.
Small Molecule Inhibition of Ligand-Stimulated RAGE-DIAPH1 Signal Transduction
Authors: Manigrasso Michaele B. , Pan Jinhong , Rai Vivek , Zhang Jinghua , Reverdatto Sergey , Quadri Nosirudeen , DeVita Robert J. , Ramasamy Ravichandran , Shekhtman Alexander , Schmidt Ann Marie
Published: March 2016

The receptor for advanced glycation endproducts (RAGE) binds diverse ligands linked to chronic inflammation and disease. NMR spectroscopy and x-ray crystallization studies of the extracellular domains of RAGE indicate that RAGE ligands bind by distinct charge- and hydrophobicity-dependent mechanisms. The cytoplasmic tail (ct) of RAGE is essential for RAGE ligand-mediated signal transduction and consequent modulation of gene expression and cellular properties. RAGE signaling requires interaction of ctRAGE with the intracellular effector, mammalian diaphanous 1 or DIAPH1. We screened a library of 58,000 small molecules and identified 13 small molecule competitive inhibitors of ctRAGE interaction with DIAPH1. These compounds, which exhibit in vitro and in vivo inhibition of RAGE-dependent molecular processes, present attractive molecular scaffolds for the development of therapeutics against RAGE-mediated diseases, such as those linked to diabetic complications, Alzheimer’s disease, and chronic inflammation, and provide support for the feasibility of inhibition of protein-protein interaction (PPI).
Functioning free gracilis transfer to reconstruct elbow flexion and quality of life in global brachial plexus injured patients
Authors: Yang Yi , Yang Jian-Tao , Fu Guo , Li Xiang-Ming , Qin Ben-Gang , Hou Yi , Qi Jian , Li Ping , Liu Xiao-Lin , Gu Li-Qiang
Published: March 2016

In the study, the functional recovery and relative comprehensive quality of life of cases of global brachial plexus treated with free functioning muscle transfers were investigated. Patients who received functioning gracilis muscle transfer between August 1999 and October 2014 to reconstruct elbow flexion, wrist and fingers extension were recruited. The mean age of the patients was 26.36 (range, 16–42) years. The mean period of time from gracilis transfer to the last follow-up was 54.5 months (range, 12–185 months). Muscle power, active range of motion of the elbow flexion, wrist extension and total active fingers extension were recorded. SDS, SAS and DASH questionnaires were given to estimate patients’ quality of life. 35.71% reported good elbow flexion and 50.00% reported excellent elbow flexion. The average ROM of the elbow flexion was 106.5° (range, 0–142°) and was 17.00° (range, 0–72°) for wrist extension. The average DASH score was 51.14 (range, 17.5–90.8). The prevalence of anxiety and depression were 42.86% and 45.24%. Thrombosis and bowstringing were the most common short and long-term complications. Based on these findings, free gracilis transfer using accessory nerve as donor nerve is a satisfactory treatment to reconstruct the elbow flexion and wrist extension in global-brachial-plexus-injured patients.
On the Dynamical Regimes of Pattern-Accelerated Electroconvection
Authors: Davidson Scott M. , Wessling Matthias , Mani Ali
Published: March 2016

Recent research has established that electroconvection can enhance ion transport at polarized surfaces such as membranes and electrodes where it would otherwise be limited by diffusion. The onset of such overlimiting transport can be influenced by the surface topology of the ion selective membranes as well as inhomogeneities in their electrochemical properties. However, there is little knowledge regarding the mechanisms through which these surface variations promote transport. We use high-resolution direct numerical simulations to develop a comprehensive analysis of electroconvective flows generated by geometric patterns of impermeable stripes and investigate their potential to regularize electrokinetic instabilities. Counterintuitively, we find that reducing the permeable area of an ion exchange membrane, with appropriate patterning, increases the overall ion transport rate by up to 80%. In addition, we present analysis of nonpatterned membranes and find a novel regime of electroconvection where a multivalued current is possible due to the coexistence of multiple convective states.
Directly Predicting Water Quality Criteria from Physicochemical Properties of Transition Metals
Authors: Wang Ying , Wu Fengchang , Mu Yunsong , Zeng Eddy Y. , Meng Wei , Zhao Xiaoli , Giesy John P. , Feng Chenglian , Wang Peifang , Liao Haiqing , Chen Cheng
Published: March 2016

Transition metals are a group of elements widespread in aquatic environments that can be hazardous when concentrations exceeding threshold values. Due to insufficient data, criteria maximum concentrations (CMCs) of only seven transition metals for protecting aquatic life have been recommended by the USEPA. Hence, it is deemed necessary to develop empirical models for predicting the threshold values of water quality criteria (WQC) for other transition metals for which insufficient information on toxic potency is available. The present study established quantitative relationships between recommended CMCs and physicochemical parameters of seven transition metals, then used the developed relationships to predict CMCs for other transition metals. Seven of 26 physicochemical parameters examined were significantly correlated with the recommended CMCs. Based on this, five of the seven parameters were selected to construct a linear free energy model for predicting CMCs. The most relevant parameters were identified through principle component analysis and the one with the best correlation with the recommended CMCs was a combination of covalent radius, ionic radius and electron density. Predicted values were largely consistent with their toxic potency values. The present study provides an alternative approach to develop screening threshold level for metals which have insufficient information to use traditional methods.
Effects of whole-body vibration training on physical function, bone and muscle mass in adolescents and young adults with cerebral palsy
Authors: Gusso Silmara , Munns Craig F , Colle Patrícia , Derraik José G B , Biggs Janene B , Cutfield Wayne S , Hofman Paul L
Published: March 2016

We performed a clinical trial on the effects of whole-body vibration training (WBVT) on muscle function and bone health of adolescents and young adults with cerebral palsy. Forty participants (11.3–20.8 years) with mild to moderate cerebral palsy (GMFCS II–III) underwent 20-week WBVT on a vibration plate for 9 minutes/day 4 times/week at 20 Hz (without controls). Assessments included 6-minute walk test, whole-body DXA, lower leg pQCT scans, and muscle function (force plate). Twenty weeks of WBVT were associated with increased lean mass in the total body (+770 g; p = 0.0003), trunk (+410 g; p = 0.004), and lower limbs (+240 g; p = 0.012). Bone mineral content increased in total body (+48 g; p = 0.0001), lumbar spine (+2.7 g; p = 0.0003), and lower limbs (+13 g; p < 0.0001). Similarly, bone mineral density increased in total body (+0.008 g/cm2; p = 0.013), lumbar spine (+0.014 g/cm2; p = 0.003), and lower limbs (+0.023 g/cm2; p < 0.0001). Participants reduced the time taken to perform the chair test, and improved the distance walked in the 6-minute walk test by 11% and 35% for those with GMFCS II and III, respectively. WBVT was associated with increases in muscle mass and bone mass and density, and improved mobility of adolescents and young adults with cerebral palsy.
Diagnosis of the phase function of random media from light reflectance
Authors: Xu Min
Published: March 2016

Light reflectance has been widely used to diagnose random media in both in situ and in vivo applications. The quantification of the phase function of the medium from reflectance measurements, however, remains elusive due to the lack of an explicit connection between the light reflectance profile and the phase function. Here we first present an analytical model for reflectance of scattered light at an arbitrary source-detector separation by forward-peaked scattering media such as biological tissue and cells. The model incorporates the improved small-angle scattering approximation (SAA) to radiative transfer for sub-diffusive light reflectance and expresses the dependence of the light reflectance on the phase function of the scattering medium in a closed form. A spreading length scale, lΘ, is found to characterise subdiffusive light reflectance at the high spatial frequency (close separation) limit. After validation by Monte Carlo simulations, we then demonstrate the application of the model in accurate determination of the complete set of optical properties and the phase function of a turbid medium from the profile of subdiffusive and diffusive light reflectance.
Understanding Ammonium Transport in Bioelectrochemical Systems towards its Recovery
Authors: Liu Ying , Qin Mohan , Luo Shuai , He Zhen , Qiao Rui
Published: March 2016

We report an integrated experimental and simulation study of ammonia recovery using microbial electrolysis cells (MECs). The transport of various species during the batch-mode operation of an MEC was examined experimentally and the results were used to validate the mathematical model for such an operation. It was found that, while the generated electrical current through the system tends to acidify (or basify) the anolyte (or catholyte), their effects are buffered by a cascade of chemical groups such as the NH3/NH4+ group, leading to relatively stable pH values in both anolyte and catholyte. The transport of NH4+ ions accounts for ~90% of the total current, thus quantitatively confirming that the NH4+ ions serve as effective proton shuttles during MEC operations. Analysis further indicated that, because of the Donnan equilibrium at cation exchange membrane-anolyte/catholyte interfaces, the Na+ ion in the anolyte actually facilitates the transport of NH4+ ions during the early stage of a batch cycle and they compete with the NH4+ ions weakly at later time. These insights, along with a new and simple method for predicting the strength of ammonia diffusion from the catholyte toward the anolyte, will help effective design and operation of bioeletrochemical system-based ammonia recovery systems.
Activation of innate antiviral immune response via double-stranded RNA-dependent RLR receptor-mediated necroptosis
Authors: Wang Wei , Wang Wei-Hua , Azadzoi Kazem M. , Su Ning , Dai Peng , Sun Jianbin , Wang Qin , Liang Ping , Zhang Wentao , Lei Xiaoying , Yan Zhen , Yang Jing-Hua
Published: March 2016

Viruses induce double-stranded RNA (dsRNA) in the host cells. The mammalian system has developed dsRNA-dependent recognition receptors such as RLRs that recognize the long stretches of dsRNA as PAMPs to activate interferon-mediated antiviral pathways and apoptosis in severe infection. Here we report an efficient antiviral immune response through dsRNA-dependent RLR receptor-mediated necroptosis against infections from different classes of viruses. We demonstrated that virus-infected A549 cells were efficiently killed in the presence of a chimeric RLR receptor, dsCARE. It measurably suppressed the interferon antiviral pathway but promoted IL-1β production. Canonical cell death analysis by morphologic assessment, phosphatidylserine exposure, caspase cleavage and chemical inhibition excluded the involvement of apoptosis and consistently suggested RLR receptor-mediated necroptosis as the underlying mechanism of infected cell death. The necroptotic pathway was augmented by the formation of RIP1-RIP3 necrosome, recruitment of MLKL protein and the activation of cathepsin D. Contributing roles of RIP1 and RIP3 were confirmed by gene knockdown. Furthermore, the necroptosis inhibitor necrostatin-1 but not the pan-caspase inhibitor zVAD impeded dsCARE-dependent infected cell death. Our data provides compelling evidence that the chimeric RLR receptor shifts the common interferon antiviral responses of infected cells to necroptosis and leads to rapid death of the virus-infected cells. This mechanism could be targeted as an efficient antiviral strategy.
All-optical control of three-photon spectra and time asymmetry in a strongly coupled cavity polariton system
Authors: Zhang X. , Li R. , Wu Haibin
Published: March 2016

Manipulating the nature of photons emission is one of the basic tasks in quantum optics and photonics. The ever growing list of quantum applications requires a robust means of controlling the strongly coupled coherent interaction of photons and matter. Here, we investigate three-photon transmission spectra in a strongly coupled cavity polariton system and show that the correlation functions and transmitted photon stream can be optically manipulated. The dynamics of single photons and photon pairs at the polariton resonances can be changed by light from a single external coupling laser. At the “dark-state polariton,” three-photon transmission is a perfectly coherent field in contrast to the strong photon-bunching behavior of a typical cavity quantum electrodynamics system. When the detuned probe light is tuned to the “bright polariton,” the light exhibits a dramatic photon antibunching effect. Remarkably, the Fano-resonant asymmetric three-photon transmission caused by the interference between the dressed states leads to a new quantum feature that is strongly nonclassical (the third-order correlation function g(3)(0, 0) ≪ 1) and has a wide and tunable bandwidth. The dependence of the intrinsic third-order correlation and time symmetry of the photon stream on the controlled parameters is also examined. Strongly nonclassical, all-optically controllable multi-photon dynamics are very important for future quantum devices and metrology.
Toll-like Receptor 9 Can be Activated by Endogenous Mitochondrial DNA to Induce Podocyte Apoptosis
Authors: Bao Wenduona , Xia Hong , Liang Yaojun , Ye Yuting , Lu Yuqiu , Xu Xiaodong , Duan Aiping , He Jing , Chen Zhaohong , Wu Yan , Wang Xia , Zheng Chunxia , Liu Zhihong , Shi Shaolin
Published: March 2016

Toll-like receptor 9 (TLR9) senses bacterial DNA characteristic of unmethylated CpG motifs to induce innate immune response. TLR9 is de novo expressed in podocytes of some patients with glomerular diseases, but its role in podocyte injury remains undetermined. Since TLR9 activates p38 MAPK and NFkB that are known to mediate podocyte apoptosis, we hypothesized that TLR9 induces podocyte apoptosis in glomerular diseases. We treated immortalized podocytes with puromycin aminonucleosides (PAN) and observed podocyte apoptosis, accompanied by TLR9 upregulation. Prevention of TLR9 upregulation by siRNA significantly attenuated NFκB p65 or p38 activity and apoptosis, demonstrating that TLR9 mediates podocyte apoptosis. We next showed that endogenous mitochondrial DNA (mtDNA), whose CpG motifs are also unmethylated, is the ligand for TLR9, because PAN induced mtDNA accumulation in endolysosomes where TLR9 is localized, overexpression of endolysosomal DNase 2 attenuated PAN-induced p38 or p65 activity and podocyte apoptosis and DNase 2 silencing was sufficient to activate p38 or p65 and induce apoptosis. In PAN-treated rats, TLR9 was upregulated in the podocytes, accompanied by increase of apoptosis markers. Thus, de novo expressed TLR9 may utilize endogenous mtDNA as the ligand to facilitate podocyte apoptosis, a novel mechanism underlying podocyte injury in glomerular diseases.
Berberine Ameliorates Hepatic Steatosis and Suppresses Liver and Adipose Tissue Inflammation in Mice with Diet-induced Obesity
Authors: Guo Ting , Woo Shih-Lung , Guo Xin , Li Honggui , Zheng Juan , Botchlett Rachel , Liu Mengyang , Pei Ya , Xu Hang , Cai Yuli , Zeng Tianshu , Chen Lulu , Li Xiaodong , Li Qifu , Xiao Xiaoqiu , Huo Yuqing , Wu Chaodong
Published: March 2016

Increasing evidence demonstrates that berberine (BBR) is beneficial for obesity-associated non-alcoholic fatty liver disease (NAFLD). However, it remains to be elucidated how BBR improves aspects of NAFLD. Here we revealed an AMP-activated protein kinase (AMPK)-independent mechanism for BBR to suppress obesity-associated inflammation and improve hepatic steatosis. In C57BL/6J mice fed a high-fat diet (HFD), treatment with BBR decreased inflammation in both the liver and adipose tissue as indicated by reduction of the phosphorylation state of JNK1 and the mRNA levels of proinflammatory cytokines. BBR treatment also decreased hepatic steatosis, as well as the expression of acetyl-CoA carboxylase and fatty acid synthase. Interestingly, treatment with BBR did not significantly alter the phosphorylation state of AMPK in both the liver and adipose tissue of HFD-fed mice. Consistently, BBR treatment significantly decreased the phosphorylation state of JNK1 in both hepatoma H4IIE cells and mouse primary hepatocytes in both dose-dependent and time-dependent manners, which was independent of AMPK phosphorylation. BBR treatment also caused a decrease in palmitate-induced fat deposition in primary mouse hepatocytes. Taken together, these results suggest that BBR actions on improving aspects of NAFLD are largely attributable to BBR suppression of inflammation, which is independent of AMPK.
SAMHD1 transcript upregulation during SIV infection of the central nervous system does not associate with reduced viral load
Authors: Buchanan Erin L. , Espinoza Diego A. , McAlexander Melissa A. , Myers Stephanie L. , Moyer Adam , Witwer Kenneth W.
Published: March 2016

Restriction of HIV-1 in myeloid-lineage cells is attributed in part to the nucleotidase activity of the SAM-domain and HD-domain containing protein (SAMHD1), which depletes free nucleotides, blocking reverse transcription. In the same cells, the Vpx protein of HIV-2 and most SIVs counteracts SAMHD1. Both Type I and II interferons may stimulate SAMHD1 transcription. The contributions of SAMHD1 to retroviral restriction in the central nervous system (CNS) have been the subject of limited study. We hypothesized that SAMHD1 would respond to interferon in the SIV-infected CNS but would not control virus due to SIV Vpx. Accordingly, we investigated SAMHD1 transcript abundance and association with the Type I interferon response in an SIV model. SAMHD1 transcript levels were IFN responsive, increasing during acute phase infection and decreasing during a more quiescent phase, but generally remaining elevated at all post-infection time points.In vitro, SAMHD1 transcript was abundant in macaque astrocytes and further induced by Type I interferon, while IFN produced a weaker response in the more permissive environment of the macrophage. We cannot rule out a contribution of SAMHD1 to retroviral restriction in relatively non-permissive CNS cell types. We encourage additional research in this area, particularly in the context of HIV-1 infection.
Comparative evaluation of p5+14 with SAP and peptide p5 by dual-energy SPECT imaging of mice with AA amyloidosis
Authors: Martin Emily B. , Williams Angela , Richey Tina , Stuckey Alan , Heidel R. Eric , Kennel Stephen J. , Wall Jonathan S.
Published: March 2016

Amyloidosis is a protein-misfolding disorder characterized by the extracellular deposition of amyloid, a complex matrix composed of protein fibrils, hyper-sulphated glycosaminoglycans and serum amyloid P component (SAP). Accumulation of amyloid in visceral organs results in the destruction of tissue architecture leading to organ dysfunction and failure. Early differential diagnosis and disease monitoring are critical for improving patient outcomes; thus, whole body amyloid imaging would be beneficial in this regard. Non-invasive molecular imaging of systemic amyloid is performed in Europe by using iodine-123-labelled SAP; however, this tracer is not available in the US. Therefore, we evaluated synthetic, poly-basic peptides, designated p5 and p5+14, as alternative radiotracers for detecting systemic amyloidosis. Herein, we perform a comparative effectiveness evaluation of radiolabelled peptide p5+14 with p5 and SAP, in amyloid-laden mice, using dual-energy SPECT imaging and tissue biodistribution measurements. All three radiotracers selectively bound amyloid in vivo; however, p5+14 was significantly more effective as compared to p5 in certain organs. Moreover, SAP bound principally to hepatosplenic amyloid, whereas p5+14 was broadly distributed in numerous amyloid-laden anatomic sites, including the spleen, liver, pancreas, intestines and heart. These data support clinical validation of p5+14 as an amyloid radiotracer for patients in the US.
Bifunctional hairy silica nanoparticles as high-performance additives for lubricant
Authors: Sui Tianyi , Song Baoyu , Wen Yu-ho , Zhang Feng
Published: March 2016

Bifunctional hairy silica nanoparticles (BHSNs), which are silica nanoparticles covered with alkyl and amino organic chains, were prepared as high-performance additives for lubricants. Compared with hairy silica nanoparticles covered by a single type of organic chain, binary hairy silica nanoparticles exhibit the advantages of both types of organic chains, which exhibit excellent compatibility with lubricants and adsorbability to metal surfaces. Nanoparticles with different ratios of amino and alkyl ligands were investigated. In comparison to an untreated lubricant, BHSNs reduce the friction coefficient and wear scar diameter by 40% and 60%, respectively. The wear mechanism of BHSNs was investigated and the protective and filling effect of the nanoparticles improved because of collaboration of amino and alkyl ligands.
Probing Leader Cells in Endothelial Collective Migration by Plasma Lithography Geometric Confinement
Authors: Yang Yongliang , Jamilpour Nima , Yao Baoyin , Dean Zachary S. , Riahi Reza , Wong Pak Kin
Published: March 2016

When blood vessels are injured, leader cells emerge in the endothelium to heal the wound and restore the vasculature integrity. The characteristics of leader cells during endothelial collective migration under diverse physiological conditions, however, are poorly understood. Here we investigate the regulation and function of endothelial leader cells by plasma lithography geometric confinement generated. Endothelial leader cells display an aggressive phenotype, connect to follower cells via peripheral actin cables and discontinuous adherens junctions, and lead migrating clusters near the leading edge. Time-lapse microscopy, immunostaining, and particle image velocimetry reveal that the density of leader cells and the speed of migrating clusters are tightly regulated in a wide range of geometric patterns. By challenging the cells with converging, diverging and competing patterns, we show that the density of leader cells correlates with the size and coherence of the migrating clusters. Collectively, our data provide evidence that leader cells control endothelial collective migration by regualting the migrating clusters.
A combined method for synthesis of superconducting Cu doped Bi2Se3
Authors: Wang Meng , Song Yanru , You Lixing , Li Zhuojun , Gao Bo , Xie Xiaoming , Jiang Mianheng
Published: March 2016

We present a two-step technique for the synthesis of superconducting CuxBi2Se3. Cu0.15Bi2Se3 single crystals were synthesized using the melt-growth method. Although these samples are non-superconducting, they can be employed to generate high quality superconducting samples if used as precursors in the following electrochemical synthesis step. Samples made from Cu0.15Bi2Se3 reliably exhibit zero-resistance even under the non-optimal quenching condition, while samples made from pristine Bi2Se3 require fine tuning of the quenching conditions to achieve similar performance. Moreover, under the optimal quenching condition, the average superconducting shielding fraction was still lower in the samples made from pristine Bi2Se3 than in the samples made from Cu0.15Bi2Se3. These results suggest that the pre-doped Cu atoms facilitate the formation of a superconducting percolation network. We also discuss the useful clues that we gathered about the locations of Cu dopants that are responsible for superconductivity.
Structural transition control between dipole–dipole and hydrogen bonds induced chirality and achirality
Authors: Hu Yi , Miao Kai , Peng Shan , Zha Bao , Xu Li , Miao Xinrui , Deng Wenli
Published: March 2016

This study presents efficient strategies on manipulation of hydrogen bonds and dipole–dipole induced chiral and achiral self-assembly nanostructures.
Role of S and Se atoms on the microstructural properties of kesterite Cu2ZnSn(SxSe1−x)4thin film solar cells
Authors: Dimitrievska Mirjana , Fairbrother Andrew , Gunder Rene , Gurieva Galina , Xie Haibing , Saucedo Edgardo , Pérez-Rodríguez Alejandro , Izquierdo-Roca Victor , Schorr Susan
Published: March 2016

Grazing incidence X-ray diffraction of kesterite shows a strong dependence of microstructural properties (domain size, microstrain) on the anion composition.
Interface properties between a low band gap conjugated polymer and a calcium metal electrode
Authors: Zhang Wei , Pan Xiao , Feng Xuefei , Wang Chia-Hsin , Yang Yaw-Wen , Ju Huanxin , Zhu Junfa
Published: March 2016

Downward band bending and chemical reactions occur simultaneously upon Ca deposition on the APFO3 film with a high degree of orientational ordering.
(Pyridyl)benzoazole palladium(ii) complexes as homogeneous catalysts in hydrogenation of alkenes and alkynes
Authors: Ojwach Stephen O. , Ogweno Aloice O. , Akerman Matthew P.
Published: March 2016

Complexes 1–6 form “cocktail” catalysts in the hydrogenation and isomerization of alkenes and alkynes where the active species are homogeneous.
Enhanced electrocatalytic activities of three dimensional PtCu@Pt bimetallic alloy nanofoams for oxygen reduction reaction
Authors: Fu Shaofang , Zhu Chengzhou , Shi Qiurong , Du Dan , Lin Yuehe
Published: March 2016

Three dimensional PtCu@Pt bimetallic alloy nanofoams show enhanced electrocatalytic activities for oxygen reduction reaction.
Temperature and pressure variations of d–d luminescence band maxima of bis(pyridylalkenolato)palladium(ii) complexes with different ligand substituents: opposite-signed trends
Authors: Poirier Stéphanie , Czympiel Lisa , Bélanger-Desmarais Nicolas , Mathur Sanjay , Reber Christian
Published: March 2016

Ligand substituents R are used to vary the sign of pressure-induced variations of luminescence maxima Emax, leading to a rare negative shift for a square-planar palladium(ii) compound.
Critical length scales and strain localization govern the mechanical performance of multi-layer graphene assemblies
Authors: Xia Wenjie , Ruiz Luis , Pugno Nicola M. , Keten Sinan
Published: March 2016

Three critical length scales govern the deformation mechanisms and constitutive response of multi-layer graphene.
Lightweight flexible polyurethane/reduced ultralarge graphene oxide composite foams for electromagnetic interference shielding
Authors: Gavgani Jaber Nasrollah , Adelnia Hossein , Zaarei Davood , Moazzami Gudarzi Mohsen
Published: March 2016

Multifunctional flexible polyurethane (PU)/reduced ultralarge graphene oxide (rUL-GO) composite foams with low density in the range of ∼53–92 kg m−3 were fabricated through the in situ polymerization of PU in the presence of rUL-GO.
An inorganic anionic polymer filter disc: direct crystallization of a layered silicate nanosheet on a glass fiber filter
Authors: Okada Tomohiko , Shimizu Kei , Yamakami Tomohiko
Published: March 2016

Cation-exchangeable layered silicate nanosheet fine crystals covered thoroughly a commercially available silica fiber filter paper through hydrothermal reactions with LiF, MgCl2 and urea.
Synthesis of allyl-aziridines from α-halo oxime ethers and allyl zinc bromides
Authors: Zheng Songlin , Zhang Songlin
Published: March 2016

A novel method for the preparation of allyl aziridines by reacting α-halo oxime ethers with allylic zinc reagents under mild conditions. Some advantages of using organozinc reagents are that they are easily prepared, non-toxic, and more selective than Grignard reagents.
Preparation of water-soluble, PEGylated, mixed-dispersant quantum dots, with a preserved photoluminescence quantum yield
Authors: Zaba C. , Bixner O. , Part F. , Zafiu C. , Tan C.-W. , Sinner E.-K.
Published: March 2016

We present the preparation of PEGylated mixed dispersant QDs from water-soluble nanocrystals, relevant for biomedical applications and environmental monitoring. We mastered control over grafting densities and PEG-conformation while retaining PLQY.
Cigarette smoke compounds induce cellular redox imbalance, activate NF-κB, and increase TNF-α/CRP secretion: a possible pathway in the pathogenesis of COPD
Authors: Dey Tapan , Dutta Prachurjya , Manna Prasenjit , Kalita Jatin , Boruah Hari Prasanna Deka , Buragohain Alak Kumar , Unni Balagopalan , Ozah Dibyajyoti , Kumar Goswami Mihir , Kotokey Ratan Kumar
Published: March 2016

Cigarette smoke has always been considered as a risk factor for chronic obstructive pulmonary diseases (COPD).
A disposable chemical heater and dry enzyme preparation for lysis and extraction of DNA and RNA from microorganisms
Authors: Buser J. R. , Zhang X. , Byrnes S. A. , Ladd P. D. , Heiniger E. K. , Wheeler M. D. , Bishop J. D. , Englund J. A. , Lutz B. , Weigl B. H. , Yager P.
Published: March 2016

A simple dry enzyme and sample heating approach for point-of-care molecular diagnostic devices is demonstrated.
Digital droplet LAMP as a microfluidic app on standard laboratory devices
Authors: Schuler Friedrich , Siber Clara , Hin Sebastian , Wadle Simon , Paust Nils , Zengerle Roland , von Stetten Felix
Published: March 2016

Digital droplet LAMP is performed on a disposable chip (DropChip) with the size of a microscope slide using only standard laboratory devices.
Interlocked multi-armed carbon for stable oxygen reduction
Authors: Li Yiming , Li Lei , Zhu Longfeng , Gu Li , Cao Xuebo
Published: March 2016

N-Doped multi-armed carbon with an interlocked structure shows high oxygen reduction activity and resistance to methanol crossover effects.
The ruthenium-catalysed selective synthesis of mono-deuterated terminal alkynes
Authors: Chatterjee Basujit , Gunanathan Chidambaram
Published: March 2016

A highly efficient catalytic system is reported for chemoselective synthesis of mono-deuterated terminal alkynes using deuterium oxide in which the reaction proceeds via Ru–acetylide intermediates formed by selective activation of the sp-CH bond.
Introduction of Co3O4 into activated honeycomb-like carbon for the fabrication of high performance electrode materials for supercapacitors
Authors: Kim Myeongjin , Oh Ilgeun , Ju Hyun , Kim Jooheon
Published: March 2016

In this work, a three-dimensional hierarchical carbon framework/Co3O4 hybrid composite was fabricated.
Rechargeable dual-metal-ion batteries for advanced energy storage
Authors: Yao Hu-Rong , You Ya , Yin Ya-Xia , Wan Li-Jun , Guo Yu-Guo
Published: March 2016

Possible configurations of hybrid-ion batteries based on dual-metal-ions are summarized: these could be promising rechargeable battery systems as they combine the respective advantages of each single-metal-ion.
Inorganic dendrimers: recent advances for catalysis, nanomaterials, and nanomedicine
Authors: Caminade Anne-Marie
Published: March 2016

Among inorganic dendrimers, phosphorhydrazone dendrimers and carbosilane dendrimers are the most widely used as nanotools for catalysis, materials, and biology.
Synthesis of monosubstituted thioureas by vapour digestion and mechanochemical amination of thiocarbamoyl benzotriazoles
Authors: Đud Mateja , Magdysyuk Oxana V. , Margetić Davor , Štrukil Vjekoslav
Published: March 2016

N-monosubstituted thioureas have been rapidly accessed from thiocarbamoyl benzotriazoles by ammonia vapour digestion and solvent-free mechanochemical milling in near-quantitative yields.
BF3·OEt2 mediated metal-free one-pot sequential multiple annulation cascade (SMAC) synthesis of complex and diverse tetrahydroisoquinoline fused hybrid molecules
Authors: Shinde Anand H. , Vidyacharan Shinde , Sharada Duddu S.
Published: March 2016

A highly efficient and distinct BF3·OEt2 mediated one-pot metal-free sequential multiple annulation cascade (SMAC) protocol for the synthesis of complex and diverse THIQ fused hybrid molecules has been presented.
Application of calcium carbonate nanoparticles and microwave irradiation in submerged fermentation production and recovery of fumaric acid: a novel approach
Authors: Das Ratul Kumar , Brar Satinder Kaur , Verma Mausam
Published: March 2016

First ever report on the applications of calcium carbonate nanoparticles and microwave irradiation in fumaric acid production and recovery, respectively.
Porous β-MnO2nanoplates derived from MnCO3nanoplates as highly efficient electrocatalysts toward oxygen evolution reaction
Authors: Kim Jun , Kim Ju Seong , Baik Hionsuck , Kang Kisuk , Lee Kwangyeol
Published: March 2016

Porous β-MnO2nanoplates obtained from calcination of MnCO3nanoplates act as excellent electrocatalysts toward oxygen evolution reaction.
Discovery of anti-Ebola drugs: a computational drug repositioning case study
Authors: Kharkar Prashant S. , Ramasami Ponnadurai , Choong Yee Siew , Rhyman Lydia , Warrier Sona
Published: March 2016

Computational drug repositioning has complemented and guided the experimental drug repositioning assignments in the recent past.
Cucurbit[6]uril-OSO3H: a novel acidic nanocatalyst for the one-pot preparation of 14-aryl-14H-dibenzo[a,j]xanthenes and 1,8-dioxo-octahydro-xanthenes
Authors: Saghanezhad Seyyed Jafar , Nazari Yaser , Davod Fereshteh
Published: March 2016

One-pot preparation of 14-aryl-14H-dibenzo[a,j]xanthenes (3a–h) and 1,8-dioxo-octahydro-xanthenes (5a–h).
Functionalization of silica through thiol-yne radical chemistry: a catalytic system based on gold nanoparticles supported on amino-sulfide-branched silica
Authors: Ballarin Barbara , Barreca Davide , Boanini Elisa , Bonansegna Elisa , Cassani Maria Cristina , Carraro Giorgio , Fazzini Silvia , Mignani Adriana , Nanni Daniele , Pinelli Davide
Published: March 2016

Synthesis of a novel catalytic system based on gold nanoparticles supported on silica functionalized via a thiol-yne radical reaction.
Surface labeling of enveloped virus with polymeric imidazole ligand-capped quantum dots via the metabolic incorporation of phospholipids into host cells
Authors: Zhao Xia , Shen Yi , Adogla Enoch A. , Viswanath Anand , Tan Rui , Benicewicz Brian C. , Greytak Andrew B. , Lin Yuan , Wang Qian
Published: March 2016

The successful modification of enveloped virus with polymeric imidazole ligand coated quantum dots was achieved by metabolic labeling and the click reaction.
Calcium-insensitive splice variants of mammalian E1 subunit of 2-oxoglutarate dehydrogenase complex with tissue-specific patterns of expression
Authors: Denton Richard M. , Pullen Timothy J. , Armstrong Craig T. , Heesom Kate J. , Rutter Guy A.
Published: March 2016

The 2-oxoglutarate dehydrogenase (OGDH) complex is an important control point in vertebrate mitochondrial oxidative metabolism, including in the citrate cycle and catabolism of alternative fuels including glutamine. It is subject to allosteric regulation by NADH and the ATP/ADP ratio, and by Ca2+ through binding to the E1 subunit. The latter involves a unique Ca2+-binding site which includes D114ADLD (site 1). Here, we describe three splice variants of E1 in which either the exon expressing this site is replaced with another exon (loss of site 1, LS1) or an additional exon is expressed leading to the insertion of 15 amino acids just downstream of site 1 (Insert), or both changes occur together (LS1/Insert). We show that all three variants are essentially Ca2+-insensitive. Comparison of massive parallel sequence (RNA-Seq) databases demonstrates predominant expression of the Ca2+-sensitive archetype form in heart and skeletal muscle, but substantial expression of the Ca2+-insensitive variants in brain, pancreatic islets and other tissues. Detailed proteomic and activity studies comparing OGDH complexes from rat heart and brain confirmed the substantial difference in expression between these tissues. The evolution of OGDH variants was explored using bioinformatics, and this indicated that Ca2+-sensitivity arose with the emergence of chordates. In all species examined, this was associated with the co-emergence of Ca2+-insensitive variants suggesting a retained requirement for the latter in some settings. Tissue-specific expression of OGDH splice variants may thus provide a mechanism that tunes the control of the enzyme to the specialized metabolic and signalling needs of individual cell types.
Development of a stable ERroGFP variant suitable for monitoring redox dynamics in the ER
Authors: Hoseki Jun , Oishi Asami , Fujimura Takaaki , Sakai Yasuyoshi
Published: March 2016

The endoplasmic reticulum (ER) is an essential organelle for cellular metabolic homeostasis including folding and maturation of secretory and membrane proteins. Disruption of ER proteostasis has been implicated in the pathogenesis of various diseases such as diabetes and neurodegenerative diseases. The ER redox state, which is an oxidative environment suitable for disulfide-bond formation, is essential for ER protein quality control. Hence, detection of the ER redox state, especially in living cells, is essential to understand the mechanism by which the redox state of the ER is maintained. However, methods to detect the redox state of the ER have not been well-established because of inefficient folding and stability of roGFP variants with oxidative redox potential like roGFP-iL. Here we have improved the folding efficiency of ER-targeted roGFP-iL (ERroGFP-iL) in cells by introducing superfolder GFP (sfGFP) mutations. Four specific amino acid substitutions (S30R, Y39N, T105N and I171V) greatly improved folding efficiency in Escherichia coli and in the ER of HeLa cells, as well as the thermostability of the purified proteins. Introduction of these mutations also enhanced the dynamic range for redox change both in vitro and in the ER of living cells. ER-targeted roGFP-S4 (ERroGFP-S4) possessing these four mutations could detect physiological redox changes within the ER. ERroGFP-S4 is therefore a novel probe suitable for monitoring redox change in the ER. ERroGFP-S4 can be applied to detect aberrant ER redox states associated with various pathological conditions and to identify the mechanisms used to maintain the redox state of the ER.