bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effects of an Echinacea Preparation on Synaptic Transmission and the Firing Properties of CA1 Pyramidal Cells in the Hippocampus
Authors: Hájos Norbert , Holderith Noémi , Németh Beáta , Papp Orsolya I. , Szabó Gergely G. , Zemankovics Rita , Freund Tamás F. , Haller József
Published: June 2011

Traditionally, Echinacea preparations are used as antiinflammatory agents and immune‐enhancers. In addition to these effects, their anxiolytic potency has been recognized recently in laboratory tests. Our aim in this study was to uncover the potential effects of an Echinacea preparation on neuronal operations in the hippocampus, a brain region that is involved in anxiety and anxiety‐related behaviors. Using in vitro electrophysiological techniques, we observed that excitatory synaptic transmission in hippocampal slices was significantly suppressed by an Echinacea extract found to be effective in anxiety tests. In contrast, no change in inhibitory synaptic transmission could be detected upon application of this extract. In addition, our experiments revealed that at low concentration the Echinacea extract reduced the spiking activity of CA1 pyramidal cells, while at high concentration increased it. This latter observation was parallel to the reduction in the magnitude of the h‐current‐mediated voltage responses in pyramidal cells. At any concentrations, the passive membrane properties of CA1 pyramidal cells were found to be unaltered by the Echinacea extract. In summary, the Echinacea extract can significantly regulate excitatory, but not inhibitory, synaptic transmission in the hippocampus, and this action might be involved in its anxiolytic effects observed in behaviour tests. Copyright © 2011 John Wiley & Sons, Ltd.
Effects of 12‐week Oral Supplementation of Ecklonia cava Polyphenols on Anthropometric and Blood Lipid Parameters in Overweight Korean Individuals: A Double‐blind Randomized Clinical Trial
Authors: Shin Hyeon‐Cheol , Kim Seong Ho , Park Yongju , Lee Bong Ho , Hwang Hye Jeong
Published: June 2011

The effects of 12‐week supplementation with a polyphenol extract from Ecklonia cava (ECP) on anthropometry, serum biochemistry and hematology have been investigated. Ninety‐seven overweight male and female adults (average age 40.5 ± 9.2 yr and body mass index (BMI) of 26.5 ± 1.6 kg/m2) were enrolled in a randomized, double‐blind, placebo‐controlled trial with parallel‐group design. Subjects were randomly allocated into three groups designated as PC (placebo), LD (low‐dose, 72 mg‐ECP/day) and HD (high‐dose, 144 mg‐ECP/day). Both LD and HD groups showed significant decreases in BMI, body fat ratio, waist circumference, waist/hip ratio, total cholesterol, low‐density lipoprotein (LDL) cholesterol, total cholesterol/high‐density lipoprotein (HDL) cholesterol and atherogenic index (AI) after 12 weeks, as compared with the placebo group. The HD group also showed a significant increase in serum HDL cholesterol as compared with the placebo group. Only the HD group showed significant decreases in serum glucose and systolic blood pressure after 12 weeks. There was no significant adverse event related with ingestion of ECP, and serum biochemical and hematological parameters were maintained within normal range during the intervention period. In conclusion, these results demonstrated that ECP supplementation significantly contributed to lowering body fat and serum lipid parameters such as total and LDL cholesterols with dose dependence. Further studies using different populations, dosages or biological markers are highly recommended to better understand the physiological features of this polyphenol. Copyright © 2011 John Wiley & Sons, Ltd.
Effects of Treatment Time by Sulfur Hexafluoride (SF6) Plasma on Barrier and Mechanical Properties of Paperboard
Authors: Jinkarn T. , Thawornwiriyanan S. , Boonyawan D. , Rachtanapun P. , Sane S.
Published: June 2011

Sulfur hexafluoride (SF6) plasma, using inductively coupled plasma technique, was applied on paperboard surfaces. Effects of different treatment times on water and oil resistances, mechanical properties (through tensile, compression and folding endurance tests) and barrier properties [through water vapor transmission rate (WVTR) and oxygen transmission rate (OTR)] were determined. Results showed that SF6 plasma treatment can improve water resistance properties of paperboard significantly, beginning with only a 2 s treatment time (p ≤ 0.05), whereas oil resistance properties can be improved over a longer time period. Plasma treatment had no effect on tensile strength of treated paperboard; however, machine direction (MD) compression strength, as well as MD and CD folding endurance, of treated paperboard was significantly lower than that for an untreated sample (p ≤ 0.05). WVTR and OTR of treated paperboard were higher with increasing treatment time, because of fluorine atoms and electron bombardment causing etching of cellulose fibres. Copyright © 2011 John Wiley & Sons, Ltd.
Leading‐order behavior of the correlation energy in the uniform electron gas
Authors: Loos Pierre‐François , Gill Peter M. W.
Published: June 2011

We show that, in the high‐density limit, restricted Møller‐Plesset (RMP) perturbation theory yields E = π−2(1 − ln 2) ln rs + O(r) for the correlation energy per electron in the uniform electron gas, where rs is the Seitz radius. This contradicts an earlier derivation which yielded E = O(ln|ln rs|). The reason for the discrepancy is explained. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Computational study of the catalytic effect of platinum on the decomposition of DNT
Authors: Lenz Annika , Pohl Anna , Ojamäe Lars , Persson Petter
Published: June 2011

The catalytic decomposition of dinitrotoluene (DNT; 3‐4‐DNT), a by‐product of the explosive trinitrotoluene (trotyl), on a platinum surface is investigated computationally. Reaction paths have been computed for a DNT molecule interacting with a Pt‐cluster under varying temperatures using quantum‐chemical density functional theory. Two possible initiation steps where DNT split either into nitro‐tolyl and NO2, or in nitro‐tolyl‐oxidanyl and NO, are considered. The energy barrier for the catalytic process is found to decrease significantly for the Pt catalyzed reaction compared with the uncatalyzed reaction. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 112: 1852–1858, 2012
Cell death‐independent functions of granzymes: hit viruses where it hurts
Authors: van Domselaar Robert , Bovenschen Niels
Published: June 2011

Granule exocytosis by cytotoxic lymphocytes is the key mechanism of our immune response to eliminate virus‐infected cells. These lytic granules contain the pore‐forming protein perforin and a set of five serine proteases called granzymes (GrA, GrB, GrH, GrK, GrM) that display distinct substrate specificities. Granzymes have mostly been studied for their ability to induce cell death. However, viruses have evolved many inhibitors to effectively block apoptosis. Evidence is emerging that granzymes also use noncytotoxic strategies to inhibit viral replication and potential viral reactivation from latency. Granzymes directly cleave viral or host cell proteins that are required in the viral life cycle. Furthermore, granzymes induce a pro‐inflammatory cytokine response to create an antiviral environment. In this review, we summarize and discuss these novel strategies by which the immune system counteracts viral infections, and we will address the potential therapeutic applications that could emerge from this intriguing mechanism. Copyright © 2011 John Wiley & Sons, Ltd.
GETTING TO SCALE WITH ENVIRONMENTAL FLOW ASSESSMENT: THE WATERSHED FLOW EVALUATION TOOL
Authors: Sanderson J. S. , Rowan N. , Wilding T. , Bledsoe B. P. , Miller W. J. , Poff N. L.
Published: June 2011

Growing water demand across the world is increasing the stress on river ecosystems, causing concern for both biodiversity and people. River‐specific environmental flow assessments cannot keep pace with the rate and geographic extent of water development. Society needs methods to assess ecological impacts of flow management at broad scales so that appropriate regional management can be implemented. To meet this need in Colorado, USA, we developed a Watershed Flow Evaluation Tool (WFET) to estimate flow‐related ecological risk at a regional scale. The WFET entails four steps: (i) modelling natural and developed daily streamflows; (ii) analysing the resulting flow time series; (iii) describing relationships between river attributes and flow metrics (flow–ecology relationships); and (iv) mapping of flow‐related risk for trout, native warm‐water species and riparian plant communities. We developed this tool in two watersheds with differing geomorphic settings and data availability. In one of the two watersheds, the WFET was successfully implemented to assess ecological risk across the 3400‐km2 watershed, providing consistent watershed‐wide information on flow‐related risk. In the other watershed, active channel change and limited data precluded a successful application. In Colorado, the WFET will be used to evaluate the risk of impacts on river ecosystems under future climate change and water development scenarios (e.g. for energy development or municipal water supply). As water continues to be developed for people, the WFET and similar methods will provide a cost‐effective means to evaluate and balance ecosystem needs at large scales. Copyright © 2011 John Wiley & Sons, Ltd.
A percolation process on the square lattice where large finite clusters are frozen
Authors: van den Berg Jacob , de Lima Bernardo N.B. , Nolin Pierre
Published: June 2011

In (Aldous, Math. Proc. Cambridge Philos. Soc. 128 (2000), 465–477), Aldous constructed a growth process for the binary tree where clusters freeze as soon as they become infinite. It was pointed out by Benjamini and Schramm that such a process does not exist for the square lattice.

This motivated us to investigate the modified process on the square lattice, where clusters freeze as soon as they have diameter larger than or equal to N, the parameter of the model. The non‐existence result, mentioned above, raises the question if the N‐ parameter model shows some ‘anomalous’ behaviour as N →∞. For instance, if one looks at the cluster of a given vertex, does, as N →∞, the probability that it eventually freezes go to 1? Does this probability go to 0? More generally, what can be said about the size of a final cluster? We give a partial answer to some of such questions. © 2011 Wiley Periodicals, Inc. Random Struct. Alg., 2012
Sequential change‐point detection based on direct density‐ratio estimation
Authors: Kawahara Yoshinobu , Sugiyama Masashi
Published: June 2011

Change‐point detection is the problem of discovering time points at which properties of time‐series data change. This covers a broad range of real‐world problems and has been actively discussed in the community of statistics and data mining. In this paper, we present a novel nonparametric approach to detecting the change of probability distributions of sequence data. Our key idea is to estimate the ratio of probability densities, not the probability densities themselves. This formulation allows us to avoid nonparametric density estimation, which is known to be a difficult problem. We provide a change‐point detection algorithm based on direct density‐ratio estimation that can be computed very efficiently in an online manner. The usefulness of the proposed method is demonstrated through experiments using artificial and real‐world datasets. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 2011
The interaction of CO2 and CO with Fe‐doped SrTiO3(100) surfaces
Authors: Voigts F. , Argirusis Chr. , Maus‐Friedrichs W.
Published: June 2011

The interaction of CO2 and CO with 0.013 at.% Fe‐doped SrTiO3(100) was investigated in situ with Metastable Induced Electron Spectroscopy (MIES) and XPS at room temperature. To clear up the influence of surface defects, cleaned and sputtered SrTiO3 surfaces were investigated. Sputtering results in the breaking of TiO bonds in the surface and the formation of oxygen‐related defects as well as reduced titanium on the surface.

Cleaned SrTiO3 surfaces do neither interact with CO2 nor with CO. Sputtered surfaces show a CO formation during CO2 exposure and—to a lesser extent—during CO exposure. The CO groups can be detected very well with MIES because of its extreme surface sensitivity. With XPS, the characteristic carbonate peak shift of the C 1s orbitals can be detected. Copyright © 2011 John Wiley & Sons, Ltd.
Maximum likelihood estimation in generalized linear models with multiple covariates subject to detection limits
Authors: May Ryan C. , Ibrahim Joseph G. , Chu Haitao
Published: June 2011

The analysis of data subject to detection limits is becoming increasingly necessary in many environmental and laboratory studies. Covariates subject to detection limits are often left censored because of a measurement device having a minimal lower limit of detection. In this paper, we propose a Monte Carlo version of the expectation–maximization algorithm to handle large number of covariates subject to detection limits in generalized linear models. We model the covariate distribution via a sequence of one‐dimensional conditional distributions, and sample the covariate values using an adaptive rejection metropolis algorithm. Parameter estimation is obtained by maximization via the Monte Carlo M‐step. This procedure is applied to a real dataset from the National Health and Nutrition Examination Survey, in which values of urinary heavy metals are subject to a limit of detection. Through simulation studies, we show that the proposed approach can lead to a significant reduction in variance for parameter estimates in these models, improving the power of such studies. Copyright © 2011 John Wiley & Sons, Ltd.
Bayesian methods for fitting mixture models that characterize branching tree processes: An application to development of resistant TB strains
Authors: Izu Alane , Cohen Ted , Mitnick Carole , Murray Megan , De Gruttola Victor
Published: June 2011

For pathogens that must be treated with combinations of antibiotics and acquire resistance through genetic mutation, knowledge of the order in which drug‐resistance mutations occur may be important for determining treatment policies. Diagnostic specimens collected from patients are often available; this makes it possible to determine the presence of individual drug resistance‐conferring mutations and combinations of these mutations. In most cases, these specimens are only available from a patient at a single point in time; it is very rare to have access to multiple specimens from a single patient collected over time as resistance accumulates to multiple drugs. Statistical methods that use branching trees have been successfully applied to such cross‐sectional data to make inference on the ordering of events that occurred prior to sampling. Here, we propose a Bayesian approach to fitting branching tree models that has several advantages, including the ability to accommodate prior information regarding measurement error or cross resistance and the natural way it permits the characterization of uncertainty. Our methods are applied to a data set for drug‐resistant TB in Peru; the goal of the analysis was to determine the order with which patients develop resistance to the drugs commonly used for treating TB in this setting. Copyright © 2011 John Wiley & Sons, Ltd.
Incremental reflexion analysis
Authors: Koschke Rainer
Published: June 2011

Architecture conformance checking is implemented in many commercial and research tools. These tools typically implement the reflexion analysis originally proposed by Murphy, Notkin, and Sullivan. This analysis allows for structural validation of an architecture model against a source model connected by a mapping from source entities onto architecture entities. Given this mapping, the reflexion analysis computes the discrepancies between the architecture model and source model automatically. The mapping process is usually highly interactive and the most time‐consuming activity in the reflexion analysis. In current tools, the reflexion analysis must be repeated completely whenever the underlying source or architecture models or the mapping changes. In large systems, the recomputation can hinder interactive use as users expect an immediate response to their changes. This paper describes an incremental reflexion analysis that does not require a complete repetition of the reflexion analysis. Instead, it repeats the analysis only for those parts that are actually influenced by a change. The incremental reflexion analysis is evaluated on large real‐world systems. Copyright © 2011 John Wiley & Sons, Ltd.
Strain Rate Dependent Flow Stress and Energy Absorption Behaviour of Cast CrMnNi TRIP/TWIP Steels
Authors: Krüger L. , Wolf S. , Martin S. , Martin U. , Jahn A. , Weiß A. , Scheller P.R.
Published: June 2011

Modern steel developments often use additional deformation mechanisms like the deformation induced martensitic transformation (TRIP‐effect) and mechanical twinning (TWIP‐effect) to enhance elongation and strength. Three high‐alloyed cast CrMnNi‐steels with different austenite stabilities were examined. Dependent on the austenite stability, TRIP‐effect and TWIP‐effect were found. A low austenite stability causes a distinctive formation of deformation induced α'‐martensite and therefore a strong strain hardening. The increase of strain rate leads to an increase in yield strength and flow stress, but also to a counteractive adiabatic heating of the specimen. Dependent on the degree of deformation, low austenite stabilities and high strain rates lead to excellent values in specific energy absorption.
Strength and Failure Behaviour of Spark Plasma Sintered Steel‐Zirconia Composites Under Compressive Loading
Authors: Krüger L. , Decker S. , Ohser‐Wiedemann R. , Ehinger D. , Martin S. , Martin U. , Seifert H.J.
Published: June 2011

Several composites, consisting of a metastable austenitic steel matrix and varying amounts of MgO partially stabilized zirconia particles (Mg‐PSZ), were produced through spark plasma sintering (SPS). Compression tests were carried out at room temperature in a wide range of strain rate (4 · 10−4 s−1, 2 · 10−3 s−1, 10−1 s−1, 1 s−1, 102 s−1). In conjunction with subsequent microstructural investigations, the mechanical material behaviour was clarified. All composites showed a good ductility and a high strength. The strength increased with an increase of the ceramic content and with higher strain rates. Both, the martensitic transformation of the steel matrix and of the ceramic particles, could be proved at all strain rates. In this study no significant influence of the strain rate on the amount of transformed ceramic could be detected while the steel matrix showed less α′‐martensite after compression at rising strain rates. Local material failure occurred around 0.3 true compressive strain depending on the applied strain rate and the amount of the Mg‐PSZ powder. The main reason for the damage is the relatively weak ceramic‐ceramic interface within the ceramic clusters.
Selective Oxidation and Sub‐Surface Phase Transformation of TWIP Steel during Continuous Annealing
Authors: Gong Young Feng , De Cooman Bruno Charles
Published: June 2011

The selective oxidation of Twinning Induced Plasticity (TWIP) steel during annealing at 800 °C in a N2 + 10%H2 gas atmosphere with a dew point of −17 °C and −3 °C was investigated by means of high resolution transmission electron microscopy of cross‐sectional samples. The annealing resulted in the selective oxidation of Mn and Si and the austenite‐to‐ferrite phase transformation of the sub‐surface region. In the low dew point atmosphere, the annealing resulted in the formation of a MnO layer at the surface. Crystalline c–xMnO · SiO2 (x ≥ 2) particles and amorphous a–xMnO · SiO2 (x < 0.9) particles were found at the interface between the MnO layer and the steel matrix. In a narrow zone of the sub‐surface, the Mn depletion resulted in the transformation of the initial austenite. In the high dew point atmosphere, a thicker MnO layer was formed on the surface and no mixed manganese‐silicon oxides particles were observed at the MnO/steel matrix interface. In the sub‐surface, Mn was significantly depleted in the range of 2–3 µm below the surface and the initial austenite in this zone was transformed to ferrite. MnO particles were found at the grain boundaries and in the interior of grains.
Physicochemical, crystalline, and thermal properties of native, oxidized, acid, and enzyme hydrolyzed Chinese yam (Dioscorea opposite Thunb) starch
Authors: Xia Li , Wenyuan Gao , Qianqian Jiang , Yanli Wang , Xinhua Guo , Luqi Huang
Published: June 2011

Native yam starch was modified by oxidation (with sodium hypochlorite), acid, and enzyme (with gluco‐amylase), respectively. Ash content, fat content, protein, and AM contents were reduced following modifications. All the modifications reduced swelling capacity whereas improved the solubility. The SEM of the native starch showed the presence of large oval or spherical to small irregular‐shaped granules, however, oxidation and hydrolysis caused collapse of the granules. From the XRD, the typical C‐type XRD pattern of the native starch changed to the typical A‐type XRD pattern of the three modified starches. The above results also demonstrated that amorphous region of yam starch granules was preferentially degraded than crystalline region of granules. DSC showed that oxidation and acid/enzyme hydrolysis reduced peak temperature of gelatinization (Tp) of native starch significantly. Enthalpy of gelatinization (ΔH) of oxidation and enzyme starch was reduced but it has no obviously change following acid modification.
Brief Report: Benchmarking Human Pluripotent Stem Cell Markers During Differentiation Into the Three Germ Layers Unveils a Striking Heterogeneity: All Markers Are Not Equal
Authors: Ramirez Jean-Marie , Gerbal-Chaloin Sabine , Milhavet Ollivier , Qiang Bai , Becker Fabienne , Assou Said , Lemaître Jean-Marc , Hamamah Samir , De Vos John
Published: June 2011

Pluripotent stem cells (PSC) are functionally characterized by their capacity to differentiate into all the cell types from the three germ layers. A wide range of markers, the expression of which is associated with pluripotency, has been used as surrogate evidence of PSC pluripotency, but their respective relevance is poorly documented. Here, we compared by polychromatic flow cytometry the kinetics of loss of expression of eight widely used pluripotency markers (SSEA3, SSEA4, TRA-1-60, TRA-1-81, CD24, OCT4, NANOG, and alkaline phosphatase [AP]) at days 0, 5, 7, and 9 after induction of PSC differentiation into cells representative of the three germ layers. Strikingly, each marker showed a different and specific kinetics of disappearance that was similar in all the PSC lines used and for all the induced differentiation pathways. OCT4, SSEA3, and TRA-1-60 were repeatedly the first markers to be downregulated, and their expression was completely lost at day 9. By contrast, AP activity, CD24, and NANOG proteins were still detectable at day 9. In addition, we show that differentiation markers are coexpressed with pluripotency markers before the latter begin to disappear. These results suggest that OCT4, SSEA3, and TRA-1-60 might be better to trace in vitro the emergence of pluripotent cells during reprogramming.
Expression of Tlx in Both Stem Cells and Transit Amplifying Progenitors Regulates Stem Cell Activation and Differentiation in the Neonatal Lateral Subependymal Zone
Authors: Obernier Kirsten , Simeonova Ina , Fila Tatiana , Mandl Claudia , Hölzl-Wenig Gabriele , Monaghan-Nichols Paula , Ciccolini Francesca
Published: June 2011

Niche homeostasis in the postnatal subependymal zone of the lateral ventricle (lSEZ) requires coordinated proliferation and differentiation of neural progenitor cells. The mechanisms regulating this balance are scarcely known. Recent observations indicate that the orphan nuclear receptor Tlx is an intrinsic factor essential in maintaining this balance. However, the effect of Tlx on gene expression depends on age and cell-type cues. Therefore, it is essential to establish its expression pattern at different developmental ages. Here, we show for the first time that in the neonatal lSEZ activated neural stem cells (NSCs) and especially transit-amplifying progenitors (TAPs) express Tlx and that its expression may be regulated at the posttranscriptional level. We also provide evidence that in both cell types Tlx affects gene expression in a positive and negative manner. In activated NSCs, but not in TAPs, absence of Tlx leads to overexpression of negative cell cycle regulators and impairment of proliferation. Moreover, in both cell types, the homeobox transcription factor Dlx2 is downregulated in the absence of Tlx. This is paralleled by increased expression of Olig2 in activated NSCs and glial fibrillary acidic protein in TAPs, indicating that in both populations Tlx decreases gliogenesis. Consistent with this, we found a higher proportion of cells expressing glial makers in the neonatal lSEZ of mutant mice than in the wild type counterpart. Thus, Tlx playing a dual role affects the expression of distinct genes in these two lSEZ cell types.
Zebrafish neurotoxicity from aphantoxins—cyanobacterial paralytic shellfish poisons (PSPs) from Aphanizomenon flos‐aquae DC‐1
Authors: Zhang Delu , Hu Chunxiang , Wang Gaohong , Li Dunhai , Li Genbao , Liu Yongding
Published: June 2011

Aphanizomenon flos‐aquae (A. flos‐aquae), a cyanobacterium frequently encountered in water blooms worldwide, is source of neurotoxins known as PSPs or aphantoxins that present a major threat to the environment and to human health. Although the molecular mechanism of PSP action is well known, many unresolved questions remain concerning its mechanisms of toxicity. Aphantoxins purified from a natural isolate of A. flos‐aquae DC‐1 were analyzed by high‐performance liquid chromatography (HPLC), the major component toxins were the gonyautoxins1 and 5 (GTX1 and GTX5, 34.04% and 21.28%, respectively) and the neosaxitoxin (neoSTX, 12.77%). The LD50 of the aphantoxin preparation was determined to be 11.33 μg/kg (7.75 μg saxitoxin equivalents (STXeq) per kg) following intraperitoneal injection of zebrafish (Danio rerio). To address the neurotoxicology of the aphantoxin preparation, zebrafish were injected with low and high sublethal doses of A. flos‐aquae DC‐1 toxins 7.73 and 9.28 μg /kg (5.3 and 6.4 μg STXeq/kg, respectively) and brain tissues were analyzed by electron microscopy and RT‐PCR at different timepoints postinjection. Low‐dose aphantoxin exposure was associated with chromatin condensation, cell‐membrane blebbing, and the appearance of apoptotic bodies. High‐dose exposure was associated with cytoplasmic vacuolization, mitochondrial swelling, and expansion of the endoplasmic reticulum. At early timepoints (3 h) many cells exhibited characteristic features of both apoptosis and necrosis. At later timepoints apoptosis appeared to predominate in the low‐dose group, whereas necrosis predominated in the high‐dose group. RT‐PCR revealed that mRNA levels of the apoptosis‐related genes encoding p53, Bax, caspase‐3, and c‐Jun were upregulated after aphantoxin exposure, but there was no evidence of DNA laddering; apoptosis could take place by pathways independent of DNA fragmentation. These results demonstrate that aphantoxin exposure can cause cell death in zebrafish brain tissue, with low doses inducing apoptosis and higher doses inducing necrosis. © 2011 Wiley Periodicals, Inc. Environ Toxicol, 2013.
Recent developments and applications of the CHARMM force fields
Authors: Zhu Xiao , Lopes Pedro E. M. , MacKerell Alexander D.
Published: June 2011

Empirical force fields (FFs) commonly used to describe the condensed‐phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds, and new theoretical developments (e.g., polarizable methods) make FF development a dynamic domain of research. Accordingly, a number of improvements and extensions of the Chemistry at HARvard Molecular Mechanics (CHARMM) FFs have occurred over the years. The objective of the present review is to provide an up‐to‐date overview of the CHARMM FFs. A limited presentation on the historical aspects of FFs will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable FFs, including examples of recent applications of those FFs. © 2011 John Wiley & Sons, Ltd.

This article is categorized under:

Molecular and Statistical Mechanics > Molecular Mechanics
Transfer RNA‐derived fragments: origins, processing, and functions
Authors: Sobala Andrew , Hutvagner Gyorgy
Published: June 2011

Deep sequencing approaches have revealed multiple types of small RNAs with known and unknown functions. In this review we focus on a recently identified group of small RNAs that are derived from transfer RNAs (tRNAs), tRNA fragments (tRFs). We review the mechanism of their processing and their functions in mammalian cells, and highlight points of possible cross‐talk between tRFs and the canonical small RNA pathway characterized by small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi‐interacting RNAs (piRNAs). We also propose a nomenclature that is based on their processing characteristics. WIREs RNA 2011 2 853–862 DOI: 10.1002/wrna.96

This article is categorized under:

RNA Processing > tRNA Processing

Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Metal Complexes of Biologically Important Ligands, CLXXVI.[1] Formation of Peptides within the Coordination Sphere of Metal Ions and of Classical and Organometallic Complexes and Some Aspects of Prebiotic Chemistry
Authors: Beck Wolfgang
Published: June 2011

The formation of peptide bonds in the neighborhood of metal ions is reviewed. The metal ions can function as activating and catalytic groups; they can act as templates. Metal ions can play a role as stabilizing spectators when peptides are formed within their ligands and they are able to protect the amino or carboxylate group of amino acids during peptide synthesis. Some related chemistry of metal‐peptide conjugates is included. This survey represents an attractive combination of coordination, organic, organometallic chemistry and biochemistry and reveals some interesting aspects of prebiotic chemistry.
Two Manganese(II) Complexes with a Bulky Fluorene‐Based Carboxylate Ligand: Syntheses, Crystal Structures, and Luminescent Properties
Authors: Wang Junjie , Shi Yunfeng , Li Sujuan
Published: June 2011

To explore the coordination possibilities of fluorene‐based ligands, two manganese(II) complexes with the ligand 9,9‐dibutyl‐9H‐fluorene‐2,7‐carboxylate (L) were synthesized and characterized: [Mn2(L)2(DMF)3]∞ (1) and [Mn2(L)2(DMF)]∞ (2). X‐ray single‐crystal diffraction analyses show that complex 1 has a two‐dimensional (2D) (4,4) structure, whereas complex 2 consits of a three‐dimensional (3D) (4,5)‐connected topology framework. The results indicate that the steric bulk of the fluorene ring in H2L plays an important role in the formations of 1 and 2. Additional pyridine‐based ligands govern the formation of the final frameworks of 2. Moreover, the luminescent properties of these complexes were briefly investigated.
Carbon Halide Bond Activation of Benzyl Chloride and Benzyl Bromide Using An NHC‐Stabilized Nickel(0) Complex
Authors: Zell Thomas , Radius Udo
Published: June 2011

A first example of the application of an NHC‐stabilized nickel complex as a catalyst in Suzuki–Miyaura cross‐coupling reactions of alkyl halides is reported. The complexes trans‐[Ni(iPr2Im)2(X)(CH2Ph)] (X = Cl 2 and Br 3) were prepared from the reactions of benzyl chloride and benzyl bromide and the dinuclear complex [Ni2(iPr2Im)4(COD)] (1). These compounds were fully characterized by elemental analysis, IR spectroscopy, multinuclear NMR spectroscopy, and X‐ray crystallography. Based on these stoichiometric oxidative addition reactions catalytic Suzuki–Miyaura cross‐coupling reactions have been performed. Complex 1 is an effective catalyst for the Suzuki–Miyaura cross‐coupling reaction of benzyl chloride and phenylboronic acid. Quantitative conversion of benzyl chloride with a high selectivity to the cross‐coupling product diphenylmethane was achieved after two hours reaction time using three equivalents phenylboronic acid, three equivalents cesium fluoride and 1.22 mol‐% [Ni2(iPr2Im)4(COD)] (1) as a catalyst.
Syntheses and Molecular Structure of Dinuclear Transition Metal Complexes Bridged by Dipyridylamine Derivative Ligands
Authors: Gupta Gajendra , Park Sunhong , Lee Shim Sung , Kim Jinkwon
Published: June 2011

Stable dinuclear transition metal complexes,[(η6‐C6H6)2Ru2(L1)Cl2]2+ (1), [(η6‐p‐iPrC6H4Me)2Ru2(L1)Cl2]2+ (2), [(η6‐C6Me6)2Ru2(L1)Cl2]2+ (3), [(η6‐C6H6)2Ru2(L2)Cl2]2+ (4),[(η6‐p‐iPrC6H4Me)2Ru2(L2)Cl2]2+ (5), [(η6‐C6Me6)2Ru2(L2)Cl2]2+ (6), [(η5‐C5Me5)2Rh2(L1)Cl2]2+ (7), [(η5‐C5Me5)2Ir2(L1)Cl2]2+ (8),[(η5‐C5Me5)2Rh2(L2)Cl2]2+ (9), and [(η5‐C5Me5)2Rh2(L2)Cl2]2+ (10), with the bis‐bidentate ligands 1,3‐bis(di‐2‐pyridylaminomethyl)benzene (L1) and 1,4‐bis(di‐2‐pyridylaminomethyl)benzene (L2), which contain two chelating dipyridylamine units connected by an aromatic spacer, were synthesized. The cationic dinuclear complexes were isolated as their hexafluorophosphate salts and characterized by using a combination of NMR, IR, and UV/Vis spectroscopic methods and mass spectrometry. The solid‐state structure of complex 8 as a representative was determined by X‐ray structure analysis.
Effect of Metal Ions on the Structures of Coordination Polymers Based on Biphenyl‐2,2′,4,4′‐Tetracarboxylate
Authors: Wang Ji‐Jiang , Lv Jun‐Fang , Cao Pei‐Xiang , Zhang Mei‐Li , Gao Lou‐Jun , Lv Lei , Ren Yi‐Xia , Hou Xiang‐Yang
Published: June 2011

Two new coordination polymers, {[Cd2(btc)(2,2′‐bpy)2]·H2O}n (1) and [Zn2(btc)(2,2′‐bpy)(H2O)]n (2) (H4btc = biphenyl‐2,2′,4,4′‐tetracarboxylic acid, 2,2′‐bpy = 2,2′‐bipyridine), were synthesized hydrothermally under similar conditions and characterized by elemental analysis, IR spectra, TGA, and single‐crystal X‐ray diffraction analysis. In complexes 1 and 2, the (btc)4– ligand acts as connectors to link metal ions to give a 2D bilayer network of 1 and a 3D metal‐organic framework of 2, respectively. The differences in the structures are induced by diverging coordination modes of the (btc)4– ligand, which can be attributed to the difference metal ions in sizes. The results indicate that metal ions have significant effects on the formation and structures of the final complexes. Additionally, the fluorescent properties of the two complexes were also studied in the solid state at room temperature.
Li35Ln9Si30N59O2F with Ln = Ce, Pr – Highly Condensed Nitridosilicates
Authors: Lupart Saskia , Durach Dajana , Schnick Wolfgang
Published: June 2011

The isotypic nitridosilicates Li35Ln9Si30N59O2F (Ln = Ce, Pr) were synthesized by reaction of LnF3 and LiN3 with Si(NH)2 in liquid lithium flux in weld shut tantalum ampoules. The crystal structures of the isotypic compounds were solved and refined on the basis of single‐crystal X‐ray diffraction (P$\bar{3}$c1 (no. 165), Z = 2; Li35Ce9Si30N59O2F:, a = 1479.9(2), c = 1538.3(3) pm, R1 = 0.0526, 1671 data, 175 parameters; Li35Pr9Si30N59O2F: a = 1477.3(2), c = 1533.9(3) pm, R1 = 0.0441, 1331 data, 175 parameters). The silicate substructure represents a 3D network of all side corner sharing SiN4 tetrahedra. At one discrete and not condensed mixed anion position an atomic ratio O:F = 2:1 is assumed in order to achieve charge neutrality. With an atomic ratio Si:N = 30:59, the degree of condensation of the silicate substructure is slightly above κ = 1/2. Accordingly, there are triply crosslinking N[3] atoms in the silicate substructure. The obtained structures prove that by employing the lithium flux technique not only nitridosilicates with a low degree of condensation can be obtained by using rather mild reaction conditions at low temperatures. Lattice energy calculations (MAPLE) and EDX measurements confirmed the electrostatic bonding interactions and the chemical composition.
Risk Factors for Stroke During Surgery for Carotid Body Tumors
Authors: Gwon Jun Gyo , Kwon Tae‐Won , Kim Hyangkyoung , Cho Yong‐Pil
Published: June 2011

Background

Removing carotid body tumors (CBTs) carry the risk of operative morbidity including stroke. We evaluated the risk factors for stroke related to resection of CBTs.

Methods

We retrospectively reviewed the records of 17 procedures performed on 16 patients with CBT between March 1998 and September 2008.

Results

The study population consisted of 5 men and 11 women, of mean age 41.7 years (range: 23–62 years). At surgery, 8 cases (47%) were localized and classified as Shamblin class I, 4 cases (23.5%) as class II, and 5 cases (29.4%) as class III. Four patients had postoperative stroke (23.5%), with Shamblin classification related to the incidence of stroke (P = 0.041). In contrast, neither tumor size (P = 0.412) nor heparin injection before internal carotid artery (ICA) manipulation (P = 0.538) was associated with stroke. Although preoperative embolization of the tumor feeder did not significantly reduce the stroke rate (P = 0.579), early external carotid artery (ECA) division in patients with class II and III tumors was effective (P = 0.008). Internal carotid artery (ICA) manipulation, including reconstruction, ligation, and repair of injury, significantly increased the incidence of stroke (P = 0.029), as did ICA ligation without reconstruction (P = 0.044).

Conclusions

Internal carotid artery manipulation, including reconstruction, ligation, and repair of injury, significantly increased the incidence of stroke. For uncomplicated CBT resection, careful preoperative planning, especially for patients with class II and III tumors, is mandatory to avoid inadvertent ICA manipulation necessitated by bleeding. Early ECA division during the operation rather than preoperative percutaneous embolization in patients with class II and III tumors was significantly effective in reducing the stroke rate
Liver Resection of Colorectal Liver Metastases in Elderly Patients
Authors: Kulik U. , Framke T. , Großhennig A. , Ceylan A. , Bektas H. , Klempnauer J. , Lehner F.
Published: June 2011

Background

The percentage of elderly patients with colorectal liver metastases (CLM) has increased. Liver resection remains the only curative therapy; data evaluating the outcome in this age group is limited. Aim of the present study was to determine if postoperative morbidity, mortality, and other independent predictors influence survival in patients ≥70 years undergoing liver resection for CLM.

Methods

Clinical data on primary tumor and metastases of 939 patients after liver resection for CLM between 1994 and 2008 were retrospectively collected and subdivided in three age‐groups (≥70, 40–69, <40). Independent predictors of survival were evaluated with overall and age‐specific univariate and multivariate Cox regression models.

Results

A total of 939 patients underwent liver resection for CLM, 20.3% aged ≥70 years. Overall postoperative mortality and morbidity were 1.08 and 14.82%, revealing no age‐related differences. With 5‐year survival of 31.8% in the elderly and 37.5% in the mid‐age population, age ≥70 years was linked with decreased survival (Hazard Ratio [HR] = 1.305; P = 0.0186). Multivariate overall analyses showed size of CLM > 50 mm (HR = 1.376; P = 0.0060), a high amount of transfusion during surgery (HR = 1.676; P = 0.0110), duration of surgery >210 min (HR = 1.241; P = 0.0322), primary UICC (International Union Against Cancer) stage IV (HR = 2.297; P < 0.0001), and performance of repeat resections (HR = 0.652; P = 0.0107) as independent predictors of survival. In the elderly group, effects of UICC IV (HR = 3.260; P = 0.0148) and high numbers of transfusions (HR = 3.647; P = 0.0129) were confirmed; the others did not show statistical significance.

Conclusions

Resection of CLM at older age is feasible with morbidity and mortality rates similar to those in younger patients. Although age ≥70 was shown to be associated with poorer overall outcome, reasonable 5‐year survival was observed.
Multidisciplinary Discussion and Management of Rectal Cancer: A Population‐based Study
Authors: Swellengrebel H. A. M. , Peters E. G. , Cats A. , Visser O. , Blaauwgeers H. G. T. , Verwaal V. J. , van Velthuysen M. L. , Cense H. A. , Bruin S. C. , Marijnen C. A. M.
Published: June 2011

Background

The purpose of the present study was to evaluate the value of discussing rectal cancer patients in a multidisciplinary team (MDT).

Methods

All treated rectal cancer patients (>T1M0) diagnosed in 2006–2008 were included. According to the national guidelines, neoadjuvant (chemo)radiotherapy should be given to all rectal cancer patients. Patients were scored as “discussed” (MDT+) only if documented proof was available. The primary endpoint was the number of positive circumferential resection margins (CRM ≤1 mm).

Results

Of the 275 patients included, 210 were analyzed (exclusions: (recto)sigmoid tumor, acute laparotomy, and inoperability). Neoadjuvant treatment was applied in 174 (83%) patients and followed by total mesorectal excision in 171 (81%) patients. Patients considered not to require downstaging, received short‐course radiotherapy (SCRT) (n = 116) or no radiotherapy (no RT) (n = 36), whereas 58 more advanced patients received chemoradiotherapy (CRT). The MDT discussion took place in 116 cases (55%). In the MDT+ group an MRI was used more often (p = 0.001) and TNM staging was more complete (p < 0.001). The proportion of patients with advanced disease was higher in the MDT+ group (88% ≥T3/N+ versus 68%; p = 0.001). The overall CRM+ rate was 13% and did not differ between the MDT+ and the MDT− group (p = 0.392). In patients receiving SCRT or no RT, the CRM+ rate was 10%, whereas the rate was 20% for patients receiving CRT.

Conclusions

Although no difference in CRM+ rate was found for those patients who were discussed and those who were not, our results demonstrate room for improvement, especially in the selection of patients for SCRT or no RT. We advocate standardized documentation of treatment decisions and pathology reports.
Facilitation of plant species richness and endangered species by a tussock grass in a moist tall grassland revealed using hierarchical Bayesian analysis
Authors: Wang Zhe , Nishihiro Jun , Washitani Izumi
Published: June 2011

Using hierarchical Bayesian analysis, we tested the hypothesis that a perennial tussock grass, Ischaemum aristatum var. glaucum, facilitates the species diversity of vegetation and the regeneration of individual native vascular plants in Ukishima Marsh, a moist tall grassland of eastern Japan. We analyzed microscale distribution patterns of sympatric plant species in response to ground height. Both the species richness of the whole plant assemblage and the occurrence of many native vascular plants, including two endangered species, were positively correlated with ground elevation, which was directly mediated by I. aristatum var. glaucum tussocks and/or the occurrence of mosses on tussocks. Susceptibility to late spring inundation of microsites on the tussocks was significantly lower than that on bare ground. These results suggest that the facilitation by I. aristatum var. glaucum contributes to maintaining the high species richness of the marsh. Consideration of the facilitation among native vascular plants is necessary for establishing sound conservation plans of wetland vegetation.
Changes in the Composition of Triacylglycerols in the Fat Bodies of Bumblebee Males During Their Lifetime
Authors: Jiroš Pavel , Cvačka Josef , Hanus Robert , Kindl Jiří , Kofroňová Edita , Valterová Irena
Published: June 2011

The age‐dependent changes in the composition of triacylglycerols (TAG) in the fat bodies of bumblebee males were studied using HPLC/MS. Two related species (Bombus terrestris and B. lucorum) were compared, with the age of the males being 0–30 days. The total amount of TAG in B. lucorum was about 2.7 times higher than that in B. terrestris for all of the ages studied. One to three‐day‐old males had the highest content of TAG in their fat bodies (1.6–2.3 mg/individual in B. terrestris and 3.8–4.2 mg/individual in B. lucorum). The analytical data show different patterns in both species. The qualitative composition of fatty acids in TAG was similar, but the mean relative abundance between B. terrestris and B. lucorum differed: 14:0, 7 and 14%; 16:0, 20 and 44%; 18:3, 62 and 23%; 18:1, 3 and 8%, respectively (the data is based on a GC/MS integration). A statistical evaluation of the dynamic changes in the TAG composition revealed that in B. terrestris different age classes were well separated according to their TAG composition while in B. lucorum the TAG did not change substantially during the male's life. The TAG analyses provide more precise information on the differences between the classes studied than the FA composition alone.
The immediate early genes Fos and Egr1 become STAT1 transcriptional targets in the absence of STAT3
Authors: Schiavone Davide , Avalle Lidia , Dewilde Sarah , Poli Valeria
Published: June 2011

Signal transducer and activators of transcription (STAT)1 and STAT3 cross‐regulate their activity downstream of gp130 cytokines, and eliminating STAT3 leads to IFN‐γ‐like responses to IL‐6 correlating with prolonged STAT1 phosphorylation. Here we demonstrate that the increased gp130‐mediated induction of the IFN‐γ‐responsive interferon regulatory factor 1 gene observed in STAT3−/− cells correlates with prolonged STAT1 binding to its promoter. Intriguingly, gp130‐mediated induction of the immediate early genes FBJ osteosarcoma oncogene and early growth response 1 is also prolonged in STAT3−/− cells, with STAT1 binding to their promoters. Thus the abrogation of STAT3 expression, perturbing the signaling balance, directs the STAT1 oncosuppressor to transcribe new target genes, known to drive mitogen responses and tumor transformation.
The competitive determinants of a firm's environmental management activities: Evidence from US manufacturing industries
Authors: Hofer Christian , Cantor David E. , Dai Jing
Published: June 2011

Environmental management (EM) issues have received substantial attention in operations management. While the link between EM practices and firm performance has been well studied, little is known about the competitive drivers of a firm's EM activities. In this research, a Schumpeterian economics perspective is adopted to investigate competitive interactions among leader and challenger firms in the domain of EM, with a particular focus on operational EM activities. Using econometric methods, the empirical analysis of panel data from a broad cross‐section of US manufacturing firms reveals that such rivalry does exist and that the effect of a rival's past EM activity on a focal firm's EM activity is greater for more profitable and smaller firms. In addition, firm characteristics such as market leadership, firm size and firm profitability are found to significantly affect the magnitude of a firm's EM activities. This study presents theoretical and empirical evidence of rivalrous behaviors in the domains of EM and OM and, thus, has interesting implications for operations management research and practice.