bluuebunny/crossref_metadata_2025 huggingface dataset:
An Integrated Miniature Bioprocessing for Personalized Human Induced Pluripotent Stem Cell Expansion and Differentiation into Neural Stem Cells
Authors: Lin Haishuang , Li Qiang , Lei Yuguo
Published: January 2017

Human induced pluripotent stem cells (iPSCs) are ideal cell sources for personalized cell therapies since they can be expanded to generate large numbers of cells and differentiated into presumably all the cell types of the human body in vitro. In addition, patient specific iPSC-derived cells induce minimal or no immune response in vivo. However, with current cell culture technologies and bioprocessing, the cost for biomanufacturing clinical-grade patient specific iPSCs and their derivatives are very high and not affordable for majority of patients. In this paper, we explored the use of closed and miniature cell culture device for biomanufacturing patient specific neural stem cells (NSCs) from iPSCs. We demonstrated that, with the assist of a thermoreversible hydrogel scaffold, the bioprocessing including iPSC expansion, iPSC differentiation into NSCs, the subsequent depletion of undifferentiated iPSCs from the NSCs, and concentrating and transporting the purified NSCs to the surgery room, could be integrated and completed within two closed 15 ml conical tubes.
Mean Platelet Volume and Arterial Stiffness – Clinical Relationship and Common Genetic Variability
Authors: Panova-Noeva Marina , Arnold Natalie , Hermanns M. Iris , Prochaska Jürgen H. , Schulz Andreas , Spronk Henri M. , Binder Harald , Pfeiffer Norbert , Beutel Manfred , Blankenberg Stefan , Zeller Tanja , Lotz Johannes , Münzel Thomas , Lackner Karl J. , ten Cate Hugo , Wild Philipp S.
Published: January 2017

Vessel wall stiffening is an important clinical parameter, but it is unknown whether platelets, key elements in the pathogenesis of arterial thrombosis, are associated with arterial stiffness. The present studies sought to determine whether mean platelet volume (MPV), a potential marker of platelet activation, is linked to vascular elasticity as assessed by the augmentation index (AIx), in 15,010 individuals from the population-based Gutenberg Health Study. Multivariable analysis showed that MPV in both males (β 0.776; 95thCI [0.250;1.16]; p = 0.0024) and females (β 0.881[0.328;1.43]; p = 0.0018) is strongly associated with AIx. Individuals with MPV and AIx above the sex-specific medians had worse survival. Association analysis between MPV-related genetic variants and arterial stiffness identified four genetic variants in males and one in females related with AIx. Cox regression analysis for mortality identified one of these joint genetic variants close to ring finger protein 145 gene (RNF145, rs10076782) linked with increased mortality (hazard ratio 2.02; 95thCI [1.35;3.02]; p = 0.00061). Thus, these population-based data demonstrate a close relation between platelet volume as a potential marker of platelet activation and arterial stiffness in both sexes. Further research is warranted to further elucidate the mechanisms underlying larger platelets‘ role in arterial stiffening including the role of shared common genetics.
Hemispherical platinum : silver core : shell nanoparticles for miRNA detection
Authors: Spain Elaine , Adamson Kellie , Elshahawy Mohammad , Bray Isabella , Keyes Tia E. , Stallings Raymond L. , Forster Robert J.
Published: January 2017

Novel electrochemical detection based on regioselective functionalised electrocatalytic nanoparticles suitable for the detection of low-abundance molecular biomarkers, miR-132 of neuroblastoma.
Method optimization for trans fatty acid determination by CZE-UV under direct detection with a simple sample preparation
Authors: Prado T. L. A. , Porto B. L. S. , Oliveira M. A. L.
Published: January 2017

An alternative method for trans fatty acid (TFA) determination, expressed in elaidic acid, by capillary zone electrophoresis using UV-VIS direct detection (200 nm) with a simple sample preparation is proposed.
Improvement in the single and simultaneous generation of As, Bi, Sb and Se hydrides using a vapor generation accessory (VGA) coupled to axially viewed inductively coupled plasma optical emission spectrometry (ICP OES)
Authors: Welna Maja , Szymczycha-Madeja Anna , Pohl Pawel
Published: January 2017

Hydride generation (HG) using a vapor generation accessory (VGA) coupled to an inductively coupled plasma optical emission spectrometer (ICP OES) for the ultrasensitive measurement of As, Bi, Sb and Se was investigated.
Highly versatile SPION encapsulated PLGA nanoparticles as photothermal ablators of cancer cells and as multimodal imaging agents
Authors: Sivakumar Balasubramanian , Aswathy Ravindran Girija , Romero-Aburto Rebeca , Mitcham Trevor , Mitchel Keith A. , Nagaoka Yutaka , Bouchard Richard R. , Ajayan Pulickel M. , Maekawa Toru , Sakthikumar Dasappan Nair
Published: January 2017

SPION encapsulated polymeric nanoformulation as photothermal ablators of cancer cells and as multimodal imaging agents.
Electron-transporting polymers based on a double B←N bridged bipyridine (BNBP) unit
Authors: Long Xiaojing , Gao Yao , Tian Hongkun , Dou Chuandong , Yan Donghang , Geng Yanhou , Liu Jun , Wang Lixiang
Published: January 2017

A series of BNBP-based polymer semiconductors are developed, which show good electron-transporting properties in organic thin film transistors.
Coupling of C(sp3)–H bonds with C(sp2)–O electrophiles: mild, general and selective
Authors: Gui Yong-Yuan , Liao Li-Li , Sun Liang , Zhang Zhen , Ye Jian-Heng , Shen Guo , Lu Zhi-Peng , Zhou Wen-Jun , Yu Da-Gang
Published: January 2017

The general coupling of amine/ether C(sp3)–H bonds with alkenyl/(hetero)aryl C–O electrophiles is reported with high selectivity.
Taco complex-templated highly regio- and stereo-selective photodimerization of a coumarin-containing crown ether
Authors: Wei Peifa , Wang Haoze , Jie Kecheng , Huang Feihe
Published: January 2017

We design a coumarin-containing bis(m-phenylene)-32-crown-10 derivative which efficiently controls the regio- and stereo-selectivity of the photodimerization of its two terminal coumarin groups templated by taco-type host–guest complex formation to selectively produce the syn-head-to-tail cryptand isomer in quantitative yield.
Controlled solvent vapor annealing of a high χ block copolymer thin film
Authors: Lundy Ross , Flynn Shauna P. , Cummins Cian , Kelleher Susan M. , Collins Maurice N. , Dalton Eric , Daniels Stephen , Morris Michael A. , Enright Ryan
Published: January 2017

Wafer scale high χ block copolymer patterning via dynamic solvent vapor annealing.
Electric field tunable half-metallic characteristic at Fe3O4/BaTiO3 interfaces
Authors: Hou Xueyao , Wang Xiaocha , Chen Guifeng , Mi Wenbo
Published: January 2017

The interfacial electronic structure of Fe3O4/BaTiO3 heterostructures was investigated using first-principles calculations.
Hidden negative linear compressibility in lithiuml-tartrate
Authors: Yeung Hamish H.-M. , Kilmurray Rebecca , Hobday Claire L. , McKellar Scott C. , Cheetham Anthony K. , Allan David R. , Moggach Stephen A.
Published: January 2017

Normal mechanical behaviour at ambient pressure precedes anomalous mechanics as a result of competing strut compression and angle opening.
Strategies for sensing neurotransmitters with responsive MRI contrast agents
Authors: Angelovski Goran , Tóth Éva
Published: January 2017

This review introduces current and potential chemistry approaches in molecular fMRI that allow direct imaging of neurotransmitters.
Effects of mesoporous calcium magnesium silicate on setting time, compressive strength, apatite formation, degradability and cell behavior to magnesium phosphate based bone cements
Authors: Cao Liehu , Weng Weizong , Chen Xiao , Zhang Jun , Zhou Qirong , Cui Jin , Wang Lin , Shin Jung-Woog , Su Jiacan
Published: January 2017

Mesoporous calcium magnesium silicate was doped into magnesium phosphate to fabricate magnesium phosphate based composite cements (MBC).
Energetics of cellulose and cyclodextrin glycosidic bond cleavage
Authors: Zhu Cheng , Krumm Christoph , Facas Gregory G. , Neurock Matthew , Dauenhauer Paul J.
Published: January 2017

Thermochemical conversion of lignocellulosic materials for production of biofuels and renewable chemicals utilizes high temperature to thermally decompose long-chain cellulose to volatile organic compounds.
Nanoporous film-mediated growth of ultrathin and continuous metal–organic framework membranes for high-performance hydrogen separation
Authors: Zhang Shenxiang , Wang Zhenggong , Ren Huiting , Zhang Feng , Jin Jian
Published: January 2017

An ultrathin and continuous ZIF-8 membrane was fabricated via a spatially confined contra-diffusion process, which exhibits a high H2 permeance and simultaneously maintains a high ideal selectivity for H2/CO2.
Synthesis of low band gap polymers based on pyrrolo[3,2-d:4,5-d′]bisthiazole (PBTz) and thienylenevinylene (TV) for organic thin-film transistors (OTFTs)
Authors: Patra Dhananjaya , Lee Jaehyuk , Lee Jongbok , Sredojevic Dusan N. , White Andrew J. P. , Bazzi Hassan S. , Brothers Edward N. , Heeney Martin , Fang Lei , Yoon Myung-Han , Al-Hashimi Mohammed
Published: January 2017

New low band gap copolymers P1–P4, based on thienylenevinylene (TV) and pyrrolo[3,2-d:4,5-d′]bisthiazole (PBTz).
Structure and inhibitor specificity of the PCTAIRE-family kinase CDK16
Authors: Dixon-Clarke Sarah E. , Shehata Saifeldin N. , Krojer Tobias , Sharpe Timothy D. , von Delft Frank , Sakamoto Kei , Bullock Alex N.
Published: January 2017

CDK16 (also known as PCTAIRE1 or PCTK1) is an atypical member of the cyclin-dependent kinase (CDK) family that has emerged as a key regulator of neurite outgrowth, vesicle trafficking and cancer cell proliferation. CDK16 is activated through binding to cyclin Y via a phosphorylation-dependent 14-3-3 interaction and has a unique consensus substrate phosphorylation motif compared with conventional CDKs. To elucidate the structure and inhibitor-binding properties of this atypical CDK, we screened the CDK16 kinase domain against different inhibitor libraries and determined the co-structures of identified hits. We discovered that the ATP-binding pocket of CDK16 can accommodate both type I and type II kinase inhibitors. The most potent CDK16 inhibitors revealed by cell-free and cell-based assays were the multitargeted cancer drugs dabrafenib and rebastinib. An inactive DFG-out binding conformation was confirmed by the first crystal structures of CDK16 in separate complexes with the inhibitors indirubin E804 and rebastinib, respectively. The structures revealed considerable conformational plasticity, suggesting that the isolated CDK16 kinase domain was relatively unstable in the absence of a cyclin partner. The unusual structural features and chemical scaffolds identified here hold promise for the development of more selective CDK16 inhibitors and provide opportunity to better characterise the role of CDK16 and its related CDK family members in various physiological and pathological contexts.
Volar Plate Fixation in Patients Older Than 70 Years with AO Type C Distal Radial Fractures: Clinical and Radiologic Outcomes
Authors: Zaidenberg Ezequiel , Duarte Matias , Boretto Jorge , Donndorff Agustin , Gallucci Gerardo , De Carli Pablo , Piuzzi Nicolas
Published: January 2017

Introduction Treatment of unstable distal radial fractures (DRFs) in elderly patients is controversial, and considering the increasing life expectancy, their appropriate treatment is of growing importance. Our aim was to analyze the clinical and radiologic outcomes in the elderly patients with AO type C DRF treated with volar locking plate (VLP).

Materials and Methods Between 2007 and 2011, 572 DRFs were operated on in our hospital with open reduction and internal fixation with VLP. Of these, only 64 patients (66 DRFs) met the selection criteria (AO type C DRF, age > 70 years, minimum 12-month follow-up). Mean follow-up was 28 months. Outcome assessment included range of motion, grip strength, VAS pain, Mayo Clinic Score, and DASH score. Analysis of pre- and postoperative radiographs was performed. Complications were recorded. Statistical analysis was performed comparing the results with the contralateral side.

Results Mean postoperative range of motion of the injured wrist compared with the control contralateral side was 86% for flexion (p < 0.001), 92% for extension (p < 0.001). The average DASH was 12. Mayo Clinic Wrist Score showed 43 excellent results, 15 good, 4 satisfactory, and 4 poor. Articular step-offs were reduced in 34 of 38 wrists. Five (7%) patients required plate removal.

Conclusion The treatment of articular DRF (AO type C) with VLP in the elderly patients achieved greater than 90% of the wrist range of motion and grip strength with no residual pain in greater than 90% of the patients.

Level of Evidence Therapeutic IV, case series.
Relationship between the potential energy landscape and the dynamic crossover in a water-like monatomic liquid with a liquid-liquid phase transition
Authors: Sun Gang , Xu Limei , Giovambattista Nicolas
Published: January 2017

In the case of fragile liquids, dynamical properties such as the structural relaxation time evolve from Arrhenius at high-temperatures to non-Arrhenius at low temperatures. Computational studies show that (i) in the Arrhenius dynamic domain, the liquid samples regions of the potential energy landscape (PEL) that are insensitive to temperature (PEL-independent regime) and the relaxation is exponential, while (ii) in the non-Arrhenius dynamic domain, the topography of the PEL explored by the liquid varies with temperature (PEL-influenced regime) and the relaxation is non-exponential. In this work we explore whether the correlation between dynamics and PEL regimes, points (i) and (ii), holds for the Fermi-Jagla (FJ) liquid. This is a monatomic model liquid that exhibits many of the water anomalous properties, including maxima in density and diffusivity. The FJ model is a rather complex liquid that exhibits a liquid-liquid phase transition and a liquid-liquid critical point (LLCP), as hypothesized for the case of water. We find that, for the FJ liquid, the correlation between dynamics and the PEL regimes is not always present and depends on the density of the liquid. For example, at high density, the liquid exhibits Arrhenius/non-Arrhenius (AnA) dynamical crossover, exponential/non-exponential (EnE) relaxation crossover, and a PEL-independent/PEL-influenced regime crossover, consistent with points (i) and (ii). However, in the vicinity of the LLCP, the AnA crossover is absent but the liquid exhibits EnE relaxation and PEL regime crossovers. At very low density, crystallization intervenes and the PEL regime crossover is suppressed. Yet, the AnA dynamical crossover and the EnE relaxation crossover remain. It follows that the dynamics in liquids (AnA and EnE crossovers) are not necessarily correlated with the changes between the PEL regimes, as one could have expected. Interestingly, the AnA crossover in the FJ liquid is not related to the presence of the Widom line. This result may seem to be at odds with previous studies of polymorphic model liquids, and a simple explanation is provided.
The effect of surface charge convection and shape deformation on the settling velocity of drops in nonuniform electric field
Authors: Mandal Shubhadeep , Bandopadhyay Aditya , Chakraborty Suman
Published: January 2017

The electrohydrodynamic settling of a leaky dielectric drop suspended in another leaky dielectric medium of unbounded extent in the combined presence of gravity and a nonuniform (combination of uniform and quadrupole) electric field is investigated theoretically in the Stokes flow limit. The present study incorporates both the effects of surface charge convection and shape deformation on the drop settling speed. The drop settling speed in the presence of an electric field is governed by three dimensionless groups: (i) capillary number Ca (the ratio of viscous to capillary stresses), (ii) electric Reynolds number ReE (the ratio of charge relaxation to convection time scales), and (iii) Masson number M (the ratio of electric to viscous stresses). Depending on the material properties of the drop and suspending medium, the strength of the applied electric field, and the drop radius, the following two different kinds of physical systems are identified for which asymptotic solutions for the settling velocity is obtained: (i) weak charge convection and small shape deformation (i.e., ReE≪1, Ca≪1) but with appreciable electric field strength (M∼1) and (ii) weak electric field (i.e., M≪1) but with appreciable charge convection ReE∼1. For a perfectly conducting drop suspended in a leaky (or perfectly) dielectric medium, the application of a uniform and/or quadrupole electric field always deforms the drop into a prolate shape which leads to an increase in drop settling speed. For a perfectly dielectric drop suspended in a perfectly dielectric medium, the application of a quadrupole electric field can deform the drop into either a prolate or an oblate shape which leads to an increase or decrease in the drop speed depending on the drop to medium permittivity ratio. Combined presence of uniform and quadrupole fields induces a dielectrophoretic force on the drop which not only alters the drop speed but also can change the direction of drop motion depending on the values of physical parameters. The present study establishes that surface charge convection plays an important role in determining the drop settling speed for a leaky dielectric drop suspended in a leaky dielectric medium. It is shown that the charge-convection-induced correction in the drop settling speed is larger in magnitude in the presence of a quadrupole electric field as compared to a uniform electric field; this is due to a more intense circulation inside the drop in the presence of a quadrupole electric field.
Spin crossover in Fe(phen)2(NCS)2 complexes on metallic surfaces
Authors: Gruber Manuel , Miyamachi Toshio , Davesne Vincent , Bowen Martin , Boukari Samy , Wulfhekel Wulf , Alouani Mebarek , Beaurepaire Eric
Published: January 2017

In this review, we give an overview on the spin crossover of Fe(phen)2(NCS)2 complexes adsorbed on Cu(100), Cu2N/Cu(100), Cu(111), Co/Cu(111), Co(100), Au(100), and Au(111) surfaces. Depending on the strength of the interaction of the molecules with the substrates, the spin crossover behavior can be drastically changed. Molecules in direct contact with non-magnetic metallic surfaces coexist in both the high- and low-spin states but cannot be switched between the two. Our analysis shows that this is due to a strong interaction with the substrate in the form of a chemisorption that dictates the spin state of the molecules through its adsorption geometry. Upon reducing the interaction to the surface either by adding a second molecular layer or inserting an insulating thin film of Cu2N, the spin crossover behavior is restored and molecules can be switched between the two states with the help of scanning tunneling microscopy. Especially on Cu2N, the two states of single molecules are stable at low temperature and thus allow the realization of a molecular memory. Similarly, the molecules decoupled from metallic substrates in the second or higher layers display thermally driven spin crossover as has been revealed by X-ray absorption spectroscopy. Finally, we discuss the situation when the complex is brought into contact with a ferromagnetic substrate. This leads to a strong exchange coupling between the Fe spin in the high-spin state and the magnetization of the substrate as deduced from spin-polarized scanning tunneling spectroscopy and ab initio calculation.
Quantum shielding effects on the Gamow penetration factor for nuclear fusion reaction in quantum plasmas
Authors: Lee Myoung-Jae , Jung Young-Dae
Published: January 2017

The quantum shielding effects on the nuclear fusion reaction process are investigated in quantum plasmas. The closed expression of the classical turning point for the Gamow penetration factor in quantum plasmas is obtained by the Lambert W-function. The closed expressions of the Gamow penetration factor and the cross section for the nuclear fusion reaction in quantum plasmas are obtained as functions of the plasmon energy and the relative kinetic energy by using the effective interaction potential with the WKB analysis. It is shown that the influence of quantum screening suppresses the Sommerfeld reaction factor. It is also shown that the Gamow penetration factor increases with an increase of the plasmon energy. It is also shown that the quantum shielding effect enhances the deuterium formation by the proton-proton reaction in quantum plasmas. In addition, it is found that the energy dependences on the reaction cross section and the Gamow penetration factor are more significant in high plasmon-energy domains.
Nonlinear effects associated with kinetic Alfvén wave in magnetic islands
Authors: Rai Rajesh Kumar , Sharma Swati , Yadav Nitin , Sharma R. P.
Published: January 2017

Observations show that kinetic Alfvén waves (KAWs) play a very important role in turbulence as well as in magnetic reconnection and have also been a topic of debate in the context of particle heating. In this paper, we aim to investigate the effect of magnetic islands on the dynamics of the nonlinear KAW. The formation of current sheet/coherent structures has been explored due to the propagation of the nonlinear KAW through the chain of pre-existing fully developed chain of magnetic islands. It is found that the field localization is more intense when the density perturbation due to nonlinearity and the field perturbation due to background islands are taken into account in comparison to the perturbation created by both the sources separately. Thus, it is expected that both nonlinearity and islands (reconnection generated) will aid the field localization and hence turbulence. Based on these coherent structures, we have evaluated the power spectrum and found the scaling after first breakpoint to be consistent with the observation by Chaston et al. [Phys. Rev. Lett. 102, 015001 (2009)] in the ion diffusion region of the magnetotail.
Frequency dispersion of flexoelectricity in PMN-PT single crystal
Authors: Shu Longlong , Wan Meiqian , Jiang Xiaoning , Li Fei , Zhou Naigen , Huang Wenbin , Wang Tong
Published: January 2017

The mechanism of the recent discovered enhanced flexoelectricity in perovskites has brought about numerous controversies which still remain unclear. In this paper, we employed relaxor 0.68Pb(Mg2/3Nb1/3)O3 -0.32PbTiO3 (PMN-PT) single crystals for study. The observed flexoelectric coefficient in PMN-PT single crystal reaches up to 100 μC/m, and in a relative low frequency range, exhibits an abnormal frequency dispersion phenomenon with a positive relationship with frequency. Such frequency dispersion regulation is different from the normal relaxation behavior that usually occur a time delay, and hence proves the flexoelectricity acting more like bulk effect rather than surface effect in this kind of materials.
Communication: Alamethicin can capture lipid-like molecules in the membrane
Authors: Afanasyeva Ekaterina F. , Syryamina Victoria N. , Dzuba Sergei A.
Published: January 2017

Alamethicin (Alm) is a 19-mer antimicrobial peptide produced by fungus Trichoderma viride. Above a threshold concentration, Alm forms pores across the membrane, providing a mechanism of its antimicrobial action. Here we show that at a small concentration which is below the threshold value, Alm participates in formation of nanoscale lipid-mediated clusters of guest lipid-like molecules in the membrane. These results are obtained by electron spin echo (ESE) technique—a pulsed version of electron paramagnetic resonance—on spin-labeled stearic acid in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer with Alm added at 1/200 peptide-to-lipid ratio. ESE decay measurements are interpreted assuming that stearic acid molecules in the membrane are assembling around the Alm molecule. One may suggest that this Alm capturing effect on the guest lipid-like molecules could be important for the peptide antimicrobial action.
Simultaneous measurement of erythrocyte deformability and blood viscoelasticity using micropillars and co-flowing streams under pulsatile blood flows
Authors: Kang Yang Jun
Published: January 2017

The biophysical properties of blood provide useful information on the variation in hematological disorders or diseases. In this study, a simultaneous measurement method of RBC (Red Blood Cell) deformability and blood viscoelasticity is proposed by evaluating hemodynamic variations through micropillars and co-flowing streams under sinusoidal blood flow. A disposable microfluidic device is composed of two inlets and two outlets, two upper side channels, and two lower side channels connected to one bridge channel. First, to measure the RBC deformability, the left-lower side channel has a deformability assessment chamber (DAC) with narrow-sized micropillars. Second, to evaluate the blood viscoelasticity in co-flowing streams, a phosphate buffered saline solution is supplied at a constant flow rate. By closing or opening a pinch valve connected to the outlet of DAC, blood flows in forward or back-and-forth mode. A time-resolved micro-particle image velocimetry technique and a digital image processing technique are used to quantify the blood velocity and image intensity. Then, RBC deformability is evaluated by quantifying the blood volume passing through the DAC under forward flow, and quantifying the variations of blood velocity and image intensity in the DAC under back-and-forth flow. Using a discrete circuit model, blood viscoelasticity is obtained by evaluating variations of blood velocity and co-flowing streams. The effect of several factors (period, hematocrit, and base solution) on the performance is quantitatively evaluated. Based on the experimental results, the period of sinusoidal flow and hematocrit are fixed at 30 s and 50%, respectively. As a performance demonstration, the proposed method is employed to detect the homogeneous and heterogeneous blood composed of normal RBCs and hardened RBCs. These experimental results show that the RBC deformability is more effective to detect minor subpopulations of heterogeneous bloods, compared with blood viscoelasticity. Therefore, it leads to the conclusion that the proposed method has the ability to evaluate RBC deformability and blood viscoelasticity under sinusoidal blood flow, with sufficient accuracy and high-throughput.
Contribution of canonical nonhomologous end joining to chromosomal rearrangements is enhanced by ATM kinase deficiency
Authors: Bhargava Ragini , Carson Caree R. , Lee Gabriella , Stark Jeremy M.
Published: January 2017

Significance

Chromosomal rearrangements, such as large deletions, can cause loss of tumor suppressor genes. Rearrangements can be formed by aberrant end-joining (EJ) repair that ligates ends from different double-strand breaks. Two distinct EJ pathways could potentially cause rearrangements [canonical nonhomologous end joining (C-NHEJ) and alternative EJ], which are mediated by different factors and cause distinct repair junction patterns. Using a reporter for a 0.4-Mbp deletion rearrangement, we found that cells deficient in the Ataxia Telangiectasia Mutated (ATM) signaling pathway show an increase in the frequency of this rearrangement and a shift toward C-NHEJ–mediated rearrangements. Thus, the relative contribution of distinct EJ pathways to rearrangement formation is affected by ATM signaling, which provides insight into the tumor suppressor function of ATM.
Cocapture of cognate and bystander antigens can activate autoreactive B cells
Authors: Sanderson Nicholas S. R. , Zimmermann Maria , Eilinger Luca , Gubser Céline , Schaeren-Wiemers Nicole , Lindberg Raija L. P. , Dougan Stephanie K. , Ploegh Hidde L. , Kappos Ludwig , Derfuss Tobias
Published: January 2017

Significance

The immune system normally produces antibodies against pathogens and avoids making antibodies against self-proteins. In some individuals, antibodies against self-proteins (autoantibodies) are made and can cause debilitating disease, but the reasons for this failure of self-tolerance are not known. The experiments described test the following hypothesis linking viral infections and production of autoantibodies: A B cell whose immunoglobulin receptor recognizes a self-membrane protein can capture that protein from the membrane of a virus-infected cell and simultaneously cocapture viral proteins; fragments of the viral protein can then be presented to antiviral T cells and qualify for the positive signals for proliferation and antibody production known as T-cell help. We observed this phenomenon in vitro and in vivo.
Place satisfaction, place attachment and quality of life: development of a conceptual framework for island destinations.
Authors: Ramkissoon H.
Published: January 2017

This chapter can be perceived as the first step in the development of a conceptual framework contributing to our understanding of how visitor experiences are shaped by environmental psychological constructs. It develops and proposes a conceptual framework for island destinations, extending the theoretical interrelationships between local visitors' place satisfaction, place attachment (affect, identity, dependence, and social bonding), pro-environmental behaviour and their overall quality of life in island economies.
The ultrastructural organization of actin and myosin II filaments in the contractile ring: new support for an old model of cytokinesis
Authors: Henson John H. , Ditzler Casey E. , Germain Aphnie , Irwin Patrick M. , Vogt Eric T. , Yang Shucheng , Wu Xufeng , Shuster Charles B.
Published: January 2017

Despite recent advances in our understanding of the components and spatial regulation of the contractile ring (CR), the precise ultrastructure of actin and myosin II within the animal cell CR remains an unanswered question. We used superresolution light microscopy and platinum replica transmission electron microscopy (TEM) to determine the structural organization of actin and myosin II in isolated cortical cytoskeletons prepared from dividing sea urchin embryos. Three-dimensional structured illumination microscopy indicated that within the CR, actin and myosin II filaments were organized into tightly packed linear arrays oriented along the axis of constriction and restricted to a narrow zone within the furrow. In contrast, myosin II filaments in earlier stages of cytokinesis were organized into small, discrete, and regularly spaced clusters. TEM showed that actin within the CR formed a dense and anisotropic array of elongate, antiparallel filaments, whereas myosin II was organized into laterally associated, head-to-head filament chains highly reminiscent of mammalian cell stress fibers. Together these results not only support the canonical “purse-string” model for contractile ring constriction, but also suggest that the CR may be derived from foci of myosin II filaments in a manner similar to what has been demonstrated in fission yeast.
Regulation of yeast ESCRT-III membrane scission activity by the Doa4 ubiquitin hydrolase
Authors: Johnson Natalie , West Matt , Odorizzi Greg
Published: January 2017

ESCRT-III executes membrane scission during the budding of intralumenal vesicles (ILVs) at endosomes. The scission mechanism is unknown but appears to be linked to the cycle of assembly and disassembly of ESCRT-III complexes at membranes. Regulating this cycle is therefore expected to be important for determining the timing of ESCRT-III–mediated membrane scission. We show that in Saccharomyces cerevisiae, ESCRT-III complexes are stabilized and ILV membrane scission is delayed by Doa4, which is the ubiquitin hydrolase that deubiquitinates transmembrane proteins sorted as cargoes into ILVs. These results suggest a mechanism to delay ILV budding while cargoes undergo deubiquitination. We further show that deubiquitination of ILV cargoes is inhibited via Doa4 binding to Vps20, which is the subunit of ESCRT-III that initiates assembly of the complex. Current models suggest that ESCRT-III complexes surround ubiquitinated cargoes to trap them at the site of ILV budding while the cargoes undergo deubiquitination. Thus our results also propose a mechanism to prevent the onset of ILV cargo deubiquitination at the initiation of ESCRT-III complex assembly.
Alarming Prevalence of Emergency Hypertension Levels in the General Public Identified by a Hypertension Awareness Campaign
Authors: Caligiuri Stephanie P. B. , Austria Jose Alejandro , Pierce Grant N.
Published: January 2017

BACKGROUND

Hypertension is a major cause of mortality and morbidity today. The “silent” nature of hypertension makes it critical to determine its prevalence and its severity in the general public and to identify strategies to identify people unaware of its presence. A mobile hypertension awareness campaign was created to: (i) determine the prevalence and types of hypertension in an urban North American center, (ii) increase hypertension awareness, and (iii) identify reasons for lack of therapy adherence.

METHODS

Mobile clinics were provided at shopping malls, workplaces, hospitals, and community centres to measure blood pressure in the public. Blood pressure recordings were done on a voluntary basis.

RESULTS

Of 1097 participants, 50% presented with high blood pressure which was higher than expected. Of particular clinical significance, an unexpectedly large number of participants (2%) exhibited a hypertensive urgency/emergency. Most of these people were not adherent to medications (if their hypertension was detected previously), were unaware of their hypertensive state, and/or unwilling to acknowledge or ignored the clinical significance of the extremely high blood pressure readings. Reasons for lack of adherence included: denial, being unaware of health consequences, and proper management of hypertension.

CONCLUSIONS

A relatively large segment of an urban population lives unaware of severe emergency levels of hypertension. A public mobile hypertension clinic provides a valuable strategy for identifying hypertension in the general public and for knowledge translation of hypertension management.
Malignant Hypertension Revisited—Does This Still Exist?
Authors: Shantsila Alena , Lip Gregory Y.H.
Published: January 2017

Malignant or accelerated hypertension is the most severe form of hypertension, defined clinically by very high blood pressure (diastolic above 130 mm Hg) accompanied by bilateral retinal hemorrhages and/or exudates, with or without papilledema. The aim of this review is to discuss if malignant hypertension still poses a clinically relevant entity and to highlight the diagnostic challenges of this form of hypertension. The substantial improvement in prognosis in patients with malignant hypertension over the last decades is well documented, but there is no strong evidence to suggest a significant change in its incidence. In fact, with the growing population and improving life expectancy, malignant hypertension is likely to become even more prevalent worldwide, especially in the developing countries with less advanced health care services. Despite simple diagnostic criteria of malignant hypertension, the diagnoses may be difficult in many patients. Malignant hypertension patients often have the diagnosis established only when the target organ damage occur. Furthermore, retrospective diagnosis is problematic, as malignant hypertensive retinopathy gradually resolves over a relatively short period of time, while persistent target organ damage will, however, lead to the development of complications and much poorer prognosis than in nonmalignant hypertension patients. Certainly, malignant hypertension still poses a clinically relevant and challenging form of hypertension and its possibility should be always considered during the assessment of patients with poorly controlled hypertension.
AFS: identification and quantification of species composition by metagenomic sequencing
Authors: Liu Yongchao , Ripp Fabian , Koeppel Rene , Schmidt Hanno , Hellmann Sören Lukas , Weber Mathias , Krombholz Christopher Felix , Schmidt Bertil , Hankeln Thomas
Published: January 2017

DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol. Cost-saving short (50-bp) single-end reads and Nextera® library preparation yield reliable results.

Availability and Implementation

Datasets, binaries and usage instructions are available under http://all-food-seq.sourceforge.net. Raw data is available at NCBI’s SRA with accession number PRJNA271645.

Supplementary information

Supplementary data are available at Bioinformatics online.
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library
Authors: Litfin Thomas , Zhou Yaoqi , Yang Yuedong
Published: January 2017

Motivation

The high cost of drug discovery motivates the development of accurate virtual screening tools. Binding-homology, which takes advantage of known protein–ligand binding pairs, has emerged as a powerful discrimination technique. In order to exploit all available binding data, modelled structures of ligand-binding sequences may be used to create an expanded structural binding template library.

Results

SPOT-Ligand 2 has demonstrated significantly improved screening performance over its previous version by expanding the template library 15 times over the previous one. It also performed better than or similar to other binding-homology approaches on the DUD and DUD-E benchmarks.

Availability and Implementation

The server is available online at http://sparks-lab.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest
Authors: Hou Qingzhen , De Geest Paul F G , Vranken Wim F , Heringa Jaap , Feenstra K Anton
Published: January 2017

Motivation

Genome sequencing is producing an ever-increasing amount of associated protein sequences. Few of these sequences have experimentally validated annotations, however, and computational predictions are becoming increasingly successful in producing such annotations. One key challenge remains the prediction of the amino acids in a given protein sequence that are involved in protein–protein interactions. Such predictions are typically based on machine learning methods that take advantage of the properties and sequence positions of amino acids that are known to be involved in interaction. In this paper, we evaluate the importance of various features using Random Forest (RF), and include as a novel feature backbone flexibility predicted from sequences to further optimise protein interface prediction.

Results

We observe that there is no single sequence feature that enables pinpointing interacting sites in our Random Forest models. However, combining different properties does increase the performance of interface prediction. Our homomeric-trained RF interface predictor is able to distinguish interface from non-interface residues with an area under the ROC curve of 0.72 in a homomeric test-set. The heteromeric-trained RF interface predictor performs better than existing predictors on a independent heteromeric test-set. We trained a more general predictor on the combined homomeric and heteromeric dataset, and show that in addition to predicting homomeric interfaces, it is also able to pinpoint interface residues in heterodimers. This suggests that our random forest model and the features included capture common properties of both homodimer and heterodimer interfaces.

Availability and Implementation

The predictors and test datasets used in our analyses are freely available (http://www.ibi.vu.nl/downloads/RF_PPI/).

Supplementary information

Supplementary data are available at Bioinformatics online.
Cyst Fluid From Cystic, Malignant Brain Tumors: A Reservoir of Nutrients, Including Growth Factor-Like Nutrients, for Tumor Cells
Authors: Dahlberg Daniel , Struys Eduard A. , Jansen Erwin E. , Mørkrid Lars , Midttun Øivind , Hassel Bjørnar
Published: January 2017

BACKGROUND: Brain tumors may have cysts, whose content of nutrients could influence tumor cell microenvironment and growth.

OBJECTIVE: To measure nutrients in cyst fluid from glioblastoma multiforme (GBM) and metastatic brain tumors.

METHODS: Quantification of nutrients in cyst fluid from 12 to 18 GBMs and 4 to 10 metastatic brain tumors.

RESULTS: GBM cysts contained glucose at 2.2 mmol/L (median value; range <0.8-3.5) and glutamine at 1.04 mmol/L (0.17-4.2). Lactate was 7.1 mmol/L (2.4-12.5) and correlated inversely with glucose level (r = –0.77; P < .001). Amino acids, including glutamate, varied greatly, but median values were similar to previously published serum values. Ammonia was 75 μmol/L (11-241). B vitamins were present at previously published serum values, and riboflavin, nicotinamide, pyridoxal 5΄-phosphate, and cobalamin were higher in cyst fluid than in cerebrospinal fluid. Inorganic phosphate was 1.25 mmol/L (0.34-3.44), which was >3 times higher than in ventricular cerebrospinal fluid: 0.35 mmol/L (0.22-0.66; P < .001). Tricarboxylic acid cycle intermediates were in the low micromolar range, except for citrate, which was 240 μmol/L (140-590). In cystic metastatic malignant melanomas and lung tumors values were similar to those in GBMs.

CONCLUSION: Tumor cysts may be a nutrient reservoir for brain tumors, securing tumor energy metabolism and synthesis of cell constituents. Serum is one likely source of cyst fluid nutrients. Nutrient levels in tumor cyst fluid are highly variable, which could differentially stimulate tumor growth. Cyst fluid glutamate, lactate, and phosphate may act as tumor growth factors; these compounds have previously been shown to stimulate tumor growth at concentrations found in tumor cyst fluid.
A measurement of interstellar polarization and an estimation of Galactic extinction for the direction of the X-ray black hole binary V404 Cygni
Authors: Itoh Ryosuke , Tanaka Yasuyuki T. , Kawabata Koji S. , Uemura Makoto , Watanabe Makoto , Fukazawa Yasushi , Kanda Yuka , Akitaya Hiroshi , Moritani Yuki , Nakaoka Tatsuya , Kawabata Miho , Shiki Kensei , Yoshida Michitoshi , Oasa Yumiko , Takahashi Jun
Published: January 2017

V404 Cygni is a well-known candidate for the black hole binary thought to have relativistic jets. It showed extreme outbursts in 2015 June, characterized by a large amplitude and short time variation of flux in the radio, optical, and X-ray bands. Not only disk emission but also synchrotron radiation from the relativistic jets was suggested by radio observations. However, it is difficult to measure the accurate spectral shape in the optical/near-infrared band because there are uncertainties of interstellar extinction. To estimate the extinction value for V404 Cygni, we performed photopolarimetric and spectroscopic observations of V404 Cygni and nearby field stars. Here, we estimate the Galactic extinction using interstellar polarization based on the observation that the origin of the optical polarization is the interstellar medium, and investigate the properties of interstellar polarization around V404 Cygni. We found a good correlation between the color excess and polarization degree in the field stars. We also confirmed that the wavelength dependence of the polarization degree in the highly polarized field stars was similar to that of V404 Cygni. Using the highly polarized field stars, we estimated the color excess for the (B − V) color and the extinction in the V band to be E(B − V) = 1.2 ± 0.2 and 3.0 < A(V) < 3.6, respectively. A tendency for a bluer peak of polarization (λmax < 5500 Å) was commonly seen in the highly polarized field stars, suggesting that the dust grains toward this region are generally smaller than the Galactic average. The corrected spectral energy distribution of V404 Cygni in the near-infrared and optical bands in our results indicated a spectral break between 2.5 × 1014 Hz and 3.7 × 1014 Hz, which might originate in the synchrotron self-absorption.
Coronary Plaque Progression and Regression in Asymptomatic African American Chronic Cocaine Users With Obstructive Coronary Stenoses: A Preliminary Study
Authors: Sandfort Veit , Bluemke David A. , Vargas Jose , Brinker Jeffrey A. , Gerstenblith Gary , Kickler Thomas , Zheng Gang , Li Ji , Chen Shaoguang , Lai Hong , Fishman Elliot K. , Lai Shenghan
Published: January 2017

Objective:

Although rapid progression of coronary atherosclerosis was observed in chronic cocaine users, it is unknown whether reduced cocaine use retards the progression of atherosclerosis. We investigated whether reduced cocaine use over a 12-month period was associated with coronary plaque regression in cocaine users.

Methods:

Fifteen African American chronic cocaine users with previously coronary computed tomography angiography (CCTA)-confirmed >50% coronary stenosis in Baltimore, Maryland, were enrolled in a study to investigate whether reduced cocaine use is associated with changes in coronary plaque burden over a 12-month period of cash-based incentive intervention, which was implemented to systematically reinforce cocaine abstinence. In addition to previous CCTA (preintervention), CCTA was performed at the intervention baseline and at postintervention. Plaque analyses were performed to determine the trajectory of plaque changes in the absence of intervention by comparing the preintervention with the intervention baseline studies; the trajectory of plaque changes associated with the intervention by comparing the intervention baseline with the postintervention studies; and (3) whether reduced cocaine use was independently associated with changes in coronary plaque burden.

Results:

During the 12-month cash-based incentive intervention period, cocaine use in participants was lower. The medians of noncalcified plaque indices were 37.8 (interquartile range [IQR] 29.3–44.0), 43.1 (IQR 38.3–49.0), and 38.7 (IQR 31.2–46.8) mm2 at preintervention, intervention baseline, and postintervention, respectively. Multivariable generalized estimating equation analysis showed that both total plaque and noncalcified plaque indices at preintervention were significantly lowered as compared with intervention baseline levels; both total plaque and noncalcified plaque indices after intervention were significantly lowered as compared with intervention baseline levels; and reduced cocaine use was independently associated with lower total plaque volume index (P < 0.0001) and noncalcified plaque volume index (P = 0.010).

Conclusions:

Our findings suggest that continued cocaine use may be associated with noncalcified plaque progression, whereas reduced cocaine use may be associated with noncalcified plaque regression. Larger studies are needed to confirm these findings.