bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hidden partners: Using cross‐docking calculations to predict binding sites for proteins with multiple interactions
Authors: Lagarde Nathalie , Carbone Alessandra , Sacquin‐Mora Sophie 
Published: April 2018

AbstractProtein‐protein interactions control a large range of biological processes and their identification is essential to understand the underlying biological mechanisms. To complement experimental approaches, in silico methods are available to investigate protein‐protein interactions. Cross‐docking methods, in particular, can be used to predict protein binding sites. However, proteins can interact with numerous partners and can present multiple binding sites on their surface, which may alter the binding site prediction quality. We evaluate the binding site predictions obtained using complete cross‐docking simulations of 358 proteins with 2 different scoring schemes accounting for multiple binding sites. Despite overall good binding site prediction performances, 68 cases were still associated with very low prediction quality, presenting individual area under the specificity‐sensitivity ROC curve (AUC) values below the random AUC threshold of 0.5, since cross‐docking calculations can lead to the identification of alternate protein binding sites (that are different from the reference experimental sites). For the large majority of these proteins, we show that the predicted alternate binding sites correspond to interaction sites with hidden partners, that is, partners not included in the original cross‐docking dataset. Among those new partners, we find proteins, but also nucleic acid molecules. Finally, for proteins with multiple binding sites on their surface, we investigated the structural determinants associated with the binding sites the most targeted by the docking partners.
Immobile populations as anchors of rural ethnic identity: Contemporary Kazakh narratives of place and migration in Mongolia
Authors: Barcus Holly R. , Shugatai Amangul 
Published: April 2018

AbstractMigration to rapidly expanding global urban landscapes and the questions surrounding population growth in these places continue to fuel interest amongst academics, policy makers, and news outlets. Less attention is paid to those individuals who do not head for the big city, immobile populations in rural places. In this paper, we argue that rather than being “those left behind,” immobile populations play a key role in maintaining and perpetuating cultural narratives for ethnic minority populations by anchoring cultural narratives to place. These narratives become reinterpreted and reimagined by outmigrants but remain firmly connected to place through immobile populations. The concept of place elasticity allows us to imagine how these local narratives of place remain intact. It describes the ways in which individuals maintain a continuous, meaningful engagement with a place, even if they reside a long distance from that place. We utilise the case study of Mongolian Kazakhs, an ethnic minority population with strong place attachments as well as significant outmigration from their rural home region in western Mongolia, to explore the idea of place elasticity and evolving place identities for rural populations in developing and transitioning countries. Through analysis of our questionnaires and life history interview data, we find that nonmigrants (immobile) facilitate rural place attachments and identities for this population. This finding suggests that rather than being “left behind,” nonmigrants or immobile populations play an important role in perpetuating place identities and attachments for outmigrants.
Highly Fluorescent Magnetic Nanobeads with a Remarkable Stokes Shift as Labels for Enhanced Detection in Immunoassays
Authors: Salis Francesca , Descalzo Ana B. , Benito‐Peña Elena , Moreno‐Bondi María C. , Orellana Guillermo 
Published: April 2018

AbstractFluorescence immunoassays are popular for achieving high sensitivity, but they display limitations in biological samples due to strong absorption of light, background fluorescence from matrix components, or light scattering by the biomacromolecules. A powerful strategy to overcome these problems is introduced here by using fluorescent magnetic nanobeads doped with two boron‐dipyrromethane dyes displaying intense emission in the visible and near‐infrared regions, respectively. Careful matching of the emission and absorption features of the dopants leads to a virtual Stokes shift larger than 150 nm achieved by an intraparticle Förster resonance energy transfer (FRET) process between the donor and the acceptor dyes. Additionally, the magnetic properties of the fluorescent beads allow preconcentration of the sample. To illustrate the usefulness of this approach to increase the sensitivity of fluorescence immunoassays, the novel nanoparticles are employed as labels for quantification of the widely used Tacrolimus (FK506) immunosuppressive drug. The FRET‐based competitive inhibition immunoassay yields a limit of detection (LOD) of 0.08 ng mL−1, with a dynamic range (DR) of 0.15–2.0 ng mL−1, compared to a LOD of 2.7 ng mL−1 and a DR between 4.1 and 130 ng mL−1 for the immunoassay carried out with direct excitation of the acceptor dye.
Silver‐Assisted Synthesis of Gold Nanorods: the Relation between Silver Additive and Iodide Impurities
Authors: Jessl Sarah , Tebbe Moritz , Guerrini Luca , Fery Andreas , Alvarez‐Puebla Ramon A. , Pazos‐Perez Nicolas 
Published: April 2018

AbstractSeed‐mediated methods employing cetyltrimethylammonium bromide (CTAB) as a surfactant, and silver salts as additives, are the most common synthetic strategies for high‐yield productions of quality Au nanorods. However, the mechanism of these reactions is not yet fully understood and, importantly, significant lab‐to‐lab reproducibility issues still affect these protocols. In this study, the direct correlation between the hidden content of iodide impurities in CTAB reagents, which can drastically differ from different suppliers or batches, and the optimal concentration of silver required to maximize the nanorods yield is demonstrated. As a result, high‐quality nanorods are obtained at different iodide contents. These results are interpreted based on the different concentrations of CTAB and cetyltrimethylammonium iodide (CTAI) complexes with Ag+ and Au+ metal ions in the growth solution, and their different binding affinity and reduction potential on distinct crystallographic planes. Notably, the exhaustive conversion of CTAI–Au+ to CTAI–Ag+ appears to be the key condition for maximizing the nanorod yield.
Ultrahigh Conductive Copper/Large Flake Size Graphene Heterostructure Thin‐Film with Remarkable Electromagnetic Interference Shielding Effectiveness
Authors: Wang Zhe , Mao Boyang , Wang Qianlong , Yu Jun , Dai Jixiang , Song Rongguo , Pu Zonghua , He Daping , Wu Zhi , Mu Shichun 
Published: April 2018

AbstractTo guarantee the normal operation of next generation portable electronics and wearable devices, together with avoiding electromagnetic wave pollution, it is urgent to find a material possessing flexibility, ultrahigh conductive, and superb electromagnetic interference shielding effectiveness (EMI SE) simultaneously. In this work, inspired by a building bricks toy with the interlock system, we design and fabricate a copper/large flake size graphene (Cu/LG) composite thin film (≈8.8 μm) in the light of high temperature annealing of a large flake size graphene oxide film followed by magnetron sputtering of copper. The obtained Cu/LG thin‐film shows ultrahigh thermal conductivity of over 1932.73 (±63.07) W m−1 K−1 and excellent electrical conductivity of 5.88 (±0.29) × 106 S m−1. Significantly, it also exhibits a remarkably high EMI SE of over 52 dB at the frequency of 1–18 GHz. The largest EMI SE value of 63.29 dB, accorded at 1 GHz, is enough to obstruct and absorb 99.99995% of incident radiation. To the best of knowledge, this is the highest EMI SE performance reported so far in such thin thickness of graphene‐based materials. These outstanding properties make Cu/LG film a promising alternative building block for power electronics, microprocessors, and flexible electronics.
Nanoscale Lacing by Electrons
Authors: Cheng Han‐Wen , Wang Jie , Li Yong‐Jun , Li Jing , Yan Shan , Shan Shiyao , Wang Lingyan , Skeete Zakiya , Zhong Chuan‐Jian 
Published: April 2018

AbstractThe ability to harness the optical or electrical properties of nanoscale particles depends on their assembly in terms of size and spatial characteristics which remains challenging due to lack of size focusing. Electrons provide a clean and focusing agent to initiate the assembly of nanoclusters or nanoparticles. Here an intriguing route is demonstrated to lace gold nanoclusters and nanoparticles in string assembly through electron‐initiated nucleation and aggregative growth of Au(I)‐thiolate motifs on a thin film substrate. This size‐focused assembly is demonstrated by controlling the electron dose under transmission electron microscopic imaging conditions. The Au(I)‐thiolate motifs, in combination with the molecularly mediated alignment, facilitate the interstring electrostatic and intrastring aurophilic interactions, which functions as a molecular template to aid electron‐initiated 1D lacing. The findings demonstrate a hierarchical route for the 1D assemblies with size and spatial tunable catalytic, optical, sensing, and diagnostic properties.
Notch Signaling Regulates Lgr5+ Olfactory Epithelium Progenitor/Stem Cell Turnover and Mediates Recovery of Lesioned Olfactory Epithelium in Mouse Model
Authors: Dai Qi , Duan Chen , Ren Wenwen , Li Fangqi , Zheng Qian , Wang Li , Li Wenyan , Lu Xiaoling , Ni Wenli , Zhang Yanping , Chen Yan , Wen Tieqiao , Yu Yiqun , Yu Hongmeng 
Published: April 2018

Abstract
The Notch signaling pathway regulates stem cell proliferation and differentiation in multiple tissues and organs, and is required for tissue maintenance. However, the role of Notch in regulation of olfactory epithelium (OE) progenitor/stem cells to maintain tissue function is still not clear. A recent study reported that leucine-rich repeat-containing G-protein-coupled receptor 5 (Lgr5) is expressed in globose basal cells (GBCs) localized in OE. Through lineage tracing in vivo, we found that Lgr5+ cells act as progenitor/stem cells in OE. The generation of daughter cells from Lgr5+ progenitor/stem cells is delicately regulated by the Notch signaling pathway, which not only controls the proliferation of Lgr5+ cells and their immediate progenies but also affects their subsequent terminal differentiation. In conditionally cultured OE organoids in vitro, inhibition of Notch signaling promotes neuronal differentiation. Besides, OE lesion through methimazole administration in mice induces generation of more Notch1+ cells in the horizontal basal cell (HBC) layer, and organoids derived from lesioned OE possesses more proliferative Notch1+ HBCs. In summary, we concluded that Notch signaling regulates Lgr5+ GBCs by controlling cellular proliferation and differentiation as well as maintaining epithelial cell homeostasis in normal OE. Meanwhile, Notch1 also marks HBCs in lesioned OE and Notch1+ HBCs are transiently present in OE after injury. This implies that Notch1+ cells in OE may have dual roles, functioning as GBCs in early development of OE and HBCs in restoring the lesioned OE.
Shaking table model test and numerical analysis of a long‐span cantilevered structure
Authors: Chen Shiming , Ge Kang , Xue Weichen , Lin Yingru , Lin Gao 
Published: April 2018

SummaryThis paper presents an earthquake‐resistance study program of a long‐span cantilevered story building. The program consists of a shaking table test study and nonlinear seismic analysis using finite element modeling technique. A 1/30 scale model of the prototype structure was designed and manufactured and then tested via the shaking table facility. Dynamic responses of the prototype structure under different earthquake excitation loadings were simulated. Dynamic properties, acceleration, and deformation responses of the scale down model under different intensity levels of earthquake were studied. The dynamic behavior, cracking pattern, and the likely governing failure mechanism of the structure were analyzed and discussed as well. The seismic responses of the prototype building were deduced and analyzed in terms of the similitude law. Furthermore, elaborate finite element models were established, and nonlinear numerical analysis of the prototype structure was conducted. The errors in the seismic response of the structure caused by structural simplification of scale down modeling are found small, and the dynamic behavior of the structure was not altered in the earthquake excitations. This test study provides a benchmark to calibrate the finite element model and a tentative guide in seismic design of such long‐span cantilevered story buildings.
Experimental study on steel reinforced concrete columns subjected to combined bending–torsion cyclic loading
Authors: Chen Shicai , Peng Wei , Yan Weiming 
Published: April 2018

SummaryAn experimental investigation and analysis of the mechanical behavior of steel reinforced concrete (SRC) columns under combined bending–torsion cyclic loads is presented in this paper. Seven SRC columns with the same cross‐sectional construction were tested under various torsion moment to bending moment ratios and axial load levels. The effect of the torsion to bending moment ratio on the failure characteristics, hysteretic behavior, bearing capacity, and deformation characteristics of the SRC columns was studied. Results indicate that both bending and torsion bearing capacity are reduced under combined bending and torsion loads and that the torsion–bending ratio is the key parameter that determines the failure mode of the SRC columns. Based on the tests results, an equation expressing the interaction curve between the bending and torsion is proposed.
Glabridin induces apoptosis and cell cycle arrest in oral cancer cells through the JNK1/2 signaling pathway
Authors: Chen Chang‐Tai , Chen Yi‐Tzu , Hsieh Yi‐Hsien , Weng Chia‐Jui , Yeh Jung‐Chun , Yang Shun‐Fa , Lin Chiao‐Wen , Yang Jia‐Sin 
Published: April 2018

AbstractGlabridin, a flavonoid extracted from licorice (Glycyrrhiza glabra), possesses various biological properties, including anticancer activities. However, the effect of glabridin on oral cancer cell apoptosis and the underlying molecular mechanisms has not been elucidated. In this study, we demonstrated that glabridin treatment significantly inhibits cell proliferation in human oral cancer SCC‐9 and SAS cell lines. Flow cytometric assays demonstrated that glabridin induced several features of apoptosis, such as sub‐G1 phase cell increase and phosphatidylserine externalization. Furthermore, glabridin induced apoptosis dose‐dependently in SCC‐9 cells through caspase‐3, −8, and −9 activation and poly (ADP‐ribose) polymerase cleavage. Moreover, glabridin increased the phosphorylation of the extracellular signal–regulated kinase, p38, and c‐Jun N‐terminal kinase (JNK) pathways in a dose‐dependent manner. Moreover, the inhibition of the JNK1/2 inhibitor significantly reversed the glabridin‐induced activation of the caspase pathway. In conclusion, our findings suggest that glabridin induces oral cancer cell apoptosis through the JNK1/2 pathway and is a potential therapeutic agent for oral cancer.
Clustering of nonstationary data streams: A survey of fuzzy partitional methods
Authors: Abdullatif Amr , Masulli Francesco , Rovetta Stefano 
Published: April 2018

Data streams have arisen as a relevant research topic during the past decade. They are real‐time, incremental in nature, temporally ordered, massive, contain outliers, and the objects in a data stream may evolve over time (concept drift). Clustering is often one of the earliest and most important steps in the streaming data analysis workflow. A comprehensive literature is available about stream data clustering; however, less attention is devoted to the fuzzy clustering approach, even though the nonstationary nature of many data streams makes it especially appealing. This survey discusses relevant data stream clustering algorithms focusing mainly on fuzzy methods, including their treatment of outliers and concept drift and shift.This article is categorized under

Technologies > Machine Learning
Technologies > Computational Intelligence
Fundamental Concepts of Data and Knowledge > Data Concepts
Double network hydrogel for tissue engineering
Authors: Gu Zhipeng , Huang Keqing , Luo Yan , Zhang Laibao , Kuang Tairong , Chen Zhou , Liao Guochao 
Published: April 2018

Double network (DN) hydrogels, a kind of promising soft and tough hydrogels, are produced by two unique contrasting networks with designed network entanglement burst into the field of materials science as versatile functional systems for a very broad range of applications. A part of the DN hydrogels is characterized by extraordinary mechanical properties providing efficient biocompatible and high strength for holding considerable promise in tissue engineering. Following DN hydrogels principles and consideration of biomedical applications, we provide an overall view of the present various DN hydrogels and look forward to the future of DN hydrogels for tissue engineering. In this review, the preparation methods, structure, properties, current situation, and challenges are mainly discussed for the purpose of tissue engineering.This article is categorized under:Implantable Materials and Surgical Technologies > Nanomaterials and ImplantsImplantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement
New closed‐form solutions for functionally graded longitudinally vibrating bar
Authors: Elishakoff Isaac , Armstrong Hailey , Hashemi Javad 
Published: April 2018

AbstractIn this paper we present new closed‐form solutions for functionally graded longitudinally vibrating bar. The modulus of elasticity is represented as a continuous function varying along the axial coordinate. It is postulated that the mode shape represents the sixth order polynomial. Six closed form solutions are presented: four for clamped‐clamped bar, and two for clamped‐free bar.
Die Relevanz kleiner Gemeinden und kleinteiliger Flächen für die Innenentwicklung. Ein quantitatives Monitoring am Beispiel Deutschlands
Authors: Schiller Georg , Blum Andreas , Oertel Holger 
Published: April 2018

The limitation of land use and the protection of soil is an important target set in European and national sustainability strategies. To this end, the use of brownfields, vacant and underutilised sites within existing settlement structures for urban development, frequently called infill development, is a primary strategy. This paper presents the results of a nationwide survey to generate reliable data on the potential for infill development in German cities and towns. In contrast to earlier studies, in particular infill development potential in small communities and small-scale potential, usually on vacant lots, are focused and discussed with regard to their relevance for land-saving settlement-policy making. The data generated allow to determine a reliable range of overall infill development potential per capita of at least 15 m2. Often underestimated, the survey also reveals, that more than a quarter of infill development potential is located in smaller communities below 5.000 inhabitants, which were not included in earlier surveys. With respect to lot sizes the results also show that small-scale potential on vacant lots makes up more than half of the overall potential. It is thus recommended that policy making towards sustainable land use put more emphasis on small-scale land uses and awareness rising in smaller communities which clearly tend to underestimate their infill potential.
Biological Reconstruction of Varus Deformity in Primary Total Knee Replacement Using Bone Graft and Description of a New Technique
Authors: Singh Luthra Jatinder , Habsi Salim A.L. 
Published: April 2018

Peripheral bony defects of the tibia can be seen in patients with osteoarthritis of the knee. These defects must be corrected at the time of total knee replacement to ensure correct placement and alignment of the components. We describe a new technique for correcting large tibial defect by using bone graft, where the uncontained defects were converted to contained defects using bone graft and the contained defect was impacted with cancellous bone. Between 2006 and 2010, 48 cases of primary total knee arthroplasty were reconstructed using autologous bone graft. Of 48 cases, five cases had large tibial defect and were treated with the new technique. Collapse was seen in one knee at 5 months postoperative. The rest of the patients showed improvement in total knee score and limb alignment. We now use this technique to treat large tibial defect during total knee replacement.
Albian infaunal Pholadomyida (Cretaceous Bivalvia), Comanchean Carbonate Shelf, Texas
Authors: Scott Robert W. , Claggett Bradley W. 
Published: April 2018

AbstractSpecies of the megaorder Poromyata, although common and relatively diverse in Albian–lower Cenomanian Comanchean strata in Texas and northern Mexico, have been neglected as biostratigraphic markers and paleoecological indicators. Since 1852, more than a dozen species have been identified asHomomyaAgassiz, order Pholadomyida, superfamily Pholadomyoidea orPleuromyaAgassiz, order Pholadida, superfamily Pleuromyoidea. Because valve morphologies of the two genera are similar in many ways, casts are difficult to separate. Statistical analysis of key morphological properties objectively defines species concepts and assesses synonymies. Eight species are retained inHomomya; four are synonymized with these. Two species are provisionally retained in “Homomya” although they differ significantly. One species is reassigned toLiopistha (Sergipemya) alta(Roemer, 1852).Pleuromya henselli(Hill, 1893) is reassigned toPanopea.Homomyid species range from upper Aptian to lower Cenomanian of the Comanchean Series in Texas and Mexico. Their ranges vary in duration from one million years up to eight million years. These infaunal suspension feeders occupied calcareous mud and carbonate shelf substrates. Two sets of species are distinct morphotypes: a smaller-sized set ofH. knowltoniHill, 1895;H. tarrantensisPerkins, 1961;H. tlahualiloensisPerkins, 1961; andH. kellumiPerkins, 1961 and a larger-sized set ofH. cymbiformisPerkins, 1961;H. austinensisShattuck, 1903;H. vulgarisShattuck, 1903;H. budaensisWhitney, 1911; andH. auroraensisPerkins, 1961. Two end-member morphotypes are represented by the “streamlined”Homomya knowltoni, which is an elongate, slightly inflated form with a relatively high umbo, and the cylindricalHomomya budaensis, which is a very elongate, tubular, inflated form with a very low umbo.
Winners and Losers of the Ballot: Electronic vs. Traditional Paper Voting Systems in Brazil
Authors: Schneider Rodrigo , Senters Kelly N. 
Published: April 2018

AbstractScholars concur that free and fair elections are essential for proper democratic functioning, but our understanding of the political effects of democratic voting systems is incomplete. This article mitigates the gap by exploiting the gradual transformation of voting systems and ballot structures in Brazil’s 1998 executive elections to study the relationship between voting systems and viable and nonviable candidates’ vote shares, using regression discontinuity design. It finds that the introduction of electronic voting concentrated vote shares among viable candidates and thus exhibited electoral bias. We posit that this result occurred because viable candidates were better able to communicate the information that electronic voters needed to cast valid ballots than were their nonviable counterparts. The article uses survey data to demonstrate that electronic voters responded to changes in ballot design and internalized the information viable candidates made available to them.