bluuebunny/crossref_metadata_2025 huggingface dataset:
Human endometrial mesenchymal stem cells exhibit intrinsic anti-tumor properties on human epithelial ovarian cancer cells
Authors: Bu Shixia , Wang Qian , Zhang Qiuwan , Sun Junyan , He Biwei , Xiang Charlie , Liu Zhiwei , Lai Dongmei
Published: November 2016

Epithelial ovarian cancer (EOC) is the most lethal tumor of all gynecologic tumors. There is no curative therapy for EOC thus far. The tumor-homing ability of adult mesenchymal stem cells (MSCs) provide the promising potential to use them as vehicles to transport therapeutic agents to the site of tumor. Meanwhile, studies have showed the intrinsic anti-tumor properties of MSCs against various kinds of cancer, including epithelial ovarian cancer. Human endometrial mesenchymal stem cells (EnSCs) derived from menstrual blood are a novel source for adult MSCs and exert restorative function in some diseases. Whether EnSCs endow innate anti-tumor properties on EOC cells has never been reported. By using tumor-bearing animal model and ex vivo experiments, we found that EnSCs attenuated tumor growth by inducing cell cycle arrest, promoting apoptosis, disturbing mitochondria membrane potential and decreasing pro-angiogenic ability in EOC cells in vitro and/or in vivo. Furthermore, EnSCs decreased AKT phosphorylation and promoted nuclear translocation of Forkhead box O-3a (FoxO3a) in EOC cells. Collectively, our findings elucidated the potential intrinsic anti-tumor properties of EnSCs on EOC cells in vivo and in vitro. This research provides a potential strategy for EnSC-based anti-cancer therapy against epithelial ovarian cancer.
Quantifying side-chain conformational variations in protein structure
Authors: Miao Zhichao , Cao Yang
Published: November 2016

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.
Decoding intentions from movement kinematics
Authors: Cavallo Andrea , Koul Atesh , Ansuini Caterina , Capozzi Francesca , Becchio Cristina
Published: November 2016

How do we understand the intentions of other people? There has been a longstanding controversy over whether it is possible to understand others’ intentions by simply observing their movements. Here, we show that indeed movement kinematics can form the basis for intention detection. By combining kinematics and psychophysical methods with classification and regression tree (CART) modeling, we found that observers utilized a subset of discriminant kinematic features over the total kinematic pattern in order to detect intention from observation of simple motor acts. Intention discriminability covaried with movement kinematics on a trial-by-trial basis, and was directly related to the expression of discriminative features in the observed movements. These findings demonstrate a definable and measurable relationship between the specific features of observed movements and the ability to discriminate intention, providing quantitative evidence of the significance of movement kinematics for anticipating others’ intentional actions.
Modeling of hydrogen atom diffusion and response behavior of hydrogen sensors in Pd–Y alloy nanofilm
Authors: Liu Yi , Li Yanli , Huang Pengcheng , Song Han , Zhang Gang
Published: November 2016

To detect hydrogen gas leakage rapidly, many types of hydrogen sensors containing palladium alloy film have been proposed and fabricated to date. However, the mechanisms and factors that determine the response rate of such hydrogen sensor have not been established theoretically. The manners in which response time is forecasted and sensitive film is designed are key issues in developing hydrogen sensors with nanometer film. In this paper, a unilateral diffusion model of hydrogen atoms in Pd alloy based on Fick’s second law is proposed to describe the Pd–H reaction process. Model simulation shows that the hydrogen sensor response time with Pd alloy film is dominated by two factors (film thickness and hydrogen diffusion coefficient). Finally, a series of response rate experiments with varying thicknesses of Pd–Y (yttrium) alloy film are implemented to verify model validity. Our proposed model can help researchers in the precise optimization of film thickness to realize a simultaneously speedy and sensitive hydrogen sensor. This study also aids in evaluating the influence of manufacturing errors on performances and comparing the performances of sensors with different thicknesses.
Adenoviral vectors encoding CRISPR/Cas9 multiplexes rescue dystrophin synthesis in unselected populations of DMD muscle cells
Authors: Maggio Ignazio , Liu Jin , Janssen Josephine M. , Chen Xiaoyu , Gonçalves Manuel A. F. V.
Published: November 2016

Mutations disrupting the reading frame of the ~2.4 Mb dystrophin-encoding DMD gene cause a fatal X-linked muscle-wasting disorder called Duchenne muscular dystrophy (DMD). Genome editing based on paired RNA-guided nucleases (RGNs) from CRISPR/Cas9 systems has been proposed for permanently repairing faulty DMD loci. However, such multiplexing strategies require the development and testing of delivery systems capable of introducing the various gene editing tools into target cells. Here, we investigated the suitability of adenoviral vectors (AdVs) for multiplexed DMD editing by packaging in single vector particles expression units encoding the Streptococcus pyogenes Cas9 nuclease and sequence-specific gRNA pairs. These RGN components were customized to trigger short- and long-range intragenic DMD excisions encompassing reading frame-disrupting exons in patient-derived muscle progenitor cells. By allowing synchronous and stoichiometric expression of the various RGN components, we demonstrate that dual RGN-encoding AdVs can correct over 10% of target DMD alleles, readily leading to the detection of Becker-like dystrophin proteins in unselected muscle cell populations. Moreover, we report that AdV-based gene editing can be tailored for removing mutations located within the over 500-kb major DMD mutational hotspot. Hence, this single DMD editing strategy can in principle tackle a broad spectrum of mutations present in more than 60% of patients with DMD.
Non-invasive Quantitative Analysis of Specific Fat Accumulation in Subcutaneous Adipose Tissues using Raman Spectroscopy
Authors: Meksiarun Phiranuphon , Andriana Bibin B. , Matsuyoshi Hiroko , Sato Hidetoshi
Published: November 2016

Subcutaneous adipose tissue (SAT), visceral adipose tissue (VAT), and fat beneath the dermis layer were investigated using a ball lens top hollow optical fiber Raman probe (BHRP). Hamsters were fed with trilinolein (TL) and tricaprin (TC) for six weeks and measurements were carried out every two weeks. The BHRP with an 800 μm diameter fused-silica ball lens was able to obtain information on the subcutaneous fat in a totally non-invasive manner. Changes in the concentration of TL and TC during the treatment were analyzed, and the relationship between fat accumulation and dietary fat was studied. It was found that SAT had, in general, a higher degree of unsaturation than VAT. The accumulation rate of TC found in SAT and VAT was 0.52 ± 0.38 and 0.58 ± 0.4%, respectively, while the TL accumulation rate was 4.45 ± 1.6 and 4.37 ± 2.4%, respectively. The results suggest different metabolic pathways for TC, a typical medium-chain fatty acid, and TL, a long-chain unsaturated fatty acid. Raman subsurface spectra were successfully obtained and used to analyze the subcutaneous fat layer. The accumulation rates of TL and TC found in skin fat were 5.01 ± 3.53% and 0.45 ± 0.36%, respectively. The results demonstrate the high feasibility of Raman spectroscopy for non-invasive analysis of adipose tissue.
First steps to define murine amniotic fluid stem cell microenvironment
Authors: Bertin E. , Piccoli M. , Franzin C. , Spiro G. , Donà S. , Dedja A. , Schiavi F. , Taschin E. , Bonaldo P. , Braghetta P. , De Coppi P. , Pozzobon M.
Published: November 2016

Stem cell niche refers to the microenvironment where stem cells reside in living organisms. Several elements define the niche and regulate stem cell characteristics, such as stromal support cells, gap junctions, soluble factors, extracellular matrix proteins, blood vessels and neural inputs. In the last years, different studies demonstrated the presence of cKit+ cells in human and murine amniotic fluid, which have been defined as amniotic fluid stem (AFS) cells. Firstly, we characterized the murine cKit+ cells present both in the amniotic fluid and in the amnion. Secondly, to analyze the AFS cell microenvironment, we injected murine YFP+ embryonic stem cells (ESC) into the amniotic fluid of E13.5 wild type embryos. Four days after transplantation we found that YFP+ sorted cells maintained the expression of pluripotency markers and that ESC adherent to the amnion were more similar to original ESC in respect to those isolated from the amniotic fluid. Moreover, cytokines evaluation and oxygen concentration analysis revealed in this microenvironment the presence of factors that are considered key regulators in stem cell niches. This is the first indication that AFS cells reside in a microenvironment that possess specific characteristics able to maintain stemness of resident and exogenous stem cells.
Regional probabilistic risk assessment of heavy metals in different environmental media and land uses: An urbanization-affected drinking water supply area
Authors: Peng Chi , Cai Yimin , Wang Tieyu , Xiao Rongbo , Chen Weiping
Published: November 2016

In this study, we proposed a Regional Probabilistic Risk Assessment (RPRA) to estimate the health risks of exposing residents to heavy metals in different environmental media and land uses. The mean and ranges of heavy metal concentrations were measured in water, sediments, soil profiles and surface soils under four land uses along the Shunde Waterway, a drinking water supply area in China. Hazard quotients (HQs) were estimated for various exposure routes and heavy metal species. Riverbank vegetable plots and private vegetable plots had 95th percentiles of total HQs greater than 3 and 1, respectively, indicating high risks of cultivation on the flooded riverbank. Vegetable uptake and leaching to groundwater were the two transfer routes of soil metals causing high health risks. Exposure risks during outdoor recreation, farming and swimming along the Shunde Waterway are theoretically safe. Arsenic and cadmium were identified as the priority pollutants that contribute the most risk among the heavy metals. Sensitivity analysis showed that the exposure route, variations in exposure parameters, mobility of heavy metals in soil, and metal concentrations all influenced the risk estimates.
Effect of bovine pericardial extracellular matrix scaffold niche on seeded human mesenchymal stem cell function
Authors: Liu Zhi Zhao , Wong Maelene L. , Griffiths Leigh G.
Published: November 2016

Numerous studies have focused on generation of unfixed bovine pericardium (BP) extracellular matrix (ECM) for clinical application. However, the extent to which maintenance of native ECM niche is capable of directing behavior of repopulating cells remains relatively unexplored. By exploiting the sidedness of BP scaffolds (i.e., serous or fibrous surface), this study aims to determine the effect of ECM niche preservation on cellular repopulation using different scaffold generation methods. BP underwent either sodium dodecyl sulfate (SDS) decellularization or stepwise, solubilization-based antigen removal using amidosulfobetaine-14 (ASB-14). SDS scaffolds were toxic to repopulating human mesenchymal stem cells (hMSC). Scanning electron microscopy revealed distinct surface ultrastructure of ASB-14 scaffolds based on native BP sidedness. Basement membrane structures on the serous side stimulated hMSC cell monolayer formation, whereas fibrous side facilitated cell penetration into scaffold. Additionally, serous side seeding significantly increased hMSC adhesion and proliferation rate compared to the fibrous side. Furthermore, scaffold ECM niche stimulated sidedness dependent differential hMSC human leukocyte antigen expression, angiogenic and inflammatory cytokine secretion. This work demonstrates that ECM scaffold preparation method and preservation of BP side-based niches critically affects in vitro cell growth patterns and behavior, which has implications for use of such ECM biomaterials in clinical practice.
Detecting trap states in planar PbS colloidal quantum dot solar cells
Authors: Jin Zhiwen , Wang Aiji , Zhou Qing , Wang Yinshu , Wang Jizheng
Published: November 2016

The recently developed planar architecture (ITO/ZnO/PbS-TBAI/PbS-EDT/Au) has greatly improved the power conversion efficiency of colloidal quantum dot photovoltaics (QDPVs). However, the performance is still far below the theoretical expectations and trap states in the PbS-TBAI film are believed to be the major origin, characterization and understanding of the traps are highly demanded to develop strategies for continued performance improvement. Here employing impedance spectroscopy we detect trap states in the planar PbS QDPVs. We determined a trap state of about 0.34 eV below the conduction band with a density of around 3.2 × 1016 cm−3 eV−1. Temperature dependent open-circuit voltage analysis, temperature dependent diode property analysis and temperature dependent build-in potential analysis consistently denotes an below-bandgap activation energy of about 1.17–1.20 eV.
Two-stage (photoautotrophy and heterotrophy) cultivation enables efficient production of bioplastic poly-3-hydroxybutyrate in auto-sedimenting cyanobacterium
Authors: Monshupanee Tanakarn , Nimdach Palida , Incharoensakdi Aran
Published: November 2016

Sustainable production of bioplastics by heterotrophic microbes has been restricted by the limited resources of organic substrates and the energy required for biomass harvest. Here, the easy-to-harvest cyanobacterium (Chlorogloea fritschii TISTR 8527), from which the biomass instantaneously settled to the bottom of liquid culture, was utilized to produce poly-3-hydroxybutyrate (PHB) using a two-stage cultivation strategy. The cells were first pre-grown under normal photoautotrophy to increase their biomass and then recultivated under a heterotrophic condition with a single organic substrate to produce the product. Through optimization of this two-stage cultivation, the mass conversion efficiency of acetate substrate to PHB was obtained at 51 ± 7% (w/w), the comparable level to the theoretical biochemical conversion efficiency of acetate to PHB. This two-stage cultivation that efficiently converted the substrate to the product, concurrent with a reduced culture biomass, may be applicable for the production of other biopolymers by cyanobacteria.
Odour-induced analgesia mediated by hypothalamic orexin neurons in mice
Authors: Tashiro Shogo , Yamaguchi Ran , Ishikawa Sodemi , Sakurai Takeshi , Kajiya Katsuko , Kanmura Yuichi , Kuwaki Tomoyuki , Kashiwadani Hideki
Published: November 2016

Various folk remedies employ certain odorous compounds with analgesic effects. In fact, linalool, a monoterpene alcohol found in lavender extracts, has been found to attenuate pain responses via subcutaneous, intraperitoneal, intrathecal, and oral administration. However, the analgesic effects of odorous compounds mediated by olfaction have not been thoroughly examined. We performed behavioural pain tests under odourant vapour exposure in mice. Among six odourant molecules examined, linalool significantly increased the pain threshold and attenuated pain behaviours. Olfactory bulb or epithelium lesion removed these effects, indicating that olfactory sensory input triggered the effects. Furthermore, immunohistochemical analysis revealed that linalool activated hypothalamic orexin neurons, one of the key mediators for pain processing. Formalin tests in orexin neuron-ablated and orexin peptide-deficient mice showed orexinergic transmission was essential for linalool odour-induced analgesia. Together, these findings reveal central analgesic circuits triggered by olfactory input in the mammalian brain and support a potential therapeutic approach for treating pain with linalool odour stimulation.
Production of selenium nanoparticles in Pseudomonas putida KT2440
Authors: Avendaño Roberto , Chaves Nefertiti , Fuentes Paola , Sánchez Ethel , Jiménez Jose I. , Chavarría Max
Published: November 2016

Selenium (Se) is an essential element for the cell that has multiple applications in medicine and technology; microorganisms play an important role in Se transformations in the environment. Here we report the previously unidentified ability of the soil bacterium Pseudomonas putida KT2440 to synthesize nanoparticles of elemental selenium (nano-Se) from selenite. Our results show that P. putida is able to reduce selenite aerobically, but not selenate, to nano-Se. Kinetic analysis indicates that, in LB medium supplemented with selenite (1 mM), reduction to nano-Se occurs at a rate of 0.444 mmol L−1 h−1 beginning in the middle-exponential phase and with a final conversion yield of 89%. Measurements with a transmission electron microscope (TEM) show that nano-Se particles synthesized by P. putida have a size range of 100 to 500 nm and that they are located in the surrounding medium or bound to the cell membrane. Experiments involving dynamic light scattering (DLS) show that, in aqueous solution, recovered nano-Se particles have a size range of 70 to 360 nm. The rapid kinetics of conversion, easy retrieval of nano-Se and the metabolic versatility of P. putida offer the opportunity to use this model organism as a microbial factory for production of selenium nanoparticles.
Harnessing Nature’s Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins
Authors: Jacob Reed B. , Michaels Kenan C. , Anderson Cathy J. , Fay James M. , Dokholyan Nikolay V.
Published: November 2016

Organophosphate poisoning can occur from exposure to agricultural pesticides or chemical weapons. This exposure inhibits acetylcholinesterase resulting in increased acetylcholine levels within the synaptic cleft causing loss of muscle control, seizures, and death. Mitigating the effects of organophosphates in our bodies is critical and yet an unsolved challenge. Here, we present a computational strategy that integrates structure mining and modeling approaches, using which we identify novel candidates capable of interacting with a serine hydrolase probe (with equilibrium binding constants ranging from 4 to 120 μM). One candidate Smu. 1393c catalyzes the hydrolysis of the organophosphate omethoate (kcat/Km of (2.0 ± 1.3) × 10−1 M−1s−1) and paraoxon (kcat/Km of (4.6 ± 0.8) × 103 M−1s−1), V- and G-agent analogs respectively. In addition, Smu. 1393c protects acetylcholinesterase activity from being inhibited by two organophosphate simulants. We demonstrate that the utilized approach is an efficient and highly-extendable framework for the development of prophylactic therapeutics against organophosphate poisoning and other important targets. Our findings further suggest currently unknown molecular evolutionary rules governing natural diversity of the protein universe, which make it capable of recognizing previously unseen ligands.
The RNA-binding protein CsrA plays a central role in positively regulating virulence factors in Erwinia amylovora
Authors: Ancona Veronica , Lee Jae Hoon , Zhao Youfu
Published: November 2016

The GacS/GacA two-component system (also called GrrS/GrrA) is a global regulatory system which is highly conserved among gamma-proteobacteria. This system positively regulates non-coding small regulatory RNA csrB, which in turn binds to the RNA-binding protein CsrA. However, how GacS/GacA-Csr system regulates virulence traits in E. amylovora remains unknown. Results from mutant characterization showed that the csrB mutant was hypermotile, produced higher amount of exopolysaccharide amylovoran, and had increased expression of type III secretion (T3SS) genes in vitro. In contrast, the csrA mutant exhibited complete opposite phenotypes, including non-motile, reduced amylovoran production and expression of T3SS genes. Furthermore, the csrA mutant did not induce hypersensitive response on tobacco or cause disease on immature pear fruits, indicating that CsrA is a positive regulator of virulence factors. These findings demonstrated that CsrA plays a critical role in E. amylovora virulence and suggested that negative regulation of virulence by GacS/GacA acts through csrB sRNA, which binds to CsrA and neutralizes its positive effect on T3SS gene expression, flagellar formation and amylovoran production. Future research will be focused on determining the molecular mechanism underlying the positive regulation of virulence traits by CsrA.
Biomechanics of subcellular structures by non-invasive Brillouin microscopy
Authors: Antonacci Giuseppe , Braakman Sietse
Published: November 2016

Cellular biomechanics play a pivotal role in the pathophysiology of several diseases. Unfortunately, current methods to measure biomechanical properties are invasive and mostly limited to the surface of a cell. As a result, the mechanical behaviour of subcellular structures and organelles remains poorly characterised. Here, we show three-dimensional biomechanical images of single cells obtained with non-invasive, non-destructive Brillouin microscopy with an unprecedented spatial resolution. Our results quantify the longitudinal elastic modulus of subcellular structures. In particular, we found the nucleoli to be stiffer than both the nuclear envelope (p < 0.0001) and the surrounding cytoplasm (p < 0.0001). Moreover, we demonstrate the mechanical response of cells to Latrunculin-A, a drug that reduces cell stiffness by preventing cytoskeletal assembly. Our technique can therefore generate valuable insights into cellular biomechanics and its role in pathophysiology.
Impact of small-scale vegetation structure on tephra layer preservation
Authors: Cutler Nick A. , Shears Olivia M. , Streeter Richard T. , Dugmore Andrew J.
Published: November 2016

The factors that influence tephra layer taphonomy are poorly understood, but vegetation cover is likely to play a role in the preservation of terrestrial tephra deposits. The impact of vegetation on tephra layer preservation is important because: 1) the morphology of tephra layers could record key characteristics of past land surfaces and 2) vegetation-driven variability in tephra thickness could affect attempts to infer eruption and dispersion parameters. We investigated small- (metre-) scale interactions between vegetation and a thin (<10 cm), recent tephra layer. We conducted surveys of vegetation structure and tephra thickness at two locations which received a similar tephra deposit, but had contrasting vegetation cover (moss vs shrub). The tephra layer was thicker and less variable under shrub cover. Vegetation structure and layer thickness were correlated on the moss site but not under shrub cover, where the canopy reduced the influence of understory vegetation on layer morphology. Our results show that vegetation structure can influence tephra layer thickness on both small and medium (site) scales. These findings suggest that some tephra layers may carry a signal of past vegetation cover. They also have implications for the sampling effort required to reliably estimate the parameters of initial deposits.
Glycine increases preimplantation development of mouse oocytes following vitrification at the germinal vesicle stage
Authors: Cao Xin-Yan , Rose Jack , Wang Shi-Yong , Liu Yong , Zhao Meng , Xing Ming-Jie , Chang Tong , Xu Baozeng
Published: November 2016

Ice-free cryopreservation, referred to as vitrification, is receiving increased attention in the human and animal assisted reproduction. However, it introduces the detrimental osmotic stress by adding and removing high contents of cryoprotectants. In this study, we evaluated the effects of normalizing cell volume regulation by adding glycine, an organic osmolyte, during vitrification of mouse germinal vesicle stage oocyte and/or subsequent maturation on its development. The data showed that glycine supplementation in either vitrification/thawing or maturation medium significantly improved the cytoplasmic maturation of MII oocytes manifested by spindle assembly, chromosomal alignment, mitochondrial distribution, euploidy rate, and blastocyst development following fertilization in vitro, compared to the control without glycine treatment. Furthermore, glycine addition during both vitrification/thawing and maturation further enhanced the oocyte quality demonstrated by various markers, including ATP contents and embryo development. Lastly, the effect of anti-apoptosis was also observed when glycine was added during vitrification. Our result suggests that reducing osmotic stress induced by vitrification could improve the development of vitrified mouse oocyte.
Proliferation rates and gene expression profiles in human lymphoblastoid cell lines from patients with depression characterized in response to antidepressant drug therapy
Authors: Breitfeld J , Scholl C , Steffens M , Brandenburg K , Probst-Schendzielorz K , Efimkina O , Gurwitz D , Ising M , Holsboer F , Lucae S , Stingl J C
Published: November 2016

The current therapy success of depressive disorders remains in need of improvement due to low response rates and a delay in symptomatic improvement. Reliable functional biomarkers would be necessary to predict the individual treatment outcome. On the basis of the neurotrophic hypothesis of antidepressant’s action, effects of antidepressant drugs on proliferation may serve as tentative individual markers for treatment efficacy. We studied individual differences in antidepressant drug effects on cell proliferation and gene expression in lymphoblastoid cell lines (LCLs) derived from patients treated for depression with documented clinical treatment outcome. Cell proliferation was characterized by EdU (5-ethynyl-2'-deoxyuridine) incorporation assays following a 3-week incubation with therapeutic concentrations of fluoxetine. Genome-wide expression profiling was conducted by microarrays, and candidate genes such as betacellulin—a gene involved in neuronal stem cell regeneration—were validated by quantitative real-time PCR. Ex vivo assessment of proliferation revealed large differences in fluoxetine-induced proliferation inhibition between donor LCLs, but no association with clinical response was observed. Genome-wide expression analyses followed by pathway and gene ontology analyses identified genes with different expression before vs after 21-day incubation with fluoxetine. Significant correlations between proliferation and gene expression of WNT2B, FZD7, TCF7L2, SULT4A1 and ABCB1 (all involved in neurogenesis or brain protection) were also found. Basal gene expression of SULT4A1 (P=0.029), and gene expression fold changes of WNT2B by ex vivo fluoxetine (P=0.025) correlated with clinical response and clinical remission, respectively. Thus, we identified potential gene expression biomarkers eventually being useful as baseline predictors or as longitudinal targets in antidepressant therapy.
De novo Peptide Sequencing
Authors: Ma Bin
Published: November 2016

De novo peptide sequencing refers to the process of determining a peptide’s amino acid sequence from its MS/MS spectrum alone. The principle of this process is fairly straightforward: a high-quality spectrum may present a ladder of fragment ion peaks. The mass difference between every two adjacent peaks in the ladder is used to determine a residue of the peptide. However, most practical spectra do not have sufficient quality to support this straightforward process. Therefore, research in de novo sequencing has largely been a battle against the errors in the data. This chapter reviews some of the major developments in this field. The chapter starts with a quick review of the history in Section 1. Then manual de novo sequencing is examined in Section 2. Section 3 introduces a few commonly used de novo sequencing algorithms. An important aspect of automated de novo sequencing software is a good scoring function that serves as the optimization goal of the algorithm. Thus, Section 4 is devoted for the methods to define good scoring functions. Section 5 reviews a list of relevant software. The chapter concludes with a discussion of the applications and limitations of de novosequencing in Section 6.
Water-soluble silica-coated ZnS : Mn nanoparticles as fluorescent sensors for the detection of ultratrace copper(ii) ions in seawater
Authors: Qin Junjie , Dong Bohua , Gao Rongjie , Su Ge , Han Jiwei , Li Xue , Liu Wei , Wang Wei , Cao Lixin
Published: November 2016

In this study, silica-coated ZnS : Mn nanoparticles (ZnS : Mn/SiO2) were synthesized and proven to be sensitive and selective for Cu2+ detection in seawater.
Matrix-enhanced nanostructure initiator mass spectrometry (ME-NIMS) for small molecule detection and imaging
Authors: Moening Tara N. , Brown Victoria L. , He Lin
Published: November 2016

ME-NIMS MS imaging (right): significantly enhanced sensitivity over conventional NIMS (left) in tissue imaging.
Chirality sensing and discrimination of lysine derivatives in water with a dyn[4]arene
Authors: Vial Laurent , Dumartin Melissa , Donnier-Maréchal Marion , Perret Florent , Francoia Jean-Patrick , Leclaire Julien
Published: November 2016

For sensing purposes, we took advantage of the conformational lability of a dyn[4]arene receptor for the generation of induced circular dichroism outputs in the presence of various lysine derivatives.
Molecular tweezers target a protein–protein interface and thereby modulate complex formation
Authors: Trusch F. , Kowski K. , Bravo-Rodriguez K. , Beuck C. , Sowislok A. , Wettig B. , Matena A. , Sanchez-Garcia E. , Meyer H. , Schrader T. , Bayer P.
Published: November 2016

Supramolecular binders select few residues on a protein surface and by their unique complexation mode disrupt a critical protein–protein interaction.
Regioselective, cascade [3+2] annulation of β-naphthols (resorcinols) with Z-enoate propargylic alcohols: a novel entry for the synthesis of complex naphtho(benzo)furans
Authors: Tharra Prabhakararao , Baire Beeraiah
Published: November 2016

An unprecedented regioselective, first cascade [3+2] annulation process has been reported between propargylic alcohols and β-naphthols (resorcinols) for the synthesis of naphtho(benzo)furans.
Distance mediated electrochemiluminescence enhancement of CdS thin films induced by the plasmon coupling of gold nanoparticle dimers
Authors: Li Mei-Xing , Zhao Wei , Qian Guang-Sheng , Feng Qiu-Mei , Xu Jing-Juan , Chen Hong-Yuan
Published: November 2016

Theoretical and experimental studies of plasmon enhanced electrochemiluminescence of CdS QDs by gold nanoparticle monomers and dimers.
An autonomic self-healing organogel with a photo-mediated modulus
Authors: Xiong Yubing , Chen Zhijun , Wang Hong , Ackermann Lisa-Maria , Klapper Markus , Butt Hans-Jürgen , Wu Si
Published: November 2016

A new method is described for fabricating autonomic, self-healing, deformable organogels.
Hydration in silica based mesoporous materials: a DFT model
Authors: Gierada Maciej , Petit Ivan , Handzlik Jarosław , Tielens Frederik
Published: November 2016

In this work, calculable and realistic DFT models of MCM-41 material that follow temperature dependence of silanol density were developed. They can be easily applied in further studies of adsorption or as a support for catalysts.
Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach
Authors: Panayiotou C. , Mastrogeorgopoulos S. , Ataman M. , Hadadi N. , Hatzimanikatis V.
Published: November 2016

Comprehensive and consistent calculations of hydration quantities, including conformational contributions.
A stochastic study of electron transfer kinetics in nano-particulate photocatalysis: a comparison of the quasi-equilibrium approximation with a random walking model
Authors: Liu Baoshun , Zhao Xiujian , Yu Jiaguo , Fujishima Akira , Nakata Kazuya
Published: November 2016

A stochastic study was performed in this research, which showed that electron transport to photocatalytic centers cannot reach a quasi-equilibrium state during photocatalysis.
High-pressure dielectric behavior of BaMoO4: a combined experimental and theoretical study
Authors: Qin Tianru , Wang Qinglin , Wang Li , Yan Huacai , Liu Cailong , Han Yonghao , Ma Yanzhang , Gao Chunxiao
Published: November 2016

In situ impedance measurements were employed to investigate the electrical transport properties of BaMoO4 under pressures of up to 20.0 GPa.
Separation of water–ethanol solutions with carbon nanotubes and electric fields
Authors: Winarto Winarto , Takaiwa Daisuke , Yamamoto Eiji , Yasuoka Kenji
Published: November 2016

Under an electric field, water prefers to fill CNTs over ethanol, and electrostatic interactions within the ordered structure of the water molecules determine the separation effects.
CeO2-modified α-MoO3 nanorods as a synergistic support for Pt nanoparticles with enhanced COads tolerance during methanol oxidation
Authors: Liu Yanying , Liu Chuntao , Yu Xuefeng , Osgood Hannah , Wu Gang
Published: November 2016

A new type of Ce-doped α-MoO3 (Ce0.2Mo0.8O3−δ) nanorod support was synthesized using a two-step hydrothermal method.
Impact of the molecular structure and adsorption mode of D–π–A dye sensitizers with a pyridyl group in dye-sensitized solar cells on the adsorption equilibrium constant for dye-adsorption on TiO2 surface
Authors: Ooyama Yousuke , Yamaguchi Naoya , Ohshita Joji , Harima Yutaka
Published: November 2016

Adsorption modes of D–π–A dyes with a pyridyl group on a TiO2 electrode have been investigated for the adsorption equilibrium constant by Langmuir isotherms.
Nanostructured discotic Pd(ii) metallomesogens as one-dimensional proton conductors
Authors: Cuerva Cristián , Campo José A. , Cano Mercedes , Schmidt Rainer
Published: November 2016

Bis(isoquinolinylpyrazolate) Pd(ii) metallomesogens may be a promising step forward in the design of highly-stable proton conducting water-free electrolyte materials.
Acetaldehyde as an ethanol derived bio-building block: an alternative to Guerbet chemistry
Authors: Moore Cameron M. , Staples Orion , Jenkins Rhodri W. , Brooks Ty J. , Semelsberger Troy A. , Sutton Andrew D.
Published: November 2016

In this work, we describe a highly selective poly-aldol condensation of acetaldehyde, which can readily be obtained via dehydrogenation of ethanol.
Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer
Authors: Miah Sayem , Banks Charles A. S. , Adams Mark K. , Florens Laurence , Lukong Kiven E. , Washburn Michael P.
Published: November 2016

Understanding the complexity of cancer biology requires extensive information about the cancer proteome over the course of the disease.
Synthesis of substituted 2H-benzo[e]indazole-9-carboxylate as a potent antihyperglycemic agent that may act through IRS-1, Akt and GSK-3β pathways
Authors: Taneja Gaurav , Gupta Chandra Prakash , Mishra Shachi , Srivastava Rohit , Rahuja Neha , Rawat Arun Kumar , Pandey Jyotsana , Gupta Anand P. , Jaiswal Natasha , Gayen Jiaur R. , Tamrakar Akhilesh K. , Srivastava Arvind Kumar , Goel Atul
Published: November 2016

The synthesis andin vitroandin vivoantihyperglycemic activity of substituted 2H-benzo[e]indazole-9-carboxylate are described.
Determination and reduction of translocator protein (TSPO) ligand rs6971 discrimination
Authors: Sokias Renee , Werry Eryn L. , Chua Sook W. , Reekie Tristan A. , Munoz Lenka , Wong Erick C. N. , Ittner Lars M. , Kassiou Michael
Published: November 2016

The 18 kDa translocator protein (TSPO) is a target for development of diagnostic imaging agents for glioblastoma and neuroinflammation.
One-step modification of PU sponges for selective absorption of oil–water mixtures
Authors: Guo Jiahong , Wang Jikui , Zhang Sai , Ma Xiangyan , Qiu Zhoutong , Peng Xing , Ying Jie , Wang Yuming , Wu Genhua
Published: November 2016

Superhydrophobic PDMS–PU sponges fabricated through dipping–coating and HCl corrosion method exhibit excellent oil–water separation property.
Synergy between experimental and computational studies of aromatic stacking interactions
Authors: Hwang Jung wun , Li Ping , Shimizu Ken D.
Published: November 2016

This review highlights the synergetic exchange of ideas and results between experimental and theoretical chemistsen routeto the better understanding of aromatic stacking interactions.
Ni-catalyzed reductive coupling of α-halocarbonyl derivatives with vinyl bromides
Authors: Qiu Canbin , Yao Ken , Zhang Xinghua , Gong Hegui
Published: November 2016

This work describes the vinylation of α-halo carbonyl compounds with vinyl bromides under Ni-catalyzed reductive coupling conditions. While aryl-conjugated vinyl bromides entail pyridine as the sole labile ligand, the alkyl-substituted vinyl bromides require both bipyridine and pyridine as the co-ligands.
Correction: Transition metal-free decarboxylative alkylation reactions
Authors: Liu Ping , Zhang Guanghui , Sun Peipei
Published: November 2016

Correction for ‘Transition metal-free decarboxylative alkylation reactions’ by Ping Liu et al., Org. Biomol. Chem., 2016, DOI: 10.1039/c6ob02101h.
Monodispersed ultramicroporous semi-cycloaliphatic polyimides for the highly efficient adsorption of CO2, H2and organic vapors
Authors: Yan Jun , Zhang Biao , Wang Zhonggang
Published: November 2016

Monodispersed ultramicroporous semi-cycloaliphatic polyimides (sPIs) were synthesizedviasolution polycondensation and possess high uptakes for CO2, H2, aromatic and aliphatic vapors, exhibiting potential in gas storage and the recovery of toxic organic vapors.
Different cell behaviors induced by stereochemistry on polypeptide brush grafted surfaces
Authors: Ma Yinan , Shen Yong , Li Zhibo
Published: November 2016

Surface-grafted polyglutamate brushes with different main-chain chirality lead to different cell behaviors.
High spectral field enhancement and tunability in core–double shell metal–dielectric–metal spherical nanoparticles
Authors: Mendoza Herrera Luis J. , Scaffardi Lucía B. , Schinca Daniel C.
Published: November 2016

Full Mie theory for spherical core–double shell NPs has been developed to study plasmon resonances, optical extinction and spectral field enhancement of a generalized metal–dielectric–metal NPs, reaching an external factor of 33 for Al–SiO2–Au.
UHPLC-FT-ICR-MS combined with serum pharmacochemistry for bioactive compounds discovery of Zhi-Zi-Da-Huang-decoction against alcohol-induced hepatotoxicity in rats
Authors: Han Fei , Liu Tianfeng , Yin Ran , Zhang Xiaoshu , Ma Li , Xu Rui , Wu Yawen
Published: November 2016

In this study, a comprehensive strategy based on UHPLC-FT-ICR-MS and serum pharmacochemistry was developed to reveal the bioactive constituents of Zhi-Zi-Da-Huang decoction against alcohol-induced hepatotoxicity in rats after oral administration.
Efficient warm-white lighting using rare-earth-element-free fluorescent materials for saving energy, environment protection and human health
Authors: Lin Ching-Fuh , Tsai Tsung-Yo , Chen Kuan-Yu , Shen Pin-Chun
Published: November 2016

We explore an approach for efficient white light emission based on ZnSe:Mn nanoparticles without rare-earth and cadmium elements. This material opens up a new avenue for energy-saving, healthy, and environmentally benign lighting.
Stabilization of platinum–nickel alloy nanoparticles with a sulfur-doped graphene support in polymer electrolyte membrane fuel cells
Authors: Xu Calvin , Hoque Md Ariful , Chiu Gordon , Sung Teresa , Chen Zhongwei
Published: November 2016

Post-heat treatment of dealloyed Pt–Ni nanoparticles on sulfur-doped graphene for PEM fuel cell cathode catalysis exhibit greatly improved activity and electrochemically active surface area retention over Pt/C in half-cell conditions.
An efficacy of ‘nano’ in brannerite-type CoV2O6 conversion electrode for lithium batteries
Authors: Sivakumar M. , Prahasini P. , Subadevi R. , Liu Wei-Ren , Wang Fu-Ming
Published: November 2016

Among the classical anodes, conversion anodes play a unique role due to their capability to provide initial discharge capacity that is higher than the theoretical capacity.
Features of partial encapsulation of an ESIPT probe 3-hydroxy-2-naphthoic acid (3HNA) in the nano cavities of β- and γ-cyclodextrin: comparative study with sequestered 3HNA in micelles and reverse micelle
Authors: Samanta Sugata , Samanta Swarna Kamal , Sanyal Sagarika , Mukherjee Moumita , Sardar Pinki Saha , Ghosh Sanjib
Published: November 2016

Encapsulation of an excited state intramolecular proton transfer probe within the nanocavity of different confined media.
Self-assembly of water molecules using graphene nanoresonators
Authors: Wang Cuixia , Zhang Chao , Jiang Jin-Wu , Wei Ning , Park Harold S. , Rabczuk Timon
Published: November 2016

Inspired by macroscale self-assembly using the higher order resonant modes of Chladni plates, we use classical molecular dynamics to investigate the self-assembly of water molecules using graphene nanoresonators.
SBA-15 mesoporous silica particles loaded with cisplatin induce senescence in B16F10 cells
Authors: Edeler David , Kaluđerović Milena R. , Dojčinović Biljana , Schmidt Harry , Kaluđerović Goran N.
Published: November 2016

Nanoparticles obtained by loading of cisplatin into mesoporous silica SBA-15 (SBA-15|CP) change the phenotype of surviving B16F10 melanoma cells from malignant to senescent.
Modeling the reactivity of ozone and sulphate radicals towards organic chemicals in water using machine learning approaches
Authors: Gupta Shikha , Basant Nikita
Published: November 2016

QSRR modeling and correlative distribution of measured and model predicted values of rate constants (kO3andkSO4) of reactions of O3and SO4˙−radicals with diverse organic chemicals in aqueous medium.
In vivo target bio-imaging of cerebral ischemic stroke by real-time labeling of zinc
Authors: Zhao Chunqiu , Lai Lanmei , Rehman Fawad Ur , Qian Cheng , Teng Gaojun , Jiang Hui , Wang Xuemei
Published: November 2016

Through intravenous injection of zinc gluconate, we could readily realize in vivo fluorescence imaging by real-time labeling the relevant brain regions of CIS model mice based on the in situ biosynthesis of fluorescence zinc nanoclusters in target diseased sites.
Effect of vanadium valence state on the solution chemistry and the stability of vanadium substituted polyoxometalates
Authors: Liu Chang , Cao Jie , Wang Qian-Qian , Zang Jie-Chao , Ci Cheng-Gang
Published: November 2016

ESI-MS combined with DFT calculation revealed that the vanadium valence state and the vanadium substitution degrees can substantially affect the stabilities of vanadium-substituted POMs.
Neutral iridium catalysts with chiral phosphine-carboxy ligands for asymmetric hydrogenation of unsaturated carboxylic acids
Authors: Yang Shuang , Che Wen , Wu Hui-Ling , Zhu Shou-Fei , Zhou Qi-Lin
Published: November 2016

The new neutral iridium catalyst with chiral spiro phosphine-carboxy ligand exhibited exceptionally high enantioselectivity in the hydrogenation of 3-alkyl-3-methylenepropionic acids.
AIEgens for dark through-bond energy transfer: design, synthesis, theoretical study and application in ratiometric Hg2+ sensing
Authors: Chen Yuncong , Zhang Weijie , Cai Yuanjing , Kwok Ryan T. K. , Hu Yubing , Lam Jacky W. Y. , Gu Xinggui , He Zikai , Zhao Zheng , Zheng Xiaoyan , Chen Bin , Gui Chen , Tang Ben Zhong
Published: November 2016

A novel dark through-bond energy transfer (DTBET) strategy is proposed and applied as the design strategy to develop ratiometric Hg2+ sensors with high performance.
Iridium-catalyzed asymmetric hydrogenation of racemic α-substituted lactones to chiral diols
Authors: Yang Xiao-Hui , Yue Hai-Tao , Yu Na , Li Yi-Pan , Xie Jian-Hua , Zhou Qi-Lin
Published: November 2016

A protocol for the highly efficient iridium-catalyzed asymmetric hydrogenation of racemic α-substituted lactones via dynamic kinetic resolution is described.
Functional biomedical hydrogels for in vivo imaging
Authors: Lei Kewen , Ma Qian , Yu Lin , Ding Jiandong
Published: November 2016

In vivoimaging of biomedical hydrogels enables real-time and non-invasive visualization of the status of structure and function of hydrogels.
One-pot synthesis of gadolinium-doped carbon quantum dots for high-performance multimodal bioimaging
Authors: Pan Yi , Yang Jun , Fang Yaning , Zheng Junhui , Song Rong , Yi Changqing
Published: November 2016

A high-performance fluorescence (FL)/magnetic resonance (MR) imaging probe is synthesized by doping Gd3+ into carbon quantum dots via a one-pot pyrolysis process, and its dual-modality applications are demonstrated by the use of HeLa cells and mice as models.
The effects of gelatin–dopamine coating on polydimethylsiloxane substrates on pluripotency maintenance and myocardial differentiation of cultured mouse embryonic stem cells
Authors: Fu Jiayin , Quek Kai Yun , Chuah Yon Jin , Lim Chee Seong , Fan Changjiang , Wang Dong-an
Published: November 2016

Gelatin–dopamine coating to improve ESC culture and myocardial differentiation on PDMS substrates.
Redox- and pH-linked conformational changes in triheme cytochrome PpcA from Geobacter sulfurreducens
Authors: Morgado Leonor , Bruix Marta , Pokkuluri P. Raj , Salgueiro Carlos A. , Turner David L.
Published: November 2016

The periplasmic triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant; it is the likely reservoir of electrons to the outer surface to assist the reduction of extracellular terminal acceptors; these include insoluble metal oxides in natural habitats and electrode surfaces from which electricity can be harvested. A detailed thermodynamic characterization of PpcA showed that it has an important redox-Bohr effect that might implicate the protein in e−/H+ coupling mechanisms to sustain cellular growth. This functional mechanism requires control of both the redox state and the protonation state. In the present study, isotope-labeled PpcA was produced and the three-dimensional structure of PpcA in the oxidized form was determined by NMR. This is the first solution structure of a G. sulfurreducens cytochrome in the oxidized state. The comparison of oxidized and reduced structures revealed that the heme I axial ligand geometry changed and there were other significant changes in the segments near heme I. The pH-linked conformational rearrangements observed in the vicinity of the redox-Bohr center, both in the oxidized and reduced structures, constitute the structural basis for the differences observed in the pKa values of the redox-Bohr center, providing insights into the e−/H+ coupling molecular mechanisms driven by PpcA in G. sulfurreducens.