bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of cancer stem cells in vincristine preconditioned SGC7901 gastric cancer cell line
Authors: Xue Zengfu , Yan Hui , Li Juntang , Liang Shuli , Cai Xiqiang , Chen Xiong , Wu Qiong , Gao Liucun , Wu Kaichun , Nie Yongzhan , Fan Daiming
Published: September 2011

Cancer stem cells (CSCs), or tumor initiating cells, are a subpopulation of cancer cells with self‐renewal and differentiation properties. However, there has been no direct observation of the properties of gastric CSCs in vitro. Here we describe a vincristine (VCR)‐preconditioning approach to obtain cancer stem‐like cells (CSLCs) from the gastric cancer cell line SGC7901. The CSLCs displayed mesenchymal characteristics, including the up‐regulated mesenchymal markers Snail, Twist, and vimentin, and the down‐regulated epithelial marker E‐cadherin. Using a Matrigel‐based differentiation assay, CSLCs formed 2D tube‐like and 3D complex lumen‐like structures, which resembled differentiated gastric crypts. The characteristic of cellular differentiation was also found by transmission electron microscopy and up‐regulation of gastrointestinal genes CDX2 and SOX2. We further showed that CSLCs could self‐renew through significant asymmetric division compared with parent cells by tracing PKH‐26, BrdU, and EDU label‐retaining cells. In addition, these CSLCs also increased expression of CD44, CD90, and CXCR4 at the mRNA level, which was identified as novel targets. Furthermore, drug sensitivity assays and xenograft experiments demonstrated that the cells developed multi‐drug resistance (MDR) and significant tumorigenicity in vivo. In summary, gastric CSCs were identified from VCR‐preconditioned SGC7901 cell line, characterized by high tumorigenicity and the capacity for self‐renewal and differentiation. J. Cell. Biochem. 113: 302–312, 2012. © 2011 Wiley Periodicals, Inc.
Combination of low O2 concentration and mesenchymal stromal cells during culture of cord blood CD34+ cells improves the maintenance and proliferative capacity of hematopoietic stem cells
Authors: Hammoud Mohammad , Vlaski Marija , Duchez Pascale , Chevaleyre Jean , Lafarge Xavier , Boiron Jean‐Michel , Praloran Vincent , Brunet de la Grange Philippe , Ivanovic Zoran
Published: September 2011

The physiological approach suggests that an environment associating the mesenchymal stromal cells (MSC) and low O2 concentration would be most favorable for the maintenance of hematopoietic stem cells (HSCs) in course of ex vivo expansion of hematopoietic grafts. To test this hypothesis, we performed a co‐culture of cord blood CD34+ cells with or without MSC in presence of cytokines for 10 days at 20%, 5%, and 1.5% O2 and assessed the impact on total cells, CD34+ cells, committed progenitors (colony‐forming cells—CFC) and stem cells activity (pre‐CFC and Scid repopulating cells—SRC). Not surprisingly, the expansion of total cells, CD34+ cells, and CFC was higher in co‐culture and at 20% O2 compared to simple culture and low O2 concentrations, respectively. However, co‐culture at low O2 concentrations provided CD34+ cell and CFC amplification similar to classical culture at 20% O2. Interestingly, low O2 concentrations ensured a better pre‐CFC and SRC preservation/expansion in co‐culture. Indeed, SRC activity in co‐culture at 1.5% O2 was higher than in freshly isolated CD34+ cells. Interleukin‐6 production by MSC at physiologically low O2 concentrations might be one of the factors mediating this effect. Our data demonstrate that association of co‐culture and low O2 concentration not only induces sufficient expansion of committed progenitors (with respect to the classical culture), but also ensures a better maintenance/expansion of hematopoietic stem cells (HSCs), pointing to the oxygenation as a physiological regulatory factor but also as a cell engineering tool. J. Cell. Physiol. 227: 2750–2758, 2012. © 2011 Wiley Periodicals, Inc.
CFTR negatively regulates cyclooxygenase‐2‐PGE2 positive feedback loop in inflammation
Authors: Chen Jing , Jiang Xiao Hua , Chen Hui , Guo Jing Hui , Tsang Lai Ling , Yu Mei Kuen , Xu Wen Ming , Chan Hsiao Chang
Published: September 2011

Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations of the cystic fibrosis transmembrane conductance regulator (CFTR), a cAMP‐dependent anion channel mostly expressed in epithelia. Accumulating evidence suggests that CF airway epithelia are overwhelmed by excessive inflammatory cytokines and prostaglandins (PGs), which eventually lead to the over‐inflammatory condition observed in CF lung disease. However, the exact underlying mechanism remains elusive. In this study, we observed increased cyclooxygenase‐2 (COX‐2) expression and over‐production of prostaglandin E2 (PGE2) in human CF bronchial epithelia cell line (CFBE41o−) with elevated NF‐κB activity compared to a wild‐type airway epithelial cell line (16HBE14o−). Moreover, we demonstrated that CFTR knockout mice had inherently higher levels of COX‐2 and NF‐κB activity, supporting the notion that lack of CFTR results in hyper‐inflammatory signaling. In addition, we identified a positive feedback loop for production of PGE2 involving PKA and transcription factor, CREB. More importantly, overexpression of wild‐type CFTR significantly suppressed COX‐2 expression in CFBE41o− cells, and wild‐type CFTR protein expression was significantly increased when 16HBE14o− cells were challenged with LPS as well as PGE2, indicating possible involvement of CFTR in negative regulation of COX‐2/PGE2. In conclusion, CFTR is a negative regulator of PGE2‐mediated inflammatory response, defect of which may result in excessive activation of NF‐κB, leading to over production of PGE2 as seen in inflammatory CF tissues. J. Cell. Physiol. 227: 2759–2766, 2012. © 2011 Wiley Periodicals, Inc.
Insect Allergy
Authors: Tracy James M.
Published: September 2011

Anaphylaxis is a life‐threatening allergic condition. The 3 most common triggers for anaphylaxis are food, medications, and insects. All of these triggers are the sources of considerable morbidity and mortality, but of the 3, only insect allergy is treatable through means other than trigger avoidance. Because ≥40 deaths per year are attributed to insect stings, it is critical that healthcare providers and the public understand the proper diagnosis as well as the long‐term treatment of this potentially life‐threatening allergy. Unlike food and medication allergy, which are managed primarily by allergen avoidance, Hymenoptera allergy is managed prospectively using venom immunotherapy; this results in a protective level of up to 98%. Insects of the order Hymenoptera include bees, wasps, hornets, yellowjackets, and ants. They are responsible for the majority of the fatal and near‐fatal sting events. Understanding the biology and habitat of the various Hymenoptera species is helpful in recommending insect‐avoidance strategies. The diagnosis of insect allergy relies on a history of a systemic allergic reaction with appropriate testing for venom‐specific immunoglobulin E. If the history of a systemic reaction to an insect sting and the presence of venom specific immunoglobulin E is confirmed, venom immunotherapy is indicated. The proper and primary means of treating acute anaphylaxis is immediate epinephrine—and studies suggest that it is underutilized in the acute setting. However, it is venom immunotherapy, a disease‐modifying therapy, that provides the affected individual with the most effective protection against future sting reactions. Long‐term management of insect allergy and anaphylaxis includes appropriate referral to an allergist familiar with insect allergy and, if indicated, venom immunotherapy. Mt Sinai J Med 78:773–783, 2011. © 2011 Mount Sinai School of Medicine
Eczema
Authors: Sohn Andrew , Frankel Amylynne , Patel Rita V. , Goldenberg Gary
Published: September 2011

Atopic dermatitis, commonly known as eczema, is a common chronic, relapsing skin disease characterized by pruritus, disrupted epidermal barrier function, and immunoglobulin E–mediated sensitization to food and environmental allergens. Atopic dermatitis is a complex disease that arises from interactions between genes and the environment. Loci on several chromosomes have been identified, including a family of epithelium‐related genes called the epidermal differentiation complex on chromosome 1q21. Mutations in filaggrin, a key protein in epidermal differentiation, have also been identified in early‐onset and severe atopic dermatitis. There are 3 classical stages of eczema: infantile, childhood, and adulthood. The spectrum of eczema presentation varies widely from a variant that only affect the hand to major forms where a patient presents with erythroderma. The acute and subacute lesions of atopic dermatitis are often characterized by intensely pruritic, erythematous papules and vesicles with excoriations and a serous exudate. Chronic atopic dermatitis is exemplified by lichenified plaques and papules with excoriations. Atopic dermatitis patients are also at higher risk for skin infections, including bacterial and viral superinfections. Conventional therapy includes avoidance of irritants and potential allergens, as well as continued hydration of the skin with thick emollients. Topical corticosteroids and topical immunomodulators are often used primarily. Other therapies including phototherapy, antimicrobials, antihistamines, and systemic immunosuppressives are also options in certain situations. Mt Sinai J Med 78:730–739, 2011. © 2011 Mount Sinai School of Medicine
Ocular Allergy
Authors: Bielory Leonard
Published: September 2011

The eye is probably the most common site for the development of allergic inflammatory disorders, because it has no mechanical barrier to prevent the impact of allergens such as pollen on its surface. Physicians in various specialties and subspecialties who provide some form of primary care frequently encounter various forms of inflammation of the anterior surface of the eye that present as “red eye.” However, the eye is rarely the only target for an immediate allergic‐type response. Typically, many patients have other combinations of allergic disorders, such as rhinoconjunctivitis, rhinosinusitis, asthma, urticaria, or eczema. Even so, ocular signs and symptoms can frequently be the most prominent features of the entire allergic response for which a patient visits his or her physician. An improved differential diagnosis provides the basis for improved treatment algorithms. Over the past 20 years, we have witnessed an astonishing growth in therapeutic advances, ranging essentially from derivatives of simple aspirin to various newly developed biologic immunomodulatory agents, utilizing implantable drug‐delivery devices that exceed the safety and efficacy of those available for other organ systems, and resorting to advanced surgical techniques for the correction of sight‐threatening, disease‐related complications. Overall, with the expanding knowledge base, the intricacy of ocular inflammation appears to be becoming ever more manageable and, with the team approach between the primary care physician, the ophthalmologist, and the clinical allergist/immunologist, the new “immuno‐ophthalmology” approach improves patient outcomes. Mt Sinai J Med 78:740–758, 2011. © 2011 Mount Sinai School of Medicine
Ultrasonography in severe carpal tunnel syndrome
Authors: Kasius Kristel M. , Claes Franka , Verhagen Wim Im , Meulstee Jan
Published: September 2011

Introduction: In up to 30% of patients with carpal tunnel syndrome (CTS), the cross‐sectional area (CSA) of the median nerve may not be enlarged. We hypothesize that this could be the result of secondary atrophy of the nerve in severe CTS. The aim of this study was to measure the ultrasonographic CSA of the median nerve at the wrist in patients with severe CTS. Methods: In 14 consecutive patients with clinically and electrophysiologically defined severe CTS, the CSA of the median nerve was measured and compared with that of control subjects. Results: CSA of the median nerve exceeded the upper limit of normal in the majority of patients with severe CTS. Conclusions: Atrophy of the median nerve in severe CTS does not explain negative ultrasonographic test results. Instead, the CSA of the median nerve is enlarged in most patients with severe CTS. Muscle Nerve, 2012
Sensory Guillain–Barré syndrome and related disorders: An attempt at systematization
Authors: Uncini Antonino , Yuki Nobuhiro
Published: September 2011

The possibility that some patients diagnosed with an acute sensory neuropathy could actually have Guillain–Barré syndrome (GBS) has been repeatedly advanced in the literature, but the number of cases reported is small. The reports have shown different clinical presentations and electrophysiological findings and are variously named, thus generating terminological and nosological confusion. We operatively defined sensory GBS as an acute, monophasic, widespread neuropathy characterized clinically by exclusive sensory symptoms and signs that reach their nadir in a maximum of 6 weeks without related systemic disorders and other diseases or conditions. We reviewed the literature through searches of PubMed from 1980 to March 2011 and our own files. On the basis of the size of fibers involved and the possible site of primary damage, we propose tentatively classifying sensory GBS and related disorders into three subtypes: acute sensory demyelinating polyneuropathy; acute sensory large‐fiber axonopathy–ganglionopathy; and acute sensory small‐fiber neuropathy–ganglionopathy. Muscle Nerve, 2012
Can neck muscle spindle afferents activate fusimotor neurons of the lower limb?
Authors: Sasaki Hiroshi , Polus Barbara I.
Published: September 2011

Introduction: We investigated whether vibratory stimulation of the dorsal neck muscles activates fusimotor neurons of lower limb muscles in relaxed human subjects. Methods: The triceps surae (TS) muscles of seated subjects (n = 15) were conditioned to leave their muscle spindles in either an insensitive (hold‐long) or sensitive (hold‐short) state. A vibrator (80 HZ) was applied to the dorsal neck muscles for 10 seconds. The tendon jerk was evoked from the right TS immediately before (during) or 5 seconds after (interposed) the offset of vibration. Results: The size of the reflex after hold‐long muscle conditioning and after neck vibration was significantly smaller than the control hold‐short reflex (P < 0.001). However, after hold‐short conditioning, neck vibration significantly increased tendon jerk amplitude, both during (P = 0.001) and interposed (P = 0.026). Conclusion: Dorsal neck vibration increases spinal reflex excitability of the TS in relaxed and seated subjects, but not through fusimotor excitation. Muscle Nerve, 2012
A comparative study on the mechanical and degradation properties of plant fibers reinforced polyethylene composites
Authors: Zaman Haydar U , Khan Mubarak A. , Khan Ruhul A.
Published: September 2011

Coir and abaca fiber‐reinforced linear low density polyethylene (LLDPE) composites (30 wt% fiber) were prepared by compression molding. Coir and abaca fibers were treated with methyl methacrylate (MMA) using ultraviolet radiation to improve the mechanical properties of the composites. Concentration of MMA and radiation dose was optimized. It was found that 30% MMA in methanol along with photoinitiator Darocur‐1173 (2%) and 15th pass of radiation rendered better performance. Chemically treated fiber‐reinforced specimens yielded better mechanical properties compared to the untreated composites, whereas coir fiber composites had better mechanical properties than abaca fiber reinforced ones. For the improvement of the properties, optimized coir (coir fiber treated with 30% MMA) and abaca (abaca fiber treated with 40% MMA) fibers were again treated with aqueous starch solution (2%–8%, w/w) for 2–7 min. Composites made of 3%‐starch‐treated coir fiber (5 min soaking time) showed the best mechanical properties than that of abaca‐fiber‐based composites. Water uptake and soil degradation tests of the composites were also performed. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Synthesis and proton conductivity studies of 5‐aminotetrazole‐doped sulfonated polymer electrolyte membranes
Authors: Boroglu Mehtap Safak , Celik Sevim Unugur , Bozkurt Ayhan , Boz Ismail
Published: September 2011

This work reports the preparation and characterization of a new anhydrous proton conducting membrane based on poly(vinyl alcohol) (PVA), sulfosuccinic acid (SSA), and 5‐aminotetrazole (ATet) at various stoichiometric ratios. The proton conductivities of membranes were investigated as a function of ATet composition, SSA composition, and temperature. New anhydrous proton conducting membranes were characterized by infrared spectra, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), dynamic mechanical analysis (DMA), methanol permeability, and impedance measurements for proton conductivity. TGA showed that the samples were thermally stable up to 150°C. DSC results illustrated the homogeneity of the materials. Mechanical analysis showed that the storage modulus of the PVA–SSA–ATet blend polymer membranes decreased with increasing ATet content. The membranes with higher tetrazole content, or higher acid doping level presented the higher proton conductivity. PVA–SSA–ATet4 can exhibit an anhydrous proton conductivity of 1.7 × 10−3 S/cm at 130°C and the proton conductivity increased with increasing temperature and acid doping level. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Surface‐activated nanosilica treated with silane coupling agents/polypropylene composites: Mechanical, morphological, and thermal studies
Authors: Lin Ong Hui , Akil Hazizan Md , Mohd Ishak Z.A.
Published: September 2011

This work reports the mechanical, morphological, and thermal properties of the polypropylene (PP) nanocomposites containing nanosilica (nano‐SiO2) which were treated by different functional group silane coupling agents. Four types of silane coupling agents namely aminopropyltriethoxy silane (APTES), glycidyloxypropyltrimethoxy silane (GPTMS), trimethoxysilylpropyl methacrylate (TMPM), and dichlorodimethyl silane (DCMS) were used to modify the surface‐activated nanosilica. To enhance the effectiveness of the coupling, nanosilica was chemically activated and analyzed through FTIR and X‐ray photo electron spectroscopy (XPS). The highest tensile strength was recorded by the activated nanocomposites treated with APTES followed by nanocomposite treated with GPTMS, TMPM, and DCMS, respectively. The addition of silane coupling agents into nano‐SiO2/PP system further improved the tensile modulus of the PP nanocomposites. From the transmission electron microscopy (TEM) analysis, activated nanosilica treated with APTES showed better nanosilica dispersion in the PP matrix and lesser agglomeration occurred when compared with the other silane coupling agents which were used in this study. Surface activation process does not effectively increase the degree of crystallinity and thermal stability on the PP nanocomposites. However, with the assistance of the surface treatment, it was found that the thermal behavior of the PP nanocomposites had been enhanced. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
How well can renewable resources mimic commodity monomers and polymers?
Authors: Mathers Robert T.
Published: September 2011

This highlight discusses the recent progress aimed at maximizing the potential of biomass for commodity monomers and polymers. These efforts are no longer solely academic issues. In recent years, a variety of alkene, diene, aromatic, and condensation type monomers have utilized renewable resources, such as cellulose, lignin, plant oils, starches, and monoterpenes in commercial polymers. Generally, these multifaceted efforts involve pretreatment of biomass with thermal, chemical, or physical methods followed by a catalyst sequence that entails a combination of acid‐catalysis, bio‐catalysis, or metal‐based catalysis. In this regard, synthesis strategies for ethylene, propylene, α‐olefins, methylmethacrylate, 1,3‐butadiene, 1,3‐cyclohexadiene, isoprene, 1,3‐propanediol, 1,4‐butanediol, and terephthalic acid are discussed as well as opportunities for other renewable‐based monomers. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Synthesis and characterization of UV‐curable ladder‐like polysilsesquioxane
Authors: Choi Seung–Sock , Lee Albert S. , Lee He Seung , Jeon Hyeon Yeol , Baek Kyung–Youl , Choi Dong Hoon , Hwang Seung Sang
Published: September 2011

Various ladder‐like structured poly(phenyl‐co‐methacryl silsesquioxane)s (LPMSQ)s with high molecular weight (Mw = 10,000 ∼ 40,000) were synthesized by direct hydrolysis and polymerization in the presence of base catalyst at 25 °C. Synthesized LPMSQs mainly showed ladder‐like structure and photo‐cure reaction by 100 mW/cm2 (360 nm) for 10 s without any photo‐cure initiators. Chemical composition and structural analysis of the obtained LPMSQs were characterized using 1H NMR, 29Si NMR, Fourier transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC), and X‐ray diffraction (XRD). Physical properties of LPMSQs before and after photcuring were analyzed by Nanoindentation. Surface modulus increased to 8GPa and hardness of thin films increased from 100 to 400 MPa. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Synthesis of copolyamides based on PA 66 bearing lithium sulfonate groups and having unique thermal properties
Authors: Cammage Geoffroy , Spitz Roger , Boisson Christophe , Rossin René , Jéol Stéphane , Touraud Franck
Published: September 2011

Copolyamides of PA 66/6 lithium 5‐sulfoisophthalic acid (LiSIPA) containing up to 40 mol % of LiSIPA were prepared in a 1L‐pilot reactor operating at high pressures and high temperatures. Interestingly, the presence of lithium sulfonate moieties highly impacted the glass transition temperature of the polyamide. The Tg increased from 59 °C for PA 66 to 155 °C for a copolymer containing about 40 mol % of LiSIPA. 1,3‐Dihexylbenzenedicarboxamide and lithium p‐toluenesulfonate were synthesized as model compounds to investigate the interaction of lithium sulfonate moieties and amide functions. Infrared spectroscopy using ATR technology performed on mixture of both compounds showed that the carbonyl group of amide functions interacts with the lithium cation of lithium sulfonate moieties. Similar SO and CO adsorption bands were observed in copolyamides PA 66/6LiSIPA and in mixture of model compounds, which strongly suggest the formation in the copolyamides of physical cross‐linking points centered on lithium cations coordinated by carbonyl groups of amide functions. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Star macromolecules with hyperbranched poly(arylene oxindole) cores and polyacid arms: Synthesis and solution behavior
Authors: Kowalczuk Agnieszka , Trzebicka Barbara , Rangelov Stanislav , Smet Mario , Dworak Andrzej
Published: September 2011

The synthesis of pH‐sensitive star polymers with 100% hyperbranched cores and polyacrylic or polymethacrylic acid arms is reported. A series of stars obtained via atom transfer polymerization of tert‐butyl acrylate and methacrylate onto poly(arylene oxindole)s were subjected to acidic hydrolysis to obtain structures with polyacid arms. The obtained polyacid stars were characterized by NMR and FTIR spectroscopy. Dynamic and static light scattering experiments were performed to provide information regarding the shape of these macromolecules in solution. In an aqueous solution, the stars formed aggregates with a radius of gyration reaching 130 nm and aggregation numbers of up to 280 stars per particle. Similar to other polyacid‐based copolymers with different branched topologies, the dimensions and aggregation numbers were found to decrease with increasing pH. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Thermoplastic polyurethane/silica nanocomposite fibers by electrospinning
Authors: Zhang Xu‐Cheng , Chen Yi‐Zhang , Yu Jian , Guo Zhao‐Xia
Published: September 2011

Thermoplastic polyurethane/silica nanocomposite fibers with good mechanical properties were prepared by electrospinning, using colloidal silica as the source of silica and dimethyl formamide as the solvent. The fiber morphology was examined by field emission scanning electron microscopy. The average fiber diameter is about 0.8 μm with 0–10 wt % silica, and silica nanoparticles were observed on all fiber surfaces. X‐ray photoelectron spectroscopy analysis of Si in combination with transmission electron microscopy observation suggest that silica nanoparticles have a fairly uniform distribution in the fibers rather than enriching on the fiber surfaces. Tensile tests show that the incorporation of silica nanoparticles can bring about a significant reinforcing effect without decreasing the ductility. The reinforcing effect is further confirmed by dynamic mechanical analysis. The thermoplastic polyurethane/silica composite fiber mats can adsorb gold nanoparticles after further treatment with 3‐aminopropyltriethoxysilane, demonstrating that the composite fibers could be used as functional fibers by using the properties of silica nanoparticles. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Assessment of ligand‐binding residue predictions in CASP9
Authors: Schmidt Tobias , Haas Jürgen , Cassarino Tiziano Gallo , Schwede Torsten
Published: September 2011

Interactions between proteins and their ligands play central roles in many physiological processes. The structural details for most of these interactions, however, have not yet been characterized experientially. Therefore, various computational tools have been developed to predict the location of binding sites and the amino acid residues interacting with ligands. In this manuscript, we assess the performance of 33 methods participating in the ligand‐binding site prediction category in CASP9. The overall accuracy of ligand‐binding site predictions in CASP9 appears rather high (average Matthews correlation coefficient of 0.62 for the 10 top performing groups) and compared to previous experiments more groups performed equally well. However, this should be seen in context of a strong bias in the test data toward easy template‐based models. Overall, the top performing methods have converged to a similar approach using ligand‐binding site inference from related homologous structures, which limits their applicability for difficult de novo prediction targets. Here, we present the results of the CASP9 assessment of the ligand‐binding site category, discuss examples for successful and challenging prediction targets in CASP9, and finally suggest changes in the format of the experiment to overcome the current limitations of the assessment. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Raptorx: Exploiting structure information for protein alignment by statistical inference
Authors: Peng Jian , Xu Jinbo
Published: September 2011

This work presents RaptorX, a statistical method for template‐based protein modeling that improves alignment accuracy by exploiting structural information in a single or multiple templates. RaptorX consists of three major components: single‐template threading, alignment quality prediction, and multiple‐template threading. This work summarizes the methods used by RaptorX and presents its CASP9 result analysis, aiming to identify major bottlenecks with RaptorX and template‐based modeling and hopefully directions for further study. Our results show that template structural information helps a lot with both single‐template and multiple‐template protein threading especially when closely‐related templates are unavailable, and there is still large room for improvement in both alignment and template selection. The RaptorX web server is available at http://raptorx.uchicago.edu. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Reduction of switching time in pentalayer magnetic tunnel junctions with a composite‐free layer
Authors: Makarov Alexander , Sverdlov Viktor , Osintsev Dmitry , Selberherr Siegfried
Published: September 2011

We have performed micromagnetic simulations of the magnetization dynamics of the composite‐free magnetic layer in a pentalayer structure. We have found a substantial decrease of the switching time in this system as compared to the pentalayer structure of similar dimensions with a monolithic free layer. The physical reasons for the switching time reduction at the same current density are discussed. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Defect engineering of room‐temperature ferromagnetism of carbon‐doped ZnO
Authors: Hsu H. S. , Tung Y. , Chen Y. J. , Chen M. G. , Lee J. S. , Sun S. J.
Published: September 2011

This study investigates the role of carbon (C) in room‐temperature (RT) ferromagnetic C:ZnO films. RT ferromagnetism can be observed in air‐annealed C:ZnO samples. However, no feature that could be attributed to the incorporation of carbon at O sites (CO) was observed. An analysis of MCD spectra of the ferromagnetic C:ZnO sample included a non‐ferromagnetic peak and a ferromagnetic one. These are related to the loss of carbon and the creation of defects in an air‐annealed C:ZnO film by the reaction between C dopants and oxygen. We suggest even if the C dopants are not at CO sites, C is still a novel dopant to make ZnO ferromagnetic in controlling the defects in the structure formed by suitable post‐annealing. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nanoscale hot electron transport across Cu/n‐Si(100) and Cu/n‐Si(111) interfaces
Authors: Parui S. , van der Ploeg J. R. R. , Rana K. G. , Banerjee T.
Published: September 2011

Ballistic electron emission microscopy (BEEM) has been used to investigate hot electron transmission, at the nanoscale, in thin films of Cu on Si(100) and Si(111). For all Cu thicknesses studied here, the BEEM transmission is observed to be twice larger for Si(111) than for Si(100). Further, the attenuation length in Cu is found to be larger for Si(111) than for Si(100) substrates, in spite of the highly textured growth of Cu on both the substrates. Our results can be explained by the incorporation of elastic scattering at the metal–semiconductor (M/S) interface as well as the increased availability of parallel momentum states at the interface. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The impact of global and local cohesion on innovation in the pharmaceutical industry
Authors: Guler Isin , Nerkar Atul
Published: September 2011

In this paper, we examine how the configuration of intraorganizational networks, and in particular, cohesion among members of an organization, influences organizations' innovative output. We argue that the cohesion among R&D scientists could be at a local level or a global level, and that local and global cohesion may have different impacts on firms' innovation performance. We test our hypotheses by examining the structure of the R&D collaboration networks within firms that operated in the pharmaceutical industry between 1981 and 1989, and their innovative outcomes—patents that led to new product launches. We find that local cohesion has a positive impact on the innovative performance of a firm, and global cohesion has a negative impact. Copyright © 2011 John Wiley & Sons, Ltd.
Plasmonic Coupling Interference (PCI) Nanoprobes for Nucleic Acid Detection
Authors: Wang Hsin‐Neng , Vo‐Dinh Tuan
Published: September 2011

A label‐free approach using plasmonic coupling interference (PCI) nanoprobes for nucleic acid detection using surface‐enhanced Raman scattering (SERS) is described. To induce a strong plasmonic coupling effect, a nanonetwork of silver nanoparticles with the Raman label located between adjacent nanoparticles is assembled by Raman‐labeled DNA‐locked nucleic acid (LNA) duplexes. The PCI method then utilizes specific nucleic acid sequences of interest as competitor elements for the Raman‐labeled DNA strands to interfere the formation of nanonetworks in a competitive binding process. As a result, the plasmonic coupling effect induced through the formation of the nanonetworks is significantly diminished, resulting in a reduced SERS signal. The potential of the PCI technique for biomedical applications is illustrated by detecting single‐nucleotide polymorphism (SNP) and microRNA sequences involved in breast cancers. The results of this study could lead to the development of nucleic acid diagnostic tools for biomedical diagnostics and biosensing applications using SERS detection.
Extraordinary Responsive Intermetallic Compounds: the R5T4 Family (R = Rare Earth, T = Group 13–15 Element)
Authors: Mudryk Yaroslav , Pecharsky Vitalij K. , Gschneidner, Jr. Karl A.
Published: September 2011

The R5T4 intermetallic compounds of rare earth elements (R) with the group 14 elements (T) adopt a number of layered crystal structures that reversibly transform into each other. The transformations proceed through massive shear displacements of their main structural units, i.e. slabs, which are pseudo two dimensional blocks of atoms stacked along a certain crystallographic direction. These transformations can be triggered by change in chemical composition of the compounds (including partial substitutions of the group 14 elements by the group 13 or 15 elements), temperature, applied pressure, or applied magnetic field. The physical properties of these compounds are usually intimately related to their crystallography, and especially the concomitant magnetic and crystallographic transitions. As a result, strong magnetocaloric, magnetostrictive, magnetoresistance, and other effects are commonly observed. Consequently, a large change of the materials' properties can be achieved by a relatively weak change of external thermodynamic conditions.
Risk Factor Analysis of Postoperative Complications After Robotic Rectal Cancer Surgery
Authors: Kang Jeonghyun , Min Byung Soh , Park Yoon Ah , Hur Hyuk , Baik Seung Hyuk , Kim Nam Kyu , Sohn Seung Kook , Lee Kang Young
Published: September 2011

Background

The robotic system has been adopted as the new modality for minimally invasive surgery for rectal cancer. However, analysis of risk factors for complications after robotic rectal cancer surgery (RRS) has been limited. This study aimed to identify the risk factors for complications after RRS.

Methods

The records of 389 consecutive patients who underwent RRS between June 2006 and October 2010 were retrieved from our prospectively collected database.

Results

The overall complication rate was 19%. The most common complication was anastomotic leakage (7.0%), followed by voiding difficulty, intrapelvic abscess, and ileus/obstruction. Multivariate analysis revealed the following as risk factors for postoperative complications: male gender, history of previous abdominal surgery, and lower tumor level (hazard ratio [HR] = 1.8, 95% confidence interval [CI] = 1.0–3.1, p = 0.041; HR = 2.3; 95% CI = 1.2–4.6, p = 0.012; and HR = 1.9, 95% CI = 1.1–3.3, p = 0.020, respectively). With regard to pelvic septic complications, lower tumor level, large tumor size, and preoperative chemoradiation remained variables that retained their statistical significance in multivariate analysis (HR = 2.6, 95% CI = 1.1–6.1, p = 0.029; HR = 2.7, 95% CI = 1.1–6.1, p = 0.017; HR = 2.9, 95% CI = 1.3–6.5, p = 0.007, respectively). The rate of postoperative complications was not influenced by the difference in laparoscopic surgery experience or the technique of robotic surgery.

Conclusion

Surgeons should be more cautious with these patient factors to optimize the benefits of robotic rectal resection.
Rethinking theoretical and methodological issues in intergenerational family relations research
Authors: LOWENSTEIN ARIELA , KATZ RUTH , BIGGS SIMON
Published: September 2011

This paper introduces some key theoretical and methodological developments in the study of intergenerational family relations. It draws on observations that a number of social issues are emerging that have an intergenerational dimension, that there is growing recognition that to study adult ageing one has also to study intergenerational relationships, and that a new architecture for social relations is beginning to take shape in the wake of demographic change. How individuals, families and societies cope with such changes provokes the question of how gerontologically-informed research, theorisation and policy will also adapt. Seven positions are summarised which attempt two things. First, to map out some new conceptual directions for intergenerational research through a critical use of concepts such as transition, generational self-awareness and empathy, metaphors of cultural translation, and the deployment of social and moral capital. Second, to examine changing gender roles, the balance between family and welfare-state support frameworks, ethnicity and immigration as important elements of this process. A critical review of approaches to intergenerational relationships hopefully emerges.
Air Traffic Control Separation Minima: Part 2 – Transition to a Trajectory-based System
Authors: Brooker Peter
Published: September 2011

Current strategic plans for Air Traffic Management (ATM) envisage a transition from radar control to a trajectory-based system. Part 1 sketched the historical origins of separation minima and then analysed the safety thinking behind current minima and the issues involved in risk modelling. Part 2 examines the future situation. This focuses on the intermediate steps to the final system – upgraded capabilities in a mixed-equipage system. Future traffic mixes two categories of traffic: V aircraft, i.e. vectored traditional ATC-handled, and 4D aircraft, i.e. flying on 4D trajectories. Conflict probe and other decision support tools will need to be in place, inter alia to prevent controller workload from increasing. Conceptually, future risks in the transition period will be the sum of three types of aircraft encounter risk: V/V, 4D/4D and 4D/V. These pose different kinds of problem for ATC, appropriate conflict alerting systems and risk assessment. The numbers of 4D/V encounters increase rapidly with growth in the proportion of 4D aircraft. With reduced minima, airborne collision avoidance systems would be unlikely to resolve higher relative velocity encounters were the ATC system to fail. It would be a difficult decision to reduce markedly ATC separation minima for any category of aircraft encounters during the transition period.
Estimating Reception Coverage Characteristics of AIS
Authors: Lapinski Anna-Liesa S. , Isenor Anthony W.
Published: September 2011

The Automatic Identification System (AIS) is now well established and widely used in commercial shipping. The system originated from a safety mandate but AIS messages have also been shown to be useful from a security situational awareness perspective. In terms of coastal security, AIS messages are often received by land-based receivers positioned along a nation's coastline. The operational range of the receivers is controlled by complex variable VHF propagation characteristics, power of the transmitter, etc. However, certain characteristics of the reception coverage area can be determined from the AIS message receptions themselves. This paper presents an algorithm to compute coverage characteristics using AIS messages. The algorithm is applied to synthetic data with known coverage characteristics, and also real AIS data obtained from the Maritime Safety and Security Information System. Results from the Norwegian, North and Baltic Seas show how the coverage estimate is influenced by the coverage edge, lack of vessel activity, and diversity in the source data.
Circle Approximations on Spheroids
Authors: Ahn Young Joon , Cui Jian , Hoffmann Christoph
Published: September 2011

We present an approximation method for geodesic circles on a spheroid. Our ap­proximation curve is the intersection of two spheroids whose axes are parallel, and it interpolates four points of the geodesic circle. Our approximation method has two merits. One is that the approximation curve can be obtained algebraically, and the other is that the approximation error is very small. For example, our approximation of a circle of radius 1000 km on the Earth has error 1·13 cm or less. We analyze the error of our approximation using the Hausdorff distance and confirm it by a geodesic distance computation.
Estimating the force of infection for HCV in injecting drug users using interval-censored data
Authors: CASTRO-SÁNCHEZ A. , SHKEDY Z. , HENS N. , AERTS M. , GESKUS R. , PRINS M. , WIESSING L. , KRETZSCHMAR M.
Published: September 2011

Injecting drug users (IDUs) account for most new HCV infections. The objectives of this study were: to estimate the force of infection for hepatitis C virus in IDUs within the interval-censoring framework and to determine the impact of risk factors such as frequency of injection, drug injected, sharing of syringes and time of first injection on the time to HCV infection. We used data from the Amsterdam Cohort Study collected in The Netherlands and focused on those individuals who were HCV negative upon entry into the study. Based on the results, the force of infection was found to vary with time of first injection. The risk of infection was higher in the first 3 years of an IDU's career, implying estimates based on single cross-sectional studies could be biased. Frequency of injection and type of drug injected were found to be highly significant predictors, whereas sharing syringes was not.
The BinProlog experience: Architecture and implementation choices for continuation passing Prolog and first-class logic engines
Authors: TARAU PAUL
Published: September 2011

We describe theBinPrologsystem's compilation technology, runtime system and its extensions supporting first-class Logic Engines while providing a short history of its development, details of some of its newer re-implementations as well as an overview of the most important architectural choices involved in their design. With focus on its differences with conventional Warren Abstract Machine (WAM) implementations, we explain key details ofBinProlog's compilation technique, which replaces the WAM with a simplifiedcontinuation passingruntime system (the “BinWAM”), based on a mapping of full Prolog tobinary logic programs. This is followed by a description of aterm compressiontechnique using a “tag-on-data” representation. Later derivatives, the Java-basedJinni Prologcompiler and the recently developedLean Prologsystem refine theBinPrologarchitecture withfirst-class Logic Engines, made generic through the use of anInteractorinterface. An overview of their applications with focus on the ability to express at source level a wide variety of Prolog built-ins and extensions covers these newer developments.
ECLiPSe – From LP to CLP
Authors: SCHIMPF JOACHIM , SHEN KISH
Published: September 2011

ECLiPSe is a Prolog-based programming system, aimed at the development and deployment of constraint programming applications. It is also used for teaching most aspects of combinatorial problem solving, for example, problem modelling, constraint programming, mathematical programming and search techniques. It uses an extended Prolog as its high-level modelling and control language, complemented by several constraint solver libraries, interfaces to third-party solvers, an integrated development environment and interfaces for embedding into host environments. This paper discusses language extensions, implementation aspects, components, and tools that we consider relevant on the way from Logic Programming to Constraint Logic Programming.
SICStus Prolog—The first 25 years
Authors: CARLSSON MATS , MILDNER PER
Published: September 2011

SICStus Prolog has evolved for nearly 25 years. This is an appropriate point in time for revisiting the main language and design decisions, and try to distill some lessons. SICStus Prolog was conceived in a context of multiple, conflicting Prolog dialect camps and a fledgling standardization effort. We reflect on the impact of this effort and role model implementations on our development. After summarizing the development history, we give a guided tour of the system anatomy, exposing some designs that were not published before. We give an overview of our new interactive development environment, and describe a sample of key applications. Finally, we try to identify key good and not so good design decisions.
SWI-Prolog
Authors: WIELEMAKER JAN , SCHRIJVERS TOM , TRISKA MARKUS , LAGER TORBJÖRN
Published: September 2011

SWI-Prolog is neither a commercial Prolog system nor a purely academic enterprise, but increasingly a community project. The core system has been shaped to its current form while being used as a tool for building research prototypes, primarily forknowledge-intensiveandinteractivesystems. Community contributions have added several interfaces and the constraint (CLP) libraries. Commercial involvement has created the initial garbage collector, added several interfaces and two development tools: PlDoc (a literate programming documentation system) and PlUnit (a unit testing environment).

In this article, we present SWI-Prolog as an integrating tool, supporting a wide range of ideas developed in the Prolog community and acting as glue betweenforeignresources. This article itself is the glue between technical articles on SWI-Prolog, providing context and experience in applying them over a longer period.
Oceanographer tracks marine debris from the Japan tsunami and other incidents
Authors: Showstack Randy
Published: September 2011

In the wake of the 11 March 2011 Tohoku earthquake and resulting tsunami that struck Japan, much of the debris that washed out to sea continues to float slowly on ocean currents across the Pacific Ocean. The leading edge of a dispersed field of debris that has not already sunk or biodegraded was estimated by a computer model to be about halfway across the Pacific, north of Midway Island, as of 31 July, 142 days after the tsunami. According to Curtis Ebbesmeyer, a consulting oceanographer who has been involved with tracking various kinds of ocean flotsam for decades, the debris field, which encompasses an area about the size of California, could begin to reach the U.S. West Coast by March 2012. The National Oceanic and Atmospheric Administration's (NOAA) Satellite and Information Service was able to track the debris field until mid‐April, when the debris became too dispersed to be detected in satellite imagery. Ebbesmeyer, formerly an oceanographer with Mobil and Standard Oil, told Eos that he does not have any recent physical evidence of the debris field because it is now widely dispersed and still far away from any landfall. Ebbesmeyer said, though, that his confidence level for the debris field's estimated size and location is “very high.”