bluuebunny/crossref_metadata_2025 huggingface dataset:
Peptide Spectrum Matching via Database Search and Spectral Library Search
Authors: Netzel Brian , Dasari Surendra
Published: November 2016

High-throughput shotgun proteomics is the mainstay of protein identification in biological samples. Efficient proteomic analysis requires streamlined and accurate workflows for protein identification. Database searching has been the most basic and reliable workflow for identifying the peptides and proteins that are present in the sample. This method derives peptides from a list of protein sequences and matches them against the experimental MS2 spectra. The resulting peptide spectrum matches are scored to quantify their goodness of fit. Spectral library searching has been recently developed as a fast, and viable, alternative to sequence database searching. This method attempts to identify the peptides by matching their corresponding experimental MS2 spectra to a library of curated MS2 peptide spectra. Each method has its own merit and application in the proteomics field. This chapter aims to highlight the foundations of peptide spectrum matching via protein sequence database and spectral library searching.
PSM Scoring and Validation
Authors: Wright James C. , Choudhary Jyoti S.
Published: November 2016

Identification and quantification of proteins by shotgun proteomics experiments is underpinned by the use of accurate masses and fragmentation patterns generated by tandem mass spectrometry. Assigning peptide sequences to tandem MS data is supported by a plethora of informatics tools. The majority of spectral identification software report arbitrary fitness scores reflecting the quality of a match, however, valid statistical metrics must be used to make sense of these scores and attribute a confidence to the peptide identifications. Accurately estimating the error and devising filtering routines to minimise incorrect and random identifications is essential for making valid and reproducible conclusions about the biology of the sample being analysed. This chapter discusses the statistical approaches used to evaluate and validate shotgun proteomics peptide to spectrum matches and provides a summary of software available for this purpose.
Protein Inference and Grouping
Authors: Jones Andrew R.
Published: November 2016

A key process in many proteomics workflows is the identification of proteins, following analysis of tandem MS (MS/MS) spectra, for example by a database search. The core unit of identification from a database search is the identification of peptides, yet most researchers wish to know which proteins have been confidently identified in their samples. As such, following peptide identification, a second stage of data analysis is performed, either internally in the search engine or in a second package, called protein inference. Protein inference is challenging in the common case that proteins have been digested into peptides early in the proteomics workflow, and thus there is no direct link between a peptide and its parent protein. Many peptides could theoretically have been derived from more than one protein in the database searched, and thus it is not straightforward to determine which is the correct assignment. A variety of algorithms and implementations have been developed, which are reviewed in this chapter. Most approaches now report “protein groups” as a the core unit of identification from protein inference, since it is common for more than one database protein to share the same-set of evidence, and thus be indistinguishable. The chapter also describes scoring and statistical values that can be assigned during the protein identification process, to give confidence in the resulting values.
Identification and Localization of Post-Translational Modifications by High-Resolution Mass Spectrometry
Authors: Matthiesen Rune , Carvalho Ana Sofia
Published: November 2016

Cells either in response to stimulus or in homeostasis require dynamic signaling through alterations in protein composition. Identification and temporospatial profiling of post translational modifications constitutes one of the most challenging tasks in biology. These challenges comprise both experimental and computational aspects. From the computational point of view identification of post translational modifications by mass spectrometry analysis frequently leads to algorithms with exponential complexity which in practice is approached by algorithms with lower complexity. Regulation of post translational modifications has been implicated in a number of diseases such as cancer, neurodegenerative diseases and metabolic diseases. Furthermore, some post translational modifications are considered as biomarkers and surrogate markers. Consequently, there is a high interest in methodologies that can identify and quantify post translational modifications. We found few papers addressing the issue of which modifications should be considered in a standard database dependent search of MS data for protein analysis. Furthermore, the few papers on the topic are from a time where MS instruments with high precision in both MS and MS/MS were not available. Therefore, based on literature search and extensive analysis we provide recommendations on post translational modifications to be included in mass spectrometry database searches of MS data with high precision in both MS and MS/MS (e.g. <5 ppm).
Data Analysis for Data Independent Acquisition
Authors: Navarro Pedro , Trevisan-Herraz Marco , Röst Hannes L.
Published: November 2016

Mass spectrometry-based proteomics using soft ionization techniques has been used successfully to identify large numbers of proteins from complex biological samples. However, reproducible quantification across a large number of samples is still highly challenging with commonly used “shotgun proteomics” which uses stochastic sampling of the peptide analytes (data dependent acquisition; DDA) to analyze samples. Recently, data independent acquisition (DIA) methods have been investigated for their potential for reproducible protein quantification, since they deterministically sample all peptide analytes in every single run. This increases reproducibility and sensitivity, reduces the number of missing values and removes stochasticity from the acquisition process. However, one of the major challenges for wider adoption of DIA has been data analysis. In this chapter we will introduce the five most well-known of these techniques, as well as their data analysis methods, classified either as targeted or untargeted; then, we will discuss briefly the meaning of the false discovery rate (FDR) in DIA experiments, to finally close the chapter with a review of the current challenges in this subject.
OpenMS: A Modular, Open-Source Workflow System for the Analysis of Quantitative Proteomics Data
Authors: Nilse Lars
Published: November 2016

OpenMS is a software framework for the analysis and visualisation of proteomics data. It consists of over 100 individual tools which can be combined to simple or more complex analysis workflows. The tools are based on a well-documented, open-source C++ library that can also be accessed via a Python interface. Besides these tools, OpenMS provides wrappers for many popular external software solutions such as search engines and protein inference algorithms. The workflows can be run on simple desktop computers as well as powerful computing clusters. In this chapter, we will discuss four workflows of increasing complexity and thereby introduce new users to the basic concepts of OpenMS.
Proteogenomics: Proteomics for Genome Annotation
Authors: Ghali Fawaz , Jones Andrew R.
Published: November 2016

One of major bottlenecks in omics biology is the generation of accurate gene models, including correct calling of the start codon, splicing of introns (taking account of alternative splicing), and the stop codon – collectively called genome annotation. Current genome annotation approaches for newly sequenced genomes are generally based on automated or semi-automated methods, usually involving gene finding software to look for intrinsic gene-like signatures (motifs) in the DNA sequence, the propagation of annotations from other (more well annotated) related species, and the mapping of experimental data sets, particularly from RNA Sequencing (RNA-Seq). Large scale proteomics data can also play an important role for confirming and correcting gene models. While proteomics approaches tend not to have the same level of sensitivity as RNA-Seq, they have the advantage that they can provide evidence that a predicted gene/transcript is indeed protein-coding. The use of proteomics data for genome annotation is called proteogenomics, and forms the basis for this chapter. We describe the theoretical underpinnings, different software packages that have been developed for proteogenomics, statistical approaches for validating the evidence, and support for proteogenomics data in file formats, standards and databases.
Proteomics Informed by Transcriptomics
Authors: Saha Shyamasree , Matthews David , Bessant Conrad
Published: November 2016

The choice of protein sequence database used for peptide spectrum matching has a major impact on the extent and significance of protein identifications obtained in a given experiment. Finding a suitable database can be a major challenge, particularly when working with non-model organisms and complex samples containing proteins from multiple species. This chapter introduces the proteomics informed by transcriptomics (PIT) methodology, in which RNA-seq transcriptomics is used to generate a sample-specific protein database against which proteomic mass spectra can be searched. This approach extends the application of proteomics to studies in which it was not previously tractable, and is well suited to the discovery of novel translated genomic elements.
A protocol for rapid, label-free histochemical imaging of fibrotic liver
Authors: Bird B. , Rowlette J.
Published: November 2016

Mid-infrared microscopy is a non-destructive, quantitative and label-free spectroscopic imaging technique that, as a result of recent instrument advancements, is now at the point of enabling high-throughput automated biochemical screening of whole histology samples.
Characteristics of chemical bonding of pentavalent uranium in La-doped UO2
Authors: Butorin Sergei M. , Kvashnina Kristina O. , Prieur Damien , Rivenet Murielle , Martin Philippe M.
Published: November 2016

HERFD-XAS studies clearly reveal U(v) formation in the cubic environment in UO2as a result of La doping.
Enhanced visible light photocatalysis over Pt-loaded Bi2O3: an insight into its photogenerated charge separation, transfer and capture
Authors: Yang Kailun , Li Jia , Peng Yang , Lin Jun
Published: November 2016

Crystalline metallic Pt nanoparticles loaded on Bi2O3 promote the efficient separation of photogenerated electron–hole pairs by rapidly transferring electrons to the surface oxygen to form H2O2, leaving holes on the valence band to drive the degradation of organic compounds and the production of ˙OH radicals.
Dipolar molecules inside C70: an electric field-driven room-temperature single-molecule switch
Authors: Foroutan-Nejad Cina , Andrushchenko Valery , Straka Michal
Published: November 2016

A dipolar molecule enclosed inside C70 works as a single-molecule switch driven by an external electric field.
Bioisosteric ferrocenyl-containing quinolines with antiplasmodial and antitrichomonal properties
Authors: Adams Muneebah , Stringer Tameryn , de Kock Carmen , Smith Peter J. , Land Kirkwood M. , Liu Nicole , Tam Christina , Cheng Luisa W. , Njoroge Mathew , Chibale Kelly , Smith Gregory S.
Published: November 2016

Bioisosteric (C, Si) ferrocenyl-containing quinolines and ferrocenylamines were prepared and evaluated as antiplasmodial and antitrichomonal agents.
Syntheses, photoluminescence and electroluminescence of two novel platinum(ii) complexes
Authors: Lu Guang-Zhao , Li Yan , Jing Yi-Ming , Zheng You-Xuan
Published: November 2016

Highly efficient green OLEDs based on two platinum complexes showed a peak current efficiency of 48.3 cd A−1 with low efficiency roll-off; and even at a brightness of 1000 cd m−2, a current efficiency of 47.0 cd A−1 could still be obtained.
Gotta catch ‘em all: the microscale quest to understand cancer biology
Authors: Ma Zhenwei , Moraes Christopher
Published: November 2016

We highlight recent advances in the innovative use of microscale engineered technologies to gain new insight into the integrative biophysical mechanisms that drive cancer initiation and progression.
Growth of centimeter-sized [(CH3)2NH2][Mn(HCOO)3] hybrid formate perovskite single crystals and Raman evidence of pressure-induced phase transitions
Authors: Xin Lipeng , Fan Zhen , Li Guanghui , Zhang Ming , Han Yonghao , Wang John , Ong Khuong P. , Qin Lei , Zheng Yanzhen , Lou Xiaojie
Published: November 2016

The fewer the number of the nucleation sites formed in the vessel, the larger the size of the obtained crystals.
Which fullerenols are water soluble? Systematic atomistic investigation
Authors: Chaban Vitaly V. , Fileti Eudes Eterno
Published: November 2016

Insights to guide a choice of most soluble fullerenols.
Synthesis, crystal structure and spectroscopic studies of a series of hexavanadate hybrids with multiple functional groups
Authors: Huang Bo , Xiao Zicheng , Wu Baolin , Hu Xiaokang , Hu Xunliang , Wu Pingfan , Wei Yongge
Published: November 2016

POV hybrids incorporated with the CC double bond can be prepared with DMAP-catalyzed esterification for the first time.
Syntheses, structures, and properties of sulfides constructed by SbS4teeter-totter polyhedra: Ba3La4Ga2Sb2S15and BaLa3GaSb2S10
Authors: Duan Rui-Huan , Shen Jin-Ni , Lin Chen-Sheng , Liu Peng-Fei , Lin Hua , Huang-Fu Shang-Xiong , Zhao Hua-Jun , Khan Muhammad Ali , Chen Ling
Published: November 2016

Two new pentanary sulfides Ba3La4Ga2Sb2S15(1) and BaLa3GaSb2S10(2) have been discovered.
In situ SERS monitored photoactive yellow protein (PYP) chromophore model elimination, nano-catalyzed phenyl redox and I2 addition reactions
Authors: Li Wei , Chu Wenlei , Jin Wen , Han Xijiang , Ma Yufei , Dai Bin , Xu Ping , Liang Yuwei , Chen Dengtai
Published: November 2016

PhS nitration products absorbed on Ag/Au NPs underwent nitro- and amino-group redox cycle reactions monitored using SERS spectra. I2 addition to the CC double bond was also confirmed with SERS.
Active bioparticle manipulation in microfluidic systems
Authors: Md Ali Mohd Anuar , Ostrikov Kostya (Ken) , Khalid Fararishah Abdul , Majlis Burhanuddin Y. , Kayani Aminuddin A.
Published: November 2016

The motion of bioparticles in a microfluidic environment can be actively controlled using several tuneable mechanisms, including hydrodynamic, electrophoresis, dielectrophoresis, magnetophoresis, acoustophoresis, thermophoresis and optical forces.
Triester–amide based on thiophene and ricinoleic acid as an innovative primary plasticizer for poly(vinyl chloride)
Authors: Satavalekar Sneha D. , Savvashe Prashant B. , Mhaske Shashank T.
Published: November 2016

The synthesized triester amide (THPRABA) gives an alternative to the phthalate plasticizers.
Luminescence properties of a Zn(ii) supramolecular framework: easily tunable optical properties by variation of the alkyl substitution of (E)-N-(pyridine-2-ylethylidyne)arylamine ligands
Authors: Dong Yu-Wei , Fan Rui-Qing , Chen Wei , Zhang Hui-Jie , Song Yang , Du Xi , Wang Ping , Wei Li-Guo , Yang Yu-Lin
Published: November 2016

The easily tunable luminescence properties of Zn(ii) complexes based on the different alkyl substituents of the Schiff-base ligand have been studied in detail.
A potentiostatic approach of growing polyaniline nanofibers in fractal morphology by interfacial electropolymerization
Authors: Gupta Rajeev , Singhal Monika , Nataraj Sanna Kotrappanavar , Srivastava Divesh N.
Published: November 2016

Potentiostatically electropolymerized polyaniline fractals at platinum foil through organic/aqueous interface.
Synthesis of LaNiO3perovskite using an EDTA-cellulose method and comparison with the conventional Pechini method: application to steam CO2reforming of methane
Authors: Yang Eun-hyeok , Moon Dong Ju
Published: November 2016

LaNiO3type perovskite was synthesized by two different methods, and characterized by various techniques such asin situandex situXRD, TPR, N2physisorption, CO chemisorption, TGA, FT-IR, XPS, TPH, TPSR and TEM-EDS.
Synthesis and application of ternary photocatalyst with a gradient band structure from two-dimensional nanosheets as precursors
Authors: Zhou Chenjuan , Yan Jing , Chen Binhe , Li Peiran , Dong Xiaoping , Xi Fengna , Liu Jiyang
Published: November 2016

A ternary photocatalyst (CNNS/CdS/rGO) with a gradient band structure exhibited prominent photocatalytic performance under visible light irradiation.
Star-shape paclitaxel prodrug self-assembled nanomedicine: combining high drug loading and enhanced cytotoxicity
Authors: Jiang Mengjuan , Han Xiangfei , Guo Weiling , Li Wei , Chen Jinling , Ren Guolian , Sun Bingjun , Wang Yongjun , He Zhonggui
Published: November 2016

Star-shape paclitaxel prodrugs self-assembled nanoparticles combining high drug loading and enhanced cytotoxicity.
Correlation of the stoichiometries of poly(ε-caprolactone) and α-cyclodextrin pseudorotaxanes with their solution rheology and the molecular orientation, crystallite size, and thermomechanical properties of their nanofibers
Authors: Narayanan Ganesh , Chung Ching-Chang , Aguda Remil , Boy Ramiz , Hartman Matthew , Mehraban Nahid , Gupta Bhupender S. , Tonelli Alan E.
Published: November 2016

Pseudorotaxane nanofibers based on biomedical polymers, such as poly(ε-caprolactone) (PCL), and α-cyclodextrins (α-CD) open new horizons for a variety of biomedical applications.
Synthesis of ZnO nano-powders via a novel PVA-assisted freeze-drying process
Authors: Liu Bolin , You Yangguang , Zhang Haifei , Wu Hao , Jin Junsu , Liu Hongtao
Published: November 2016

ZnO nano-powder samples obtained by a novel PVA-assisted freeze-drying process with different PVA/Zn(NO3)2·6H2O mass ratios.
Integration of TiO2 photoanode and perovskite solar cell for overall solar-driven water splitting
Authors: Sun Bo , Shi Tielin , Liu Zhiyong , Tang Zirong , Zhou Jianxin , Liao Guanglan
Published: November 2016

Fully integrated device based on TiO2 photoanode and perovskite solar cell for overall solar-driven water splitting.
Electrical anisotropy and multidimensional pressure sensor of aligned Fe3O4@silver nanowire/polyaniline composite films under an extremely low magnetic field
Authors: Fang Fang , Li Yuan-Qing , Huang Gui-Wen , Xiao Hong-Mei , Feng Qing-Ping , Hu Ning , Fu Shao-Yun
Published: November 2016

The PDMS sealed aligned Ag nanowire/PANI composite film as a multi-dimensional pressure sensor.
In situ preparation of Ca0.5Mn0.5O/C as a novel high-activity catalyst for the oxygen reduction reaction
Authors: Lyu Yu-Qi , Chen Chi , Gao Yang , Saccoccio Mattia , Ciucci Francesco
Published: November 2016

Ca-substituted rock-salt MnO/C (Ca0.5Mn0.5O/C) is prepared using an in situ approach and shows enhanced activity for the oxygen reduction reaction (ORR).
Development of ionic strength/pH/enzyme triple-responsive zwitterionic hydrogel of the mixed l-glutamic acid and l-lysine polypeptide for site-specific drug delivery
Authors: Ma Guanglong , Lin Weifeng , Yuan Zhefan , Wu Jiang , Qian Haofeng , Xu Liangbo , Chen Shengfu
Published: November 2016

Environmentally responsive hydrogels for drug delivery.
A ratiometric nanoprobe consisting of up-conversion nanoparticles functionalized with cobalt oxyhydroxide for detecting and imaging ascorbic acid
Authors: Han Qingxin , Dong Zhe , Tang Xiaoliang , Wang Li , Ju Zhenghua , Liu Weisheng
Published: November 2016

A new ratiometric probe based on up-conversion nanoparticles displayed excellent selectivity and pronounced sensitivity in the detection of ascorbic acid.
Quantum spin Hall phase in Mo2M2C3O2(M = Ti, Zr, Hf) MXenes
Authors: Si Chen , You Jinxuan , Shi Wujun , Zhou Jian , Sun Zhimei
Published: November 2016

A new family of quantum spin Hall materials characterized by topologically protected helical edge states are predicted in Mo2MC2O3(M = Ti, Zr, Hf) MXenes.
Shared Responsibilities for Full Participation in Society: Planning Further Integration of the ICF Into AAC
Authors: Huer Mary Blake , Threats Travis T.
Published: November 2016

The World Health Organization's (WHO's) 2001 International Classification of Functioning Disability and Health (ICF) has as one of its central tenets the full inclusion of persons with disabilities in society. It acknowledges the need for medical and rehabilitation intervention in its biopscychosocial framework. However, the WHO realizes that society must do its part to facilitate this full participation and empowerment. Persons with complex communication needs (PWCCN) often need augmentative and alternative communication (AAC) in order to express themselves. However, in order to access and successfully use AAC, PWCCN need access to the necessary AAC devices and services, as well as a willing society to interact with them as full contributing members of society. The factors outside of a person's specific physical and/or cognitive functional limitations are addressed in the ICF via the Personal and Environmental Factors. Personal Factors include the individual's personality traits, lifestyle, experiences, social/educational/professional background, race, gender, and age. Environmental Factors include community support systems, social service agencies, governments, social networks, and those persons that interact with the PWCCN. This article addresses the sociopolitical influences on PWCCN and their functioning from a human rights perspective. The necessary introspective role of speech-language pathologists in this process is explored.
The Limited Resource View of Self-regulation: Implications for Vocal Behavior Change
Authors: Vinney Lisa A.
Published: November 2016

Successful self-regulation is likely an important construct underlying the learning of new vocal behaviors and lasting vocal behavior change. In this short survey article, review of established and emerging understanding of self-regulatory phenomena, in general and in relationship to vocal behavior, will be discussed. Potential future research avenues, integrating self-regulation experimental paradigms, and the ways in which they may inform and improve voice therapy practice and outcomes will also be highlighted.
Security‐oriented distributed access selection for D2D underlaying cellular networks
Authors: Kang Xiaolei , Ji Xinsheng , Huang Kaizhi , Li Xiangyu
Published: November 2016

In device‐to‐device (D2D) underlaying cellular networks, interference generated by D2D communications can be exploited to improve secrecy rate of cellular users (CUE). The security‐oriented distributed access selection algorithm is proposed, in which each D2D pair decides whether to access to radio resources according to its local channel state information without considering the locations of D2D pairs and Eve. The ergodic secrecy rate of CUE and the data rate of D2D pairs in the proposed scheme are investigated. Simulation results show that the proposed scheme can achieve an impressive secrecy performance gain.
Dual CDS scheme embedded in SAR‐based ADCs for low‐noise CMOS imagers without a PGA
Authors: Kim M.‐K. , Hong S.‐K. , Gou J. , Kwon O.‐K.
Published: November 2016

A dual correlated double sampling (CDS) scheme, which can be embedded into a successive approximation register (SAR) or SAR/single‐slope analogue‐to‐digital converters (ADCs) for low‐noise CMOS imagers without the use of a power‐consuming programmable gain amplifier (PGA) is proposed. To reduce the noise of the readout channel, the proposed dual CDS scheme removes the sampling error, which occurs in the capacitor digital‐to‐analogue converter (DAC), by storing only a reset voltage of the pixel into the capacitor DAC. In addition, without using the PGA, it amplifies the output of the readout channel by controlling the reference voltages of the ADC. The readout channel using the proposed CDS scheme was designed using a 90 nm CMOS imager process technology. The simulation results show that the signal‐to‐noise‐distortion ratio of the readout channel using the proposed dual CDS scheme is 81.8 dB, which is an improvement of 10.8 dB over the digital CDS scheme. In addition, the output of the readout channel is amplified without the use of a PGA.
Cyber‐physical attacks and defences in the smart grid: a survey
Authors: He Haibo , Yan Jun
Published: November 2016

The smart grid is arguably one of the most complex cyber‐physical systems (CPS). Complex security challenges have been revealed in both the physical and the cyber parts of the smart grid, and an integrative analysis on the cyber‐physical (CP) security is emerging. This paper provides a comprehensive and systematic review of the critical attack threats and defence strategies in the smart grid. We start this survey with an overview of the smart grid security from the CP perspective, and then focuses on prominent CP attack schemes with significant impact on the smart grid operation and corresponding defense solutions. With an in‐depth review of the attacks and defences, we then discuss the opportunities and challenges along the smart grid CP security. We hope this paper raises awareness of the CP attack threats and defence strategies in complex CPS‐based infrastructures such as the smart grid and inspires research effort toward the development of secure and resilient CP infrastructures.
Optimal WDG planning in active distribution networks based on possibilistic–probabilistic PEVs load modelling
Authors: Ahmadian Ali , Sedghi Mahdi , Elkamel Ali , Aliakbar‐Golkar Masoud , Fowler Michael
Published: November 2016

Distribution network operators and planners usually model the load demand of plug‐in electric vehicles (PEVs) to evaluate their effects on operation and planning procedures. Increasing the PEVs’ load modelling accuracy leads to more precise and reliable operation and planning approaches. This study presents a methodology for possibilistic–probabilistic‐based PEVs’ load modelling in order to be employed in optimal wind distributed generation (WDG) planning. The proposed methodology considers not only the PEVs temporal uncertainty, but also the uncertain spatial effect of PEVs on WDGs as renewable‐based distributed resources. The WDG planning is considered as an optimisation problem which is solved under technical and economic constraints. A hybrid modified particle swarm optimisation/genetic algorithm is proposed for optimisation that is more robust than the conventional algorithms. The effectiveness of the proposed load modelling of PEVs and the proposed algorithm is evaluated in several scenarios.
Research on the fault diagnosis method for slip ring device in doubly‐fed induction generators based on vibration
Authors: Ma Hongzhong , Chen Taotao , Zhang Yan , Ju Ping , Chen Zhenfei
Published: November 2016

The brush and slip ring system is an important part of excitation system in doubly‐fed induction generators, but the excitation instability caused by the surface damage of slip ring often occurs, which brings a great security trouble to the stable operation in the generator. To solve this problem, the method that the vibration signal is used to carry out diagnosis of slip ring surface in different fault states was proposed. First, the principle based on vibration, the transmission route and failure mechanism of the slip ring were analysed. Then, the experiment platform of the brush and slip ring was set up; the real‐time vibration signal was collected before and after fault; the wavelet energy spectrum was applied to the vibration signal processing. The abnormal vibration band was found by the contrast and proportion analysis of the wavelet energy spectrum distribution of vibration signals before and after fault, which can be the basis for fault diagnosis of the slip ring device.
Cretaceous fire in Australia: a review with new geochemical evidence, and relevance to the rise of the angiosperms
Authors: Carpenter Raymond J. , Holman Alexander I. , Abell Andrew D. , Grice Kliti
Published: November 2016

Much of the Australian flora has high flammability. It is therefore of interest whether burning was a feature in the Cretaceous, the geological period in which angiosperms rose to dominance, and in which fossil and molecular evidence suggests the presence of lineages now prominent in regularly burnt habitats. Determining the extent of fire in the Australian Cretaceous is limited by a paucity of surface exposures of strata, and of published reports of definite charcoal from exploration cores. Nevertheless, charcoalified tissues occur much more widely than is currently reported in the international literature, and there are also numerous references to inertinite macerals in Australian Cretaceous coals. Combustion-related hydrocarbons can also be detected in ancient sediments using organic geochemical methods, and we demonstrate the potential of this approach here. Overall, the available evidence is in concert with that from elsewhere on Earth: fire was apparently widespread in the Australian Cretaceous, and can reasonably be invoked as a force that influenced the evolution of modern Australian environments. Just as in extant open, nutrient-limited regions, proteaceous lineages seem to have been important in burnt, open habitats in the Late Cretaceous, perhaps retaining dominance of such niches for >70 million years. However, there is so far no fossil evidence for the Cretaceous presence of Eucalyptus, the principal tree genus of modern Australian fire-prone vegetation.
Aptamer-Based Fluorescent Switch for Sensitive Detection of Oxytetracycline
Authors: Babaei Mahsa , Jalalian Seyed Hamid , Bakhtiari Hadi , Ramezani Mohammad , Abnous Khalil , Taghdisi Seyed Mohammad
Published: November 2016

Oxytetracycline (OTC) is one of the most used antibiotics in veterinary medicine. There is a large concern about developing antibiotic resistance in humans as a result of the consumption of products contaminated with OTC, so a fast detection technique for an on-field screening test is highly in demand. Here we introduce a novel aptasensor for fast detection of OTC, based on a triple helix molecular switch (THMS) complex formation. The limit of detection (LOD) of this sensor was 1.67 and 6.44 nM in phosphate buffer and milk samples, respectively. Moreover, the sensor showed a high selectivity towards OTC.
Yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double-stranded RNA
Authors: Samuel Glady Hazitha , Wiley Michael R. , Badawi Atif , Adelman Zach N. , Myles Kevin M.
Published: November 2016

Significance

Until it was demonstrated that the
Aedes aegypti
mosquito transmitted yellow fever, the disease was possibly the most feared pestilence in the western hemisphere. This finding, by Walter Reed’s Yellow Fever Commission, is credited with eradication of the disease in many areas, through sanitation programs designed to eliminate the vector. Since this discovery, the mosquito has been widely believed to be complicit in the transmission of viral diseases, earning the enmity of humans everywhere. However, we show here that yellow fever virus encodes a protein that blocks the mosquito’s immune response, suggesting the pathogen’s continued existence in nature depends on staying one step ahead of the vector’s antiviral defense.
Global patterns of kelp forest change over the past half-century
Authors: Krumhansl Kira A. , Okamoto Daniel K. , Rassweiler Andrew , Novak Mark , Bolton John J. , Cavanaugh Kyle C. , Connell Sean D. , Johnson Craig R. , Konar Brenda , Ling Scott D. , Micheli Fiorenza , Norderhaug Kjell M. , Pérez-Matus Alejandro , Sousa-Pinto Isabel , Reed Daniel C. , Salomon Anne K. , Shears Nick T. , Wernberg Thomas , Anderson Robert J. , Barrett Nevell S. , Buschmann Alejandro H. , Carr Mark H. , Caselle Jennifer E. , Derrien-Courtel Sandrine , Edgar Graham J. , Edwards Matt , Estes James A. , Goodwin Claire , Kenner Michael C. , Kushner David J. , Moy Frithjof E. , Nunn Julia , Steneck Robert S. , Vásquez Julio , Watson Jane , Witman Jon D. , Byrnes Jarrett E. K.
Published: November 2016

Significance

Kelp forests support diverse and productive ecological communities throughout temperate and arctic regions worldwide, providing numerous ecosystem services to humans. Literature suggests that kelp forests are increasingly threatened by a variety of human impacts, including climate change, overfishing, and direct harvest. We provide the first globally comprehensive analysis of kelp forest change over the past 50 y, identifying a high degree of variation in the magnitude and direction of change across the geographic range of kelps. These results suggest region-specific responses to global change, with local drivers playing an important role in driving patterns of kelp abundance. Increased monitoring aimed at understanding regional kelp forest dynamics is likely to prove most effective for the adaptive management of these important ecosystems.
Socioecological transitions trigger fire regime shifts and modulate fire–climate interactions in the Sierra Nevada, USA, 1600–2015 CE
Authors: Taylor Alan H. , Trouet Valerie , Skinner Carl N. , Stephens Scott
Published: November 2016

Significance

Twenty-first–century climate change is projected to increase fire activity in California, but predictions are uncertain because humans can amplify or buffer fire–climate relationships. We combined a tree-ring–based fire history with 20th-century area burned data to show that large fire regime shifts during the past 415 y corresponded with socioecological change, and not climate variability. Climate amplified large-scale fire activity after Native American depopulation reduced the buffering effect of Native American burns on fire spread. Later Euro-American settlement and fire suppression buffered fire activity from long-term temperature increases. Our findings highlight a need to enhance our understanding of human–fire interactions to improve the skill of future projections of fire driven by climate change.
Long-term empirical evidence of ocean warming leading to tropicalization of fish communities, increased herbivory, and loss of kelp
Authors: Vergés Adriana , Doropoulos Christopher , Malcolm Hamish A. , Skye Mathew , Garcia-Pizá Marina , Marzinelli Ezequiel M. , Campbell Alexandra H. , Ballesteros Enric , Hoey Andrew S. , Vila-Concejo Ana , Bozec Yves-Marie , Steinberg Peter D.
Published: November 2016

Significance

Most studies of the impact of global warming focus on the direct physiological impacts of climate change. However, global warming is shifting the distribution of many species and leading to novel interactions between previously separated species that have the potential to transform entire ecological communities. This study shows that an increase in the proportion of warmwater species (“tropicalization”) as oceans warm is increasing fish herbivory in kelp forests, contributing to their decline and subsequent persistence in alternate “kelp-free” states. These tropical and subtropical herbivores are increasingly impacting temperate algal communities worldwide, posing a significant threat to the long-term stability of these iconic ecosystems and the valuable services they provide.
Synergistic reaction of silver nitrate, silver nanoparticles, and methylene blue against bacteria
Authors: Li Runze , Chen Jie , Cesario Thomas C. , Wang Xin , Yuan Joshua S. , Rentzepis Peter M.
Published: November 2016

Significance

Bacteria are increasingly becoming resistant to antibiotics; therefore, other means must be found for their inactivation. Efficient inactivation of bacteria cannot be achieved simply by increasing the dose because of toxicity limitation. Therefore, it is critical to search for a combination of agents, within a safe dose, that is more effective in killing bacteria than agents reacting alone. Here, we show that the combination of methylene blue (MB) and silver nitrate can be up to three orders of magnitude more effective in killing bacteria than the two agents reacting alone against bacteria. This synergistic mechanism is due to silver ion increasing the penetration of MB into the bacteria interior, allowing photogenerated single oxygen to react with DNA and prevent replication.
Notch1 controls development of the extravillous trophoblast lineage in the human placenta
Authors: Haider Sandra , Meinhardt Gudrun , Saleh Leila , Fiala Christian , Pollheimer Jürgen , Knöfler Martin
Published: November 2016

Significance

Progenitor trophoblast cells of the human placenta either fuse to form a syncytium or develop into invasive trophoblasts invading the maternal uterus. However, regulatory pathways controlling their development and distinct differentiation programs are poorly understood. In the present study, we demonstrate that Notch1 is a critical regulator of early pregnancy, promoting development of the invasive, extravillous trophoblast lineage and survival of its progenitors. In vivo, Notch1 is detected in extravillous trophoblast progenitors and clusters of villous trophoblast initiating the invasive differentiation program. In vitro, Notch1 repressed genes involved in self-renewal of fusogenic precursors, but induced genes specifically expressed by extravillous trophoblast progenitors. Our data delineate Notch1 as a key regulator promoting development of the human extravillous trophoblast lineage.
Plant nodulation inducers enhance horizontal gene transfer of
Azorhizobium caulinodans
symbiosis island
Authors: Ling Jun , Wang Hui , Wu Ping , Li Tao , Tang Yu , Naseer Nawar , Zheng Huiming , Masson-Boivin Catherine , Zhong Zengtao , Zhu Jun
Published: November 2016

Significance

Pathogenic or symbiosis islands are mobile genetic elements that can provide recipient bacteria the capacity to establish intimate interactions with eukaryotic hosts. For example, legume symbionts have evolved via horizontal transfer of symbiotic plasmids or genomic islands. Here, we show that the transfer of the symbiosis island of the
Sesbania rostrata
symbiont,
Azorhizobium caulinodans
, to other rhizobia is enhanced by plant flavonoids that also serve as signals to initiate the symbiotic process. These data suggest that eukaryotic hosts are involved in bacterial horizontal gene transfer to promote symbiotic interactions between rhizobia and legumes.
Nanoparticle engineered TRAIL-overexpressing adipose-derived stem cells target and eradicate glioblastoma via intracranial delivery
Authors: Jiang Xinyi , Fitch Sergio , Wang Christine , Wilson Christy , Li Jianfeng , Grant Gerald A. , Yang Fan
Published: November 2016

Significance

Current treatment for glioblastoma multiforme (GBM) fails to address its highly infiltrative nature; treatment often leaves behind microscopic neoplastic satellites, resulting in eventual tumor recurrence. Here we report polymeric nanoparticle-engineered human adipose-derived stem cells (hADSCs) overexpressing the cancer-specific TNF-related apoptosis-inducing ligand for targeting and eradicating glioblastoma cells. Engineered hADSCs exhibited long-range directional migration toward tumor in patient-derived GBM orthotropic xenografts and showed significant inhibition of tumor growth and extension of animal survival. Repetitive injection further prolonged animal survival compared with single injection. Together, our data suggest that nanoparticle-engineered hADSCs exhibit the therapeutically relevant behavior of “seek-and-destroy” tumortropic migration, and may offer a promising therapy for substantial enhancement of GBM treatment.
Atomic determinants of BK channel activation by polyunsaturated fatty acids
Authors: Tian Yutao , Aursnes Marius , Hansen Trond Vidar , Tungen Jørn Eivind , Galpin Jason D. , Leisle Lilia , Ahern Christopher A. , Xu Rong , Heinemann Stefan H. , Hoshi Toshinori
Published: November 2016

Significance

Polyunsaturated ω-3 fatty acids such as docosahexaenoic acid (DHA) are found abundantly in fish oil. Potential health benefits of these fatty acids continue to draw public interest; however, mechanistic information on how the fatty acids regulate their specific molecular targets is only beginning to be elucidated. One of the high-affinity targets of DHA is the large-conductance Ca
2+
- and voltage-gated Slo1 K
+
channel important in exerting a negative feedback influence on cell excitability. Here, we have manipulated the structures of the channel and DHA and defined the detailed atomic principles underling the activating effect of DHA on the channel. Our findings could lead to discovery and development of fatty-acid–based therapeutics targeting Slo1 K
+
channels.
Relationship Between Cesarean Delivery Rate and Maternal and Neonatal Mortality
Authors: Molina George , Weiser Thomas G. , Lipsitz Stuart R. , Esquivel Micaela M. , Uribe-Leitz Tarsicio , Azad Tej , Shah Neel , Semrau Katherine , Berry William R. , Gawande Atul A. , Haynes Alex B.
Published: November 2016

(JAMA 2015;314(21):2263–2270)

Cesarean deliveries can be lifesaving for women with obstructed labor and other emergency conditions. As per the World Health Organization (WHO) recommendation, cesarean delivery rates should not exceed 10% to 15% of deliveries. However, actual rates are higher in many countries. The aim of this study was to provide better estimates of the contemporary relationship between national cesarean delivery rates and neonatal and maternal mortality.
Pharmacokinetics and Pharmacodynamics of Drugs Commonly Used in Pregnancy and Parturition
Authors: Ansari Jessica , Carvalho Breandan , Shafer Steven L. , Flood Pamela
Published: November 2016

(Anesth Analg 2016;122:786–804)

There is a lack of pharmacokinetic and pharmacodynamic studies in parturients. In addition, while current regulations require such studies to be conducted in women of childbearing potential, very few medications have been studied in the setting of pregnancy, with most drugs being used off-label. As such, there are inadequate data for physicians and patients to make informed decisions regarding drug use during pregnancy and lactation. In this review, the authors discussed known alterations in drug pharmacokinetics and pharmacodynamics that occur during pregnancy as well as the impact of acute changes in physiology during childbirth.
In Vitro Comparative Effect of Carbetocin and Oxytocin in Pregnant Human Myometrium With and Without Oxytocin Pretreatment
Authors: Cole N.M. , Carvalho J.C. , Erik-Soussi M. , Ramachandran N. , Balki M.
Published: November 2016

(Anesthesiology 2016;124:378–386)

Oxytocin remains the first-line uterotonic agent for the prevention and treatment of postpartum hemorrhage (PPH) secondary to uterine atony, but its routine use has limitations that include many side effects. Hence there is a search for newer agents for the prevention of PPH with greater efficacy and fewer side effects. The objective of this study was to compare the effects of oxytocin and carbetocin in human term pregnant myometrium in vitro, with and without oxytocin pretreatment.
Checklists and Multidisciplinary Team Performance During Simulated Obstetric Hemorrhage
Authors: Hilton G. , Daniels K. , Goldhaber-Fiebert S.N. , Lipman S. , Carvalho B. , Butwick A.
Published: November 2016

(Int J Obstet Anesth. 2016;25:9–16)

Postpartum hemorrhage (PPH) rates have increased in the United States and some other developed countries over the past several years. PPH is also one of the leading causes of maternal morbidity and mortality. In an attempt to address these problems and improve outcomes, there has been a major focus on the development of protocols and checklists for use during PPH episodes. Studies have shown that adherence to recommended protocols and procedures during critical anesthetic events are improved when checklists and/or cognitive aids are used. The aim of this study was to evaluate checklist use and multidisciplinary team performance during a simulation of major PPH after vaginal delivery.
A Systematic Review and Network Meta-Analysis Comparing the Use of Foley Catheters, Misoprostol, and Dinoprostone for Cervical Ripening in the Induction of Labor
Authors: Chen W. , Xue J. , Peprah M.K. , Wen S.W. , Walker M. , Gao Y. , Tang Y.
Published: November 2016

(BJOG. 2016;123:346–354)

Induction of labor often begins with cervical ripening as other induction techniques, such as oxytocin, are less effective if the cervix is not in a favorable condition. There are various methods available, both mechanical and pharmacological, that soften, thin, and dilate the cervix. It is still debatable which of these cervical ripening techniques is optimal. The goal of this systematic review and network meta-analysis was to compare methods for cervical ripening as a component of labor induction.
Cervical Pessary Placement for Prevention of Preterm Birth in Unselected Twin Pregnancies: A Randomized Controlled Trial
Authors: Nicolaides K.H. , Syngelaki A. , Poon L.C. , De Paco Matallana C. , Plasencia W. , Molina F.S. , Picciarelli G. , Tul N. , Celik E. , Lau T.K. , Conturso R.
Published: November 2016

(Am J Obstet Gynecol. 2016;214:3.e1–e.9)

Preterm birth is responsible for >70% of all neonatal and infant deaths. Twins, with a prevalence of 1.5% of pregnancies, account for about 25% of preterm births. Randomized controlled trials in singleton pregnancies with short cervical length reported that the prophylactic use of progesterone reduced significantly the rate of preterm birth and neonatal morbidity. In twin pregnancies, progestogens and cervical cerclage have been shown to be ineffective in reducing preterm birth. The aim of this multicenter Randomized controlled trial was to test the hypothesis that the insertion of a cervical pessary in twin pregnancies, compared with expectant management, would reduce the rate of spontaneous birth at <34 weeks’ gestation.
Spinal Ultrasound Versus Palpation for Epidural Catheter Insertion in Labour: A Randomized Controlled Trial
Authors: Arzola C. , Mikhael R. , Margarido C. , Carvalho J.C.
Published: November 2016

(Eur J Anaesthesiol. 2015;32(7):499–505)

Ultrasound guidance has gained increasing acceptance among anesthesiologists as a means to potentially improve the efficacy and safety of various procedures, including vascular access, peripheral nerve blockade, and neuraxial anesthesia. Although several studies have been published on the use of spinal ultrasound, a common limitation is that a single expert investigator or selected group of anesthesiologists performed the ultrasound scanning while an experienced or novice operator carried out the neuraxial technique.
Pain and Psychological Distress Following Orthopedic Trauma: A Call for Collaborative Models of Care
Authors: Castillo Renan C. , Archer Kristin R. , Bradford Newcomb Anna , Wegener Stephen T.
Published: November 2016

Numerous studies have documented that orthopedic trauma patients’ experience long-term disability, even after complete clinical recovery. For many patients, the level of disability is not fully explained by the extent and severity of their injuries. These studies have also identified risk and protective factors that may explain why some patients experience full recovery while others suffer from life-long disability. Key factors that may play a central role as both predictors and mediators of disability are pain, depression, and anxiety, and posttraumatic stress disorder (PTSD). Anxiety, which in this population can take the form of acute and PTSD, has gained particular attention in the past few decades and is the subject of intense study, particularly among veteran populations and those experiencing life-threatening injuries. Depression has been studied far longer and may constitute both a major risk factor preinjury and a detrimental factor in both the acute and long-term recovery phases. Pain has always been understood as a symptom of traumatic injuries, but is a focus of concern now also due to its role in the use of opioids and PTSD. In this manuscript we will briefly review the scope of the problem, discuss risk factors and potential intervention points, and broadly propose secondary prevention approaches suitable for implementation in the trauma setting, with a particular focus on the role of collaborative care models.