bluuebunny/crossref_metadata_2025 huggingface dataset:
RANK Ligand Modulation of Autophagy in Oral Squamous Cell Carcinoma Tumor Cells
Authors: Sambandam Yuvaraj , Sakamuri Sashank , Balasubramanian Sundaravadivel , Haque Azizul
Published: June 2015

Autophagy is a cellular process to recycle nutrients and has been implicated in cancer treatment. Oral squamous cell carcinoma (OSCC) is the most common oral cancer which ranks 3% of cancers in men and 2% in women. In this study, immunohistochemical staining of OSCC tumor specimens from human subjects and an athymic mouse model demonstrated high levels of autophagy markers LC3‐II and ATG5 expression. Further, we identified high levels LC3‐II expression in OSCC tumor cell lines (SCC‐1, SCC‐12, and SCC‐14a) compared to normal human epithelial (RWPE‐1) cells. OSCC cells express high levels of RANK ligand (RANKL); however, a functional role in autophagy is unknown. Interestingly, RANKL stimulation significantly increased autophagosome‐related gene expressions such as LC3, ATG5, BECN1, and PI3KC3 mRNA expression in OSCC cells. Further, Western blot analysis of total cell lysates demonstrated a dose‐dependent increase in LC3‐II and ATG5 expression in RANKL‐stimulated cells. In addition, RANKL increased expression of LC3‐I and LC3‐II, essential for autophagosome formation. Confocal microscopy analysis of LC3‐II and localization with lysosome further confirms autophagosome formation in response to RANKL treatment in OSCC cells. Collectively, our results indicate a novel function of RANKL to induce autophagosome formation, and could be a potential therapeutic target to control OSCC tumor progression. J. Cell. Biochem. 117: 118–125, 2016. © 2015 Wiley Periodicals, Inc.
Zdhhc15b Regulates Differentiation of Diencephalic Dopaminergic Neurons in zebrafish
Authors: Wang Fen , Chen Xueran , Shi Wei , Yao Linli , Gao Ming , Yang Yang , Hao Aijun
Published: June 2015

The aspartate‐histidine‐histidine‐cysteine (DHHC) protein family shares a 50‐amino acid cysteine‐rich domain with a conserved DHHC signature motif. DHHC proteins play a critical role in several biological processes. Several DHHC family members have been implicated in neuronal differentiation and synaptic plasticity. And disruptions to their function can lead to disease in the nervous system. Here, we investigate the role of Zdhhc15b, a DHHC family member, in neuro development in zebrafish. Whole‐mount in situ hybridization (WISH) revealed that zdhhc15b, an ortholog to human ZDHHC15, is abundant in zebrafish (Danio rerio) forebrain, especially in the diencephalon. Downregulation of zdhhc15b resulted in a smaller diencephalon and a reduction in mature dopaminergic neurons (DA neurons). In the meanshile, mutant zdhhc15b zebrafish was associated with poor learning behavior as detected by T‐maze testing. The expression of zdhhc15b was upregulated during DA neuronal differentiation whereas knock‐down of zdhhc15b diminished DA neuronal differentiation. Tyrosine hydroxylase (TH) immunofluorescence of cultured DA neurons in vitro also showed that DA neurons were immature following zdhhc15b knock‐down. Consistent with the decreased number of DA neurons following knock‐down of zdhhc15b, the expression of fate determination‐related transcription factors such as nurr1, foxA2, and lmx1a were also reduced in morphant zebrafish. Our results reveal that zdhhc15b controls DA neuronal fate decisions by regulating differentiation but not progenitor cell proliferation or DA neuronal survival. J. Cell. Biochem. 116: 2980–2991, 2015. © 2015 Wiley Periodicals, Inc.
Accounting for observed small angle X‐ray scattering profile in the protein–protein docking server cluspro
Authors: Xia Bing , Mamonov Artem , Leysen Seppe , Allen Karen N. , Strelkov Sergei V. , Paschalidis Ioannis Ch. , Vajda Sandor , Kozakov Dima
Published: June 2015

The protein‐protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near‐native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small angle X‐ray scattering (SAXS) is an experimental technique for obtaining low resolution structural information in solution. While not sufficient on its own to uniquely predict complex structures, accounting for SAXS data improves the ranking of models and facilitates the identification of the most accurate structure. Although SAXS profiles are currently available only for a small number of complexes, due to its simplicity the method is becoming increasingly popular. Since combining docking with SAXS experiments will provide a viable strategy for fairly high‐throughput determination of protein complex structures, the option of using SAXS restraints is added to the ClusPro server. © 2015 Wiley Periodicals, Inc.
Tamoxifen Inhibits TGF‐β‐Mediated Activation of Myofibroblasts by Blocking Non‐Smad Signaling Through ERK1/2
Authors: Carthy Jon M. , Sundqvist Anders , Heldin Angelos , van DAM Hans , Kletsas Dimitris , Heldin Carl‐Henrik , Moustakas Aristidis
Published: June 2015

Transforming growth factor‐β (TGF‐β) is a multifunctional cytokine which stimulates the differentiation of fibroblasts into myofibroblasts. Myofibroblasts are critical for normal wound healing, but also accumulate pathologically in a number of chronic inflammatory conditions where they are key contributors to aberrant tissue remodeling and fibrosis, and in cancer stroma. In the current study, we identified a role for tamoxifen as a potent inhibitor of the TGF‐β‐mediated activation of primary human skin and breast fibroblasts. Our data indicate that tamoxifen does not interfere with canonical Smad signaling downstream of TGF‐β but rather blocks non‐Smad signaling through ERK1/2 MAP‐kinase and the AP‐1 transcription factor FRA2. We further demonstrate by siRNA‐mediated knockdown that FRA2 is critical for the induced expression of myogenic proteins in response to TGF‐β. Functionally, TGF‐β‐stimulated fibroblast‐mediated contraction of collagen gels was impaired in the presence of tamoxifen. Altogether, these data demonstrate that tamoxifen prevents myofibroblast differentiation and, therefore, may provide therapeutic benefits to patients suffering from chronic inflammatory conditions or cancer. J. Cell. Physiol. 230: 3084–3092, 2015. © 2015 Wiley Periodicals, Inc.
Critical Role of AMPK/FoxO3A Axis in Globular Adiponectin‐Induced Cell Cycle Arrest and Apoptosis in Cancer Cells
Authors: Shrestha Anup , Nepal Saroj , Kim Mi Jin , Chang Jae Hoon , Kim Sang‐Hyun , Jeong Gil‐Saeng , Jeong Chul‐Ho , Park Gyu Hwan , Jung Sunghee , Lim Jaecheong , Cho Eunha , Lee Soyoung , Park Pil‐Hoon
Published: June 2015

Adiponectin predominantly secreted from adipose tissue has exhibited potent anti‐proliferative properties in cancer cells via modulating cell cycle and apoptosis. FoxO3A, a Forkhead box O member of the transcription factor, plays a critical role in modulating expression of genes involved in cell death and/or survival. In this study, we investigated the role of FoxO3A signaling in anti‐cancer activities of adiponectin. Herein, we have shown that treatment with globular adiponectin (gAcrp) increases p27 but decreases cyclinD1 expression in human hepatoma (HepG2) and breast (MCF‐7) cancer cells. Gene ablation of FoxO3A prevented gAcrp‐induced increase in p27 and decreased in cyclin D1 expression, and further ameliorated cell cycle arrest by gAcrp, indicating a critical role of FoxO3A in gAcrp‐induced cell cycle arrest of cancer cells. Moreover, treatment with gAcrp also induced caspase‐3/7 activation and increased Fas ligand (FasL) expression in both HepG2 and MCF‐7 cells. Transfection with FoxO3A siRNA inhibited gAcrp‐induced caspase‐3/7 activation and FasL expression, suggesting that FoxO3A signaling also plays an important role in gAcrp‐induced apoptosis of cancer cells. We also found that gene silencing of AMPK prevented gAcrp‐induced nuclear translocation of FoxO3A in HepG2 and MCF‐7 cells. In addition, suppression of AMPK also blocked gAcrp‐induced cell cycle arrest and further attenuated gAcrp‐induced caspase‐3/7 activation, indicating that AMPK signaling plays a pivotal role in both gAcrp‐induced cell cycle arrest and apoptosis via acting as an upstream signaling of FoxO3A. Taken together, our findings demonstrated that AMPK/FoxO3A axis plays a cardinal role in anti‐proliferative effect of adiponectin in cancer cells. J. Cell. Physiol. 231: 357–369, 2016. © 2015 Wiley Periodicals, Inc.
Platelet‐Derived CCL5 Regulates CXC Chemokine Formation and Neutrophil Recruitment in Acute Experimental Colitis
Authors: Yu Changhui , Zhang Songen , Wang Yongzhi , Zhang Su , Luo Lingtao , Thorlacius Henrik
Published: June 2015

Accumulating data suggest that platelets not only regulate thrombosis and haemostasis but also inflammatory processes. Platelets contain numerous potent pro‐inflammatory compounds, including the chemokines CCL5 and CXCL4, although their role in acute colitis remains elusive. The aim of this study is to examine the role of platelets and platelet‐derived chemokines in acute colitis. Acute colitis is induced in female Balb/c mice by administration of 5% dextran sodium sulfate (DSS) for 5 days. Animals receive a platelet‐depleting, anti‐CCL5, anti‐CXCL4, or a control antibody prior to DSS challenge. Colonic tissue is collected for quantification of myeloperoxidase (MPO) activity, CXCL5, CXCL2, interleukin‐6 (IL‐6), and CCL5 levels as well as morphological analyses. Platelet depletion reduce tissue damage and clinical disease activity index in DSS‐exposed animals. Platelet depletion not only reduces levels of CXCL2 and CXCL5 but also levels of CCL5 in the inflamed colon. Immunoneutralization of CCL5 but not CXCL4 reduces tissue damage, CXC chemokine expression, and neutrophil recruitment in DSS‐treated animals. These findings show that platelets play a key role in acute colitis by regulating CXC chemokine generation, neutrophil infiltration, and tissue damage in the colon. Moreover, our results suggest that platelet‐derived CCL5 is an important link between platelet activation and neutrophil recruitment in acute colitis. J. Cell. Physiol. 231: 370–376, 2016. © 2015 Wiley Periodicals, Inc.
Synthesis of Novel Heterocycles Derived from 4‐Arylmethylene‐2‐phenyl‐1,3‐oxazole‐5(4H)‐ones
Authors: Youssef Ahmed S. A. , Kandeel Kamal A. , Abou‐Elmagd Wael S. I. , Haneen David S. A.
Published: June 2015

The acid hydrazide derivatives 2 were converted into pyrazolone, triazinone, and schiff bases. However, the reaction of Schiff base 12 with malononitrile or thioglycolic acid gives the pyrazolotriazinone or thiazolidinone derivative, respectively. The structures of the newly synthesized compounds were established on the basis of IR, 1H‐NMR, mass spectral data, and elemental analyses. The antimicrobial activities of the synthesized compounds were examined against two types of bacteria and two types of fungi. Some of the tested compounds showed promising activities.
Mouse lung‐adapted mutation of E190G in hemagglutinin from H5N1 influenza virus contributes to attenuation in mice
Authors: Han Pengfei , Hu Yi , Sun Wei , Zhang Sen , Li Yuchang , Wu Xiaoyan , Yang Yinhui , Zhu Qingyu , jiang Tao , Li Jing , Qin Chengfeng
Published: June 2015

The highly pathogenic H5N1 avian influenza virus is one of the greatest influenza pandemic threats since 2003. The association of the receptor binding domain (RBD) with the virulence of influenza virus is rarely addressed, particularly of H5N1 influenza viruses. In this study, BALB/c mice were intranasally infected with A/Vietnam/1194/2004 (VN1194, H5N1). The mouse lung‐adapted variants were isolated and the mutation of E190G (H3 numbering) in the RBD was recognized. The recombinant virus, rVN‐E190G carrying E190G in hemagglutinin (HA) was designed and rescued using reverse genetics techniques. The receptor binding activity, growth curve and pathogenicity in mice of the rVN‐E190G were investigated. Results demonstrated that rVN‐E190G virus increased the binding avidity to α2,6 SA (sialic acid) and reduced the affinity to α2,3 SA, meanwhile weakened the viral replication in vitro. Moreover, the virulence assessment demonstrated that rVN‐E190G was attenuated in mice. These results indicated that the mutation E190G in HA decreases H5N1 viral replication in vitro and significantly attenuates virulence in vivo. These findings identify one of the determinants in RBD which can be associated with H5N1 virulence in mice. J. Med. Virol. 87:1816–1822, 2015. © 2015 Wiley Periodicals, Inc.
Contribution of tropical cyclones to extreme rainfall in Australia
Authors: Villarini Gabriele , Denniston Rhawn F.
Published: June 2015

The contribution by tropical cyclones (TCs) to extreme rainfall in Australia is examined using daily rainfall measurements from over 2000 rain gauges. Analyses focus on the period beginning with regular satellite monitoring of TCs (1969/1970) through the year 2012/2013 and consider daily and multi‐daily annual maximum rainfall series. Our results indicate that TCs play a prominent role in extreme rainfall over much Australia, with more than half of the highest annual rainfall events associated with these storms over the coastal regions and in particular over Western Australia. Moreover, the TC fractional contribution to extreme rainfall increases as we focus on the largest rainfall events, with approximately 66–100% of annual maxima in excess of 100 mm (∼4 inches) over Western Australia associated with TCs at over one third of the locations. Given the well‐established controls on Australian TC activity by the El Niño–Southern Oscillation (ENSO), we also examined the relationship between extreme rainfall associated with TCs and ENSO using logistic regression. A larger probability of having an annual rainfall maximum related to TCs occurs during La Niña years, consistent with enhanced Australian cyclogenesis during these phases of ENSO. We also highlighted regional differences in the link between ENSO and extreme rainfall events, highlighting the stronger connection along the coastal areas and in particular over Western Australia.
Unambiguous warming in the western tropical Pacific primarily caused by anthropogenic forcing
Authors: Wang Guomin , Power Scott B. , McGree Simon
Published: June 2015

Small Island Developing States in the tropical western Pacific are among the most vulnerable to climate change. While a great deal of information on the observed climate change trends and their cause is available for many other regions and for the globe as a whole, much less information has been available specifically for the Pacific. Here, we show that warming over the past 50 years in the western Pacific is evident in recently homogenized tropical station data, and in gridded surface temperature data sets for the region. The warming has already emerged from the background climate variability. The observational data and Coupled Model Intercomparison Project Phase 5 climate model output are used to show that the observed warming was primarily caused by human‐forced changes to the earth's radiative balance. Further warming is projected to occur in the same models under all three Representative Concentration Pathways (RCPs) considered (RCP2.6, RCP4.5 and RCP8.5), with the magnitude far exceeding the warming to date under the two scenarios with higher emissions (RCP4.5 and RCP8.5).
Unified chromatography: Fundamentals, instrumentation and applications†
Authors: Silva Meire R. , Andrade Felipe N. , Fumes Bruno H. , Lanças Fernando M.
Published: June 2015

The concept of unified chromatography has been in existence for 50 years after the work of Giddings proposing that all modes of chromatography (gas chromatography, liquid chromatography, supercritical fluid chromatography and so on) may be treated together under a single unified theory. His idea was partially fulfilled 23 years later by Ishii, Takeuchi and colleagues, who demonstrated for the first time the possibility to analyze a complex sample containing substances with a wide range of boiling points and polarities in the same instrument and column, just by varying the mobile phase pressure and temperature to change from one chromatographic mode to another. This approach has been demonstrated through application to the separation of complex mixtures in several areas including crude oil, edible oils and polymers. Still, unified chromatography has not yet been fully developed. In the present work, we will review the fundamentals, instrumentation and several applications of the technique. Also discussed are the drawbacks that still hinder development, as well as the recent developments and trends in instrumentation and columns that suggest the most feasible ways forward to the full development of unified chromatography.
Organic monolith frits encased in polyether ether ketone tubing with improved durability for liquid chromatography
Authors: Park Sin Young , Cheong Won Jo
Published: June 2015

This study introduces a preparation method for polymer‐encased monolith frits with improved durability for liquid chromatography columns. The inner surface of the polyether ether ketone tubing is pretreated with sulfuric acid in the presence of catalysts (vanadium oxide and sodium sulfate). The tubing was rinsed with water and acetone, flushed with nitrogen, and treated with glycidyl methacrylate. After washing, the monolith reaction mixture composed of lauryl methacrylate, ethylene glycol dimethacrylate, initiator, and porogenic solvent was filled in the tubing and subjected to in situ polymerization. The tubing was cut into thin slices and used as frits for microcolumns. To check their durability, the frit slices were placed in a vial and a heavy impact was applied on the vial by a vortex mixer for various periods. The frits made in the presence of catalysts were found to be more durable than those made without catalysts. Furthermore, when the monolith‐incorporated tubing was used as a chromatography column, the column prepared in the presence of catalysts resulted in a better separation efficiency. The separation performance of the columns installed with the polyether ether ketone encased monolith frits was comparable to that of the columns installed with the commercial stainless‐steel screen frits.
Correlates of excessive daytime sleepiness in de novo Parkinson's disease: A case control study
Authors: Simuni Tanya , Caspell‐Garcia Chelsea , Coffey Christopher , Chahine Lama M. , Lasch Shirley , Oertel Wolfgang H. , Mayer Geert , Högl Birgit , Postuma Ron , Videnovic Aleksandar , Amara Amy Willis , Marek Ken ,   for the PPMI Sleep Working group on behalf of the PPMI Investigators
Published: June 2015

Objective

This study was undertaken to determine the frequency and correlates of excessive daytime sleepiness in de novo, untreated Parkinson's disease (PD) patients compared with the matched healthy controls.

Methods

Data were obtained from the Parkinson's Progression Markers Initiative, an international study of de novo, untreated PD patients and healthy controls. At baseline, participants were assessed with a wide range of motor and nonmotor scales, including the Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS‐UPDRS). Excessive daytime sleepiness was assessed based on the Epworth Sleepiness scale (ESS), with a cutoff of 10.

Results

Four hundred twenty‐three PD subjects and 196 healthy controls were recruited into the study. Mean ESS (min, max) score was 5.8 (0, 20) for the PD subjects and 5.6 (0, 19) for healthy controls (P = 0.54). Sixty‐six (15.6%) PD subjects and 24 (12%) healthy controls had ESS of at least 10 (P = 0.28). No difference was seen in demographic characteristics, age of onset, disease duration, PD subtype, cognitive status, or utilization of sedatives between the PD sleepiness‐positive versus the negative group. The sleepiness‐positive group had higher MDS‐UPDRS Part I and II but not III scores, and higher depression and autonomic dysfunction scores. Sleepiness was associated with a marginal reduction of A‐beta (P = 0.05) but not alpha‐synuclein spinal fluid levels in PD.

Conclusions

This largest case control study demonstrates no difference in prevalence of excessive sleepiness in subjects with de novo untreated PD compared with healthy controls. The only clinical correlates of sleepiness were mood and autonomic dysfunction. Ongoing longitudinal analyses will be essential to further examine clinical and biological correlates of sleepiness in PD and specifically the role of dopaminergic therapy. © 2015 International Parkinson and Movement Disorder Society
Refinements in flap design and inset for pharyngoesophageal reconstruction with free thigh flaps
Authors: Zelken Jonathan A. , Kang Chung‐Jan , Huang Shiang‐Fu , Liao Chun‐Ta , Tsao Chung‐Kan
Published: June 2015

Background

Complications arising from anastomotic failure may occur after pharyngoesophageal reconstruction. In this report we present results of pharyngoesophageal reconstruction with free thigh flaps using a refined design and inset strategy in a series of patients.

Methods

From May 2011 to December 2012, pharyngoesophageal oncologic defects were reconstructed in 12 men using thigh flaps. Flaps were designed to exceed defect circumference to allow draping of the excess over injury‐prone vessels (so‐called delta‐inset). Patients were 39‐ to 68‐years‐old (mean, 51.8‐years‐old) at the time of surgery. BMI ranged from 17 to 28 kg/m2 (average, 21.5 kg/m2). The sites of defects were the hypopharynx in 11 cases and the pharynx in 1 case. Ten anterolateral thigh (ALT) flaps and 2 anteromedial thigh (AMT) flaps were used. All patients underwent radiation therapy.

Results

The average flap size was 22 × 9 cm (range: 16–26 × 7–11 cm2). There were no partial or total flap losses, and no donor site complications. Follow‐up was 19.3 months (range: 2.4–21.6 months) including 8 patients (75%) who succumbed to disease in the follow‐up period. Oral intake was achieved in all patients. Recipient site complications occurred in 50% of cases and included fistula (2 cases), fistula and stricture (2 cases), stricture (1 case), and lymphocele (1 case). Four patients required revision for fistula.

Conclusions

A refined thigh flap design and inset method in pharyngoesophageal reconstruction may circumvent complications arising from toxic drainage and vascular injury. However, there are insufficient data to make meaningful comparisons to alternative methods. © 2015 Wiley Periodicals, Inc. Microsurgery 37:112–118, 2017.
Investigation of chloromethane complexes of cryptophane‐A analogue with butoxy groups using 13C NMR in the solid state and solution along with single crystal X‐ray diffraction
Authors: Steiner Emilie , Mathew Renny , Zimmermann Iwan , Brotin Thierry , Edén Mattias , Kowalewski Jozef
Published: June 2015

Host‐guest complexes between cryptophane‐A analogue with butoxy groups (cryptophane‐But) and chloromethanes (chloroform, dichloromethane) were investigated in the solid state by means of magic‐angle spinning 13C NMR spectroscopy. The separated local fields method with 13C‐1H dipolar recoupling was used to determine the residual dipolar coupling for the guest molecules encaged in the host cavity. In the case of chloroform guest, the residual dipolar interaction was estimated to be about 19 kHz, consistent with a strongly restricted mobility of the guest in the cavity, while no residual interaction was observed for encaged dichloromethane. In order to rationalize this unexpected result, we performed single crystal X‐ray diffraction studies, which confirmed that both guest molecules indeed were present inside the cryptophane cavity, with a certain level of disorder. To improve the insight in the dynamics, we performed a 13C NMR spin‐lattice relaxation study for the dichloromethane guest in solution. The system was characterized by chemical exchange, which was slow on the chemical shift time scale but fast with respect to the relaxation rates. Despite these disadvantageous conditions, we demonstrated that the data could be analyzed and that the results were consistent with an isotropic reorientation of dichloromethane within the cryptophane cavity. Copyright © 2015 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.
The Evolution of Information and Communication Technology in Public Administration
Authors: Liu Shuhua Monica , Yuan Qianli
Published: June 2015

Over the last decades, governments all over the world have tried to take advantage of information and communication technology (ICT) to improve government operations and communication with citizens. Adoption of e‐government has increased in most countries, but at the same time, the rate of successful adoption and operation varies from country to country. This article outlines the evolution of ICT in the public sector over the past 25 years. It presents general trends by examining interactions and mutual shaping processes between ICT evolution and several inter‐related institutional changes including government operations, public services delivery, citizen participation, policy and decision making, and governance reform. The authors suggest that within a short time period, e‐governance has evolved rapidly from rudimentary uses of ICTs as simple tools to support highly structured administrative work to the integration of ICT throughout government operations. The growing use of Web 2.0, social media, and mobile and wireless ICT by citizens can also heavily impact the way public services are delivered and how citizen engagement processes are carried out. However, new management approaches, governance structures, and policy frameworks are still missing, posing a challenge for governments to operate effectively in the age of big data. Generally, developing countries are lagging behind in e‐government adoption compared with developed countries. Thus, for developing countries to successfully adopt ICT and try to leapfrog some of the obstacles encountered by early ICT adopters in developed countries, systematic analyses need to be conducted to understand the interactions among stakeholders and ICTs and co‐create the institutional environment to lead to a positive impact of ICT on public administration. Only when this relationship is clearly understood can innovative ICTs be seamlessly integrated into the governance structure. Copyright © 2015 John Wiley & Sons, Ltd.
Nicotinamide‐based poly(ether amide)s: a novel type of soluble thermally stable polyamides
Authors: Mehdipour‐Ataei Shahram , Ehsani Sara
Published: June 2015

In order to obtain a novel type of thermally stable polyamides with enhanced solubility, design and synthesis of a diamine were achieved. A nicotinamide‐based dichloro compound was obtained via nucleophilic substitution reaction of 2,6‐diaminopyridine with 6‐chloronicotinoyl chloride. The final diamine was attained through reaction of dichloro product with 5‐amino‐1‐hydroxynaphthalene. The obtained materials were completely characterized by common spectroscopic methods and elemental analysis. Polycondensation reaction of the diamine with different diacid chlorides led to the preparation of related nicotinamide‐based poly(ether amide)s. Polymers were well characterized, and their physical and thermal properties including viscosity, solubility, thermal behavior and stability, flame retardancy, and crystallinity were studied. The polymers showed high thermal stability and flame retardancy together with enhanced solubility. Copyright © 2015 John Wiley & Sons, Ltd.
Genomic landscape of adenoid cystic carcinoma of the breast
Authors: Martelotto Luciano G , De Filippo Maria R , Ng Charlotte KY , Natrajan Rachael , Fuhrmann Laetitia , Cyrta Joanna , Piscuoglio Salvatore , Wen Huei‐Chi , Lim Raymond S , Shen Ronglai , Schultheis Anne M , Wen Y Hannah , Edelweiss Marcia , Mariani Odette , Stenman Göran , Chan Timothy A , Colombo Pierre‐Emmanuel , Norton Larry , Vincent‐Salomon Anne , Reis‐Filho Jorge S , Weigelt Britta
Published: June 2015

Adenoid cystic carcinoma (AdCC) is a rare type of triple‐negative breast cancer (TNBC) characterized by the presence of the MYB–NFIB fusion gene. The molecular underpinning of breast AdCCs other than the MYB–NFIB fusion gene remains largely unexplored. Here we sought to define the repertoire of somatic genetic alterations of breast AdCCs. We performed whole‐exome sequencing, followed by orthogonal validation, of 12 breast AdCCs to determine the landscape of somatic mutations and gene copy number alterations. Fluorescence in situ hybridization and reverse‐transcription PCR were used to define the presence of MYB gene rearrangements and MYB–NFIB chimeric transcripts. Unlike common forms of TNBC, we found that AdCCs have a low mutation rate (0.27 non‐silent mutations/Mb), lack mutations in TP53 and PIK3CA and display a heterogeneous constellation of known cancer genes affected by somatic mutations, including MYB, BRAF, FBXW7, SMARCA5, SF3B1 and FGFR2. MYB and TLN2 were affected by somatic mutations in two cases each. Akin to salivary gland AdCCs, breast AdCCs were found to harbour mutations targeting chromatin remodelling, cell adhesion, RNA biology, ubiquitination and canonical signalling pathway genes. We observed that, although breast AdCCs had rather simple genomes, they likely display intra‐tumour genetic heterogeneity at diagnosis. Taken together, these findings demonstrate that the mutational burden and mutational repertoire of breast AdCCs are more similar to those of salivary gland AdCCs than to those of other types of TNBCs, emphasizing the importance of histological subtyping of TNBCs. Furthermore, our data provide direct evidence that AdCCs harbour a distinctive mutational landscape and genomic structure, irrespective of the disease site of origin. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
In‐field volatile analysis employing a hand‐held portable GC‐MS: emission profiles differentiate damaged and undamaged yellow starthistle flower heads
Authors: Beck John J. , Porter Nathan , Cook Daniel , Gee Wai S. , Griffith Corey M. , Rands Anthony D. , Truong Tai V. , Smith Lincoln , San Román Itxaso
Published: June 2015

Introduction

Understanding the complex chemical signalling of plants and insects is an important component of chemical ecology. Accordingly, the collection and analysis of chemical cues from plants in their natural environment is integral to elucidation of plant–insect communications. Remote plant locations and the need for a large number of replicates make in situ headspace analyses a daunting logistical challenge. A hand‐held, portable GC‐MS system was used to discriminate between damaged and undamaged Centaurea solstitialis (yellow starthistle) flower heads in both a potted‐plant and natural setting.

Objective

To determine if a portable GC‐MS system was capable of distinguishing between undamaged and mechanically damaged plant treatments, and plant environments.

Methodology

A portable GC‐MS utilising needle trap adsorbent technology was used to collect and analyse in situ headspace volatiles of varying yellow starthistle treatments. Principal component analysis (PCA) was used to distinguish treatments and identify biomarker volatiles. Analysis of variance (ANOVA) was used to determine differences between treatment volatile amounts.

Results

The portable GC‐MS system detected 31 volatiles from the four treatments. Each GC‐MS run was completed in less than 3 min. PCA showed four distinct clusters representing the four treatments – damaged and undamaged potted plant, and damaged and undamaged natural plant. Damage‐specific volatiles were identified.

Conclusion

The portable GC‐MS system distinguished the treatments based on their detected volatile profiles. Additional statistical analysis identified five possible biomarker volatiles for the treatments, among them cyclosativene and copaene, which indicated damaged flower heads. Copyright © 2015 John Wiley & Sons, Ltd.
The significance of gender in fetuses with increased nuchal translucency: pregnancy outcomes and long‐term outcomes of children
Authors: Äyräs Outi , Eronen Marianne , Tikkanen Minna , Rahkola‐Soisalo Päivi , Paavonen Jorma , Stefanovic Vedran
Published: June 2015

Objective

We aim to study the gender impact on the pregnancy outcome and on the long‐term outcome of children after increased fetal nuchal translucency.

Method

All singleton pregnancies with increased nuchal translucency (≥3 mm until 1 March 2004 and ≥95th percentile thereafter) referred to Helsinki University Hospital from 2002 to 2007 with known gender and normal sex chromosomes were included. The pregnancy outcome (miscarriage, termination of pregnancy, perinatal death or delivery of a healthy/unhealthy child) and the long‐term outcome (structural defects or neurodevelopmental impairment) were recorded from hospital databases and national registers.

Results

Of the 1011 fetuses, 600 were male and 411 were female, male‐to‐female ratio being 1.46 : 1. This ratio decreased by increasing NT thickness, being 1 : 1 when the NT was ≥4.0 mm. The pregnancy outcome was better among male fetuses than among female fetuses (p = 0.049). There were more chromosomal abnormalities among the females than the males (p = 0.04). Among euploid fetuses, the pregnancy outcome and the long‐term outcome were equal.

Conclusion

After increased nuchal translucency, the pregnancy outcome of male fetuses was better due to the lower incidence of chromosomal abnormalities compared with female fetuses. Among euploid fetuses, the pregnancy outcome and the long‐term outcome were equal. © 2015 John Wiley & Sons, Ltd.
Clinical outcome of subchromosomal events detected by whole‐genome noninvasive prenatal testing
Authors: Helgeson J. , Wardrop J. , Boomer T. , Almasri E. , Paxton W. B. , Saldivar J. S. , Dharajiya N. , Monroe T. J. , Farkas D. H. , Grosu D. S. , McCullough R. M.
Published: June 2015

Objective

A novel algorithm to identify fetal microdeletion events in maternal plasma has been developed and used in clinical laboratory‐based noninvasive prenatal testing. We used this approach to identify the subchromosomal events 5pdel, 22q11del, 15qdel, 1p36del, 4pdel, 11qdel, and 8qdel in routine testing. We describe the clinical outcomes of those samples identified with these subchromosomal events.

Methods

Blood samples from high‐risk pregnant women submitted for noninvasive prenatal testing were analyzed using low coverage whole genome massively parallel sequencing. Sequencing data were analyzed using a novel algorithm to detect trisomies and microdeletions.

Results

In testing 175 393 samples, 55 subchromosomal deletions were reported. The overall positive predictive value for each subchromosomal aberration ranged from 60% to 100% for cases with diagnostic and clinical follow‐up information. The total false positive rate was 0.0017% for confirmed false positives results; false negative rate and sensitivity were not conclusively determined.

Conclusion

Noninvasive testing can be expanded into the detection of subchromosomal copy number variations, while maintaining overall high test specificity. In the current setting, our results demonstrate high positive predictive values for testing of rare subchromosomal deletions. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd.
Large Scale Synthesis of Highly Stable Fluorescent Carbon Dots Using Silica Spheres as Carriers for Targeted Bioimaging of Cancer Cells
Authors: Wang Chuanxi , Xu Zhenzhu , Lin Huihui , Huang Yijun , Zhang Chi
Published: June 2015

In this paper, fluorescent carbon dots (CDs) loaded on silica (SiO2) spheres are synthesized by the one‐pot hydrothermal route, and then folic acids (FA) are covalently conjugated on the surface of SiO2 spheres. The formed SiO2@CDs‐FA composites can target specific tissues, e.g., cancer. The key of this method is the employment of (3‐aminopropyl)trimethoxysilane as bridge joint, which not only serves as surface passivation agents allowing the large scale synthesis of CDs with high quantum yield, but also enables SiO2@CDs composites further covalent conjugation of FA. The resultant SiO2@CDs composites have many advantages such as easy separation and purification, highly stable, well water‐soluble, and biocompatible. Moreover, the SiO2@CDs‐FA could be used as fluorescent probes for biological imaging in vitro. The uptake of the SiO2@CDs‐FA into HeLa cells is receptor‐mediated endocytosis, which is confirmed by a comparative study using FR‐negative 293T cells. Findings from this study suggest that the SiO2@CDs‐FA composites could be used as a platform for cancer diagnosis studies in various biological systems.
Identification of six cell surface proteins for specific liver targeting
Authors: Ducret Axel , Kux van Geijtenbeek Sabine , Röder Daniel , Simon Sandrine , Chin Daniel , Berrera Marco , Gruenbaum Lore , Ji Changhua , Cutler Paul
Published: June 2015

Purpose

Cell surface proteins are the primary means for a cell to sense and interact with its environment and their dysregulation has been linked to numerous diseases. In particular, the identification of proteins specific to a single tissue type or to a given disease phenotype may enable the characterization of novel therapeutic targets. We tested here the feasibility of a cell surface proteomics approach to identify pertinent markers directly in a clinically relevant tissue.

Experimental design

We analyzed the cell surface proteome of freshly isolated primary heptatocytes using a glycocapture‐specific approach combined with a robust bioinformatics filtering.

Results

Using primary lung epithelial cell cultures as negative controls, we identified 32 hepatocyte‐specific cell surface proteins candidates. We used mRNA expression to select six markers that may provide adequate specificity for targeting therapeutics to the liver.

Conclusions and clinical relevance

We demonstrate the feasibility and the importance of conducting such studies directly in a clinically relevant tissue. In particular, the cell surface proteome of freshly isolated hepatocytes differed substantially from cultured cell lines.
Genetic basis, evolutionary origin and spread of resistance to herbicides inhibiting acetolactate synthase in common groundsel (Senecio vulgaris)
Authors: Délye Christophe , Causse Romain , Michel Séverine
Published: June 2015

BACKGROUND

Following control failure by herbicides inhibiting acetolactate synthase (ALS) in French wheat fields and vineyards, we aimed to confirm resistance evolution and investigate the evolutionary origin and spread of resistance in the tetraploid species Senecio vulgaris (common groundsel), a widespread, highly mobile weed.

RESULTS

Sequencing of two ALS homeologues in S. vulgaris enabled the first identification and characterisation of ALS‐based resistance in this species. Cross‐resistance patterns associated with Leu‐197 and Ser‐197 ALS1 were established using eight herbicides. Sequencing and genotyping showed that ALS‐based resistance evolved by multiple, independent appearances of mutant ALS1 and ALS2 alleles followed by spread. Spread of a mutant ALS1 allele issued from one particular appearance event was observed over 60 km. Independent resistance appearance events and easy seed dispersion are the most likely reasons for populations of S. vulgaris containing different mutant ALS alleles. Accumulation of different alleles probably due to sexual reproduction was observed in the same plant.

CONCLUSION

Mutant ALS alleles and possibly other mechanisms cause resistance to ALS inhibitors in S. vulgaris. Management strategies should aim at limiting S. vulgaris establishment and seed set. Considering the mobility of this species, control coordination at a regional level is clearly necessary if resistance spread is to be contained. © 2015 Society of Chemical Industry
Transparent conductive nanoporous aluminium mesh prepared by electrochemical anodizing
Authors: Hubarevich Aliaksandr , Marus Mikita , Stsiapanau Andrei , Smirnov Aliaksandr , Zhao Junliang , Fan Weijun , Wang Hong , Sun Xiaowei
Published: June 2015

A non‐lithographic method for the fabrication of the transparent conductive nanoporous aluminium (Al) mesh is presented. The electrochemical anodizing of Al layer deposited on the glass substrate was used to obtain the mesh. The average transmittance of 10–60% in 400–800 nm wavelength range and the sheet resistance of 10–1000 Ω sq−1 have been obtained for Al mesh with disordered pores arrangement. It was found that transmittance of uniformly arranged porous mesh is increased up to 80–90% with the conductivity range of 25–100 Ω sq−1. Our results demonstrate porous Al mesh as a strong candidate of low‐cost transparent conductive electrode, especially for flexible electronics.
Solitary waves in auxetic rods with quadratic nonlinearity: Exact analytical solutions and numerical simulations
Authors: Bui Dinh T. , Cao Long V. , Wojciechowski K. W.
Published: June 2015

Special soliton analytical solutions are seeked for the so‐called double dispersion equation (or Porubov's equation), which describes the propagation of longitudinal waves in an elastic rod. Using the F‐expansion method, a new interesting class of traveling solitary waves is obtained. As a byproduct, the results obtained by other authors for some special cases are regained. Some numerical simulations are also performed. Splitting of various initial pulses during propagation into a sequence of solitary waves is considered. The dependence of the amplitude and the velocity of the solitary waves on Poisson's ratio is discussed in detail. Collisions between some obtained solitary waves are also presented. The simulation results are compared with the obtained exact analytical solutions—the latter reflect the perfect balance between the nonlinearity and dispersion. The comparison indicates that the obtained exact solutions are useful for describing more complicated wave fields studied by numerical simulations. It also indicates that the numerical results for auxetic materials are in better agreement with theoretical solutions than in the case of ordinary materials. Furthermore, one can conclude that the Secant pulse generates solitary waves closer to the analytical predictions than a Gaussian pulse. This is similar to the case of variational method, where the Secant trial function is also more proper than the Gaussian one.
A temporal correlation function for the association between patient‐reported outcome and clinical endpoints
Authors: Gong Qi , Fang Liang
Published: June 2015

For clinical trials with multiple endpoints, the primary interest is usually to evaluate the relationship of these endpoints and treatment interventions. Studying the correlation of two clinical trial endpoints can also be of interests. For example, the association between patient‐reported outcome and clinically assessed endpoint could answer important research questions and also generate interesting hypothesis for future research. However, it is not straightforward to quantify such association. In this article, we proposed a multiple event approach to profile such association with a temporal correlation function, visualized by a correlation function plot over time with a confidence band. We developed this approach by extending the existing methodology in recurrent event literature. This approach was shown to be generally unbiased and could be a useful tool for data visualization and inference. We demonstrated the use of this method with data from a real clinical trial. Although this approach was developed to evaluate the association between patient‐reported outcome and adverse events, it can also be used to evaluate the association of any two endpoints that can be translated to time‐to‐event endpoints. Copyright © 2015 John Wiley & Sons, Ltd.
Evaluation of the Logarithmic Law of the Wall for River Flows
Authors: Petrie J. , Diplas P.
Published: June 2015

The logarithmic law of the wall is commonly used to determine the shear stress applied to the river bed by the flow field. The shear stress calculation requires a velocity profile at the location of interest—data that can be obtained with a boat‐mounted acoustic Doppler current profiler (ADCP). ADCP survey procedures use either a fixed‐vessel (FV) or moving‐vessel (MV) with each providing different spatial and temporal resolution. MV procedures require significantly less field effort but the data lack the temporal resolution of FV measurements. This fact has motivated investigators to seek MV procedures and analysis techniques that provide equivalent results to FV measurements. This study compares results of the two survey procedures for depth‐averaged quantities (velocity and flow direction), mean velocity profiles, shear velocity and equivalent sand grain roughness. Mean velocity profiles are produced by time averaging for the FV measurements and spatial averaging for the MV measurements. Shear velocity and equivalent sand grain roughness are determined using simple linear regression applied to the logarithmic law of the wall. These procedures are demonstrated using data obtained during bankfull flow on the lower Roanoke River, North Carolina, USA. The results indicate comparable estimates of depth‐averaged quantities from both survey procedures. Estimates of the mean velocity profiles were found to be more variable. The agreement for shear velocity and equivalent sand grain roughness was generally poor indicating that further work is necessary to produce comparable results with MV survey procedures. Copyright © 2015 John Wiley & Sons, Ltd.
DVB‐S2X‐enabled precoding for high throughput satellite systems
Authors: Arapoglou Pantelis‐Daniel , Ginesi Alberto , Cioni Stefano , Erl Stefan , Clazzer Federico , Andrenacci Stefano , Vanelli‐Coralli Alessandro
Published: June 2015

Multi‐user multiple‐input multiple‐output (MU‐MIMO) has allowed recent releases of terrestrial long‐term evolution (LTE) standards to achieve significant improvements in terms of offered system capacity. The publication of the DVB‐S2X standard and particularly of its novel superframe structure is a key enabler for applying similar interference management techniques –such as precoding– to multibeam high throughput satellite (HTS) systems. This paper presents results from the European Space Agency‐funded R&D activities concerning the practical issues that arise when precoding is applied over an aggressive frequency re‐use HTS network. In addressing these issues, the paper also proposes pragmatic solutions that have been developed in order to overcome these limitations. Through the application of a comprehensive system simulator, it is demonstrated that important capacity gains (beyond 40%) are to be expected from applying precoding even after introducing a number of significant practical impairments. Copyright © 2015 John Wiley & Sons, Ltd.