bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Bcl‐2 Inhibitors: Discovery and Mechanism Study of Small Organic Apoptosis‐Inducing Agents
Authors: Zhang Zhichao , Jin Liji , Qian Xuhong , Wei Meijiao , Wang Yuanyuan , Wang Jing , Yang Yuanyuan , Xu Qin , Xu Yongting , Liu Fengyu 
Published: December 2006

AbstractApoptosis as a novel target for cancer chemotherapy has generated an intense demand for new apoptosis‐inducing agents. The newly revealed role of protein families involved in the apoptosis pathway, and resistance to cytotoxic therapies have opened new avenues for the development of novel anticancer strategies. We have established a novel strategy to rapidly obtain protein‐targeted, instead of conventional DNA‐targeted, apoptosis inducers as antitumor leads. First, a novel organic non‐DNA intercalative compound S1 (8‐oxo‐3‐thiomorpholin‐4‐yl‐8H‐acenaphtho[1,2‐b]pyrrole‐9‐carbonitrile, MW=331) was found with an IC50 of 10−7–10−8 μM against diverse cancer cell lines. Further biological evaluation demonstrated that it was an apoptosis‐inducer both in vivo and in vitro. The treatment of hydroperitoneum hepatoma cells (H22 cell line) with S1 at various concentrations (from 0.01 to 10 μM) for 24 h triggered these cells to enter the apoptosis process. The antitumor efficiency was also tested in the H22 xenotransplant models in mice. At a dosage of 0.3 mg kg−1, S1 exhibited significant antitumor activity with a much longer survival time, a decrease in tumor size, and increased apoptosis cells in tumor tissue. More importantly, studies of the molecular mechanism of apoptosis induction by S1 revealed that S1 inactivated the Bcl‐2 protein by binding to it, depolarizing the mitochondrial membrane, and then activating caspase 9, followed by caspase 3. Finally, structure‐based virtual modification was performed by computer modeling. As a result, a derivative, S2 (8‐oxo‐3‐[(thienylmethyl)amino]‐8H‐acenaphtho[1,2‐b]pyrrole‐9‐carbonitrile, MW=341) was identified that possessed a lower binding energy to Bcl‐2, and demonstrated better antitumor potency, even on the Bcl‐2‐overexpressing human acute myeloid leukemia (HL‐60) cells (IC50=1.3 μM) in vitro. S1 and S2 are the well‐defined Bcl‐2 inhibitors that give us a promising platform for the development of new therapeutic agents.
Generation of New Landomycins with Altered Saccharide Patterns through Over‐expression of the Glycosyltransferase Gene lanGT3 in the Biosynthetic Gene Cluster of Landomycin A in Streptomyces cyanogenus S‐136
Authors: Zhu Lili , Luzhetskyy Andriy , Luzhetska Martha , Mattingly Cynthia , Adams Val , Bechthold Andreas , Rohr Jürgen 
Published: December 2006

AbstractTwo novel landomycin compounds, landomycins I and J, were generated with a new mutant strain of Streptomyces cyanogenus in which the glycosyltransferase that is encoded by lanGT3 was over‐expressed. This mutant also produced the known landomycins A, B, and D. All these compounds consist of the same polyketide‐derived aglycon but differ in their sugar moieties, which are chains of different lengths. The major new metabolite, landomycin J, was found to consist of landomycinone with a tetrasaccharide chain attached. Combined with previous results of the production of landomycin E (which contains three sugars) by the LanGT3− mutant strain (obtained by targeted gene deletion of lanGT3), it was verified that LanGT3 is a D‐olivosyltransferase responsible for the transfer of the fourth sugar required for landomycin A biosynthesis. The experiments also showed that gene over‐expression is a powerful method for unbalancing biosynthetic pathways in order to generate new metabolites. The cytotoxicity of the new landomycins—compared to known ones—was assessed by using three different tumor cell lines, and their structure–activity relationship (SAR) with respect to the length of the deoxysugar side chain was deduced from the results.
Patent foramen ovale and migraine
Authors: Post M.C. , Luermans J.G.L.M. , Plokker H.W.M. , Budts W. 
Published: December 2006

AbstractMigraine is a common neurological disorder with a great impact on the quality of life and social activities. The patent foramen ovale (PFO) is an intra‐atrial right‐to‐left shunt with a prevalence of 25% in the general population. An increased prevalence is found in patients with migraine, especially in migraine with aura. Percutaneous PFO closure might decrease the prevalence of migraine. However, most of these observational studies were retrospective without a randomized design and the results need to be interpreted with caution. In this review we describe the association between PFO and migraine and the different pathophysiological hypotheses, which have been proposed to explain this relationship. © 2006 Wiley‐Liss, Inc.
Dynamic Combinatorial Libraries Based on Hydrogen‐Bonded Molecular Boxes
Authors: Kerckhoffs Jessica M. C. A. , Mateos‐Timoneda Miguel A. , Reinhoudt David N. , Crego‐Calama Mercedes 
Published: December 2006

AbstractThis article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self‐assembled molecular receptors together with the amplification and selection of the best binder. Receptors (1 a–d)3⋅(DEB)6 are formed by the self‐assembly of six diethyl barbiturate (DEB) and calix[4]arene dimelamine derivatives 1 a–d by using hydrogen bonds. The largest amplification factor (2.8) for a host assembly (1 a3⋅ (DEB)6) was observed after the addition of 2 a to four‐component library 1 an⋅1 b(3−n)⋅(DEB)6 (n=0–3). Addition of 2 a to twenty‐component library 1 an⋅1 bm⋅1 co⋅1 d(3−(n+m+o))⋅(DEB)6 (n, m, o=0–3; (n+m+o)≤3) also showed amplification of receptor 1 a3⋅(DEB)6. The second part of this article describes the complexation of libraries of different alizarin‐like guest molecules (2 a–d) and the self‐assembled receptor 1 a3⋅(DEB)6. This receptor is able to template the formation of the best‐fitting guest trimer.
A locally conservative least‐squares method for Darcy flows
Authors: Bochev P. B. , Gunzburger M. D. 
Published: December 2006

AbstractLeast‐squares finite‐element methods for Darcy flow offer several advantages relative to the mixed‐Galerkin method: the avoidance of stability conditions between finite‐element spaces, the efficiency of solving symmetric and positive definite systems, and the convenience of using standard, continuous nodal elements for all variables. However, conventional C0 implementations conserve mass only approximately and for this reason they have found limited acceptance in applications where locally conservative velocity fields are of primary interest. In this paper, we show that a properly formulated compatible least‐squares method offers the same level of local conservation as a mixed method. The price paid for gaining favourable conservation properties is that one has to give up what is arguably the least important advantage attributed to least‐squares finite‐element methods: one can no longer use continuous nodal elements for all variables. As an added benefit, compatible least‐squares methods inherit the best computational properties of both Galerkin and mixed‐Galerkin methods and, in some cases, yield identical results, while offering the advantages of not having to deal with stability conditions and yielding positive definite discrete problems. Numerical results that illustrate our findings are provided. Copyright © 2006 John Wiley & Sons, Ltd.
The modified Shanks transform for the solution of elastic problems by boundary integral equation (BIE) method
Authors: Antes M. Y. , Karinski Y. S. , Yankelevsky D. Z. 
Published: December 2006

AbstractA new approach which allows solving the elastic problems by the boundary integral equation (BIE) methods is presented. The solution of the integral equation is presented in the form of Neumann series and in order to accelerate its convergence the Shanks transform was applied in a modified form. Usage of this transform allows essentially the decrease of the number of Neumann series terms for complex geometrical forms of the bodies boundary. The BIE method to the class of problems characterized by mass potential forces (i.e. thermal, gravitational or centrifugal) is applied. The comparison with the known solution for the disturbed flow around a aerofoil shows good agreement. The method is demonstrated through an example of the stress analysis of a centrifugal high‐speed compressor working wheel. Copyright © 2006 John Wiley & Sons, Ltd.
A simple enzymatic method for parietal yolk sac removal in early postimplantation mouse embryos
Authors: Rivera‐Pérez Jaime A. , Diefes Hunter , Magnuson Terry 
Published: December 2006

AbstractCrucial aspects of axial development in mice occur at early postimplantation stages from the time of implantation to the appearance of the primitive streak. However, this period of development is notoriously refractory to experimental approaches due to the small size of the conceptus and to the presence of the parietal yolk sac, a protective tripartite membrane that surrounds the developing egg cylinder. Here, we describe a method that combines enzymatic digestion and mechanical manipulation to remove the parietal yolk sac of conceptuses at stages between 5.5 and 6.5 days post coitum. This method, which is compatible with whole‐mount in situ hybridization and immunostaining techniques, offers a significant improvement over conventional dissection techniques, and it will greatly facilitate research in early mammalian development. Developmental Dynamics 236:489–493, 2007. © 2006 Wiley‐Liss, Inc.
The hippocampus is required for short‐term topographical memory in humans
Authors: Hartley Tom , Bird Chris M. , Chan Dennis , Cipolotti Lisa , Husain Masud , Vargha‐Khadem Faraneh , Burgess Neil 
Published: December 2006

AbstractThe hippocampus plays a crucial role within the neural systems for long‐term memory, but little if any role in the short‐term retention of some types of stimuli. Nonetheless, the hippocampus may be specialized for allocentric topographical processing, which impacts on short‐term memory or even perception. To investigate this we developed performance‐matched tests of perception (match‐to‐sample) and short‐term memory (2 s delayed‐match‐to‐sample) for the topography and for the nonspatial aspects of visual scenes. Four patients with focal hippocampal damage and one with more extensive damage, including right parahippocampal gyrus, were tested. All five patients showed impaired topographical memory and spared nonspatial processing in both memory and perception. Topographical perception was profoundly impaired in the patient with parahippocampal damage, mildly impaired in two of the hippocampal cases, and clearly preserved in the other two hippocampal cases (including one with dense amnesia). Our results suggest that the hippocampus supports allocentric topographical processing that is indispensable when appropriately tested after even very short delays, while the presence of the sample scene can allow successful topographical perception without it, possibly via a less flexible parahippocampal representation. © 2006 Wiley‐Liss, Inc.
Characterizing interneuron and pyramidal cells in the human medial temporal lobe in vivo using extracellular recordings
Authors: Viskontas Indre V. , Ekstrom Arne D. , Wilson Charles L. , Fried Itzhak 
Published: December 2006

AbstractThe goal of this study was to characterize the electrophysiological features of single neurons recorded deep within the medial temporal lobes in humans. Using three physiological criteria to distinguish principal cells and interneurons (firing rate, burst propensity, and action potential waveform) and a large data set of human single neurons (585) from thirteen patients, we show that single neurons in the human MTL separate into two distinct classes comparable to the pyramidal cell and interneuron classes described in animals. We also find that the four different MTL brain regions that we examined (amygdala, hippocampus, entorhinal cortex, and posterior parahippocampal cortex) show unique action potential characteristics, which may in turn relate to the role that neurons from these regions play in behavior. A subset of cells were recorded while patients engaged in both slow‐wave (SWS) and rapid‐eye movement (REM) sleep and a comparison of the electrophysiological features during these different sleep stages showed that interneurons tended to burst more during SWS compared to REM, while only principal cells in the EC and hippocampus showed a greater propensity for bursting during SWS. Together, our results support the idea that human single neurons have electrophysiologically identifiable cell types, similar to those observed in other mammals, and provide insight into regional and functional differences in spike‐wave characteristics relevant to considerations about neural populations in the human brain. © 2006 Wiley‐Liss, Inc.
Diatoms in Lowland Ponds of Koshi Tappu, Eastern Nepal – Relationships with Chemical and Habitat Characteristics
Authors: Simkhada Bishnu , Jüttner Ingrid , Chimonides P. James 
Published: December 2006

AbstractEpiphytic and epipelic diatom assemblages were studied in relation to water chemistry and habitat character in lowland ponds of Koshi Tappu, Nepal. Epiphytic assemblages from different microhabitats, such as morphologically different plants, roots, stems, filamentous algae and decomposing leaves, within the same ponds were similar. Assemblage composition of epiphytic diatoms reflected gradients in water chemistry and habitat character of the pond with respect to pond vegetation and substratum type, bank profile and land use in the catchment. Epiphytic and epipelic assemblages responded to chemical gradients in the surface water, particularly concentrations of Ca, Mg and Na, but epipelic diatoms also indicated differences in SO4. Epipelic diatoms were also sensitive to interstitial water chemistry variations in PO4, Si, Ca and Mg. There were no relationships between species richness, diversity or evenness and gradients in water chemistry and habitat character. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of Seasonal Changes on Predictive Model Assessments of Streams Water Quality with Macroinvertebrates
Authors: João Feio Maria , Reynoldson Trefor B. , Graça Manuel A. 
Published: December 2006

AbstractIn this study we investigate how seasonal variability in aquatic macroinvertebrate communities affects the performance of a predictive model developed to assess environmental quality. Macroinvertebrates were sampled from nine not visibly disturbed sites located in different streams of the Mondego catchment across a full year. Organisms were identified to the lowest practicable taxonomic level and their abundances recorded at three taxonomic levels (order, family and lowest level). The seasonal samples were examined with regard to seasonal variation using three predictive models at order, family and lowest taxonomic level. The models showed increasing effect of seasonal changes across taxonomic levels, from order to the lowest level. When using the current models samples should be taken in the same season as the reference sites were sampled. Furthermore, data from more reference sites should be added to the model in order to encompass sufficient natural variation and allow the use of the model in different seasons. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Morphological and Molecular Data Reveal the Presence of the Invasive Artemia franciscana in Margherita di Savoia Salterns (Italy)
Authors: Mura Graziella , Kappas Ilias , Baxevanis Athanasios D. , Moscatello Salvatore , D'Amico Quirico , Lopez German M. , Hontoria Francisco , Amat Francisco , Abatzopoulos Theodore J. 
Published: December 2006

AbstractIntroduced populations of the American invasive Artemia franciscana have been reported in Mediterranean countries except for Italy. A recent sampling at Margherita di Savoia revealed the presence of mating pairs in a saltwork known to host only parthenogens. An integrated approach, based on scanning electron microscopy of four morphological traits, discriminant analysis of 13 morphometric characters and 16S rRNA PCR‐RFLP profiles of eight endonucleases was implemented for the identification of the invader. Patterns of variability in all assayed markers provided congruent and solid evidence that the allochthonous species is A. franciscana. Native parthenogens are still predominant (∼98.4%) in this Italian site but they can be rapidly outcompeted by A. franciscana, as it occurred in similar cases throughout Europe and elsewhere. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Recent advances in planar tetracoordinate carbon chemistry
Authors: Merino Gabriel , Méndez‐Rojas Miguel A. , Vela Alberto , Heine Thomas 
Published: December 2006

AbstractWe summarize our contributions on the quest of new planar tetracoordinate carbon entities (new carbon molecules with exotic chemical structures and strange bonding schemes). We give special emphasis on the rationalization why in this type of molecules the planar configuration is favored over the tetrahedral one. We will concentrate on the latter and will show that molecules containing planar tetracoordinate carbons have a stabilizing system of delocalized π electrons, which shows similar properties as π systems in aromatic molecules. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 362–372, 2007
Electrostatic energy in the effective fragment potential method: Theory and application to benzene dimer
Authors: Slipchenko Lyudmila V. , Gordon Mark S. 
Published: December 2006

AbstractEvaluation of the electrostatic energy within the effective fragment potential (EFP) method is presented. The performance of two variants of the distributed multipole analysis (DMA) together with two different models for estimating the charge penetration energies was studied using six homonuclear dimers. The importance of damping the higher order multipole terms, i.e. charge dipole, was also investigated. Damping corrections recover more than 70% of the charge penetration energy in all dimers, whereas higher order damping introduces only minor improvement. Electrostatic energies calculated by the numerical DMA are less accurate than those calculated by the analytic DMA. Analysis of bonding in the benzene dimer shows that EFP with inclusion of the electrostatic damping term performs very well compared to the high‐level coupled cluster singles, doubles, and perturbative triples method. The largest error of 0.4 kcal/mol occurs for the sandwich dimer configuration. This error is about half the size of the corresponding error in second order perturbation theory. Thus, EFP in the current implementation is an accurate and computationally inexpensive method for calculating interaction energies in weakly bonded molecular complexes. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 276–291, 2007
The role of radial nodes of atomic orbitals for chemical bonding and the periodic table
Authors: Kaupp Martin 
Published: December 2006

AbstractThe role of radial nodes, or of their absence, in valence orbitals for chemical bonding and periodic trends is discussed from a unified viewpoint. In particular, we emphasize the special role of the absence of a radial node whenever a shell with angular quantum number l is occupied for the first time (lack of “primogenic repulsion”), as with the 1s, 2p, 3d, and 4f shells. Although the consequences of the very compact 2p shell (e.g. good isovalent hybridization, multiple bonding, high electronegativity, lone‐pair repulsion, octet rule) are relatively well known, it seems that some of the aspects of the very compact 3d shell in transition‐metal chemistry are less well appreciated, e.g., the often weakened and stretched bonds at equilibrium structure, the frequently colored complexes, and the importance of nondynamical electron‐correlation effects in bonding. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 320–325, 2006
How resonance assists hydrogen bonding interactions: An energy decomposition analysis
Authors: Beck John Frederick , Mo Yirong 
Published: December 2006

AbstractBlock‐localized wave function (BLW) method, which is a variant of theab initiovalence bond (VB) theory, was employed to explore the nature of resonance‐assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between π delocalization and hydrogen‐bonding interactions. We examined the dimers of formic acid, formamide, 4‐pyrimidinone, 2‐pyridinone, 2‐hydroxpyridine, and 2‐hydroxycyclopenta‐2,4‐dien‐1‐one. In addition, we studied the interactions in β‐diketone enols with a simplified model, namely the hydrogen bonds of 3‐hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of π resonance, were decomposed into the Hitler‐London energy (ΔEHL), polarization energy (ΔEpol), charge transfer energy (ΔECT), and electron correlation energy (ΔEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of π conjugation on hydrogen bonding interactions. Although it has been proposed that resonance‐assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole–dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term “resonance‐assisted binding (RAB)” instead of “resonance‐assisted hydrogen bonding (RHAB)” to highlight the electrostatic, which is a long‐range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 455–466, 2007
Rehybridization as a general mechanism for maximizing chemical and supramolecular bonding and a driving force for chemical reactions
Authors: Alabugin Igor V. , Manoharan Mariappan 
Published: December 2006

AbstractDynamic variations in hybridization patterns (rehybridization) were analyzed at B3LYP/6–31G** and MP2/6–31+G* levels. Computations clearly illustrate the generality of rehybridization in a variety of chemical phenomena, which involve structural reorganization in hydrogen‐bonded complexes, nonhyperconjugative stereoelectronic effects in saturated heterocycles, Mills‐Nixon effect, and contrasting substituent effects in cycloaromatization reactions. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 373–390, 2007
Maximum probability domains from Quantum Monte Carlo calculations
Authors: Scemama Anthony , Caffarel Michel , Savin Andreas 
Published: December 2006

AbstractAlthough it would be tempting to associate the Lewis structures to the maxima of the squared wave function |Ψ|2, we prefer in this paper the use of domains of the three‐dimensional space, which maximize the probability of containing opposite‐spin electron pairs. We find for simple systems (CH4, H2O, Ne, N2, C2H2) domains comparable to those obtained with the electron localization function (ELF) or by localizing molecular orbitals. The different domains we define can overlap, and this gives an interesting physical picture of the floppiness of CHand of the symmetric hydrogen bond in FHF−. The presence of multiple solutions has an analogy with resonant structures, as shown in the trans‐bent structure of Si2H2. Correlated wave functions were used (MCSCF or Slater‐Jastrow) in the Variational Quantum Monte Carlo framework. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 442–454, 2007