bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary prediction of medicinal properties in the genus Euphorbia L.
Authors: Ernst Madeleine , Saslis-Lagoudakis C. Haris , Grace Olwen M. , Nilsson Niclas , Simonsen Henrik Toft , Horn James W. , Rønsted Nina 
Published: July 2016

AbstractThe current decrease of new drugs brought to the market has fostered renewed interest in plant-based drug discovery. Given the alarming rate of biodiversity loss, systematic methodologies in finding new plant-derived drugs are urgently needed. Medicinal uses of plants were proposed as proxy for bioactivity, and phylogenetic patterns in medicinal plant uses have suggested that phylogeny can be used as predictive tool. However, the common practice of grouping medicinal plant uses into standardised categories may restrict the relevance of phylogenetic predictions. Standardised categories are mostly associated to systems of the human body and only poorly reflect biological responses to the treatment. Here we show that medicinal plant uses interpreted from a perspective of a biological response can reveal different phylogenetic patterns of presumed underlying bioactivity compared to standardised methods of medicinal plant use classification. In the cosmopolitan and pharmaceutically highly relevant genus Euphorbia L., identifying plant uses modulating the inflammatory response highlighted a greater phylogenetic diversity and number of potentially promising species than standardised categories. Our interpretation of medicinal plant uses may therefore allow for a more targeted approach for future phylogeny-guided drug discovery at an early screening stage, which will likely result in higher discovery rates of novel chemistry with functional biological activity.
High energy X-ray phase and dark-field imaging using a random absorption mask
Authors: Wang Hongchang , Kashyap Yogesh , Cai Biao , Sawhney Kawal 
Published: July 2016

AbstractHigh energy X-ray imaging has unique advantage over conventional X-ray imaging, since it enables higher penetration into materials with significantly reduced radiation damage. However, the absorption contrast in high energy region is considerably low due to the reduced X-ray absorption cross section for most materials. Even though the X-ray phase and dark-field imaging techniques can provide substantially increased contrast and complementary information, fabricating dedicated optics for high energies still remain a challenge. To address this issue, we present an alternative X-ray imaging approach to produce transmission, phase and scattering signals at high X-ray energies by using a random absorption mask. Importantly, in addition to the synchrotron radiation source, this approach has been demonstrated for practical imaging application with a laboratory-based microfocus X-ray source. This new imaging method could be potentially useful for studying thick samples or heavy materials for advanced research in materials science.
Nature of the Insulating Ground State of the Two-Dimensional Sn Atom Lattice on SiC(0001)
Authors: Yi Seho , Lee Hunpyo , Choi Jin-Ho , Cho Jun-Hyung 
Published: July 2016

AbstractSemiconductor surfaces with narrow surface bands provide unique playgrounds to search for Mott-insulating state. Recently, a combined experimental and theoretical study of the two-dimensional (2D) Sn atom lattice on a wide-gap SiC(0001) substrate proposed a Mott-type insulator driven by strong on-site Coulomb repulsion U within a single-band Hubbard model. However, our systematic density-functional theory (DFT) study with local, semilocal, and hybrid exchange-correlation functionals shows that the Sn dangling-bond state largely hybridizes with the substrate Si 3p and C 2p states to split into three surface bands due to the crystal field. Such a hybridization gives rise to the stabilization of the antiferromagnetic order via superexchange interactions. The band gap and the density of states predicted by the hybrid DFT calculation agree well with photoemission data. Our findings not only suggest that the Sn/SiC(0001) system can be represented as a Slater-type insulator driven by long-range magnetism, but also have an implication that taking into account long-range interactions beyond the on-site interaction would be of importance for properly describing the insulating nature of Sn/SiC(0001).
Energy transmission using recyclable quantum entanglement
Authors: Ye Ming-Yong , Lin Xiu-Min 
Published: July 2016

AbstractIt is known that faster-than-light (FTL) transmission of energy could be achieved if the transmission were considered in the framework of non-relativistic classical mechanics. Here we show that FTL transmission of energy could also be achieved if the transmission were considered in the framework of non-relativistic quantum mechanics. In our transmission protocol a two-spin Heisenberg model is considered and the energy is transmitted by two successive local unitary operations on the initially entangled spins. Our protocol does not mean that FTL transmission can be achieved in reality when the theory of relativity is considered, but it shows that quantum entanglement can be used in a recyclable way in energy transmission.
Alterations of the gut microbiome of largemouth bronze gudgeon (Coreius guichenoti) suffering from furunculosis
Authors: Li Tongtong , Long Meng , Ji Cheng , Shen Zhixin , Gatesoupe François-Joël , Zhang Xujie , Zhang Qianqian , Zhang Lanli , Zhao Yuanli , Liu Xinhua , Li Aihua 
Published: July 2016

AbstractHigh-throughput sequencing was applied to compare the intestinal microbiota in largemouth bronze gudgeon either healthy or affected by furunculosis. Proteobacteria, Actinobacteria, Tenericutes, Firmicutes and Bacteroidetes were detected as the predominant bacterial phyla in the gut of both diseased and healthy fish. The abundance of Proteobacteria differed significantly between the two groups of fish, mainly due to the overwhelming prevalence of Aeromonas in the diseased fish (81% ± 17%), while the genus was unevenly spread among the apparently healthy fish (33% ± 33%). The bacterial diversity in the intestine of diseased fish was markedly lower than in healthy fish. Analysis revealed the significant dissimilarity between the gut microbiota of diseased and healthy fish. The bacterial profiles in the gut were further characterized with the 28 phylotypes that were shared by the two groups. In diseased fish, two shared OTUs (OTU0001 and OTU0013) were closely related to Aeromonas salmonicida, their total proportion exceeding 70% of the sequences in diseased fish, while averaging 5.2% ± 4.6% in the healthy fish. This result suggested the presence of healthy carriers of pathogenic A. salmonicida among the farmed fish, and the gut appeared as a probable infection source for furunculosis in largemouth bronze gudgeon.
Performance of a Heating Block System Designed for Studying the Heat Resistance of Bacteria in Foods
Authors: Kou Xiao-xi , Li Rui , Hou Li-xia , Huang Zhi , Ling Bo , Wang Shao-jin 
Published: July 2016

AbstractKnowledge of bacteria’s heat resistance is essential for developing effective thermal treatments. Choosing an appropriate test method is important to accurately determine bacteria’s heat resistances. Although being a major factor to influence the thermo-tolerance of bacteria, the heating rate in samples cannot be controlled in water or oil bath methods due to main dependence on sample’s thermal properties. A heating block system (HBS) was designed to regulate the heating rates in liquid, semi-solid and solid foods using a temperature controller. Distilled water, apple juice, mashed potato, almond powder and beef were selected to evaluate the HBS’s performance by experiment and computer simulation. The results showed that the heating rates of 1, 5 and 10 °C/min with final set-point temperatures and holding times could be easily and precisely achieved in five selected food materials. A good agreement in sample central temperature profiles was obtained under various heating rates between experiment and simulation. The experimental and simulated results showed that the HBS could provide a sufficiently uniform heating environment in food samples. The effect of heating rate on bacterial thermal resistance was evaluated with the HBS. The system may hold potential applications for rapid and accurate assessments of bacteria’s thermo-tolerances.
Solution-Processible Crystalline NiO Nanoparticles for High-Performance Planar Perovskite Photovoltaic Cells
Authors: Kwon Uisik , Kim Bong-Gi , Nguyen Duc Cuong , Park Jong-Hyeon , Ha Na Young , Kim Seung-Joo , Ko Seung Hwan , Lee Soonil , Lee Daeho , Park Hui Joon 
Published: July 2016

AbstractIn this work, we report on solution-based p-i-n-type planar-structured CH3NH3PbI3perovskite photovoltaic (PV) cells, in which precrystallized NiO nanoparticles (NPs) without post-treatment are used to form a hole transport layer (HTL). X-ray diffraction and high-resolution transmission electron microscopy showed the crystallinity of the NPs, and atomic force microscopy and scanning electron microscopy confirmed the uniform surfaces of the resultant NiO thin film and the subsequent perovskite photoactive layer. Compared to the conventional poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) HTL, the NiO HTL had excellent energy-level alignment with that of CH3NH3PbI3and improved electron-blocking capability, as analyzed by photoelectron spectroscopy and diode modeling, resulting inVoc~0.13 V higher than conventional PEDOT:PSS-based devices. Consequently, a power conversion efficiency (PCE) of 15.4% with a high fill factor (FF, 0.74), short-circuit current density (Jsc, 20.2 mA·cm−2), and open circuit voltage (Voc, 1.04 V) having negligible hysteresis and superior air stability has been achieved.
NCMine: Core-peripheral based functional module detection using near-clique mining
Authors: Tadaka Shu , Kinoshita Kengo 
Published: July 2016

Motivation: The identification of functional modules from protein–protein interaction (PPI) networks is an important step toward understanding the biological features of PPI networks. The detection of functional modules in PPI networks is often performed by identifying internally densely connected subnetworks, and often produces modules with “core” and “peripheral” proteins. The core proteins are the ones having dense connections to each other in a module. The difference between core and peripheral proteins is important to understand the functional roles of proteins in modules, but there are few methods to explicitly elucidate the internal structure of functional modules at gene level.
Results: We propose NCMine, which is a novel network clustering method and visualization tool for the core-peripheral structure of functional modules. It extracts near-complete subgraphs from networks based on a node-weighting scheme using degree centrality, and reports subgroups as functional modules. We implemented this method as a plugin of Cytoscape, which is widely used to visualize and analyze biological networks. The plugin allows users to extract functional modules from PPI networks and interactively filter modules of interest. We applied the method to human PPI networks, and found several examples with the core-peripheral structure of modules that may be related to cancer development.
Availability and Implementation: The Cytoscape plugin and tutorial are available at Cytoscape AppStore. (http://apps.cytoscape.org/apps/ncmine).
Contact: kengo@ecei.tohoku.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance
Authors: Cortina George A. , Kasson Peter M. 
Published: July 2016

Motivation
Bacterial resistance to antibiotics, particularly plasmid-encoded resistance to beta lactam drugs, poses an increasing threat to human health. Point mutations to beta-lactamase enzymes can greatly alter the level of resistance conferred, but predicting the effects of such mutations has been challenging due to the large combinatorial space involved and the subtle relationships of distant residues to catalytic function. Therefore we desire an information-theoretic metric to sensitively and robustly detect both local and distant residues that affect substrate conformation and catalytic activity.

Results
Here, we report the use of positional mutual information in multiple microsecond-length molecular dynamics (MD) simulations to predict residues linked to catalytic activity of the CTX-M9 beta lactamase. We find that motions of the bound drug are relatively isolated from motions of the protein as a whole, which we interpret in the context of prior theories of catalysis. In order to robustly identify residues that are weakly coupled to drug motions but nonetheless affect catalysis, we utilize an excess mutual information metric. We predict 31 such residues for the cephalosporin antibiotic cefotaxime. Nine of these have previously been tested experimentally, and all decrease both enzyme rate constants and empirical drug resistance. We prospectively validate our method by testing eight high-scoring mutations and eight low-scoring controls in bacteria. Six of eight predicted mutations decrease cefotaxime resistance greater than 2-fold, while only one control shows such an effect. The ability to prospectively predict new variants affecting bacterial drug resistance is of great interest to clinical and epidemiological surveillance.

Availability and implementation
Excess mutual information code is available at https://github.com/kassonlab/positionalmi

Contact
kasson@virginia.edu
Simultaneous gene finding in multiple genomes
Authors: König Stefanie , Romoth Lars W. , Gerischer Lizzy , Stanke Mario 
Published: July 2016

Motivation: As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or—if not—where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach.
Results: The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances.
Availability and implementation: The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/.
Contact: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Results of biological restoration of varus impacted proximal humeral fracture and stabilization with locked plate and calcar screws
Authors: Sharaby Mohamed M.F. 
Published: July 2016

Background:
Varus impacted proximal humeral fractures (B2.2) is a unique type of fracture with multiple sequelae and unpredictable outcome. There is a high incidence of varus collapse and loss of fixation associated with this type of fracture especially in patients with loss of medial calcar. This created the idea of reconstructing the medial calcar during internal fixation to avoid recurring deformity and malunion. The aim of this study was to evaluate the results of fixation of varus impacted proximal humeral fracture using locking plate fixation with a calcar screw and without the use of bone grafting or opening of the joint capsule for reconstruction of the medial buttress.

Methods:
A series of 39 operative procedures of varus proximal humeral fractures were fixed with locking plate and calcar screws. Clinical and radiographic outcomes were collected and evaluated.

Results:
At 2-year follow-up, the mean Constant score was 83.9±6.4 (range 68-92), with four patients lost for different reasons. At final follow-up, the head-shaft angle was 130.3±8 degrees (range 111-143 degrees), the change in the angle because of subsidence ranged between 0 to 20 degrees (4.4±5.3 degrees). The complications included two superficial wound infections, one developed greater tuberosity nonunion, and nine had subsidence of the head with minor change of the head-shaft angle at follow-up. Six patients had a change of 5 to 10 degrees, while three patients had a 10 to 20-degree change.

Conclusions:
Medial calcar comminution can be treated successfully by the use of locking plate fixation with calcar screws with no additional grafting. Long-term follow-up is required to ensure the persistence of good results.
New developments in genetics of myositis
Authors: Rothwell Simon , Lamb Janine A. , Chinoy Hector 
Published: July 2016

Purpose of review
This article reviews the advances that have been made in our understanding of the genetics of the idiopathic inflammatory myopathies (IIM) in the past 2 years, with a particular focus on polymyositis, dermatomyositis and inclusion body myositis.

Recent findings
Two large human leukocyte antigen (HLA) imputation studies have confirmed a strong association with the 8.1 ancestral haplotype in clinical subgroups of myositis and suggest multiple independent associations on this haplotype. Risk in these genes may be due to specific amino acid positions within the peptide-binding grooves of HLA molecules. A large genetic study in 2566 IIM patients revealed associations such as PTPN22, STAT4, UBE2L3 and BLK, which overlap with risk variants reported in other seropositive autoimmune diseases. There is also evidence of different genetic architectures in clinical subgroups of IIM. Candidate gene studies in the Japanese and Chinese populations have replicated previous IIM associations which suggest common aetiology between ethnicities.

Summary
International collaborations have facilitated large genetic studies in IIM that have revealed much about the genetics of this rare complex disease both within the HLA region and genome-wide. Future approaches, such as sequencing and trans-ethnic meta-analyses, will advance our knowledge of IIM genetics.
High-dose Cyclophosphamide is Effective Therapy for Pediatric Severe Aplastic Anemia
Authors: Gamper Christopher J. , Takemoto Clifford M. , Chen Allen R. , Symons Heather J. , Loeb David M. , Casella James F. , Dezern Amy E. , King Karen E. , McGonigle Andrea M. , Jones Richard J. , Brodsky Robert A. 
Published: July 2016

Objective:
Use of high-dose cyclophosphamide without hematopoietic stem cell transplant to treat severe aplastic anemia (SAA) has been controversial due to concern for increased infectious toxicity as compared with antithymocyte globulin and cyclosporine A. As children often tolerate dose-intensive therapy better than adults, we sought to perform a detailed retrospective analysis of both treatment response and toxicity in 28 patients younger than 22 years of age treated with 29 courses of high-dose cyclophosphamide as the sole form of immunosuppression.

Study Design:
Children and adolescents with SAA who lacked an human leukocyte antigen–matched sibling donor were treated with cyclophosphamide 50 mg/kg/d for 4 consecutive days then received daily granulocyte colony stimulating factor until neutrophil recovery, transfusion support, and antimicrobial prophylaxis.

Results:
Overall survival was 85%, with hematologic response of 79% and complete response of 66%. Cumulative incidences of bacterial infection (86%) and fungal infection (62%) were high but deaths due to infection were rare, as were clonal evolution (1/28), clinically relevant paroxysmal nocturnal (1/28), and relapse (2/28).

Conclusions:
Response rates and survival following high-dose cyclophosphamide in pediatric patients with SAA exceed those seen in adults and compare favorably to antithymocyte globulin/cyclosporine A with manageable infectious toxicity.
A common perceptual inference for cross-modally induced illusions of body schema
Authors: Zheng Zane Z. , Munhall Kevin G. , Johnsrude Ingrid S. 
Published: July 2016

AbstractBody-schema, or the multimodal representation of one’s own body attributes, has been demonstrated previously to be malleable. In the rubber-hand illusion (Botvinick & Cohen, 1998), synchronous visual and tactile stimulation cause a fake hand to be perceived as one’s own. Similarly, if a stranger’s voice is heard synchronously with one’s own vocal production, that voice comes to be attributed to oneself (Zheng et al., 2011). Multimodal illusions like these involve distorting body schema based on correlated input, yet the degree to which different instances of distortion are perceived within the same individuals has never been examined. Here we show that participants embraced the ownership of a fake hand and a stranger’s voice to a similar degree, controlling both for individual suggestibility and for general susceptibility to illusion of body schema. Our findings suggest that the perceptual inference that leads to the distortion of body schema is a stable trait.
Genome-wide methylation data mirror ancestry information
Authors: Rahmani Elior , Shenhav Liat , Schweiger Regev , Yousefi Paul , Huen Karen , Eskenazi Brenda , Eng Celeste , Huntsman Scott , Hu Donglei , Galanter Joshua , Oh Sam , Waldenberger Melanie , Strauch Konstantin , Grallert Harald , Meitinger Thomas , Gieger Christian , Holland Nina , Burchard Esteban , Zaitlen Noah , Halperin Eran 
Published: July 2016

AbstractGenetic data are known to harbor information about human demographics, and genotyping data are commonly used for capturing ancestry information by leveraging genome-wide differences between populations. In contrast, it is not clear to what extent population structure is captured by whole-genome DNA methylation data. We demonstrate, using three large cohort 450K methylation array data sets, that ancestry information signal is mirrored in genome-wide DNA methylation data, and that it can be further isolated more effectively by leveraging the correlation structure of CpGs with cis-located SNPs. Based on these insights, we propose a method, EPISTRUCTURE, for the inference of ancestry from methylation data, without the need for genotype data. EPISTRUCTURE can be used to infer ancestry information of individuals based on their methylation data in the absence of corresponding genetic data. Although genetic data are often collected in epigenetic studies of large cohorts, these are typically not made publicly available, making the application of EPISTRUCTURE especially useful for anyone working on public data. Implementation of EPISTRUCTURE is available in GLINT, our recently released toolset for DNA methylation analysis at:http://glint-epigenetics.readthedocs.io.