bluuebunny/crossref_metadata_2025_split huggingface dataset:
Directionally hiding objects and creating illusions above a carpet-like device by reflection holography
Authors: Cheng Qiluan , Wu Kedi , Shi Yile , Wang Hui , Wang Guo Ping 
Published: February 2015

AbstractRealization of a perfect invisibility cloak still challenges the current fabricating technologies. Most experiments, if not all, are hence focused on carpet cloaks because of their relatively low requirements to material properties. Nevertheless, present invisibility carpets are used to hide beneath objects. Here, we report a carpet-like device to directionally conceal objects and further to create illusions above it. The device is fabricated through recording a reflection hologram of objects and is used to produce a time-reversed signal to compensate for the information of the objects and further to create light field of another object so as to realize both functions of hiding the objects and creating illusions, respectively. The carpet-like device can work for macroscopic objects at visible wavelength as the distance between objects and device is at decimeter scale. Our carpet-like device to realizing invisibility and creating illusions may provide a robust way for crucial applications of magic camouflaging and anti-detection etc.
Quantification of the binding potential of cell-surface receptors in fresh excised specimens via dual-probe modeling of SERS nanoparticles
Authors: Sinha Lagnojita , Wang Yu , Yang Cynthia , Khan Altaz , Brankov Jovan G. , Liu Jonathan T. C. , Tichauer Kenneth M. 
Published: February 2015

AbstractThe complete removal of cancerous tissue is a central aim of surgical oncology, but is difficult to achieve in certain cases, especially when the removal of surrounding normal tissues must be minimized. Therefore, when post-operative pathology identifies residual tumor at the surgical margins, re-excision surgeries are often necessary. An intraoperative approach for tumor-margin assessment, insensitive to nonspecific sources of molecular probe accumulation and contrast, is presented employing kinetic-modeling analysis of dual-probe staining using surface-enhanced Raman scattering nanoparticles (SERS NPs). Human glioma (U251) and epidermoid (A431) tumors were implanted subcutaneously in six athymic mice. Fresh resected tissues were stained with an equimolar mixture of epidermal growth factor receptor (EGFR)-targeted and untargeted SERS NPs. The binding potential (BP; proportional to receptor concentration) of EGFR – a cell-surface receptor associated with cancer – was estimated from kinetic modeling of targeted and untargeted NP concentrations in response to serial rinsing. EGFR BPs in healthy, U251 and A431 tissues were 0.06 ± 0.14, 1.13 ± 0.40 and 2.23 ± 0.86, respectively, which agree with flow-cytometry measurements and published reports. The ability of this approach to quantify the BP of cell-surface biomarkers in fresh tissues opens up an accurate new approach to analyze tumor margins intraoperatively.
Optimization of the heme biosynthesis pathway for the production of 5-aminolevulinic acid in Escherichia coli
Authors: Zhang Junli , Kang Zhen , Chen Jian , Du Guocheng 
Published: February 2015

Abstract5-Aminolevulinic acid (ALA), the committed intermediate of the heme biosynthesis pathway, shows significant promise for cancer treatment. Here, we identified that in addition to hemA and hemL, hemB, hemD, hemF, hemG and hemH are also the major regulatory targets of the heme biosynthesis pathway. Interestingly, up-regulation of hemD and hemF benefited ALA accumulation whereas overexpression of hemB, hemG and hemH diminished ALA accumulation. Accordingly, by combinatorial overexpression of the hemA, hemL, hemD and hemF with different copy-number plasmids, the titer of ALA was improved to 3.25 g l−1. Furthermore, in combination with transcriptional and enzymatic analysis, we demonstrated that ALA dehydratase (HemB) encoded by hemB is feedback inhibited by the downstream intermediate protoporphyrinogen IX. This work has great potential to be scaled-up for microbial production of ALA and provides new important insights into the regulatory mechanism of the heme biosynthesis pathway.
Low-frequency magnetic fields do not aggravate disease in mouse models of Alzheimer's disease and amyotrophic lateral sclerosis
Authors: Liebl Martina P. , Windschmitt Johannes , Besemer Anna S. , Schäfer Anne-Kathrin , Reber Helmut , Behl Christian , Clement Albrecht M. 
Published: February 2015

AbstractLow-frequency magnetic fields (LF-MF) generated by power lines represent a potential environmental health risk and are classified as possibly carcinogenic by the World Health Organization. Epidemiological studies indicate that LF-MF might propagate neurodegenerative diseases like Alzheimer's disease (AD) or amyotrophic lateral sclerosis (ALS). We conducted a comprehensive analysis to determine whether long-term exposure to LF-MF (50 Hz, 1 mT) interferes with disease development in established mouse models for AD and ALS, namely APP23 mice and mice expressing mutant Cu/Zn-superoxide dismutase (SOD1), respectively. Exposure for 16 months did not aggravate learning deficit of APP23 mice. Likewise, disease onset and survival of SOD1G85R or SOD1G93A mice were not altered upon LF-MF exposure for ten or eight months, respectively. These results and an extended biochemical analysis of protein aggregation, glial activation and levels of toxic protein species suggests that LF-MF do not affect cellular processes involved in the pathogenesis of AD or ALS.
Nature of charge transport and p-electron ferromagnetism in nitrogen-doped ZrO2: An ab initio perspective
Authors: Zhu Huanfeng , Li Jing , Chen Kun , Yi Xinyu , Cheng Shuai , Gan Fuxi 
Published: February 2015

AbstractZirconium dioxide provides an exceptional prototype material for studying the redistribution of the polaron holes and its magnetic coupling with their nearby anions owning to the difference oxygen binding behavior in the monoclinic phase. Here, we perform a comprehensive study of thep-electron magnetism in the nitrogen doped 2 × 2 × 2 monoclinic ZrO2based on spin-polarized density functional theory. Nitrogen substitutions make the system display half-metallic properties and the origin of room temperature ferromagnetism ascribes to thep-pcoupling interaction between N 2pand the host 2pstates. The charge density difference and Mülliken population analyses provide evidences of charge redistributions. Our results reveal that the polaron transfer may alter the magnetic properties and it is greatly facilitated ferromagnetic coupling if the polaron holes are localized around a single anion dopant.
A strategy to design novel structure photochromic sensitizers for dye-sensitized solar cells
Authors: Wu Wenjun , Wang Jiaxing , Zheng Zhiwei , Hu Yue , Jin Jiayu , Zhang Qiong , Hua Jianli 
Published: February 2015

AbstractTwo sensitizers with novel structure were designed and synthetized by introducing photochromic bisthienylethene (BTE) group into the conjugated system. Thanks to the photochromic effect the sensitizers have under ultraviolet and visible light, the conjugated bridge can be restructured and the resulting two photoisomers showed different behaviors in photovoltaic devices. This opens up a new research way for the dye-sensitized solar cells (DSSCs).
Induced pluripotent stem cells as a model for diabetes investigation
Authors: Stepniewski J. , Kachamakova-Trojanowska N. , Ogrocki D. , Szopa M. , Matlok M. , Beilharz M. , Dyduch G. , Malecki M. T. , Jozkowicz A. , Dulak J. 
Published: February 2015

AbstractMouse and human induced pluripotent stem cells (iPSCs) may represent a novel approach for modeling diabetes. Taking this into consideration, the aim of this study was to generate and evaluate differentiation potential of iPSCs from lepdb/db (db/db) mice, the model of diabetes type 2 as well as from patients with Maturity Onset Diabetes of the Young 3 (HNF1A MODY). Murine iPSC colonies from both wild type and db/db mice were positive for markers of pluripotency: Oct3/4A, Nanog, SSEA1, CDy1 and alkaline phosphatase and differentiated in vitro and in vivo into cells originating from three germ layers. However, our results suggest impaired differentiation of db/db cells into endothelial progenitor-like cells expressing CD34 and Tie2 markers and their reduced angiogenic potential. Human control and HNF1A MODY reprogrammed cells also expressed pluripotency markers: OCT3/4A, SSEA4, TRA-1–60, TRA-1-81, formed embryoid bodies (EBs) and differentiated into cells of three germ layers. Additionally, insulin expressing cells were obtained from those partially reprogrammed cells with direct as well as EB-mediated differentiation method. Our findings indicate that disease-specific iPSCs may help to better understand the mechanisms responsible for defective insulin production or vascular dysfunction upon differentiation toward cell types affected by diabetes.
Rapid preparation of rare ginsenosides by acid transformation and their structure-activity relationships against cancer cells
Authors: Quan Kai , Liu Qun , Wan Jin-Yi , Zhao Yi-Jing , Guo Ru-Zhou , Alolga Raphael N. , Li Ping , Qi Lian-Wen 
Published: February 2015

AbstractThe anticancer activities of ginsenosides are widely reported. The structure-activity relationship of ginsenosides against cancer is not well elucidated because of the unavailability of these compounds. In this work, we developed a transformation method to rapidly produce rare dehydroxylated ginsenosides by acid treatment. The optimized temperature, time course and concentration of formic acid were 120°C, 4 h and 0.01%, respectively. From 100 mg of Rh1, 8.3 mg of Rk3 and 18.7 mg of Rh4 can be produced by acid transformation. Similarly, from 100 mg of Rg3, 7.4 mg of Rk1 and 15.1 mg of Rg5 can be produced. From 100 mg of Rh2, 8.3 mg of Rk2 and 12.7 mg of Rh3 can be generated. Next, the structure-activity relationships of 23 ginsenosides were investigated by comparing their cytotoxic effects on six human cancer cells, including HCT-116, HepG2, MCF-7, Hela, PANC-1 and A549. The results showed that: (1) the cytotoxic effect of ginsenosides is inversely related to the sugar numbers; (2) sugar linkages rank as C-3 > C-6 > C-20; (3) the protopanaxadiol-type has higher activities; (4) having the double bond at the terminal C20-21 exhibits stronger activity than that at C20-22; and (5) 20(S)-ginsenosides show stronger effects than their 20(R)-stereoisomers.
Collapsing modular counting in bounded arithmetic and constant depth propositional proofs
Authors: Buss Samuel , Kołodziejczyk Leszek , Zdanowski Konrad 
Published: February 2015

Jeřábek introduced fragments of bounded arithmetic which are axiomatized with weak surjective pigeonhole principles and support a robust notion of approximate counting. We extend these fragments to accommodate modular counting quantifiers. These theories can formalize and prove the relativized versions of Toda’s theorem on the collapse of the polynomial hierarchy with modular counting. We introduce a version of the Paris-Wilkie translation for converting formulas and proofs of bounded arithmetic with modular counting quantifiers into constant depth propositional logic with modular counting gates. We also define Paris-Wilkie translations to Nullstellensatz and polynomial calculus refutations. As an application, we prove that constant depth propositional proofs that use connectives AND, OR, and mod p gates, for

p
p

a prime, can be translated, with quasipolynomial increase in size, into propositional proofs containing only propositional formulas of depth three in which the top level is Boolean, the middle level consists of mod p gates, and the bottom level subformulas are small conjunctions. These results are improved to depth two by using refutations from the weak surjective pigeonhole principles.
specL—an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics
Authors: Panse Christian , Trachsel Christian , Grossmann Jonas , Schlapbach Ralph 
Published: February 2015

Abstract
Motivation: Targeted data extraction methods are attractive ways to obtain quantitative peptide information from a proteomics experiment. Sequential Window Acquisition of all Theoretical Spectra (SWATH) and Data Independent Acquisition (DIA) methods increase reproducibility of acquired data because the classical precursor selection is omitted and all present precursors are fragmented. However, especially for targeted data extraction, MS coordinates (retention time information precursor and fragment masses) are required for the particular entities (peptide ions). These coordinates are usually generated in a so-called discovery experiment earlier on in the project if not available in public spectral library repositories. The quality of the assay panel is crucial to ensure appropriate downstream analysis. For that, a method is needed to create spectral libraries and to export customizable assay panels.
Results: Here, we present a versatile set of functions to generate assay panels from spectral libraries for use in targeted data extraction methods (SWATH/DIA) in the area of proteomics.
Availability and implementation: specL is implemented in the R language and available under an open-source license (GPL-3) in Bioconductor since BioC 3.0 (R-3.1) http://www.bioconductor.org (Trachsel et al., 2015). A vignette with a complete tutorial describing data import/export and analysis is included in the package and can also be found as supplement material of this article.
Contact: cp@fgcz.ethz.ch or jg@fgcz.ethz.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences
Authors: Kirmitzoglou Ioannis , Promponas Vasilis J. 
Published: February 2015

Abstract
Motivation: Local compositionally biased and low complexity regions (LCRs) in amino acid sequences have initially attracted the interest of researchers due to their implication in generating artifacts in sequence database searches. There is accumulating evidence of the biological significance of LCRs both in physiological and in pathological situations. Nonetheless, LCR-related algorithms and tools have not gained wide appreciation across the research community, partly due to the fact that only a handful of user-friendly software is currently freely available.
Results: We developed LCR-eXXXplorer, an extensible online platform attempting to fill this gap. LCR-eXXXplorer offers tools for displaying LCRs from the UniProt/SwissProt knowledgebase, in combination with other relevant protein features, predicted or experimentally verified. Moreover, users may perform powerful queries against a custom designed sequence/LCR-centric database. We anticipate that LCR-eXXXplorer will be a useful starting point in research efforts for the elucidation of the structure, function and evolution of proteins with LCRs.
Availability and implementation: LCR-eXXXplorer is freely available at the URL http://repeat.biol.ucy.ac.cy/lcr-exxxplorer.
Contact: vprobon@ucy.ac.cy
Supplementary information: Supplementary data are available at Bioinformatics online.
EpiToolKit—a web-based workbench for vaccine design
Authors: Schubert Benjamin , Brachvogel Hans-Philipp , Jürges Christopher , Kohlbacher Oliver 
Published: February 2015

Abstract
Summary: EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. For inexperienced users it offers simplified interfaces to guide the users through the analysis of complex immunological data sets.
Availability and implementation: http://www.epitoolkit.de
Contact: schubert@informatik.uni-tuebingen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated benchmarking of peptide-MHC class I binding predictions
Authors: Trolle Thomas , Metushi Imir G. , Greenbaum Jason A. , Kim Yohan , Sidney John , Lund Ole , Sette Alessandro , Peters Bjoern , Nielsen Morten 
Published: February 2015

Abstract
Motivation: Numerous in silico methods predicting peptide binding to major histocompatibility complex (MHC) class I molecules have been developed over the last decades. However, the multitude of available prediction tools makes it non-trivial for the end-user to select which tool to use for a given task. To provide a solid basis on which to compare different prediction tools, we here describe a framework for the automated benchmarking of peptide-MHC class I binding prediction tools. The framework runs weekly benchmarks on data that are newly entered into the Immune Epitope Database (IEDB), giving the public access to frequent, up-to-date performance evaluations of all participating tools. To overcome potential selection bias in the data included in the IEDB, a strategy was implemented that suggests a set of peptides for which different prediction methods give divergent predictions as to their binding capability. Upon experimental binding validation, these peptides entered the benchmark study.
Results: The benchmark has run for 15 weeks and includes evaluation of 44 datasets covering 17 MHC alleles and more than 4000 peptide-MHC binding measurements. Inspection of the results allows the end-user to make educated selections between participating tools. Of the four participating servers, NetMHCpan performed the best, followed by ANN, SMM and finally ARB.
Availability and implementation: Up-to-date performance evaluations of each server can be found online at http://tools.iedb.org/auto_bench/mhci/weekly. All prediction tool developers are invited to participate in the benchmark. Sign-up instructions are available at http://tools.iedb.org/auto_bench/mhci/join.
Contact: mniel@cbs.dtu.dk or bpeters@liai.org
Supplementary information: Supplementary data are available at Bioinformatics online.
A new method to improve network topological similarity search: applied to fold recognition
Authors: Lhota John , Hauptman Ruth , Hart Thomas , Ng Clara , Xie Lei 
Published: February 2015

AbstractMotivation: Similarity search is the foundation of bioinformatics. It plays a key role in establishing structural, functional and evolutionary relationships between biological sequences. Although the power of the similarity search has increased steadily in recent years, a high percentage of sequences remain uncharacterized in the protein universe. Thus, new similarity search strategies are needed to efficiently and reliably infer the structure and function of new sequences. The existing paradigm for studying protein sequence, structure, function and evolution has been established based on the assumption that the protein universe is discrete and hierarchical. Cumulative evidence suggests that the protein universe is continuous. As a result, conventional sequence homology search methods may be not able to detect novel structural, functional and evolutionary relationships between proteins from weak and noisy sequence signals. To overcome the limitations in existing similarity search methods, we propose a new algorithmic framework—Enrichment of Network Topological Similarity (ENTS)—to improve the performance of large scale similarity searches in bioinformatics.Results: We apply ENTS to a challenging unsolved problem: protein fold recognition. Our rigorous benchmark studies demonstrate that ENTS considerably outperforms state-of-the-art methods. As the concept of ENTS can be applied to any similarity metric, it may provide a general framework for similarity search on any set of biological entities, given their representation as a network.Availability and implementation: Source code freely available upon requestContact: lxie@iscb.org
Individual specialization on fishery discards by lesser black-backed gulls (Larus fuscus)
Authors: Tyson Chris , Shamoun-Baranes Judy , Van Loon E. Emiel , Camphuysen Kees (C. J.) , Hintzen Niels T. 
Published: February 2015

Abstract
While seabird–fishery associations are well documented, this research primarily comes from ship-based surveys and consequently individual level responses to discard availability are largely unknown. As part of a long-term study on lesser black-backed gulls (Larus fuscus) in the Netherlands, the fine-scale movements of adults were tracked with GPS tags throughout the breeding period. The aim of this study was to determine if lesser black-backed gulls were utilizing fishery discards in the Wadden Sea and to examine possible consequences of this behaviour. Within the Wadden Sea during weekdays, tracked birds predominately associated with zones where fishing vessels are known to operate (deep gullies). Across all individuals combined (n = 40), there was a significantly reduced use of the Wadden Sea during weekends when the fleets were not operating. Eight females, who markedly increased their use of the Wadden Sea during weekdays throughout the breeding period, were largely responsible for this pattern. The loss of discard resources on weekends primarily resulted in these eight individuals switching to terrestrial foraging areas. Nest attendance and total foraging time were consistent between weekdays and weekends, suggesting that resource shifts on weekends did not impact daily time budgets. As such, it appears that lesser black-backed gulls specializing on discard utilization are able to flexibly respond to the temporary loss of discards by switching to alternative resources.
Selection between foreground models for global 21-cm experiments
Authors: Harker Geraint J. A. 
Published: February 2015

Abstract
The precise form of the foregrounds for sky-averaged measurements of the 21-cm line during and before the epoch of reionization is unknown. We suggest that the level of complexity in the foreground models used to fit global 21-cm data should be driven by the data, under a Bayesian model selection methodology. A first test of this approach is carried out by applying nested sampling to simplified models of global 21-cm data to compute the Bayesian evidence for the models. If the foregrounds are assumed to be polynomials of order n in log–log space, we can infer the necessity to use n = 4 rather than n = 3 with &lt;2 h of integration with limited frequency coverage, for reasonable values of the n = 4 coefficient. Using a higher order polynomial does not necessarily prevent a significant detection of the 21-cm signal. Even for n = 8, we can obtain very strong evidence distinguishing a reasonable model for the signal from a null model with 128 h of integration. More subtle features of the signal may, however, be lost if the foregrounds are this complex. This is demonstrated using a simpler model for the signal that only includes absorption. The results highlight some pitfalls in trying to quantify the significance of a detection from errors on the parameters of the signal alone.