bluuebunny/crossref_metadata_2025 huggingface dataset:
Chiral metal–organic frameworks constructed from four-fold helical chain SBUs for enantioselective recognition of α-hydroxy/amino acids
Authors: Yao Ru-Xin , Fu Huan-Huan , Yu Bo , Zhang Xian-Ming
Published: November 2017

Three chiral 3D metal–carboxylate frameworks have been successfully synthesized, featuring four-fold helical metal chains as SBUs. Co-MOFs could recognize enantio-selectively α-hydroxy/amino acids by the change of CD signals.
TiO2nanorod arrays hydrothermally grown on MgO-coated compact TiO2for efficient perovskite solar cells
Authors: Chen Wenhan , Luo Qi , Deng Xueshuang , Zheng Jianfeng , Zhang Chenxi , Chen Xiaohong , Huang Sumei
Published: November 2017

We have demonstrated efficient, stable, and hysteresis-less mesoscopic perovskite solar cells employing TiO2nanorod arrays with MgO modification.
Polyethylenimine-functionalized cellulose aerogel beads for efficient dynamic removal of chromium(vi) from aqueous solution
Authors: Guo Dong-Mei , An Qing-Da , Xiao Zuo-Yi , Zhai Shang-Ru , Shi Zhan
Published: November 2017

Cellulose aerogel beads with high a density of reactive amino groups were facilely prepared via a cross-linking reaction for efficient dynamic removal of Cr(vi) from aqueous solutions.
Synthesis, characterization and photocatalytic activity of mesoporous Na-doped TiO2 nano-powder prepared via a solvent-controlled non-aqueous sol–gel route
Authors: Singh Inderjeet , Birajdar Balaji
Published: November 2017

The superior photo-catalytic activity of mesoporous Na doped TiO2 attributed to the combined effect of electron–hole recombination rate, increased surface area and enhanced crystallinity.
In vitro and in vivo characterization of a novel long-acting GLP-1 receptor agonist, exendin-4–Fc fusion protein
Authors: Lu Lian , Su Xiaoqing , Wang Yantai , Luo Yi , Yang Jun , Xie Li , Gao Xuefeng , Ma Yaru , Tian Yaomei , Yuan Fengjiao , He Gu , Zhou Bailing , Fan Yingzi , Zhang Xueyan , Huang Rong , Lam Ying Ka , Jiang Lin , Dai Hua , Zhao Qian , Liao Xiaoyang , Yang Li
Published: November 2017

Exendin-4 (Ex-4), one of the important glucagon-like peptide-1 receptor (GLP-1R) agonists, has proven to be an effective antidiabetic agent for type 2 diabetes (T2D).
A DFT study of (WO3)3nanoclusters adsorption on defective MgO ultrathin films on Ag(001)
Authors: Zhang Hui , Zhu Jia , Fang Zhenxing , Xu Xianglan , Zhang Yongfan , Fan Yuehua
Published: November 2017

The structures and electronic properties of (WO3)3nanocluster adsorption on defective MgO ultrathin films supported on Ag(001) metal surfaces have been investigated by means of density functional theory (DFT) calculations including dispersion interactions.
Synthesis, antioxidant activity, and density functional theory study of catechin derivatives
Authors: Wang Jing , Tang Han , Hou Bo , Zhang Pan , Wang Qi , Zhang Bang-Lei , Huang Ye-Wei , Wang Ya , Xiang Ze-Min , Zi Cheng-Ting , Wang Xuan-Jun , Sheng Jun
Published: November 2017

Catechin derivatives were synthesized, and their structures were characterized by 1H-NMR, 13C-NMR, and mass spectrometry.
Role of nanoparticle surface defects in the conduction mechanism of polymer–nanoparticle electrical bistable devices
Authors: Song Jiaping , Han Huizhen , Peng Bo , Hu Yufeng , Cui Qiuhong , Lou Zhidong , Hou Yanbing , Teng Feng
Published: November 2017

Surfactant induced conduction mechanism transition from TCLC to FN tunnelling in PEO : ZnO-NP electrical bistable devices.
Synthesis of yolk–shell spheres based on molybdenum diselenide-encapsulated molybdenum oxide for efficient electrocatalytic hydrogen evolution
Authors: Xia Xiaohong , Wang Chunming , Liu Lang , Du Yonglin , Ye Weichun
Published: November 2017

Yolk–shell spheres based on molybdenum diselenide encapsulated molybdenum oxide has been synthesized, the void space between the interior core and the outer shell of this yolk–shell sphere improved the capability of adsorption and catalysis for hydrogen evolution reaction.
Development of visible-light responsive and mechanically enhanced “smart” UCST interpenetrating network hydrogels
Authors: Xu Yifei , Ghag Onkar , Reimann Morgan , Sitterle Philip , Chatterjee Prithwish , Nofen Elizabeth , Yu Hongyu , Jiang Hanqing , Dai Lenore L.
Published: November 2017

An interpenetrating polymer network, chlorophyllin-incorporated “smart” hydrogel was synthesized and exhibited enhanced mechanical properties, upper critical solution temperature swelling, and promising visible-light responsiveness.
rGO/SnS2/TiO2heterostructured composite with dual-confinement for enhanced lithium-ion storage
Authors: Wang Hong-En , Zhao Xu , Li Xuecheng , Wang Zhenyu , Liu Chaofeng , Lu Zhouguang , Zhang Wenjun , Cao Guozhong
Published: November 2017

The rGO/SnS2/TiO2heterostructured composite exhibits superior Li-ion storage property by dual-confinement from N–Sn/C–S chemical bonding and TiO2decoration.
Polyampholyte-doped aligned polymer hydrogels as anisotropic electrolytes for ultrahigh-capacity supercapacitors
Authors: Wei Junjie , Yin Chengyao , Wang Huanlei , Wang Qigang
Published: November 2017

We developed a simple and versatile way to prepare aligned hydrogel electrolytes for ultrahigh-capacity supercapacitors by building aligned pores via “hot ice” templates and copolymerizing with amphoteric monomers.
Chiral organic photonics: self-assembled micro-resonators for an enhanced circular dichroism effect in the non-linear optical signal
Authors: Venkatakrishnarao Dasari , Sahoo Chakradhar , Mamonov Evgeniy A. , Novikov Vladimir B. , Mitetelo Nikolai V. , Naraharisetty Sri Ram G. , Murzina Tatiana V. , Chandrasekar Rajadurai
Published: November 2017

Enantiomeric R and S type organic whispering-gallery-mode (WGM) optical micro-cavities display an enhanced CD-NLO effect due to increased light–matter interaction.
Continuously prepared highly conductive and stretchable SWNT/MWNT synergistically composited electrospun thermoplastic polyurethane yarns for wearable sensing
Authors: Li Yahong , Zhou Bing , Zheng Guoqiang , Liu Xianhu , Li Tingxi , Yan Chao , Cheng Chuanbing , Dai Kun , Liu Chuntai , Shen Changyu , Guo Zhanhu
Published: November 2017

Highly conductive and stretchable electrospun thermoplastic polyurethane yarns with multi-walled and single-walled CNTs were prepared.
Controlling magnetism via transition metal exchange in the series of intermetallics Eu(T1,T2)5In (T = Cu, Ag, Au)
Authors: Smetana Volodymyr , Mudryk Yaroslav , Pecharsky Vitalij K. , Mudring Anja-Verena
Published: November 2017

Evolution of the crystal structure and the magnetic properties in the series Eu(AuxCu1−x)5In.
Verifiable secret sharing scheme without dealer based on vector space access structures over bilinear groups
Authors: Wang Na , Fu Junsong , Zeng Jiwen
Published: November 2017

In general, most of the previous secret sharing schemes involve a secret dealer and a number of participants. The dealer generates a secret and then distributes the secret shares to the participants in a centralised manner, which may lead to the data tamper problem. A verifiable secret sharing scheme without dealer on vector space access structures over bilinear groups is presented. In particular, each participant can act as a ‘dealer’ and the secret in the proposed scheme is a random element generated by all the participants from a bilinear group. In addition, the performance of the proposed scheme in terms of security and computing complexity is analysed in detail and compared it with that of the scheme by Zhang and Zhang. The results show that the proposed scheme performs better in terms of computational cost.
High‐precision time transfer over a 23 km microwave link
Authors: Liu Jiye , Chen Xihong
Published: November 2017

The high‐precision time synchronisation is of vital importance in the modern communication, navigation system and weapon system. The microwave time transfer method is adopted to resolve the time synchronisation problem. After expounding the principle and system composition of the method, the microwave time transfer system has been constructed. First, the measurement of board‐level and system was conducted. The transfer bandwidth in the experiment via microwave channel is 10 Mb. The results show that the jittering of retrieval signals via microwave channel is <4 ns. Then the microwave transmission experiment of 23 km was carried out. The results show that RMS error of time signal is <2 ns and the error between the forward and backward directions is <4 ns.
A comprehensive review on cold work of AISI D2 tool steel
Authors: Abdul Rahim Mohd Aidil Shah bin , Minhat Mohamad bin , Hussein Nur Izan Syahriah Binti , Salleh Mohd Shukor bin
Published: November 2017

As a common material in mould and die application, AISI D2 cold work tool steel has proven to be a promising chosen material in the industries. However, challenges remain in using AISI D2 through a modified version with a considerable progress having been made in recent years. This paper provides a critical review of the original as-cast AISI D2 cold work tool steel up to the modified version. The main purpose is to develop an understanding of current modified tool steel trend; the machinability of AISI D2 (drilling, milling, turning, grinding and EDM/WEDM; and the microstructure evolution and mechanical properties of these cold work tool steels due to the presence of alloy materials in the steel matrix. The doping of rare earth alloy element, new steel fabrication processes, significant process parameter in machinability and surface treatment shows that there have been few empirical investigations into these cold work tool steel alloys. This study has discovered that cold work tool steel will remain to be explored in order to survive in the steel industries.
Characterization of barycenters in the Wasserstein space by averaging optimal transport maps
Authors: Bigot Jérémie , Klein Thierry
Published: November 2017

This paper is concerned by the study of barycenters for random probability measures in the Wasserstein space. Using a duality argument, we give a precise characterization of the population barycenter for various parametric classes of random probability measures with compact support. In particular, we make a connection between averaging in the Wasserstein space as introduced in Agueh and Carlier [SIAM J. Math. Anal.43(2011) 904–924], and taking the expectation of optimal transport maps with respect to a fixed reference measure. We also discuss the usefulness of this approach in statistics for the analysis of deformable models in signal and image processing. In this setting, the problem of estimating a population barycenter fromnindependent and identically distributed random probability measures is also considered.
Green Photoorganocatalytic Synthesis of Phenols from Arylboronic Acids
Authors: Kokotos Christoforos , Sideri Ioanna , Voutyritsa Errika
Published: November 2017

A green and cheap protocol for the photocatalytic hydroxylation of arylboronic acids is presented. 2,2-Dimethoxy-2-phenylacetophenone proved to be the best photoinitiator, among a range of organocatalysts in promoting this reaction. This photocatalytic protocol can be expanded into a wide substrate scope of aromatic boronic acids bearing various functional groups, leading to the corresponding phenols in good to high yields under mild reaction conditions, which include water as solvent, light irradiation provided from standard light-bulbs at room temperature.
Factor VII-Activating Protease: Hemostatic Protein or Immune Regulator?
Authors: Zeerleder Sacha
Published: November 2017

Factor VII (FVII)-activating protease (FSAP) is a serine protease in plasma, which was initially described to play a role in coagulation by activation of FVII, independent of tissue factor, and in fibrinolysis by cleavage of single-chain urokinase. Recent studies, however, suggest that FSAP-mediated FVII cleavage is negligible and that FSAP may exert procoagulant functions via cleavage of tissue factor pathway inhibitor. Meanwhile, many substrates of FSAP have been identified, such as platelet-derived growth factor, basic fibroblast growth factor/epidermal growth factor, histones, and high-molecular-weight kininogen. FSAP has also shown to induce DNA released from dead cells. Given its propensity for autoproteolysis and degradation, studies on the activation and regulation of FSAP are difficult to perform. Recent animal studies suggest a role of FSAP in the pathogenesis of arteriosclerosis, vascular integrity and probably also in the regulation of coagulation initiation. This review will focus on the biochemical properties of FSAP, regulation of FSAP activation, and finally its role in vascular disease and acute systemic inflammatory diseases, such as sepsis.
Das Ebenenmodell – Hoch differenziert befunden
Authors: Brils Henk J. M. , Steilen Axel , Schalk Burkhard , Riechert Claas , Brils Jens , Hempel Christine , Münkel Kerstin
Published: November 2017

Die Ursache für Beschwerden am Bewegungsapparat liegt nicht immer auch im Bewegungssystem. Daher ist es wichtig, in der Untersuchung beispielsweise auch neuro-, psychogene oder neuronale Faktoren zu prüfen. Ein systematisches Vorgehen hierfür bietet das Ebenenmodell des Instituts für Osteopathie und Manuelle Therapie.
Große Unterschiede in Deutschland – Ausbildungswirrwarr
Authors: Hügler Stephanie
Published: November 2017

In der kommenden Legislaturperiode steht eine Reform der Physiotherapieausbildung auf der politischen Agenda. In Deutschland bestimmt aktuell ein buntes Potpourri aus Regeln, Empfehlungen und Richtlinien die Ausbildung. Welche Art zu lernen ist sinnvoll? Muss die Ausbildung an jeder Schule gleich sein? Experten haben dazu unterschiedliche Auffassungen.
Antibiotikatherapie der pyogenen Spondylodiszitis bei Erwachsenen
Authors: Fleege Christoph , Rauschmann Michael , Wichelhaus Thomas
Published: November 2017

Für eine erfolgreiche Behandlung der pyogenen Spondylodiszitis ist eine suffiziente Antibiotikatherapie essenziell. Bei hämodynamisch stabilen Patienten mit normalem neurologischem Status sollte mit einer Antibiotikatherapie solange gewartet werden, bis die mikrobiologische Diagnostik einen Erregernachweis mit Antibiogramm erbringt und somit eine gezielte Therapie ermöglicht. Bei hämodynamisch instabilen Patienten oder bei Patienten mit fortschreitenden bzw. schweren neurologischen Symptomen sollte vor der kalkulierten Therapie eine mikrobiologische Diagnostik (Blutkulturen) eingeleitet werden. Empfehlungen zur kalkulierten und gezielten Therapie der pyogenen Spondylodiszitis sind in dieser Arbeit formuliert. In unkomplizierten Verläufen, ohne operative Instrumentation, ist eine systemische Therapiedauer von 6 Wochen ausreichend. Im Rahmen einer operativen Sanierung des Infektherdes stehen lokale Antibiotikaträger auf der Basis von Hydroxylapatit und Kalziumsulfat zur Verfügung.
Beeinflussung der Lebensqualität beim metastasierten kastrationsresistenten Prostatakarzinom – eine Übersicht
Authors: Miller Kurt
Published: November 2017

Mit dem Auftreten von Metastasen verschlechtert sich zusehends auch die gesundheitsbezogene Lebensqualität von Karzinom-Patienten. Vor allem Fatigue, Schlafstörungen, Knochenschmerzen, Obstipation und andere krankheitsassoziierte Symptome belasten die Betroffenen sehr. Infolge der verbesserten Behandlungsmöglichkeiten und längeren Überlebenszeiten stellen auch Symptomkontrolle und Verbesserung der Lebensqualität wichtige Ziele der Tumortherapie dar. Bei Patienten mit metastasiertem kastrationsresistentem Prostatakarzinom (mCRPC) konnte für Abirateronacetat und Enzalutamid neben der signifikanten Überlebensverlängerung auch ein signifikanter Nutzen hinsichtlich mehrerer Parameter der Lebensqualität gezeigt werden.
Lehre, Fort- und Weiterbildung in Public Health
Authors: Dragano Nico , Geffert Karin , Geisel Bertram , Hartmann Thomas , Hoffmann Falk , Schneider Sven , Voss Maike , Gerhardus Ansgar
Published: November 2017

Der Bedarf an Public-Health-Expertinnen und -Experten kann nur durch ein abgestimmtes Angebot von Aus-, Fort- und Weiterbildung auf Basis internationaler didaktischer Standards gedeckt werden. Zugleich sollten den Absolventinnen und Absolventen attraktive Karrierewege offenstehen. Auch in der Ausbildung der Gesundheitsberufe sowie in Studienfächern mit Bezug zur Bevölkerungsgesundheit (z. B. Stadtplanung, Agrarwissenschaften) sollten Public-Health-Kompetenzen eine wichtige Rolle spielen. Um diese Ziele zu erreichen, hat eine Arbeitsgruppe des Zukunftsforums erste Vorschläge für Strategien erarbeitet und in diesem Beitrag zusammengefasst.
Surveillance und Monitoring
Authors: Ziese Thomas , Hamouda Osamah
Published: November 2017

Evidenzorientierte Gesundheitspolitik und evidenzbasierte Maßnahmen brauchen umfassende Informationen zur Gesundheit der Bevölkerung. Die bestehende Gesundheitssurveillance liefert zu vielen gesundheitspolitischen Fragen verlässliche Antworten. Dennoch bestehen in vielen Bereichen Informationslücken, die bisher nicht oder nur über kurzfristige Projektlösungen geschlossen werden. 1. Wir brauchen eine Stärkung und einen Ausbau der bestehenden Gesundheitssurveillance bzw. -monitoring, um kontinuierlich Informationen über den Gesundheitsstatus aller Bevölkerungsgruppen zu erheben, darunter auch Gruppen, die mit den bisherigen Erhebungen und Methoden schwer zu erreichen sind, wie z. B. Menschen mit Migrationshintergrund oder sozial Benachteiligte. Diese Informationen müssen auf der nationalen, regionalen und idealerweise auch auf der lokalen Ebene regelmäßig verfügbar sein. 2. Die Nutzung von vorhandenen Daten zur Gesundheit bspw. aus der amtlichen Statistik oder der Sozialversicherung muss deutlich ausgebaut und verstärkt werden. Die Infrastruktur für wissenschaftliche Analysen von Gesundheitsdaten sowie den Informationstransfer an die Politik und die Öffentlichkeit muss gestärkt werden. Durch einen Ausbau der Ressourcen für die wissenschaftliche Bearbeitung von gesundheitspolitisch relevanten Fragestellungen kann Public Health einen wichtigen Beitrag für eine effektive Gesundheitspolitik leisten.
Unbehagen: a gallantry with excess
Authors: Zeiher Cindy
Published: November 2017

This paper has its foundation in Lacanian psychoanalytic theory as a way of understanding, from a scientific perspective, the human impact of material technology under the conditions of capitalism. Two related propositions concerning material technology are interrogated in terms of the Lacanian struggle for subjective articulation. Firstly, if following Frederick Kittler, information and communication technologies retain their autonomy beyond the subject, having emerged as a product of their storage, containment and repetitive usage, and if we as subjects embody technological developments as they occur, it could be argued that such technologies possess imaginary agency in that their ability for self-preservation and reproduction constitutes a commanding of unending enjoyment. Insofar as this command is enshrined within capitalism it tends to ignore subjective division and to bypass subjective struggle with the impossibility of language. Rather than affording the subject a new language, material technology merely hints at a contingent language yet to come. Further, in obfuscating the necessity for disinterest–the intellectual position–material technology operates as a discourse which fails to capture the subject, or more precisely, lalangue. Through its inevitable disappearance (and re-emergence transformed as another technology) material technology localises and thereby obscures conflict within the subject. This leads to the second proposition: as part of the capitalist imperative the quest for jouissance is already being played out alongside obscured subjective struggle, spectacularly so in the case of material technology. However, investment in this imperative has an unforeseen cost: in being confronted with excess of jouissance we are overwhelmed and uncertain. Material technologies command that we integrate excess into our daily lives as a unique discursive network, yet this network is at best opaque. Here, joussiance takes the form of a distinctive compulsion emanating from material technology’s intersection with capitalism. This in turn reconfigures the struggle in which the subject of language is grappling with the connection (if any) between knowledge and technological devices. In order to throw light on this struggle we could take up the position of disinterest regarding material technology under capitalism.
Salmonellosis as a neglected emerging zoonotic threat in Africa: situation in South Africa.
Authors: Oloso N. , Fasina F. O. , Fasanmi O. G. , Heerden H. van , Adesiyun A. A.
Published: November 2017

Typhoidal and non-typhoidal salmonellosis have emerged as prominent causes of bloodstream infection in Africa with high fatalities up to 47%. The transmission routes of typhoidal and reservoir hosts of non-typhoidal
Salmonella
are not fully understood in Africa. Diverse challenges with in-country peculiarities create a thriving condition for salmonellosis thus a need for an appraisal of historical and contemporary epidemiology of salmonellosis in Africa, with specific focus on each country. South Africa (SA) situation was reviewed as part of the attempt to explore the situation analysis of
Salmonella
prevalence in Africa. This will contribute towards the knowledge of epidemiology that will assist to curb the threat of salmonellosis in Africa. However with a review of accessible publications, very limited and fragmented scientific evidence of
Salmonella
epidemiology exist. SA has documented existence of
Salmonella
spp. in various ranges of food producing animals and their environment sometimes clinical incidences but no systematic link to provide full epidemiological inferences. With the existing gaps on
Salmonella
infection and salmonellosis in humans and animals in SA; there is the need for concerted efforts to determine the epidemiology of salmonellosis, and conduct conventional and molecular characterization of
Salmonella
spp. Prevention and control of
Salmonella
infection in poultry and other livestock are vital measures to counter the threat of human salmonellosis in SA. These are very important because of the role of SA as a major exporter of poultry, ostriches and livestock products globally and especially other members of Southern African Development Community (SADC).
Robust inference of population structure from next-generation sequencing data with systematic differences in sequencing
Authors: Liao Peizhou , Satten Glen A , Hu Yi-Juan
Published: November 2017

Motivation

Inferring population structure is important for both population genetics and genetic epidemiology. Principal components analysis (PCA) has been effective in ascertaining population structure with array genotype data but can be difficult to use with sequencing data, especially when low depth leads to uncertainty in called genotypes. Because PCA is sensitive to differences in variability, PCA using sequencing data can result in components that correspond to differences in sequencing quality (read depth and error rate), rather than differences in population structure. We demonstrate that even existing methods for PCA specifically designed for sequencing data can still yield biased conclusions when used with data having sequencing properties that are systematically different across different groups of samples (i.e. sequencing groups). This situation can arise in population genetics when combining sequencing data from different studies, or in genetic epidemiology when using historical controls such as samples from the 1000 Genomes Project.

Results

To allow inference on population structure using PCA in these situations, we provide an approach that is based on using sequencing reads directly without calling genotypes. Our approach is to adjust the data from different sequencing groups to have the same read depth and error rate so that PCA does not generate spurious components representing sequencing quality. To accomplish this, we have developed a subsampling procedure to match the depth distributions in different sequencing groups, and a read-flipping procedure to match the error rates. We average over subsamples and read flips to minimize loss of information. We demonstrate the utility of our approach using two datasets from 1000 Genomes, and further evaluate it using simulation studies.

Availability and implementation

TASER-PC software is publicly available at http://web1.sph.emory.edu/users/yhu30/software.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach
Authors: Ali Mehreen , Khan Suleiman A , Wennerberg Krister , Aittokallio Tero
Published: November 2017

Motivation

Proteomics profiling is increasingly being used for molecular stratification of cancer patients and cell-line panels. However, systematic assessment of the predictive power of large-scale proteomic technologies across various drug classes and cancer types is currently lacking. To that end, we carried out the first pan-cancer, multi-omics comparative analysis of the relative performance of two proteomic technologies, targeted reverse phase protein array (RPPA) and global mass spectrometry (MS), in terms of their accuracy for predicting the sensitivity of cancer cells to both cytotoxic chemotherapeutics and molecularly targeted anticancer compounds.

Results

Our results in two cell-line panels demonstrate how MS profiling improves drug response predictions beyond that of the RPPA or the other omics profiles when used alone. However, frequent missing MS data values complicate its use in predictive modeling and required additional filtering, such as focusing on completely measured or known oncoproteins, to obtain maximal predictive performance. Rather strikingly, the two proteomics profiles provided complementary predictive signal both for the cytotoxic and targeted compounds. Further, information about the cellular-abundance of primary target proteins was found critical for predicting the response of targeted compounds, although the non-target features also contributed significantly to the predictive power. The clinical relevance of the selected protein markers was confirmed in cancer patient data. These results provide novel insights into the relative performance and optimal use of the widely applied proteomic technologies, MS and RPPA, which should prove useful in translational applications, such as defining the best combination of omics technologies and marker panels for understanding and predicting drug sensitivities in cancer patients.

Availability and implementation

Processed datasets, R as well as Matlab implementations of the methods are available at https://github.com/mehr-een/bemkl-rbps.

Supplementary information

Supplementary data are available at Bioinformatics online.
Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns
Authors: Shen Hui , Jin Dongmei , Shu Jiang-Ping , Zhou Xi-Le , Lei Ming , Wei Ran , Shang Hui , Wei Hong-Jin , Zhang Rui , Liu Li , Gu Yu-Feng , Zhang Xian-Chun , Yan Yue-Hong
Published: November 2017

Background

Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial.

Results

With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata.

Conclusions

Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants.
Modeling and boundary control of infinite dimensional systems in the Brayton–Moser framework
Authors: Chaitanya Kosaraju Krishna , Pasumarthy Ramkrishna , Jeltsema Dimitri
Published: November 2017

It is well documented that shaping the energy of finite-dimensional port-Hamiltonian systems by interconnection is severely restricted due to the presence of dissipation. This phenomenon is usually referred to as the dissipation obstacle. In this paper, we show the existence of dissipation obstacle in infinite dimensional systems. Motivated by this, we present the Brayton–Moser formulation, together with its equivalent Dirac structure. Analogous to finite dimensional systems, identifying the underlying gradient structure is crucial in presenting the stability analysis. We elucidate this through an example of Maxwell’s equations with zero energy flows through the boundary. In the case of mixed-finite and infinite-dimensional systems, we find admissible pairs for all the subsystems while preserving the overall structure. We illustrate this using a transmission line system interconnected to finite dimensional systems through its boundary. This ultimately leads to a new passive map, using this we solve a boundary control problem, circumventing the dissipation obstacle.
NGC 5626: a massive fast rotator with a twist
Authors: Viaene S , Sarzi M , Baes M , Puerari I
Published: November 2017

We present a kinematic analysis of the dust-lane elliptical NGC 5626 based on MUSE observations. These data allow us to robustly classify this galaxy as a fast rotator and to infer a virial mass of 1011.7 M⊙, making it one of the most massive fast rotators known. In addition, the depth and extent of the MUSE data reveal a strong kinematic twist in the stellar velocity field (by up to 45° beyond 1.5Re). A comparison with the ATLAS3D sample underlines the rareness of this system, although we show that such a large-scale kinematic twist could have been missed by the ATLAS3D data due to the limited spatial sampling of this survey (typically extending to 0.6Re for massive early-type galaxies). MUSE thus has the potential to unveil more examples of this type of galaxies. We discuss the environment and possible formation history of NGC 5626 and finally argue how a merger between the Milky Way and Andromeda could produce a galaxy of the same class as NGC 5626.
Criteria for Identifying Patients With Staphylococcus aureus Bacteremia Who Are at Low Risk of Endocarditis: A Systematic Review
Authors: Heriot George S , Cronin Katie , Tong Steven Y C , Cheng Allen C , Liew Danny
Published: November 2017

This systematic review examines the methods and results of recent studies reporting clinical criteria able to identify patients with Staphylococcus aureus bacteremia who are at very low risk of endocarditis. We searched PubMed, EMBASE, and the Cochrane Collaboration CENTRAL database for articles published after March 1994 using a combination of MeSH and free text search terms for S. aureus AND bacteremia AND endocarditis. Studies were included if they presented a combination of clinical and microbiological criteria with a negative likelihood ratio of ≤0.20 for endocarditis. We found 8 studies employing various criteria and reference standards whose criteria were associated with negative likelihood ratios between 0.00 and 0.19 (corresponding to 0%–5% risk of endocarditis at 20% background prevalence). The benefit of echocardiography for patients fulfilling these criteria is uncertain.
Searching for moving objects in HSC-SSP: Pipeline and preliminary results
Authors: Chen Ying-Tung , Lin Hsing-Wen , Alexandersen Mike , Lehner Matthew J , Wang Shiang-Yu , Wang Jen-Hung , Yoshida Fumi , Komiyama Yutaka , Miyazaki Satoshi
Published: November 2017

The Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP) is currently the deepest wide-field survey in progress. The 8.2 m aperture of the Subaru telescope is very powerful in detecting faint/small moving objects, including near-Earth objects, asteroids, centaurs and Tran-Neptunian objects (TNOs). However, the cadence and dithering pattern of the HSC-SSP are not designed for detecting moving objects, making it difficult to do so systematically. In this paper, we introduce a new pipeline for detecting moving objects (specifically TNOs) in a non-dedicated survey. The HSC-SSP catalogs are sliced into HEALPix partitions. Then, the stationary detections and false positives are removed with a machine-learning algorithm to produce a list of moving object candidates. An orbit linking algorithm and visual inspections are executed to generate the final list of detected TNOs. The preliminary results of a search for TNOs using this new pipeline on data from the first HSC-SSP data release (2014 March to 2015 November) present 231 TNO/Centaurs candidates. The bright candidates with Hr < 7.7 and i > 5 show that the best-fitting slope of a single power law to absolute magnitude distribution is 0.77. The g − r color distribution of hot HSC-SSP TNOs indicates a bluer peak at g − r = 0.9, which is consistent with the bluer peak of the bimodal color distribution in literature.
A systematic review of sample size and power in leading neuroscience journals
Authors: Carter Alice , Tilling Kate , Munafò Marcus R
Published: November 2017

Adequate sample size is key to reproducible research findings: low statistical power can increase the probability that a statistically significant result is a false positive. Journals are increasingly adopting methods to tackle issues of reproducibility, such as by introducing reporting checklists. We conducted a systematic review comparing articles submitted to Nature Neuroscience in the 3 months prior to checklists (n=36) that were subsequently published with articles submitted to Nature Neuroscience in the 3 months immediately after checklists (n=45), along with a comparison journal Neuroscience in this same 3-month period (n=123). We found that although the proportion of studies commenting on sample sizes increased after checklists (22% vs 53%), the proportion reporting formal power calculations decreased (14% vs 9%). Using sample size calculations for 80% power and a significance level of 5%, we found little evidence that sample sizes were adequate to achieve this level of statistical power, even for large effect sizes. Our analysis suggests that reporting checklists may not improve the use and reporting of formal power calculations.
Pooled population resequencing of clam shrimp (Eulimnadia texana) from different vernal pools reveals signatures of local adaptation
Authors: Baldwin-Brown James G. , Long Anthony D.
Published: November 2017

Vernal pool clam shrimp (Eulimnadia texana) are a promising model due to ease of culturing, short generation time, modest genome size, and obligate desiccated diapaused eggs. We collected Illumina data (Poolseq) from eleven pooled wild vernal pool clam shrimp populations. We hypothesized that restricted gene flow between vernal pools, separated by distances of 0.36 to 253 km, in concert with Poolseq data from each population, could be used to identify genes important in local adaptation. We adaptedBayenv2to genome-wide Poolseq data and detected thirteen genomic regions showing a strong excess of population subdivision relative to a genome-wide background. We identified a set of regions that appear to be significantly diverged in allele frequency, above what is expected based on the relationships amongst the populations. Regions identified as significant were on average 9.5 kb in size and harbored 3.8 genes. We attempted to identify correlations between allele frequencies at each genomic region and environmental variables that may influence local adaptation in the sequences populations, but found that there were too many confounding environmental variables to draw strong conclusions. One such genomic region harbored an ortholog ofDrosophila melanogasterCG10413, a gene predicted to have sodium/potassium/chloride activity. Finally, we demonstrate that the identified regions could not have been found with less powerful statistics, i.e.FST, or with a less contiguous genome assembly.
Quaternary structure evaluation tool for protein assemblies
Authors: Korkmaz Selcuk , Duarte Jose M. , Prlić Andreas , Goksuluk Dincer , Zararsiz Gokmen , Saracbasi Osman , Burley Stephen K. , Rose Peter W.
Published: November 2017

The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. For example, it makes a difference if the protein is normally a dimer and not a monomer or a trimer or a tetramer or a hexamer in nature. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 86% correct, 9% incorrect, and 5% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org).
Cyclic nature of the REM-like state in the cuttlefish Sepia officinalis
Authors: Iglesias T. L. , Boal J. G. , Frank M.G. , Zeil J. , Hanlon R.T.
Published: November 2017

Sleep is a state of immobility characterized by three key criteria: an increased threshold of arousal, rapid reversal to an alert state, and evidence of homeostatic “rebound sleep” in which there is an increase of time spent in this quiescent state following sleep deprivation. Common European cuttlefish, Sepia officinalis, show states of quiescence during which they meet the last two of these three criteria, yet also show spontaneous bursts of arm and eye movements that accompany rapid changes in chromatophore patterns in the skin. Here we report that this rapid-eye-movement (REM)-like state is cyclic in nature. Iterations of the REM-like state last 2.42 ± 0.22 min (±SE) and alternate with 34.01 ± 1.49 min of the quiescent sleep-like state. These states alternate for durations lasting 176.89 ± 36.71 min. We found clear evidence that this REM-like state (i) occurs in animals younger than previously reported; (ii) follows an ultradian pattern; (iii) includes intermittent dynamic chromatophore patterning, representing fragments of normal patterning seen in the waking state for a wide range of signaling and camouflage; and (iv) shows variability in the intensity of expression of these skin patterns between and within individuals. These data suggest that cephalopods, which are molluscs with an elaborate brain and complex behavior, possess a sleep-like state that resembles behaviorally the vertebrate REM sleep state, although the exact nature and mechanism of this form of sleep may differ from that of vertebrates.
A Phylogenomic Study Quantifies Competing Mechanisms for Pseudogenization in Prokaryotes
Authors: Avni Eliran , Montoya Dennis , Lopez David , Modlin Robert , Pellegrini Matteo , Snir Sagi
Published: November 2017

Background

Pseudogenes are non-functional sequences in the genome with homologous sequences that are functional (i.e. genes). They are abundant in eukaryotes where they have been extensively investigated, while in prokaryotes they are significantly scarcer and less well studied. Here we conduct a comprehensive analysis of the evolution of pseudogenes in prokaryotes. For this analysis we consider a broad range of bacteria, but also focus on the leprosy pathogenMycobacterium leprae, which contains an unusually large number of pseudogenes which comprise approximately 40% of its entire genome.

Results

We have developed an informatics-based approach to characterize the evolution of pseudogenes. This approach combines tools from phylogenomics, genomics, and transcriptomics. The results we obtain suggest the presence of two mechanisms for pseudogene formation: failed horizontal gene transfer events and disruption of native genes.

Conclusions

We conclude that while in most bacteria the former is most likely responsible for the majority of pseudogenization events, in mycobacteria, and in particular inM. lepraewith its exceptionally high pseudogene numbers, the latter predominates. We believe that our study sheds new light on the evolution of pseudogenes in bacteria, by utilizing new methodologies that are applied to the unusually abundantM. lepraepseudogenes and their orthologs. As such, we anticipate that it will be of broad interest to both evolutionary biologists as well as microbiologists.
New fluorescent compounds based on zinc thiocyanate: influence of structure on spectral properties
Authors: Swiatkowski Marcin , Kruszynski Rafal
Published: November 2017

New coordination compounds based on zinc thiocyanate, namely (acetone thiosemicarbazone-κ2
N
1,S)bis(isothiocyanato-κN)zinc(II) monohydrate, [Zn(NCS)2(C4H9N3S)]·H2O, (I), and diaquatetrakis(urea-κO)zinc(II) tetrakis(isothiocyanato-κN)zinc(II), [Zn(CH4N2O)4(H2O)2][Zn(NCS)4], (II), were synthesized and studied by UV–Vis, fluorescence and IR spectroscopy. Coordination salt (II) forms a rare system composed of two different coordination units of the same metal and it is the first example of a compound with two completely different zinc coordination units, of which one contains a tetrakis(urea)zinc unit. Both (I) and (II) possess fluorescence properties and produce blue and green emissions, respectively, upon irradiation with violet light. The spectral properties were correlated with the observed molecular and supramolecular structures. The acetone thiosemicarbazone ligand of (I) exhibits (upon coordination) red shifts of bands corresponding to N=C and C=S stretching vibration frequencies, which is not typical for chelating molecules.
A combined crystallographic, thermal, Raman and computational study on polymorphism and phase transition in 1-(4-hexyloxy-3-hydroxyphenyl)ethanone
Authors: Suárez Sebastián , Manzano Veronica E. , Fantoni Adolfo C. , Halac Emilia , Baggio Ricardo , Cukiernik Fabio D.
Published: November 2017

The crystal structure of the triclinic polymorph of 1-(4-hexyloxy-3-hydroxyphenyl)ethanone, C14H20O3, differs markedly from that of the orthorhombic polymorph [Manzano et al. (2015). Acta Cryst. C71, 1022–1027]. The two molecular structures are alike with respect to their bond lengths and angles, but differ in their spatial arrangement. This gives rise to quite different packing schemes, even if built up by similar chains having the hydroxy–ethanone O—H...O hydrogen-bond synthon in common. Both phases were found to be related by a first-order thermally driven phase transformation at 338–340 K, which is discussed in detail. The relative stabilities of both polymorphs are explained on the basis of both the noncovalent interactions operating in each structure and quantum chemical calculations. The polymorphic phase transition has also been studied experimentally by means of differential scanning calorimetry (DSC) experiments, conducted on individual single crystals, Raman spectroscopy and controlled heating under a microscope of individual single crystals, which were further characterized by powder and single-crystal X-ray diffraction.
Digitalization in retailing: multi-sided platforms as drivers of industry transformation
Authors: Hänninen Mikko , Smedlund Anssi , Mitronen Lasse
Published: November 2017

Purpose

Digitalization has transformed several industries during the past two decades. In this paper the authors focus on the retail sector, where new business models help retailers and suppliers meet the ever changing and demanding needs of retail shoppers. One example of this business model innovation is multi-sided digital platforms, which have become popular as they connect consumers with suppliers from around the world with a large ecosystem to support the retail platform. The purpose of this paper is to provide an overview of how multi-sided digital platforms are transforming the retail exchange logic and assess the implications and impact of these platform-based businesses on the retail sector, especially for business managers and consumers.

Design/methodology/approach

In this paper, the authors employ literature review, conceptual analysis and qualitative case study methodology. The authors provide an overview of how the platform economy is affecting the retail sector through the illustration of four digital multi-sided platforms: Alibaba Group, Amazon.com, eBay and Rakuten Group, and what differentiates them from incumbent business models in retailing.

Findings

The findings suggest that platforms transform the transaction logic of retailing as they simply intermediate transactions between buyers and suppliers rather than handling the entire supply and logistics chain themselves. The authors highlight the role of consumer understanding and Big Data as one example of how multi-sided digital platforms differentiate from their non-platform competitors.

Practical implications

The paper highlights how incumbent retailers can compete against new forms of business, such as digital platforms, and the authors demonstrate some of the managerial capabilities needed to remain relevant amidst this new digital competition.

Originality/value

Very little empirical studies in marketing and retail literature have focused on multi-sided digital platforms and their business models. The present study fills this gap with an overview of how multi-sided digital platforms transform the retail sector.