bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tuning the π‐π stacking distance and J‐aggregation of DPP‐based conjugated polymer via introducing insulating polymer
Authors: Chen Liang , Wang Haiyang , Liu Jiangang , Xing Rubo , Yu Xinhong , Han Yanchun 
Published: January 2016

ABSTRACTThe close π–π stacking and the high J‐aggregation during the formation of fibrillar morphology in films of the poly[[2,5‐bis(2‐octyldodecyl)−2,3,5,6‐tetrahydro‐3,6‐dioxopyrrolo[3,4‐c]pyrrole‐1,4‐diyl]‐alt–[[2,2′‐(2,5‐thiophene)bis‐thieno[3,2‐b]thiophen]‐5,5′‐diyl]] (PDPPTT‐T) are demonstrated via blending with polystyrene (PS). The hydrodynamic radius (Rh) of PDPPTT‐T is decreased from 16.7 nm in the neat solution to 12.7 nm in the blend solution at the ratio of 1/20(PDPPTT‐T/PS). This phenomenon suggests that blending PS is beneficial for the disentanglement of PDPPTT‐T. The disentanglement of PDPPTT‐T facilitates the formation of fibrillar morphology. The growth of the fibrils occurs along the molecular backbones and the width of the fibrils is parallel to the π–π stacking direction. The disentanglement of PDPPTT‐T helps the molecules adjust conformation to improve J‐aggregation and decrease the π–π stacking distance. The maximum absorption is red‐shifted from 825 nm to 849 nm and the relative intensity of J‐aggregation (the 0‐0/0‐1 ratio) is increased from 1.19 to 1.60. The π–π stacking distance decreases from 3.57 to 3.52 Å. The charge‐carrier mobility will be improved in the fibrillar morphology with close π–π stacking and high J‐aggregation. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 838–847
Post‐diagnosis social networks, and lifestyle and treatment factors in the After Breast Cancer Pooling Project
Authors: Kroenke Candyce H , Michael Yvonne L. , Shu Xiao‐Ou , Poole Elizabeth M. , Kwan Marilyn L. , Nechuta Sarah , Caan Bette J. , Pierce John P. , Chen Wendy Y. 
Published: January 2016

AbstractObjectiveLarger social networks have been associated with better breast cancer survival. To investigate potential mediators, we evaluated associations of social network size and diversity with lifestyle and treatment factors associated with prognosis.MethodsWe included 9331 women from the After Breast Cancer Pooling Project who provided data on social networks within approximately two years following diagnosis. A social network index was derived from information about the presence of a spouse or intimate partner, religious ties, community participation, friendship ties, and numbers of living relatives. Diversity was assessed as variety of ties, independent of size. We used logistic regression to evaluate associations with outcomes and evaluated whether effect estimates differed using meta‐analytic techniques.ResultsAssociations were similar across cohorts though analyses of smoking and alcohol included US cohorts only because of low prevalence of these behaviors in the Shanghai cohort. Socially isolated women were more likely to be obese (OR = 1.21, 95% CI:1.03–1.42), have low physical activity (<10 MET‐hours/week, OR = 1.55, 95% CI:1.36–1.78), be current smokers (OR = 2.77, 95% CI:2.09‐3.68), and have high alcohol intake (≥15 g/d, OR = 1.23, 95% CI:1.00–1.51), compared with socially integrated women. Among node positive cases from three cohorts, socially isolated women were more likely not to receive chemotherapy (OR = 2.10, 95% CI:1.30–3.39); associations differed in a fourth cohort. Other associations (nonsignificant) were consistent with less intensive treatment in socially isolated women. Low social network diversity was independently associated with more adverse lifestyle, but not clinical, factors.ConclusionsSmall, less diverse social networks measured post‐diagnosis were associated with more adverse lifestyle factors and less intensive cancer treatment. Copyright © 2016 John Wiley & Sons, Ltd.
A de novo protein confers copper resistance in Escherichia coli
Authors: Hoegler Kenric J. , Hecht Michael H. 
Published: January 2016

AbstractTo survive environmental challenges, biological systems rely on proteins that were selected by evolution to function in particular cellular and conditional settings. With the advent of protein design and synthetic biology, it is now possible to construct novel proteins that are not biased by eons of selection in natural hosts. The availability of these sequences prompts us to ask whether natural biological organisms can use naïve—non‐biological—proteins to enhance fitness in stressful environments. To address this question, we transformed a library of DNA sequences encoding ∼1.5 × 106 binary patterned de novo proteins into E. coli, and selected for sequences that enable growth in concentrations of copper that would otherwise be toxic. Several novel sequences were discovered, and one of them, called Construct K (ConK), was studied in detail. Cells expressing ConK accumulate approximately 50% less copper than control cells. The function of ConK does not involve an oxidase, nor does it require two of the best characterized copper efflux systems. However, the ability of ConK to rescue cells from toxic concentrations of copper does require an active proton motive force. Further selections for growth in higher concentrations of copper led to the laboratory evolution of variants of ConK with enhanced levels of activity in vivo. These studies demonstrate that novel proteins, unbiased by evolutionary history in the natural world, can enhance the fitness of biological systems.Synopsis: Living systems evolve to adapt to potentially lethal environmental changes. This normally involves repurposing existing genetic information (i.e. sequences that were selected by billions of years of evolution). Here we show that a completely de novo protein, not derived from nature, can enable E. coli cells to grow in otherwise toxic concentrations of copper, demonstrating that living systems also have the capacity to incorporate and protopurpose entirely novel genetic information.
NMR reveals structural rearrangements associated to substrate insertion in nucleotide‐adding enzymes
Authors: Mohanty Biswaranjan , Geralt Michael , Wüthrich Kurt , Serrano Pedro 
Published: January 2016

AbstractThe protein NP_344798.1 from Streptococcus pneumoniae TIGR4 exhibits a head and base‐interacting neck domain architecture, as observed in class II nucleotide‐adding enzymes. Although it has less than 20% overall sequence identity with any member of this enzyme family, the residues involved in substrate‐recognition and catalysis are highly conserved in NP_344798.1. NMR studies showed binding affinity of NP_344798.1 for nucleotides and revealed μs to ms time scale rate processes involving residues constituting the active site. The results thus obtained indicate that large‐amplitude rearrangements of regular secondary structures facilitate the penetration of the substrate into the occluded nucleotide‐binding site of NP_344798.1 and, by inference based on sequence and structural homology, probably a wide range of other nucleotide‐adding enzymes.
Analysis of amino acid substitutions in AraC variants that respond to triacetic acid lactone
Authors: Frei Christopher S. , Wang Zhiqing , Qian Shuai , Deutsch Samuel , Sutter Markus , Cirino Patrick C. 
Published: January 2016

AbstractThe Escherichia coli regulatory protein AraC regulates expression of ara genes in response to l‐arabinose. In efforts to develop genetically encoded molecular reporters, we previously engineered an AraC variant that responds to the compound triacetic acid lactone (TAL). This variant (named “AraC‐TAL1”) was isolated by screening a library of AraC variants, in which five amino acid positions in the ligand‐binding pocket were simultaneously randomized. Screening was carried out through multiple rounds of alternating positive and negative fluorescence‐activated cell sorting. Here we show that changing the screening protocol results in the identification of different TAL‐responsive variants (nine new variants). Individual substituted residues within these variants were found to primarily act cooperatively toward the gene expression response. Finally, X‐ray diffraction was used to solve the crystal structure of the apo AraC‐TAL1 ligand‐binding domain. The resolved crystal structure confirms that this variant takes on a structure nearly identical to the apo wild‐type AraC ligand‐binding domain (root‐mean‐square deviation 0.93 Å), suggesting that AraC‐TAL1 behaves similar to wild‐type with regard to ligand recognition and gene regulation. Our results provide amino acid sequence–function data sets for training and validating AraC modeling studies, and contribute to our understanding of how to design new biosensors based on AraC.
The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops
Authors: Tsuchiya Yuko , Mizuguchi Kenji 
Published: January 2016

AbstractOf the complementarity‐determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen‐binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen‐binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen‐binding tendencies of all the CDR loops.
Crystal structure of the FK506 binding domain of human FKBP25 in complex with FK506
Authors: Prakash Ajit , Rajan Sreekanth , Yoon Ho Sup 
Published: January 2016

AbstractHuman FKBP25 (hFKBP25) is a nuclear immunophilin and interacts with several nuclear proteins, hence involving in many nuclear events. Similar to other FKBPs, FK506 binding domain (FKBD) of hFKBP25 also binds to immunosuppressive drugs such as rapamycin and FK506, albeit with a lower affinity for the latter. The molecular basis underlying this difference in affinity could not be addressed due to the lack of the crystal structure of hFKBD25 in complex with FK506. Here, we report the crystal structure of hFKBD25 in complex with FK506 determined at 1.8 Å resolution and its comparison with the hFKBD25–rapamycin complex, bringing out the microheterogeneity in the mode of interaction of these drugs, which could possibly explain the lower affinity for FK506.
Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases
Authors: Taberman Helena , Parkkinen Tarja , Rouvinen Juha 
Published: January 2016

AbstractThe Gfo/Idh/MocA protein family contains a number of different proteins, which almost exclusively consist of NAD(P)‐dependent oxidoreductases that have a diverse set of substrates, typically pyranoses. In this study, to clarify common structural features that would contribute to their function, the available crystal structures of the members of this family have been analyzed. Despite a very low sequence identity, the central features of the three‐dimensional structures of the proteins are surprisingly similar. The members of the protein family have a two‐domain structure consisting of a N‐terminal nucleotide‐binding domain and a C‐terminal α/β‐domain. The C‐terminal domain contributes to the substrate binding and catalysis, and contains a βα‐motif with a central α‐helix carrying common essential amino acid residues. The β‐sheet of the α/β‐domain contributes to the oligomerization in most of the proteins in the family.
Half‐Heusler compounds with a 1 eV (1.7 eV) direct band gap, lattice‐matched to GaAs (Si), for solar cell application: A first‐principles study
Authors: Belmiloud N. , Boutaiba F. , Belabbes A. , Ferhat M. , Bechstedt F. 
Published: January 2016

AbstractA systematic theoretical study of the structural and electronic properties of new half‐Heusler compounds is performed to find the appropriate target key physical parameters for photovoltaic application. As a result, five ternary half‐Heusler compounds ScAgC, YCuC, CaZnC, NaAgO, and LiCuS are studied by density functional theory for potential applications in multi‐junction solar cells. The calculated formation enthalpies indicate that these materials are thermodynamically stable. Using state‐of‐the‐art modified Becke–Johnson exchange potential approximation, we find a direct band gap close to 1 eV (1.88 eV) for ScAgC, YCuC, CaZnC, NaAgO (LiCuS) being quasi‐lattice matched to GaAs (Si). In addition, the band offsets between half‐Heusler compounds and GaAs (Si) and their consequences for heterostructures are derived using the modified Tersoff method for the branch‐point energy. Furthermore, the elastic constants and phonon dispersion curves are calculated. They indicate the respective mechanical and dynamical stability of these half‐Heusler compounds.
Diamond‐SAW devices: a reverse fabrication method
Authors: Mukherjee Debarati , Oliveira Filipe J. , Silva Rui F. , Carreira José F. , Rino Luis , Correia Maria R. , Rotter Shlomo Z. , Alves Luis N. , Mendes Joana C. 
Published: January 2016

AbstractSurface acoustic wave (SAW) devices are key components in modern wireless communication systems. Besides being used as reflective delay lines, filters or resonators, SAW devices can be used as sensors and fixed‐code identification tags. Due to their high‐acoustic velo‐city, diamond films can be combined with piezoelectric materials to fabricate diamond‐based SAW devices with potential for high frequency applications. This paper presents results of coating commercial SAW delay lines with diamond films. The films were deposited on lithium niobate under different conditions in a hot filament chemical vapour deposition system. Seeding was performed using 6‐12 μm diamond grit and 20‐30 nm nano‐diamond particles based suspensions. After tuning the deposition conditions, dies of 74 MHz delay lines were coated with diamond. The quality, morphology and conformability of the coatings were evaluated by scanning electron microscopy (SEM) and Raman spectroscopy. The integrity of the interdigitated transducers (IDTs) after deposition was evaluated by SEM. S‐parameters of as‐bought and diamond‐coated dies were measured using a network analyser. Although the frequency response is attenuated after diamond deposition, integrity of the IDTs and the operating principle of the devices are kept intact. These preliminary results open the door to a simplified fabrication procedure of diamond‐based SAW devices. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Use of robot‐specific resources and operating room times: the case of Telelap Alf‐X robotic hysterectomy
Authors: Rossitto Cristiano , Gueli Alletti Salvatore , Romano Federica , Fiore Alessandra , Coretti Silvia , Oradei Marco , Ruggeri Matteo , Cicchetti Americo , Marchetti Marco , Fanfani Francesco , Scambia Giovanni 
Published: January 2016

AbstractIntroductionThe aim of this study was to identify, quantify and evaluate the use of robotic materials and operating theatre times in Telelap ALF‐X robotic hysterectomy.Materials and methodsCost analysis was performed on 81 patients who underwent a Telelap ALF‐X robotic hysterectomy. Data were collected during a phase II study trial conducted at the University Hospital A. Gemelli, Catholic University, Rome. According to micro‐costing technique, surgical team costs, materials and operating theatre usage were recorded during each surgical intervention. Cost data were provided by the hospital's accounting office. Probabilistic sensitivity analysis was carried out in order to test the robustness of the results by assuming an Inv‐norm random variable.ResultsThe base case analysis showed a cost/patient of €3391.82. The new robotic device requires a low consumption of robotic materials. Sensitivity analysis showed that the most sensitive cost driver was use of the operating theatre.ConclusionThis study shows that Telelap ALF‐X robotic hysterectomy is feasible and safe and could offer specific advantages in terms of cost. Copyright © 2016 John Wiley & Sons, Ltd.
Patient‐specific assessment of dysmorphism of the femoral head–neck junction: a statistical shape model approach
Authors: Khanduja Vikas , Baelde Nick , Dobbelaere Andreas , Van Houcke Jan , Li Hao , Pattyn Christophe , Audenaert Emmanuel A. 
Published: January 2016

AbstractBackgroundObjective quantification of anatomical variations about the femur head–neck junction in pre‐operative planning for surgical intervention in femoro‐acetabular impingement is problematic, as no clear definition of average normal anatomy for a specific subject exists.MethodsWe have defined the normal‐equivalent of a subject's anatomy by using a statistical shape model and geometric shape optimization for finding correspondences, while excluding the femoral head–neck junction during the fitting procedure. The presented technique was evaluated on a cohort of 20 patients.ResultsDifference in α‐angle measurement between the actual morphology and the predicted normal‐equivalent, averaged 1.3° (SD 1.7°) in the control group versus 8° (SD 7.3°) in the patient group (p < 0.05).ConclusionsDefining normal equivalent anatomy is effective in quantifying anatomical dysmorphism of the femoral head–neck junction and as such can improve presurgical analysis of patients diagnosed with femoro‐acetabular impingement. Copyright © 2016 John Wiley & Sons, Ltd.
On distributed reactive power and storage control on microgrids
Authors: Cortés Andres , Martínez Sonia 
Published: January 2016

SummaryThis manuscript develops a dual decomposition algorithm for the distributed control of reactive power and charging/discharging rates in microgrids with distributed solar generation and \storage capacities. Our setting considers physical constraints inherent to storage systems and voltage regulation constraints with the objective of minimizing a cost function that encompasses two aspects: the total cost of the active power consumed by the microgrid and its associated transmission losses over a finite time horizon. We provide a complete analysis of the convergence of the proposed algorithm and introduce a novel approach for the distributed approximation of the voltage prediction over the power grid. Simulations demonstrate the performance of the dual decomposition algorithm on a particular microgrid case. Copyright © 2016 John Wiley & Sons, Ltd.
Adaptive perimeter traffic control of urban road networks based on MFD model with time delays
Authors: Haddad Jack , Mirkin Boris 
Published: January 2016

SummaryIn this work, we focus on two main themes: (i) developing a more realistic macroscopic fundamental diagram‐based nonlinear control‐oriented model of urban traffic networks with time delays incorporated into model structure; and (ii) based on its linearized form subject to input delay, designing two new perimeter control architectures for one aggregated urban traffic region under unknown bounded external disturbances and parameter uncertainties. The feedback control laws design is performed in the context of model reference adaptive control approach. Simulation results based on a linearized model are also presented, which demonstrate in this case desired closed‐loop adaptive control system performance. Copyright © 2015 John Wiley & Sons, Ltd.
Statistical efficiency and optimal design for stepped cluster studies under linear mixed effects models
Authors: Girling Alan J. , Hemming Karla 
Published: January 2016

In stepped cluster designs the intervention is introduced into some (or all) clusters at different times and persists until the end of the study. Instances include traditional parallel cluster designs and the more recent stepped‐wedge designs. We consider the precision offered by such designs under mixed‐effects models with fixed time and random subject and cluster effects (including interactions with time), and explore the optimal choice of uptake times. The results apply both to cross‐sectional studies where new subjects are observed at each time‐point, and longitudinal studies with repeat observations on the same subjects.The efficiency of the design is expressed in terms of a ‘cluster‐mean correlation’ which carries information about the dependency‐structure of the data, and two design coefficients which reflect the pattern of uptake‐times. In cross‐sectional studies the cluster‐mean correlation combines information about the cluster‐size and the intra‐cluster correlation coefficient. A formula is given for the ‘design effect’ in both cross‐sectional and longitudinal studies.An algorithm for optimising the choice of uptake times is described and specific results obtained for the best balanced stepped designs. In large studies we show that the best design is a hybrid mixture of parallel and stepped‐wedge components, with the proportion of stepped wedge clusters equal to the cluster‐mean correlation. The impact of prior uncertainty in the cluster‐mean correlation is considered by simulation. Some specific hybrid designs are proposed for consideration when the cluster‐mean correlation cannot be reliably estimated, using a minimax principle to ensure acceptable performance across the whole range of unknown values. © 2016 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd.
A Primitive Growth Factor, NME7AB, Is Sufficient to Induce Stable Naïve State Human Pluripotency; Reprogramming in This Novel Growth Factor Confers Superior Differentiation
Authors: Carter M.G. , Smagghe B.J. , Stewart A.K. , Rapley J.A. , Lynch E. , Bernier K.J. , Keating K.W. , Hatziioannou V.M. , Hartman E.J. , Bamdad Cynthia C. 
Published: January 2016

Abstract
Scientists have generated human stem cells that in some respects mimic mouse naïve cells, but their dependence on the addition of several extrinsic agents, and their propensity to develop abnormal karyotype calls into question their resemblance to a naturally occurring “naïve” state in humans. Here, we report that a recombinant, truncated human NME7, referred to as NME7AB here, induces a stable naïve-like state in human embryonic stem cells and induced pluripotent stem cells without the use of inhibitors, transgenes, leukemia inhibitory factor (LIF), fibroblast growth factor 2 (FGF2), feeder cells, or their conditioned media. Evidence of a naïve state includes reactivation of the second X chromosome in female source cells, increased expression of naïve markers and decreased expression of primed state markers, ability to be clonally expanded and increased differentiation potential. RNA-seq analysis shows vast differences between the parent FGF2 grown, primed state cells, and NME7AB converted cells, but similarities to altered gene expression patterns reported by others generating naïve-like stem cells via the use of biochemical inhibitors. Experiments presented here, in combination with our previous work, suggest a mechanistic model of how human stem cells regulate self-replication: an early naïve state driven by NME7, which cannot itself limit self-replication and a later naïve state regulated by NME1, which limits self-replication when its multimerization state shifts from the active dimer to the inactive hexamer.