bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oligonucleotides Containing 7‐Deaza‐2′‐deoxyinosine as Universal Nucleoside: Synthesis of 7‐Halogenated and 7‐Alkynylated Derivatives, Ambiguous Base Pairing, and Dye Functionalization by the Alkyne–Azide ‘Click’ Reaction
Authors: Seela Frank , Ming Xin 
Published: July 2008

AbstractOligonucleotides containing 7‐deaza‐2′‐deoxyinosine derivatives bearing 7‐halogen substituents or 7‐alkynyl groups were prepared. For this, the phosphoramidites 2b–2g containing 7‐substituted 7‐deaza‐2′‐deoxyinosine analogues 1b–1g were synthesized (Scheme 2). Hybridization experiments with modified oligonucleotides demonstrate that all 2′‐deoxyinosine derivatives show ambiguous base pairing, as 2′‐deoxyinosine does. The duplex stability decreases in the order Cd>Ad>Td>Gd when 2b–2g pair with these canonical nucleosides (Table 6). The self‐complementary duplexes 5′‐d(F7c7I‐C)6, d(Br7c7I‐C)6, and d(I7c7I‐C)6 are more stable than the parent duplex d(c7I‐C)6 (Table 7). An oligonucleotide containing the octa‐1,7‐diyn‐1‐yl derivative 1g, i.e., 27, was functionalized with the nonfluorescent 3‐azido‐7‐hydroxycoumarin (28) by the Huisgen–Sharpless–Meldal cycloaddition ‘click’ reaction to afford the highly fluorescent oligonucleotide conjugate 29 (Scheme 3). Consequently, oligonucleotides incorporating the derivative 1g bearing a terminal CC bond show a number of favorable properties: i) it is possible to activate them by labeling with reporter molecules employing the ‘click’ chemistry. ii) Space demanding residues introduced in the 7‐position of the 7‐deazapurine base does not interfere with duplex structure and stability (Table 8). iii) The ambiguous pairing character of the nucleobase makes them universal probes for numerous applications in oligonucleotide chemistry, molecular biology, and nanobiotechnology.
Chemical Approach for the Study of the ‘Kissing Complex’ of Moloney murine leukaemia Virus
Authors: Porcher Sébastien 
Published: July 2008

AbstractThe replication of Moloney murine leukaemia virus relies on the formation of a stable homodimeric ‘kissing complex’ of a GACG tetraloop interacting through only two C⋅G base pairs flanked of 5′‐adjacent unpaired adenosines A9. Previous NMR investigations of a model stem loop 1 has not permitted to reveal the origin of this interaction. Therefore, with the aim of deeper comprehension of the phenomena, the model sequence 10 was prepared where position 9 has been substituted for a nucleoside offering a wider π‐stacking. In this context, the wyosine phosphoramidite building block 2 was prepared and incorporated by adapting the conditions of the automated synthesis and developing original templated enzymatic ligation. However, no ‘kissing interaction’ has been observed for this model sequence 10 due to steric hindrance as confirmed by computational simulation. Consequently, several other model sequences, 18, 23–26, containing modified nucleosides were prepared. Finally, the importance of the cross‐loop H‐bond between G8 and G11 nucleobases was revealed by preparing a 18mer RNA hairpin 27, where the guanosine G8 has been substituted for inosine. The latter, which does not possess a C3 amino function compared to guanosine, is unable to form any ‘kissing complex’ demonstrating the importance of this secondary interaction in the formation of the complex.
DNA Interactions of the Functionalized (Mixed Polypyridine)ruthenium(II) Complex Bis(2,2′‐bipyridine‐κN1,κN1′)(methyl dipyrido[3,2‐a : 2′,3′‐c]phenazine‐11‐carboxylate‐κN4,κN5)ruthenium(2+) ([Ru(bpy)2(dppz‐11‐CO2Me)]2+)
Authors: Tan Li‐Feng , Wang Fang , Chao Hui , Zhang Sheng , Fei Jun‐Jie , Ji Liang‐Nian 
Published: July 2008

AbstractA novel polypyridine ligand, dipyrido[3,2‐a:2′,3′‐c]phenazine‐11‐carboxylic acid methyl ester (=dppz‐11‐CO2Me), and its ruthenium(II) complex, [Ru(bpy)2(dppz‐11‐CO2Me)]2+ (1), were synthesized and characterized. The binding properties of this complex to calf‐thymus DNA (CT‐DNA) were investigated by different spectrophotometric methods and viscosity measurements. The results suggest that the complex binds to DNA in an intercalative mode and serves as a molecular ‘light switch’ for DNA. When irradiated at 365 nm, the complex 1 promoted the photocleavage of plasmid pBR‐322 DNA.
Synthesis and Conformational Studies of a Hybrid Cyclic Peptide Based on cis‐β‐Furanoid Sugar Amino Acid (FSAA) and Ornithine
Authors: Chandrasekhar Srivari , Saritha Birudaraju , Naresh Police , Udayakiran Marelli , Raji Reddy Chada , Jagadeesh Bharatam 
Published: July 2008

AbstractThe conformational control of a 14‐helix nucleating template, cis‐β‐furanoid sugar amino acid (FSAA), over a flexible δ‐amino acid, ornithine is studied in a FSAA‐ornithine cyclic tetrapeptide. Extensive NMR and MD studies reveal that the cyclic peptide adopts a three‐dimentional bowl‐shape cavity, which promotes six‐ and seven‐membered intra‐ and inter‐residue H‐bonding, in polar and non‐polar solvents, respectively.
Scholastic achievement of children with lymphoma or Wilms tumor at the end of comprehensive education—A nationwide, register‐based study
Authors: Lähteenmäki Päivi M. , Sankila Risto , Pukkala Eero , Kyyrönen Pentti , Harila‐Saari Arja 
Published: July 2008

AbstractCancer treatment may affect school performance. School report grades after childhood lymphomas and Wilms tumor have not been previously reported. All Finnish patients with Wilms tumor (N = 74), Hodgkin lymphoma (HL) (N = 99) and non‐Hodgkin lymphoma (NHL) (N = 94) who were born in 1974–1986 and had achieved the age of 16 years were identified from the Finnish cancer registry. Population controls (N = 1329) were matched for age, gender and residence. Their 9th grade school reports were obtained from Statistics Finland. The overall average and grades for mother tongue, first foreign language, mathematics and physical education were compared between the patients and their controls. Almost all the patients (>98%) had finished their comprehensive school. NHL patients had lower overall averages than their controls (difference −0.27 grade units; 95% CI −0.39, −0.15). Irradiation or age at diagnosis did not explain this difference in NHL patients. The grades of NHL patients were significantly lower than those of their controls in each academic school subject, especially in mathematics (−0.45; 95% CI −0.63, −0.27). In mother tongue, girls with irradiation had greatest difference (−0.66, 95% CI −0.99, −0.34) to their controls. Patients with HL and Wilms tumor performed similarly or even better than their controls in all academic subjects. Grades for physical education were impaired in Wilms tumor patients (−0.20; 95% CI −0.33, −0.06). Impairment of school report grades was observed in patients with NHL. The difference to controls was greatest in mathematics. The patients with HL and Wilms tumor, who had not received any central nervous system directed therapy, achieved equally good grades as their controls in all the academic subjects. © 2008 Wiley‐Liss, Inc.
Nuclear microenvironments and cancer
Authors: Stein Gary S. , Davie James R. , Knowlton J. Randy , Zaidi Sayyed K. 
Published: July 2008

AbstractNucleic acids and regulatory proteins are architecturally organized in nuclear microenvironments. The compartmentalization of regulatory machinery for gene expression, replication and repair, is obligatory for fidelity of biological control. Perturbations in the organization, assembly and integration of regulatory machinery have been functionally linked to the onset and progression of tumorigenesis. The combined application of cellular, molecular, biochemical and in vivo genetic approaches, together with structural biology, genomics, proteomics and bioinformatics, will likely lead to new approaches in cancer diagnostics and therapy. J. Cell. Biochem. 104: 1949–1952, 2008. © 2008 Wiley‐Liss, Inc.
Parathyroid hormone‐related protein (107–139) increases human osteoblastic cell survival by activation of vascular endothelial growth factor receptor‐2
Authors: Alonso Verónica , de Gortázar Arancha R. , Ardura Juan A. , Andrade‐Zapata Irene , Alvarez‐Arroyo M. Victoria , Esbrit Pedro 
Published: July 2008

AbstractParathyroid hormone‐related protein (PTHrP) (107–139), in contrast to the N‐terminal fragment PTHrP (1–36), has been shown to interact with the vascular endothelial growth factor (VEGF) system to modulate human osteoblast differentiation. In this study, we evaluated whether this interaction might affect human osteoblastic cell survival. Pre‐incubation with PTHrP (107–139) for 1–24 h dose‐dependently (0.1–100 nM) inhibited dexamethasone‐ or etoposide‐induced cell death in human osteoblastic MG‐63 cells and human osteoblast‐like cells from trabecular bone. This effect, but not that elicited by PTHrP (1–36), was abolished by the VEGF receptor (VEGFR)‐2 inhibitors SU5614 and SU1498 or VEGFR‐2 siRNA transfection in these cells. PTHrP (107–139), but not PTHrP (1–36), at 100 nM, rapidly (within 2 min) increased VEGFR‐2 tyrosine‐phosphorylation in MG‐63 cells; an effect unaffected by several inhibitors of metalloproteinases, neutralizing VEGF165 or VEGFR‐2 antibodies, or the VEGF binding inhibitor CBO‐PP1. The latter two antagonists also failed to affect 125I‐[Tyr116] PTHrP (107–115) binding to these cells. Consistent with its effect on VEGFR‐2 activation, PTHrP (107–139) rapidly induced extracellular signal‐regulated kinase (ERK) 1/2 and Akt activaton, and both ERK and phosphatidylinsositol‐3 kinase (PI3K) inhibitors abolished its pro‐survival effect in human osteoblastic cells. In addition, SU5614 and the latter two types of inhibitors abrogated Runx2 activation by this peptide in MG‐63 cells. Transfection with a dominant‐negative Runx2 construct abolished the pro‐survival effect of PTHrP (107–139), associated with a decrease in Bcl‐2/Bax protein ratio. Our findings demonstrate that PTHrP (107–139) interacts with VEGFR‐2 to promote human osteoblastic cell survival by a mechanism involving Runx2 activation. J. Cell. Physiol. 217: 717–727, 2008. © 2008 Wiley‐Liss, Inc.
New pathway links from cancer‐progression determinants to gene expression of matrix metalloproteinases in breast cancer cells
Authors: DeLassus Gregory S. , Cho Hyojin , Park Janice , Eliceiri George L. 
Published: July 2008

AbstractAP‐2α, interleukin‐4 (IL‐4), E‐cadherin, fibulin 1D, p16INK4α, PTEN, RKIP, and S100A4 are determinants (suppressors, except for S100A4) of cancer cell invasiveness and other traits of cancer progression, which are located upstream of matrix metalloproteinases (MMPs) in cell signaling pathways. We will refer to them as upstream cancer‐progression determinants (UCPDs, for brevity). MMP‐1, MMP‐2, MMP‐9, MMP‐11, MMP‐13, MMP‐14, MMP‐16, and MMP‐19 are enhancers of cancer cell invasiveness and other traits of cancer progression, in MDA‐MB‐231 breast cancer cells. We are interested in pathway links from UCPDs to gene expression of cancer cell MMPs in MDA‐MB‐231 cells. To test models about these links, wild‐type copies of UCPDs were transiently overexpressed and then MMP mRNAs were measured by reverse transcription real‐time PCR. The present results show that each of eight UCPDs is linked to the gene expression of a unique set of MMPs. This indicates that the effects are sequence‐specific and that each UCPD reaches these MMP expressions through different sets of signaling pathways. We have detected 20 new pathway links, 11 are downregulatory and nine are upregulatory; 15 are new links in any cell, and five are new links in breast cancer. In seven links, three cancer‐progression suppressing UCPDs unexpectedly enhance the gene expression of five cancer‐progression promoting MMPs. J. Cell. Physiol. 217: 739–744, 2008. © 2008 Wiley‐Liss, Inc.
Cattle's effect on land and labour productivity: Evidence from Zambia
Authors: Smith Robert E. 
Published: July 2008

AbstractCattle may have become under‐appreciated as a means of boosting staple crop production in areas of recurrent food insecurity. This study tests number of cattle owned as a determinant (alongside agronomic and socio‐economic control variables) of land and labour productivity for hybrid and local maize, and for all crops aggregated by value, from a cross‐sectional sample of 266 small and medium‐sized farms in Zambia's Southern Province. For all tested derivations of productivity, cattle ownership scores strongly as a determinant—more so than, for example, fertiliser application. The strong effect on land productivity (as robust as the expected effect on labour productivity) is ascribed to cattle owners' ability to optimally time ploughing and planting vis‐à‐vis the onset of rains. Cattle re‐stocking thus appears to be an under‐utilised tool of agricultural development. Copyright © 2008 John Wiley & Sons, Ltd.
Stability analysis for the AIBO‐FDTD method
Authors: Liu Guo‐Sheng , Zhang Guo‐Ji , Hu Bin‐Jie 
Published: July 2008

AbstractThe stability of the implicit finite‐difference time‐domain (FDTD) method named alternating implicit block overlapped (AIBO) FDTD is presented in this paper. Based on separation of variables method, the spectral radius of the growth matrix for AIBO‐FDTD is obtained. Analytical results show that the AIBO‐FDTDs both in one‐dimensional and two‐dimensional cases are unconditionally stable. But it is conditionally stable in 3D case, like the conventional FDTD. Numerical results are also presented to demonstrate its effectiveness for parallel processing. Copyright © 2008 John Wiley & Sons, Ltd.
A critical role for collagen II in cartilage matrix degradation: Collagen II induces pro‐inflammatory cytokines and MMPs in primary human chondrocytes
Authors: Klatt Andreas R. , Paul‐Klausch Brigitte , Klinger Gabriele , Kühn Getrud , Renno Joerg H. , Banerjee Marc , Malchau Gebhart , Wielckens Klaus 
Published: July 2008

AbstractWe report a process that results in the acceleration of matrix degradation in human articular cartilage, a phenomenon commonly observed in osteoarthritis (OA). The study was conducted by (1) examining the potential of collagen II in modulating the gene expression profile of primary human chondrocytes (PHCs), and (2) investigating the involvement of pro‐inflammatory signaling cascades. We first tested the collagen II‐dependent induction of pro‐inflammatory cytokines and matrix metalloproteinases (MMPs) in PHCs. PHCs were incubated with or without monomeric (i.e., nonfibrillar) collagen II. Cells were then analyzed by RT‐PCR for the expression of MMP1, MMP3, MMP13, MMP14, and IL‐1β. ELISA was used to quantify IL‐6 and IL‐8 release. To examine the influence of collagen II signaling, specifically the role of MAPK p38, a p38‐inhibitor was added prior to collagen treatment. Changes in IκB concentration were monitored by immunoblot analysis to detect NFκB signaling. Results indicated that incubation of PHCs with collagen II did produce a dose‐dependent induction of MMP1, MMP3, MMP13, MMP14, as well as cytokines IL‐1β, IL‐6, and IL‐8. At the same time, inhibition of p38 and IκB degradation revealed that collagen II‐dependent gene induction also involves MAPK p38 and NFκB signaling. Thus, we provide evidence for a collagen II‐dependent feed‐forward mechanism whereby collagen II induces first MMPs and pro‐inflammatory cytokines and then release of collagen II fragments from mature collagen II fibers. This, in turn, induces more pro‐inflammatory cytokines and MMPs, and the process is repeated, which results in the acceleration and perpetuation of cartilage matrix degradation. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27:65–70, 2009
Ozonization and Cyclic Voltammetry as Efficient Methods for the Regeneration of Gelatin‐Coated SPR Chips
Authors: Van Vlierberghe Sandra , De Wael Karolien , Buschop Hans , Adriaens Annemie , Schacht Etienne , Dubruel Peter 
Published: July 2008

AbstractThe application of ozonization and cyclic voltammetry for the regeneration of gold chips containing a chemisorbed gelatin layer is reported. The efficiency of the regeneration process was analyzed using various surface analysis techniques indicating a complete removal of the biopolymer layer. The current findings open up perspectives for regeneration and multiple application of gold chips for SPR measurements.magnified image
Mechanical and corrosion behaviour of a Ti‐Al‐Nb alloy after deformation at elevated temperatures
Authors: Popa M. V. , Raducanu D. , Vasilescu E. , Drob P. , Cojocaru D. , Vasilescu C. , Ivanescu S. , Rosca J. C. Mirza 
Published: July 2008

AbstractThe mechanical properties of Ti6Al7Nb alloy deformed and heat treated at elevated temperatures were correlated with its microstructure and corrosion behaviour in Ringer (of different pH values: 2.49, 6.9 and 8.9) and Ringer–Brown solutions. Microstructural analysis revealed a Widmanstatten structure for the alloys deformed at 1100 °C (β field) and structure with α grains at 930 °C (α + β field). The thermo‐mechanical processing improved the electrochemical behaviour of Ti6Al7Nb alloys, especially their passive state. Open circuit potential variations in time reflected more compact, stable, resistant passive films on the surface of the treated alloys. Open circuit potential gradients simulating the non‐uniformities of pH along the implant surface have very low values that cannot generate galvanic corrosion. Corrosion rates and ion release are very much reduced. Impedance spectra were fitted with a two time‐constants equivalent circuit for some alloys and with three time‐constants equivalent circuit for other alloys.
Induction of p16ink4a and p19ARF by TGFβ1 contributes to growth arrest and senescence response in mouse keratinocytes
Authors: Vijayachandra Kinnimulki , Higgins William , Lee Jessica , Glick Adam 
Published: July 2008

AbstractTGFβ1 acts as a potent negative regulator of the cell cycle and tumor suppressor in part through induction of cyclin dependent kinase inhibitors p15ink4b, p21, and p57. We previously showed that primary mouse epidermal keratinocytes (MEK) expressing a v‐rasHa oncogene undergo hyperproliferation followed by growth arrest and senescence that was dependent on TGFβ1 signaling and associated with increased levels of p16ink4a and p19ARF. Here we show that the induction of both p16ink4a and p19ARF in v‐rasHa expressing keratinocytes is dependent on TGFβ1 signaling, as TGFβ1 treatment or Smad3 overexpression induces both p16ink4a and p19ARF protein and mRNA, while Smad3 depletion or Smad7 overexpression blocks induction. Genetic ablation of the cdkn2a (ink4a/arf) locus reduced sensitivity to TGFβ1 mediated cell cycle arrest and induction of senescence suggesting that alteration of TGFβ1 responses may be an additional pathway impacted by the inactivation of cdkn2a locus during tumor development. © 2008 Wiley‐Liss, Inc.
Boom in the development of non‐peptidic β‐secretase (BACE1) inhibitors for the treatment of Alzheimer's disease
Authors: Silvestri Romano 
Published: July 2008

Abstractβ‐Amyloid cleaving enzyme‐1 (BACE1) has become a significant target for the therapy of Alzheimer's disease. After the discovery of the first non‐peptidomimetic β‐secretase inhibitors by Takeda Chemicals in 2001, several research teams focused on SAR development of these agents. The non‐peptidic BACE1 inhibitors may potentially overcome the classical problems associated with the peptide structure of first generation, such as blood–brain barrier crossing, poor oral bioavailability and susceptibility to P‐glycoprotein transport. In the past 6 years a boom in research of non‐peptidic BACE1 inhibitors has disseminated findings over hundreds of publications and patents. The rapidly growing literature has been reviewed with particular emphasis on literature of pharmaceutical companies. © 2008 Wiley Periodicals, Inc. Med Res Rev, 29, No. 2, 295–338, 2009
Osteoporosis among ancient Egyptians
Authors: Zaki M. E. , Hussien F. H. , El Banna R. Abd El‐Shafy 
Published: July 2008

AbstractOsteoporosis is a condition of reduced total bone mass per unit volume for the normal ratio of bone mineral to bone matrix. The present work deals with the investigation and evaluation of osteoporosis in ancient Egyptians of two social classes from the Old Kingdom in Giza. The aims of this study are to provide information about the lifestyle and health status of ancient Egyptians, and to detect the causes of osteoporosis. The material consisted of 74 skeletons (43 males and 31 females) from two different social classes (high officials and workers). Skeletons were excavated from the Giza Necropolis and belonged to the Old Kingdom (2687–2191 BC). Dual energy X‐ray absorptiometry (DEXA) was used to measure bone mineral density (BMD) at different skeletal sites (radius, fourth lumbar vertebra and head of femur). Moreover, scanning electron microscopy (SEM) was used to show the microarchitectural structure of the bone. Results showed a significant decrease of BMD values in old age groups compared with younger ones in both sexes. In addition, SEM of trabecular bone in osteoporotic cases demonstrated that the horizontal trabeculae were more affected than the vertical trabeculae. Comparison between high officials and workers revealed that osteoporosis was more frequent in male workers than in male high officials, and in female high officials than in female workers. An elevated prevalence of osteoporosis among male workers may be related to the effects of nutritional stress and excessive workload, while a sedentary lifestyle may have played a role in the occurrence of osteoporosis among female high officials. Moreover, osteoporosis occurs earlier and more frequently in females than males, which may be related to the hormonal changes that accompany the menopause in females. This study emphasises the importance of gender and lifestyle factors in influencing the severity of osteoporosis. Age‐related bone loss at most skeletal sites is noted in both sexes of ancient Egyptians. Copyright © 2008 John Wiley & Sons, Ltd.
Cleavage and functional loss of human apolipoprotein E by digestion of matrix metalloproteinase‐14
Authors: Park Jun Hyoung , Park Sung‐Min , Park Sun‐Hyun , Cho Kyung‐Hyun , Lee Seung‐Taek 
Published: July 2008

AbstractBy means of a degradomic approach applying proteomic techniques, we previously suggested that apolipoprotein E (apoE) is a substrate of matrix metalloproteinase‐14 (MMP‐14). Here we confirm that apoE is, in fact, a substrate of MMP‐14 and also of MMP‐7 and MMP‐2 to a lesser extent. The 34 kDa apoE protein was initially processed by MMP‐14 into fragments with molecular masses of 28, 23, 21, and 11 kDa. MMP‐14 cleavage sites within the apoE protein were determined by C‐terminal labeling of MMP‐14‐digested apoE fragments with isotope (18O/16O = 1:1) and identification of the doublet fragments or peptides showing 2 Da difference by MS, along with N‐terminal sequencing of the fragments. It was determined that the primary MMP‐14 cleavage sites were A176‐I177, P183‐L184, P202‐L203, and Q249‐I250. The MMP‐14‐mediated cleavage of apoE was consistent regardless of whether apoE existed in its lipid‐bound or lipid‐free form. Upon digestion with MMP‐14, apoE loses its ability to suppress the platelet‐derived growth factor‐induced migration of rat vascular smooth muscle cells. Considering the important role of apoE for lipid metabolism and atherosclerosis protection, our findings suggest that MMP‐14 plays an essential role for the development of hyperlipidemia and atherosclerosis as a result of degradation of apoE.