bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted and controlled anticancer drug delivery and release with magnetoelectric nanoparticles
Authors: Rodzinski Alexandra , Guduru Rakesh , Liang Ping , Hadjikhani Ali , Stewart Tiffanie , Stimphil Emmanuel , Runowicz Carolyn , Cote Richard , Altman Norman , Datar Ram , Khizroev Sakhrat 
Published: February 2016

AbstractIt is a challenge to eradicate tumor cells while sparing normal cells. We used magnetoelectric nanoparticles (MENs) to control drug delivery and release. The physics is due to electric-field interactions (i) between MENs and a drug and (ii) between drug-loaded MENs and cells. MENs distinguish cancer cells from normal cells through the membrane’s electric properties; cancer cells have a significantly smaller threshold field to induce electroporation. In vitro and in vivo studies (nude mice with SKOV-3 xenografts) showed that (i) drug (paclitaxel (PTX)) could be attached to MENs (30-nm CoFe2O4@BaTiO3 nanostructures) through surface functionalization to avoid its premature release, (ii) drug-loaded MENs could be delivered into cancer cells via application of a d.c. field (~100 Oe), and (iii) the drug could be released off MENs on demand via application of an a.c. field (~50 Oe, 100 Hz). The cell lysate content was measured with scanning probe microscopy and spectrophotometry. MENs and control ferromagnetic and polymer nanoparticles conjugated with HER2-neu antibodies, all loaded with PTX were weekly administrated intravenously. Only the mice treated with PTX-loaded MENs (15/200 μg) in a field for three months were completely cured, as confirmed through infrared imaging and post-euthanasia histology studies via energy-dispersive spectroscopy and immunohistochemistry.
Feasible logic Bell-state analysis with linear optics
Authors: Zhou Lan , Sheng Yu-Bo 
Published: February 2016

AbstractWe describe a feasible logic Bell-state analysis protocol by employing the logic entanglement to be the robust concatenated Greenberger-Horne-Zeilinger (C-GHZ) state. This protocol only uses polarization beam splitters and half-wave plates, which are available in current experimental technology. We can conveniently identify two of the logic Bell states. This protocol can be easily generalized to the arbitrary C-GHZ state analysis. We can also distinguish two N-logic-qubit C-GHZ states. As the previous theory and experiment both showed that the C-GHZ state has the robustness feature, this logic Bell-state analysis and C-GHZ state analysis may be essential for linear-optical quantum computation protocols whose building blocks are logic-qubit entangled state.
Exfoliation and Raman Spectroscopic Fingerprint of Few-Layer NiPS3 Van der Waals Crystals
Authors: Kuo Cheng-Tai , Neumann Michael , Balamurugan Karuppannan , Park Hyun Ju , Kang Soonmin , Shiu Hung Wei , Kang Jin Hyoun , Hong Byung Hee , Han Moonsup , Noh Tae Won , Park Je-Geun 
Published: February 2016

AbstractThe range of mechanically cleavable Van der Waals crystals covers materials with diverse physical and chemical properties. However, very few of these materials exhibit magnetism or magnetic order, and thus the provision of cleavable magnetic compounds would supply invaluable building blocks for the design of heterostructures assembled from Van der Waals crystals. Here we report the first successful isolation of monolayer and few-layer samples of the compound nickel phosphorus trisulfide (NiPS3) by mechanical exfoliation. This material belongs to the class of transition metal phosphorus trisulfides (MPS3), several of which exhibit antiferromagnetic order at low temperature, and which have not been reported in the form of ultrathin sheets so far. We establish layer numbers by optical bright field microscopy and atomic force microscopy, and perform a detailed Raman spectroscopic characterization of bilayer and thicker NiPS3 flakes. Raman spectral features are strong functions of excitation wavelength and sample thickness, highlighting the important role of interlayer coupling. Furthermore, our observations provide a spectral fingerprint for distinct layer numbers, allowing us to establish a sensitive and convenient means for layer number determination.
Critical assessment and ramifications of a purported marine trophic cascade
Authors: Grubbs R. Dean , Carlson John K. , Romine Jason G. , Curtis Tobey H. , McElroy W. David , McCandless Camilla T. , Cotton Charles F. , Musick John A. 
Published: February 2016

AbstractWhen identifying potential trophic cascades, it is important to clearly establish the trophic linkages between predators and prey with respect to temporal abundance, demographics, distribution and diet. In the northwest Atlantic Ocean, the depletion of large coastal sharks was thought to trigger a trophic cascade whereby predation release resulted in increased cownose ray abundance, which then caused increased predation on and subsequent collapse of commercial bivalve stocks. These claims were used to justify the development of a predator-control fishery for cownose rays, the “Save the Bay, Eat a Ray” fishery, to reduce predation on commercial bivalves. A reexamination of data suggests declines in large coastal sharks did not coincide with purported rapid increases in cownose ray abundance. Likewise, the increase in cownose ray abundance did not coincide with declines in commercial bivalves. The lack of temporal correlations coupled with published diet data suggest the purported trophic cascade is lacking the empirical linkages required of a trophic cascade. Furthermore, the life history parameters of cownose rays suggest they have low reproductive potential and their populations are incapable of rapid increases. Hypothesized trophic cascades should be closely scrutinized as spurious conclusions may negatively influence conservation and management decisions.
Plain to point network reduced graphene oxide - activated carbon composites decorated with platinum nanoparticles for urine glucose detection
Authors: Hossain Mohammad Faruk , Park Jae Y. 
Published: February 2016

AbstractIn this study, a hydrothermal technique was applied to synthesize glucose-treated reduced graphene oxide-activated carbon (GRGO/AC) composites. Platinum nanoparticles (PtNP) were electrochemically deposited on the modified GRGO/AC surface, and chitosan-glucose oxidase (Chit-GOx) composites and nafion were integrated onto the modified surface of the working electrode to prepare a highly sensitive glucose sensor. The fabricated biosensor exhibited a good amperometric response to glucose in the detection range from 0.002 mM to 10 mM, with a sensitivity of 61.06 μA/mMcm2, a short response time (4 s) and a low detection limit of 2 μM (signal to noise ratio is 3). The glucose sensor exhibited a negligible response to interference and good stability. In addition, the glucose levels in human urine were tested in order to conduct a practical assessment of the proposed sensor, and the results indicate that the sensor had superior urine glucose recognition. These results thus demonstrate that the noble nano-structured electrode with a high surface area and electrocatalytic activity offers great promise for use in urine glucose sensing applications.
Effects of fragment traits, burial orientation and nutrient supply on survival and growth in Populus deltoides × P. simonii
Authors: Zhang Ping , Su Zhi-Qin , Xu Lie , Shi Xue-Ping , Du Ke-Bing , Zheng Bo , Wang Yong-Jian 
Published: February 2016

AbstractClonal propagations of shoot or root fragments play pivotal roles in adaptation of clonal trees to environmental heterogeneity, i.e. soil nutrient heterogeneity and burials after disturbance. However, little is known about whether burial orientation and nutrient supply can alter the effects of fragment traits in Populus. Shoot and root fragments of Populus deltoides × P. simonii were subjected to burials in two different fragment diameters (0.5 and 2.0 cm), two fragment lengths (5 and 15 cm) and three burial orientations (horizontal, upward and downward). For the shoot fragments, survival and growth were significantly higher in the larger pieces (either in length or diameter) and the horizontal/upward burial position. On the contrary, the effect of burial position was reversed for the root fragments. Shoot/root fragments of 15 cm in length in horizontal burial position were then subjected to two different fragment diameters (0.5 and 2.0 cm) and four types of nutrient supplies (without nutrient, low frequency, high frequency and patchy). Growth of shoot fragments of 2.0 cm in diameter significantly increased in high frequency and patchy nutrient supplies than that of without nutrient treatment. These results suggest that burial orientation and nutrient supply could be employed in clonal propagations of cuttings, afforestation or regeneration in Populus.
Genetic Improvements in Rice Yield and Concomitant Increases in Radiation- and Nitrogen-Use Efficiency in Middle Reaches of Yangtze River
Authors: Zhu Guanglong , Peng Shaobing , Huang Jianliang , Cui Kehui , Nie Lixiao , Wang Fei 
Published: February 2016

AbstractThe yield potential of rice (Oryza sativa L.) has experienced two significant growth periods that coincide with the introduction of semi-dwarfism and the utilization of heterosis. In present study, we determined the annual increase in the grain yield of rice varieties grown from 1936 to 2005 in Middle Reaches of Yangtze River and examined the contributions of RUE (radiation-use efficiency, the conversion efficiency of pre-anthesis intercepted global radiation to biomass) and NUE (nitrogen-use efficiency, the ratio of grain yield to aboveground N accumulation) to these improvements. An examination of the 70-year period showed that the annual gains of 61.9 and 75.3 kg ha−1 in 2013 and 2014, respectively, corresponded to an annual increase of 1.18 and 1.16% in grain yields, respectively. The improvements in grain yield resulted from increases in the harvest index and biomass and the sink size (spikelets per panicle) was significantly enlarged because of breeding for larger panicles. Improvements were observed in RUE and NUE through advancements in breeding. Moreover, both RUE and NUE were significantly correlated with the grain yield. Thus, our study suggests that genetic improvements in rice grain yield are associated with increased RUE and NUE.
Method parameters’ impact on mortality and variability in mouse stroke experiments: a meta-analysis
Authors: Ingberg Edvin , Dock Hua , Theodorsson Elvar , Theodorsson Annette , Ström Jakob O. 
Published: February 2016

AbstractAlthough hundreds of promising substances have been tested in clinical trials, thrombolysis currently remains the only specific pharmacological treatment for ischemic stroke. Poor quality, e.g. low statistical power, in the preclinical studies has been suggested to play an important role in these failures. Therefore, it would be attractive to use animal models optimized to minimize unnecessary mortality and outcome variability, or at least to be able to power studies more exactly by predicting variability and mortality given a certain experimental setup. The possible combinations of methodological parameters are innumerous, and an experimental comparison of them all is therefore not feasible. As an alternative approach, we extracted data from 334 experimental mouse stroke articles and, using a hypothesis-driven meta-analysis, investigated the method parameters’ impact on infarct size variability and mortality. The use of Swiss and C57BL6 mice as well as permanent occlusion of the middle cerebral artery rendered the lowest variability of the infarct size while the emboli methods increased variability. The use of Swiss mice increased mortality. Our study offers guidance for researchers striving to optimize mouse stroke models.
Clinical Relevance of Liver Kinase B1(LKB1) Protein and Gene Expression in Breast Cancer
Authors: Chen I-Chun , Chang Yuan-Ching , Lu Yen-Shen , Chung Kuei-Pin , Huang Chiun-Sheng , Lu Tzu-Pin , Kuo Wen-Hung , Wang Ming-Yang , Kuo Kuan-Ting , Wu Pei-Fang , Hsueh Tsu-Hsin , Shen Chen-Yang , Lin Ching-Hung , Cheng Ann-Lii 
Published: February 2016

AbstractLiver kinase B1 (LKB1) is a tumor suppressor, and its loss might lead to activation of the mammalian target of rapamycin (mTOR) and tumorigenesis. This study aimed to determine the clinical relevance of LKB1 gene and protein expression in breast cancer patients. LKB1 protein expression was evaluated using immunohistochemistry in tumors from early breast cancer patients in two Taiwanese medical centers. Data on LKB1 gene expression were obtained from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) data set. The correlations between LKB1 expression, clinicopathologic factors, and patient outcome were analyzed. LKB1 expression was significantly associated with estrogen receptor (ER) expression in 2 of the 4 cohorts, but not with other clinicopathologic factors. LKB1 expression was not a predictor for relapse-free survival, overall survival (OS), or breast cancer-specific survival. In a subgroup analysis of the two Taiwanese cohorts, high LKB1 protein expression was predictive of high OS in human epidermal growth factor receptor 2 (HER2)-positive breast cancer patients (P = 0.013). Our study results indicate that LKB1 expression is not prognostic in the whole population of breast cancer patients, but it is a potential predictor of OS in the subset of HER2-positive patients
Kooperation im Gesundheitswesen: Formative Evaluation des Modellprojekts Regionale Gesundheitskonferenzen in Bayern
Authors: Hollederer A. , Stühler K. 
Published: February 2016

Zusammenfassung
Ziel der Studie: Gesundheitskonferenzen bieten eine Möglichkeit zur besseren Kooperation und Steuerung im kommunalen Gesundheitsmanagement. Die explorative Evaluationsstudie hatte zum Ziel, die Strukturen, Prozesse und Ergebnisse von „Regionalen Gesundheitskonferenzen (RGK)“ in 3 Modellregionen zu bewerten, Hinweise auf Entwicklungspotenziale zu geben und die Übertragbarkeit auf andere Regionen zu prüfen.
Methodik: Am Ende der 18-monatigen Modellprojektphase (08/2013 bis 12/2014) wurde eine Vollerhebung bei 80 Teilnehmern der RGK in den 3 Regionen mittels eines teilstandardisierten Fragebogens durchgeführt. Die Rücklaufquote betrug 90%. Die Befunde wurden durch Dokumentenanalyse und separate Geschäftsstellenbefragung ergänzt.
Ergebnisse: Die RGK haben sich in den 3 Modellregionen zügig mit Geschäftsstelle und insgesamt 13 Arbeitsgruppen zur Gesundheitsversorgung etabliert. In der Perspektive fast aller Teilnehmer der RGK waren die Mitgliederzahl angemessen und alle wichtigen Akteure vertreten. Die Mehrheit beteiligte sich nach Einschätzung des Großteils der Befragten überwiegend aktiv und in der Regel hatte jeder Teilnehmer die gleichen Chancen, Themen einzubringen. Obwohl für knapp die Hälfte der Befragten Konflikte deutlich wurden, blieb die Atmosphäre für drei Viertel sehr konstruktiv. Die Wichtigkeit von Vorsitzenden und Geschäftsstellenleitern wurden ebenso wie der Einfluss der Moderatoren von nahezu allen Interviewten bestätigt. Fast alle stimmten zu, dass sich die RGK für die Optimierung der Gesundheitsversorgung und der Kooperation eignen. Aus Teilnehmersicht wurden überwiegend die wichtigsten Versorgungprobleme identifiziert. 94% der Befragten äußerten sich zustimmend, dass die bisherige Arbeit als erfolgreich eingeschätzt werden kann. Mit dem Verlauf der RGK waren 91% insgesamt zufrieden oder eher zufrieden. Während die Zufriedenheitsgrade zwischen den Modellregionen kaum divergierten, unterschieden sie sich aber deutlich zwischen den Akteursgruppen. 98% der Interviewten würden in Zukunft wieder teilnehmen.
Schlussfolgerung: Die RGK stellen nach den Rückmeldungen insgesamt eine gute Plattform für Koordination, Austausch und Zusammenarbeit der Akteure dar und haben sich als Kooperationsinstrument bewährt. Der Ansatz wird in Bayern im Rahmen des neuen Konzepts zu Gesundheitsregionenplus qualitativ und in der regionalen Reichweite ausgebaut.
Piecewise parameter estimation for stochastic models in COPASI
Authors: Bergmann Frank T. , Sahle Sven , Zimmer Christoph 
Published: February 2016

Abstract
Motivation: Computational modeling is widely used for deepening the understanding of biological processes. Parameterizing models to experimental data needs computationally efficient techniques for parameter estimation. Challenges for parameter estimation include in general the high dimensionality of the parameter space with local minima and in specific for stochastic modeling the intrinsic stochasticity.
Results: We implemented the recently suggested multiple shooting for stochastic systems (MSS) objective function for parameter estimation in stochastic models into COPASI. This MSS objective function can be used for parameter estimation in stochastic models but also shows beneficial properties when used for ordinary differential equation models. The method can be applied with all of COPASI’s optimization algorithms, and can be used for SBML models as well.
Availability and implementation: The methodology is available in COPASI as of version 4.15.95 and can be downloaded from http://www.copasi.org.
Contact: frank.bergmann@bioquant.uni-heidelberg.de or fbergman@caltech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Protein backbone ensemble generation explores the local structural space of unseen natural homologs
Authors: Schenkelberg Christian D. , Bystroff Christopher 
Published: February 2016

Abstract
Motivation: Mutations in homologous proteins affect changes in the backbone conformation that involve a complex interplay of forces which are difficult to predict. Protein design algorithms need to anticipate these backbone changes in order to accurately calculate the energy of the structure given an amino acid sequence, without knowledge of the final, designed sequence. This is related to the problem of predicting small changes in the backbone between highly similar sequences.
Results: We explored the ability of the Rosetta suite of protein design tools to move the backbone from its position in one structure (template) to its position in a close homologous structure (target) as a function of the diversity of a backbone ensemble constructed using the template structure, the percent sequence identity between the template and target, and the size of local zone being considered in the ensemble. We describe a pareto front in the likelihood of moving the backbone toward the target as a function of ensemble diversity and zone size. The equations and protocols presented here will be useful for protein design.
Availability and implementation: PyRosetta scripts available at www.bioinfo.rpi.edu/bystrc/downloads.html#ensemble
Contact: bystrc@rpi.edu
Estimating the number and assignment of clock models in analyses of multigene datasets
Authors: Duchêne Sebastián , Foster Charles S. P. , Ho Simon Y. W. 
Published: February 2016

Abstract
Motivation: Molecular-clock methods can be used to estimate evolutionary rates and timescales from DNA sequence data. However, different genes can display different patterns of rate variation across lineages, calling for the employment of multiple clock models. Selecting the optimal clock-partitioning scheme for a multigene dataset can be computationally demanding, but clustering methods provide a feasible alternative. We investigated the performance of different clustering methods using data from chloroplast genomes and data generated by simulation.
Results: Our results show that mixture models provide a useful alternative to traditional partitioning algorithms. We found only a small number of distinct patterns of among-lineage rate variation among chloroplast genes, which were consistent across taxonomic scales. This suggests that the evolution of chloroplast genes has been governed by a small number of genomic pacemakers. Our study also demonstrates that clustering methods provide an efficient means of identifying clock-partitioning schemes for genome-scale datasets.
Availability and implementation: The code and data sets used in this study are available online at https://github.com/sebastianduchene/pacemaker_clustering_methods.
Contact: sebastian.duchene@sydney.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees
Authors: Rainer Johannes , Taliun Daniel , D’Elia Yuri , Pattaro Cristian , Domingues Francisco S. , Weichenberger Christian X. 
Published: February 2016

AbstractSummary: Familial aggregation analysis is the first fundamental step to perform when assessing the extent of genetic background of a disease. However, there is a lack of software to analyze the familial clustering of complex phenotypes in very large pedigrees. Such pedigrees can be utilized to calculate measures that express trait aggregation on both the family and individual level, providing valuable directions in choosing families for detailed follow-up studies. We developed FamAgg, an open source R package that contains both established and novel methods to investigate familial aggregation of traits in large pedigrees. We demonstrate its use and interpretation by analyzing a publicly available cancer dataset with more than 20 000 participants distributed across approximately 400 families.Availability and implementation: The FamAgg package is freely available at the Bioconductor repository, http://www.bioconductor.org/packages/FamAgg.Contact: Christian.Weichenberger@eurac.eduSupplementary information: Supplementary data are available at Bioinformatics online.
The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
Authors: Barquist Lars , Mayho Matthew , Cummins Carla , Cain Amy K. , Boinett Christine J. , Page Andrew J. , Langridge Gemma C. , Quail Michael A. , Keane Jacqueline A. , Parkhill Julian 
Published: February 2016

Abstract
Summary: Transposon insertion sequencing is a high-throughput technique for assaying large libraries of otherwise isogenic transposon mutants providing insight into gene essentiality, gene function and genetic interactions. We previously developed the Transposon Directed Insertion Sequencing (TraDIS) protocol for this purpose, which utilizes shearing of genomic DNA followed by specific PCR amplification of transposon-containing fragments and Illumina sequencing. Here we describe an optimized high-yield library preparation and sequencing protocol for TraDIS experiments and a novel software pipeline for analysis of the resulting data. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. This article can serve as a general reference for the application of the TraDIS methodology.
Availability and implementation: The optimized sequencing protocol is included as supplementary information. The Bio-Tradis analysis pipeline is available under a GPL license at https://github.com/sanger-pathogens/Bio-Tradis
Contact: parkhill@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.