bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive resequence analysis of a 123‐kb region of chromosome 11q13 associated with prostate cancer
Authors: Chung Charles C. , Boland Joseph , Yeager Meredith , Jacobs Kevin B. , Zhang Xijun , Deng Zuoming , Matthews Casey , Berndt Sonja I. , Chanock Stephen J.
Published: July 2011

BACKGROUND

Genome‐wide association studies of prostate cancer have identified single nucleotide polymorphism (SNP) markers in a region of chromosome 11q13.3 in men of European decent. A fine‐mapping analysis with tag SNPs in the cancer genetic markers of susceptibility study identified three independent loci, marked by rs10896438, rs12793759, and rs10896449. This study further annotates common and uncommon variation across this region.

METHODS

A next generation resequence analysis of a 122.9‐kb region of 11q13.3 (68,642,755‐68,765,690) was conducted in 78 unrelated individuals of European background, 1 CEPH trio, and 1 YRI trio.

RESULTS

In total, 644 polymorphic loci were identified by our sequence analysis. Of these, 166 variants—118 SNPs and 48 insertion‐deletion polymorphisms (indels)—were novel, namely not present in the 1000 Genomes or International HapMap Projects. We identified 22, 25, 6, and 4 variants strongly correlated (r2 ≥ 0.8) with rs10896438, rs10896449, rs12793759, and rs11228565, respectively. HapMap SNPs were in linkage disequilibrium (r2 ≥ 0.8) with 48%, 69%, 14%, and 60% of SNPs marking bins by rs10896438, rs10896449, rs12793759, and rs11228565, respectively.

CONCLUSIONS

Our next generation resequence analysis compliments publicly available datasets of European descent (HapMap, build 28 and 1000 Genome, Pilot 1, October 2010), underscoring the value of targeted resequence analysis prior to initiating functional studies based on public databases alone. Increasing the number of common variants enables investigators to better prioritize variants for functional studies designed to uncover the biological basis of the direct association(s) in the region. Prostate 72:476–486, 2012. © 2011 Wiley Periodicals, Inc.
Assessing the risk of lymph node invasion in patients with intermediate risk prostate cancer treated with extended pelvic lymph node dissection. A novel prediction tool
Authors: Briganti Alberto , Capitanio Umberto , Abdollah Firas , Gallina Andrea , Suardi Nazareno , Bianchi Marco , Tutolo Manuela , Salonia Andrea , Freschi Massimo , Rigatti Patrizio , Montorsi Francesco
Published: July 2011

BACKGROUND

Controversy exists regarding the need for extended pelvic lymph node dissection (ePLND) in patients with intermediate risk prostate cancer (PCa).

MATERIALS AND METHODS

The study included 982 consecutive men with intermediate risk PCa (PSA 10–20 ng/ml or cT2b‐c or biopsy Gleason 3 + 4/ 4 + 3) treated with ePLND and radical prostatectomy (RP) at a single center. All patients underwent an anatomically defined ePLND. A novel risk stratification tool was developed by applying the nonparametric tree modeling technique of classification and regression tree analysis (CART) which relied on pre‐operative PSA, clinical stage, biopsy Gleason score, and percentage of positive cores. The area under the receiver characteristic curve (AUC) method was used to quantify the accuracy of the model.

RESULTS

Lymph node invasion (LNI) was found in 81 (8.2%) patients. The CART analyses identified three risk groups of having LNI: a) Low risk: Gleason 3 + 3, cT1c/cT2, PSA 10‐20 ng/ml, or Gleason 3 + 4/4 + 3, ≤63% of positive cores and PSA < 5 ng/ml (risk of LNI: 3.7 and 5.2%, respectively; 64.8% of patients included); b) Moderate risk: Gleason 3 + 4/4 + 3, ≤63% of positive cores and PSA ≥ 5 ng/ml (risk of LNI:14.4%; 23% of patients included); c)High risk: Gleason 3 + 4/4 + 3, % positive cores >63% (risk of LNI:20.1%; 12.% of patients included; P < 0.001). The accuracy of the model was 71%.

CONCLUSIONS

The risk of having LNI varies significantly (3.7–20.1%) in patients with intermediate risk PCa. Our predictive tool might help selecting those patients suitable for ePLND, allowing to spare this approach in about 60% of intermediate risk patients. Prostate 72:499–506, 2012. © 2011 Wiley Periodicals, Inc.
Prostate cancer targeting motifs: Expression of ανβ3, neurotensin receptor 1, prostate specific membrane antigen, and prostate stem cell antigen in human prostate cancer cell lines and xenografts
Authors: Taylor Robert M. , Severns Virginia , Brown David C. , Bisoffi Marco , Sillerud Laurel O.
Published: July 2011

BACKGROUND

Membrane receptors are frequent targets of cancer therapeutic and imaging agents. However, promising in vitro results often do not translate to in vivo clinical applications. To better understand this obstacle, we measured the expression differences in receptor signatures among several human prostate cancer cell lines and xenografts as a function of tumorigenicity.

METHODS

Messenger RNA and protein expression levels for integrin ανβ3, neurotensin receptor 1 (NTSR1), prostate specific membrane antigen (PSMA), and prostate stem cell antigen (PSCA) were measured in LNCaP, C4‐2, and PC‐3 human prostate cancer cell lines and in murine xenografts using quantitative reverse transcriptase polymerase chain reaction, flow cytometry, and immunohistochemistry.

RESULTS

Stable expression patterns were observed for integrin αν and PSMA in all cells and corresponding xenografts. Integrin β3 mRNA expression was greatly reduced in C4‐2 xenografts and greatly elevated in PC‐3 xenografts compared with the corresponding cultured cells. NTSR1 mRNA expression was greatly elevated in LNCaP and PC‐3 xenografts. PSCA mRNA expression was elevated in C4‐2 xenografts when compared with C4‐2 cells cultured in vitro. Furthermore, at the protein level, PSCA was re‐expressed in all xenografts compared with cells in culture.

CONCLUSIONS

The regulation of mRNA and protein expression of the cell‐surface target proteins ανβ3, NTSR1, PSMA, and PSCA, in prostate cancer cells with different tumorigenic potential, was influenced by factors of the microenvironment, differing between cell cultures and murine xenotransplants. Integrin ανβ3, NTRS1 and PSCA mRNA expression increased with tumorigenic potential, but mRNA expression levels for these proteins do not translate directly to equivalent expression levels of membrane bound protein. Prostate 72:523–532, 2012. © 2011 Wiley Periodicals, Inc.
Organ specific Gst‐pi expression of the metastatic androgen independent prostate cancer cells in nude mice
Authors: Naiki Taku , Asamoto Makoto , Toyoda‐Hokaiwado Naomi , Naiki‐Ito Aya , Tozawa Keiichi , Kohri Kenjiro , Takahashi Satoru , Shirai Tomoyuki
Published: July 2011

BACKGROUND

Elucidating the mechanisms of metastasis in prostate cancer, particularly to the bone, is a major issue for treatment of this malignancy. We previously reported that an androgen‐independent variant had higher expression of glutathione S‐transferase pi (Gst‐pi) compared with a parent androgen‐dependent transplantable rat prostate carcinoma which was established from the transgenic rat for adenocarcinoma of the prostate (TRAP).

METHODS

A new cell line, PCai1, was established from the androgen‐independent tumor and investigated its metastatic potential in nude mice. The tumorigenesis of PCai1 cells in vivo was studied by subcutaneous transplantations into nude mice. The growth in the microenvironment of the prostate was studied by orthotopic transplantation of PCai1 cells into nude mice. The metastatic potential of PCai1 cells was studied by tail vein injections. Effects of Gst‐pi knocked down were analysis in PCai1 cells.

RESULTS

PCai1 frequently formed metastatic lesions in the lung and lymph nodes after orthotopic implantation in the prostate. Intravenous injections of PCai1, metastasis to lung and bone were obvious. PCai1 had strong expression for Gst‐pi, therefore we tried knocked down Gst‐pi. Gst‐pi‐siRNA in vitro significantly suppressed cell proliferation rate. In addition, high levels of intracellular reactive oxygen species (ROS) were recognized in the Gst‐pi knockout.

CONCLUSIONS

Gst‐pi expression of the prostate cancers are dependent on metastatic site, and that Gst‐pi has an important role in adapting prostate cancer for growth and metastasis involving an alteration of ROS signals. Prostate 72:533–541, 2012. © 2011 Wiley Periodicals, Inc.
The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling
Authors: Li Jianing , Abel Robert , Zhu Kai , Cao Yixiang , Zhao Suwen , Friesner Richard A.
Published: July 2011

A novel energy model (VSGB 2.0) for high resolution protein structure modeling is described, which features an optimized implicit solvent model as well as physics‐based corrections for hydrogen bonding, π–π interactions, self‐contact interactions, and hydrophobic interactions. Parameters of the VSGB 2.0 model were fit to a crystallographic database of 2239 single side chain and 100 11–13 residue loop predictions. Combined with an advanced method of sampling and a robust algorithm for protonation state assignment, the VSGB 2.0 model was validated by predicting 115 super long loops up to 20 residues. Despite the dramatically increasing difficulty in reconstructing longer loops, a high accuracy was achieved: all of the lowest energy conformations have global backbone RMSDs better than 2.0 Å from the native conformations. Average global backbone RMSDs of the predictions are 0.51, 0.63, 0.70, 0.62, 0.80, 1.41, and 1.59 Å for 14, 15, 16, 17, 18, 19, and 20 residue loop predictions, respectively. When these results are corrected for possible statistical bias as explained in the text, the average global backbone RMSDs are 0.61, 0.71, 0.86, 0.62, 1.06, 1.67, and 1.59 Å. Given the precision and robustness of the calculations, we believe that the VSGB 2.0 model is suitable to tackle “real” problems, such as biological function modeling and structure‐based drug discovery. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Computed structures of point deletion mutants and their enzymatic activities
Authors: Berrondo Monica , Gray Jeffrey J.
Published: July 2011

Point deletions in enzymes can vary in effect from negligible to complete loss of activity; however, these effects are not generally predictable. Deletions are widely observed in nature and often result in diseases such as cancer, cystic fibrosis, or osteogenesis imperfecta. Here, we have developed an algorithm to model the perturbed structures of deletion mutants with the ultimate goal of predicting their activities. The algorithm works by deleting the specified residue from the wild‐type structure, creating a gap that is closed using a combination of local and global moves that change the backbone torsion angles of the protein structure. On a set of five proteins for which both wild‐type and deletion mutant x‐ray crystal structures are available, the algorithm produces deep, narrow energy funnels within 1.5 Å of the crystal structure for the deletion mutants. To assess the ability of our algorithm to predict activity from the predicted structures, we tested the correlation of experimental activity with several measures of the predicted structure ensemble using a set of 45 point deletions from ricin. Estimates incorporating likely prevalence of active and inactive deletion sites suggest that activity can be predicted correctly over 60% of the time from the active site root‐mean squared deviation of the lowest energy predicted structures. The predictions are stronger than simple sequence organization measures, but more fundamental work is required in structure prediction and enzyme activity determination to allow consistent prediction of activity. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Mössbauer spectroscopy analysis of iron compounds in carboxylated multiwall carbon nanotubes and their ammonium salt
Authors: Jamrozik Agnieszka , Mazurkiewicz Marta , Małolepszy Artur , Stobiński Leszek , Matlak Krzysztof , Korecki Józef , Kurzydłowski Krzysztof Jan , Burda Kvĕtoslava
Published: July 2011

Different forms of iron compounds embedded in non‐functionalized (as prepared) and functionalized multiwall carbon nanotubes (MWCNTs) were studied. Iron used to catalyze MWCNT synthesis can be found inside nanotubes and built‐in within their walls. Mössbauer spectroscopy was applied to study valence and spin states as well as magnetic ordering of the iron compounds. In the Mössbauer spectra of as prepared MWCNTs the Fe3C carbide provides the main contribution. The content of Fe3C decreases by about 20 and 40% in carboxylated carbon nanotubes (MWCNTs‐COOH) and ammonium salt of carboxylated carbon nanotubes (MWCNTs‐COONH4), respectively. A small amount of α‐Fe and FexCx iron forms are always observed in all studied carbon nanotubes. In MWCNTs‐COOH, additionally, ferrihydrates and/or FexCy with oxygen in the second coordination sphere of iron are present (at a level of about 17%). In MWCNTs‐COONH4 their content increases by a factor of 3. The experimental data shows that the purification and functionalization of as prepared MWCNTs result in removal of about 90% of iron contaminations. Additionally, we observe the modification of iron compounds inside MWCNTs. All these results are important in optimizing the as prepared MWCNT purification process and in finding a new way to produce different Fe phases inside MWCNTs.
Tailoring properties of borohydrides for hydrogen storage: A review
Authors: Rude Line H. , Nielsen Thomas K. , Ravnsbæk Dorthe B. , Bösenberg Ulrike , Ley Morten B. , Richter Bo , Arnbjerg Lene M. , Dornheim Martin , Filinchuk Yaroslav , Besenbacher Flemming , Jensen Torben R.
Published: July 2011

Hydrogen is recognized as a possible future energy carrier, which can be produced from renewable energy and water. A major challenge in a future ‘hydrogen economy’ is the development of safe, compact, robust, and efficient means of hydrogen storage, in particular for mobile applications. The present review focuses on light metal boron based hydrides, for which the general interest has expanded significantly during the past few years. Synthesis methods, physical, chemical and structural properties of novel boron based hydrides are reviewed along with new approaches for improving kinetic and thermodynamic properties: (i) anion substitution, (ii) reactive hydride composites and (iii) nanoconfinement of hydrides and chemical reactions. The light metal borohydrides reveal a fascinating structural chemistry and have the potential for storing large amounts of hydrogen. A combination of the different approaches may provide a new route to a wide range of interesting energy storage materials in the future.
Studies of Fe‐binding sites within multiwall carbon nanotubes using Mössbauer spectroscopy
Authors: Luberda‐Durnaś Katarzyna , Nieznalska Magdalena , Mazurkiewicz Marta , Małolepszy Artur , Khachataryan Gohar , Khachataryan Karen , Tomasik Piotr , Michalski Oskar , Matlak Krzysztof , Korecki Józef , Stobinski Leszek , Burda Květoslava
Published: July 2011

The potential applications of carbon nanotubes (CNTs) are strongly related to their physical and chemical properties. In this work, results of different methods for the oxidation of crude CNTs are reported. These methods changed Fe binding sites within multiwall carbon nanotubes (MWCNTs). Mössbauer spectroscopy was used to detect the chemical properties of the Fe‐phases in MWCNTs. Signals from the iron carbide Fe3C were the main components in the Mössbauer spectra of unmodified MWCNTs revealing magnetic ordering even at 300 K. In oxidized MWCNTs, the amount of Fe3C decreased and γ‐Fe and α‐Fe, ferrihydrates of iron oxides and different forms of goethite appeared. In MWCNTs oxidized with HClO4, a significant fraction (∼24%) of magnetically ordered Fe2O3 particles was detected. This study showed that traces of iron catalyst embedded in MWCNTs could be used as a sensitive probe to monitor various MWCNT modifications.
Al catalyzed growth of silicon nanowires and subsequent in situ dry etching of the catalyst for photovoltaic application
Authors: Kohen David , Tileli Vasiliki , Cayron Cyril , Faucherand Pascal , Morin Christine , Dufourcq Joël , Noël Sébastien , Levis Michel , Brioude Arnaud , Perraud Simon
Published: July 2011

Aluminum‐catalyzed epitaxial growth of silicon nanowire (SiNW) arrays was performed on Si wafer by chemical vapor deposition at 600 °C. The arrays showed a low optical total reflectance in the visible light spectrum, with a minimum of 2% around 450 nm wavelength. Following SiNW growth, dry etching of the Al catalyst was performed in situ using HCl chemistry at 600 °C. The effectiveness of aluminum etching was assessed by energy dispersive X‐ray spectroscopy, by high resolution transmission electron microscopy and by a controlled growth experiment. This SiNW array growth and subsequent catalyst dry etching opens up the possibility of an all in vacuum fabrication process of radial junction solar cells.

Al catalyst dry etching following growth using HCl gas at 600 °C.

magnified image

Al catalyst dry etching following growth using HCl gas at 600 °C.
Pentagonal puckering in a sheet of amorphous graphene
Authors: Li Y. , Inam F. , Kumar Avishek , Thorpe M. F. , Drabold D. A.
Published: July 2011

Ordered graphene has been extensively studied. In this paper, we undertake a density functional study of topologically disordered analogs of graphene, in the form of a random network, consisting predominantly of hexagonal rings, but also including pentagons and heptagons. After some preliminaries with crystalline material, we relax various random network models and find that the presence of carbon pentagons induce local curvature, thus breaking the initial planar symmetry, in some analogy with the case of fullerenes. Using density functional theory to calculate the total energy, we find that while the planar state is locally stable, there is a puckered state that has lower energy. The scale of the puckering is consistent with that expected with local maxima and minima associated with pentagons surrounded by larger rings, forming local “buckyball domes”.
Density functional theory studies on structures and absorption spectra of [Au(tpy)Cl]2+ and its derivatives: Role of basis set, functional, solvent effect, and spin orbit effect
Authors: Li Haibin , Wu Shuixing , Liao Yi , Su Zhongmin , Kan Yuhe , Tang Xueling
Published: July 2011

The geometries of [Au(tpy)Cl]2+ (tpy = 2,2′:6′,2″‐terpyridine) and its derivatives (1–4) were optimized using relativistic density functional theory (DFT) at both scalar and two‐component spin orbit coupling (SOC) level of theory via zero order regular approximation (ZORA). The combination of OPTX exchange, PW91c correlation functional (denoted as OP91), all‐electron ZORA TZ2P basis set was found to be the optimal combination for geometry. The results reveal that both SOC and substituents have little effect on the geometry of complexes 1–4. Then, their absorption spectra were investigated by scalar relativistic time dependent DFT (TDDFT)/SAOP/TZ2P in vacuum, in CH2Cl2, CH3CN solvents by means of conductor like screening model. The calculations indicate that the nature of the low‐lying spin‐allowed excited states is gold‐perturbed intraligand transition, namely charge reorganization. This fact also demonstrates that the influence of the polarity of solvent on absorption spectra of 1–4 is negligible. The spin orbit TDDFT was also performed to get further insight into the effect of SOC on the absorption spectra. It is found that the SOC has little influence on the simulation of electronic spectrum of complexes 1–4 due to no significant involvement of d‐orbitals during electronic transition. Our conclusions are reliable and are in good agreement with the previous experimental results and theoretical investigations. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
An experimental and theoretical approach to the molecular structure of 3‐{[4‐(3‐Methyl‐3‐phenyl‐cyclobutyl)‐thiazol‐2‐yl]‐hydrazono}‐1,3‐dihydro‐ indol‐2‐one
Authors: Saraçoğlu Hanİfe , Cukurovali Alaaddin
Published: July 2011

The title molecule, 3‐{[4‐(3‐methyl‐3‐phenyl‐cyclobutyl)‐thiazol‐2‐yl]‐hydrazono}‐1,3‐dihydro‐indol‐2‐one (C22H20N4O1S1), was prepared and characterized by 1H NMR, 13C NMR, IR, UV–visible, and single‐crystal X‐ray diffraction. The compound crystallizes in the monoclinic space group P21 with a = 8.3401(5), b = 5.6976(3), c = 20.8155(14) Å, and β = 95.144(5)°. Molecular geometry from X‐ray experiment and vibrational frequencies of the title compound in the ground state has been calculated using the Hartree–Fock with 6‐31G(d, p) and density functional method (B3LYP) with 6‐31G(d, p) and 6‐311G(d, p) basis sets, and compared with the experimental data. The calculated results show that optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies values show good agreement with experimental data. Density functional theory calculations of the title compound and thermodynamic properties were performed at B3LYP/6‐31G(d, p) level of theory. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
New graphical representation of a DNA sequence based on the ordered dinucleotides and its application to sequence analysis
Authors: Huang Yujuan , Wang Tianming
Published: July 2011

Graphical representation of a DNA sequence is a powerful tool for basic biological research. Based on the ordered dinucleotides, we propose a novel three dimensional (3D) graphical representation without circuit or degeneracy. Simultaneously, we derive the projection curve of the 3D graph. These two curves have good visualization for longer DNA sequences. The utility of the proposed curves is illustrated by mutation analysis, similarity analysis, and evolutionary relationships of different species. The results indicate that our method is efficient and powerful. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Vibrational contribution to static and dynamic (Hyper)polarizabilities of zigzag BN nanotubes calculated by the finite field nuclear relaxation method
Authors: Ferrabone Matteo , Kirtman Bernard , Lacivita Valentina , Rérat Michel , Orlando Roberto , Dovesi Roberto
Published: July 2011

The vibrational contribution to static and dynamic (hyper)polarizabilities for the zigzag (n,0) family of BN nanotubes, with n ranging from (6,0) to (36,0), has been obtained. Calculations were done by the finite field nuclear relaxation (FF‐NR) method for periodic systems, newly implemented in the CRYSTAL code, using the Coupled Perturbed Kohn‐Sham (CPKS) scheme at the B3LYP/6‐31G* level for the required electronic properties. Both transverse and transverse‐longitudinal tensor components are determined by applying finite, i.e. static, fields in the transverse direction. The magnitude of the vibrational term increases with the radius of the nanotube as determined by the increase in the field‐induced geometric deformation. The resulting vibrational (hyper)polarizability varies from being dominant to negligible, when compared with the corresponding static electronic contribution. This depends upon the radius, as well as the property and the component, in a systematic manner. The extension to longitudinal components, not yet available, will be implemented next. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Double icosahedron‐based motif of Nin (n = 20−30)
Authors: Song Wei , Lu Wen‐Cai , Zang Qing‐Jun , Wang C. Z. , Ho K. M.
Published: July 2011

A genetic algorithm (GA) coupled with a tight‐binding (TB) interatomic potential was used to search for the low‐energy structures of the medium‐sized Nin (n = 20−30) clusters. The low‐energy candidate structures from the GA/TB search were further optimized by using the density functional theory calculations with the Perdew, Burke, and Ernzerhof exchange‐correlation energy functional. The obtained lowest‐energy structures of the medium‐sized Nin (n = 20−30) clusters are shown to exhibit double icosahedron‐based motif. The properties of the nickel clusters including binding energies, second differences in energy, and especially magnetic properties have also been studied. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Theoretical thermochemistry: Enthalpies of formation of a set of nitrogen‐containing compounds
Authors: He Xin , Zhang Jiaheng , Gao Haixiang
Published: July 2011

Gas‐phase standard state formation enthalpies of 63 nitrogen‐containing compounds (NCCs) were studied by computational methods. Gaussian‐n and complete basis set composite methods were applied. After the calculation of the set of NCCs, the results were analyzed in several ways. All the seven selected methods depicted various precisions in this work. According to the calculations and further data processing, G4 was proven to be appropriate and capable of formation enthalpy calculations on NCCs with a mean absolute deviation of 0.63 kcal/mol. Thus, G4 calculation may help us on choosing experimental values and conducting predictions. Isodesmic reactions using G4 methods are also conducted and further correction was given. The high accuracy of G4 method makes it reliable for calculating gas‐phase enthalpies of formations and allows them to serve as a valuable check on the accuracy of reported experimental data. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Structure‐Dependence of the magnetic moment in small palladium clusters: Surprising results from the M06‐L Meta‐GGA functional
Authors: Koitz Ralph , Soini Thomas M. , Genest Alexander , Trickey S. B. , Rösch Notker
Published: July 2011

The size‐ and structure‐dependence of the magnetic moment in Pdn clusters (n = 13, 19, 38) was studied with density functional theory. We compare the Becke‐Perdew gradient‐corrected exchange‐correlation functional with the parameterized meta‐generalized gradient approximation functional by Zhao and Truhlar (M06‐L). Although the former functional shows the expected quenching of the clusters' magnetic moment with increasing nuclearity, the latter one predicts a strongly increasing magnetic moment. In a series of fixed‐spin calculations with the two functionals at different geometries, we observe a strong dependence of the magnetic moment on the cluster structure, where the untypically long metal‐metal bonds predicted by the M06‐L functional are a dominant influence on the stability of the high‐spin cluster configurations. Furthermore, we observe differing behavior of the two functionals with respect to the magnetic moment as particular bonds in the cluster are strained, indicating that, in addition to the structural contribution, the description of exchange‐correlation energy in the M06‐L functional may intrinsically favor high magnetic moments in these Pd clusters. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Wigner crystallization of quadratically dispersing electrons in graphene
Authors: Iyakutti Kombiah , Surya Velappa Jayaraman , Rajeswarapalanichamy Ratnavelu , Kawazoe Yoshiyuki
Published: July 2011

The graphene surface with the unpaired π electrons presents an ideal two‐dimensional electron system. Although the effective massless Dirac fermions are important, they are not the only carriers that describe the quantum transport in graphene. Above zero energy, the current carrying carriers in graphene are the usual electrons. This electron density may vary depending on the surface defects and π–σ interaction, and this may lead to a possible Wigner crystallization on the surface of graphene. Calculations for nonmagnetic, ferromagnetic, and antiferromagnetic Wigner crystals are carried out based on the Koster–Kohn variational principle for direct calculation of Wannier functions. The effect of positive background due to the carbon ions is suitably treated. From our results, we find that Wigner crystallization is possible in grapheme, if we consider the electrons on the surface, which obey quadratic dispersion relation. The electron crystal with ferromagnetic phase and face centered square lattice structure has the lowest energy. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Ab initio path integral simulation of AgOH(H2O)
Authors: Koizumi Akihito , Suzuki Kimichi , Shiga Motoyuki , Tachikawa Masanori
Published: July 2011

Ab initio path integral molecular dynamics simulation of MOH(H2O) (M = Cu, Ag, and Au) clusters has been performed to analyze how the hydrogen‐bonded proton can be affected by the counter noble metal cation. The CuOH(H2O) cluster does not form hydrogen bonded structure even for the static equilibrium structures. Contrary to our previous article of hydrated alkali metal hydroxide clusters (Koizumi et al., J Chem Phys 2011, 134, 031101), proton transferred distribution was not observed because of the high potential barrier heights of MOH(H2O). © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Temperature Determination of Resonantly Excited Plasmonic Branched Gold Nanoparticles by X‐ray Absorption Spectroscopy
Authors: Van de Broek Bieke , Grandjean Didier , Trekker Jesse , Ye Jian , Verstreken Kris , Maes Guido , Borghs Gustaaf , Nikitenko Sergey , Lagae Liesbet , Bartic Carmen , Temst Kristiaan , Van Bael Margriet J.
Published: July 2011

The fields of bioscience and nanomedicine demand precise thermometry for nanoparticle heat characterization down to the nanoscale regime. Since current methods often use indirect and less accurate techniques to determine the nanoparticle temperature, there is a pressing need for a direct and reliable element‐specific method. In‐situ extended X‐ray absorption fine structure (EXAFS) spectroscopy is used to determine the thermo‐optical properties of plasmonic branched gold nanoparticles upon resonant laser illumination. With EXAFS, the direct determination of the nanoparticle temperature increase upon laser illumination is possible via the thermal influence on the gold lattice parameters. More specifically, using the change of the Debye–Waller term representing the lattice disorder, the temperature increase is selectively measured within the plasmonic branched nanoparticles upon resonant laser illumination. In addition, the signal intensity shows that the nanoparticle concentration in the beam more than doubles during laser illumination, thereby demonstrating that photothermal heating is a dynamic process. A comparable temperature increase is measured in the nanoparticle suspension using a thermocouple. This good correspondence between the temperature at the level of the nanoparticle and at the level of the suspension points to an efficient heat transfer between the nanoparticle and the surrounding medium, thus confirming the potential of branched gold nanoparticles for hyperthermia applications. This work demonstrates that X‐ray absorption spectroscopy‐based nanothermometry could be a valuable tool in the fast‐growing number of applications of plasmonic nanoparticles, particularly in life sciences and medicine.
Evolution of Langmuir Film of Nanoparticles Through Successive Compression Cycles
Authors: Kim Jin Young , Raja Shilpa , Stellacci Francesco
Published: July 2011

The success of nanoparticle‐based devices will need reliable fabrication methods for well‐defined, defect‐free self‐assembled structures of nanoparticles (NPs). NP self‐assembly is a process governed by an interplay between many inter‐particle interactions, such as core–core van der Waals and dipolar attractions, as well as interactions of the ligand shells, which, when generating an interpenetration, is called interdigitation. The result of this delicate balance between strong interactions is often kinetically hindered; hence, the reaching and recognition of an equilibrium structure becomes challenging. Here, a systematic study is presented that aims at approaching equilibrium 2D NP assemblies (i.e., NP monolayers) based on cyclic compression and relaxation in Langmuir NP monolayers. Cyclic isotherm curves are taken at various surface pressures together with a complete characterization of the corresponding structural evolution of the NP structures. Results are obtained through the analysis of the images, using in‐house software that enables the analysis and visualization of the degree of ligand interdigitation as well as the NPs short‐ and long‐range order. It is found that the initial structures obtained through Langmuir assembly can be quite far from equilibrium, mostly due to inhomogeneities in the ligand shell interdigitation and interaction. A few compression cycles render the whole assembly more homogeneous and significantly increases the long‐range order. Finally, this structural analysis shows that the ligand shell can act a buffer to the size polydispersity in the particle cores.
Clustering genes with expression and beyond
Authors: Shiga Motoki , Mamitsuka Hiroshi
Published: July 2011

Clustering over gene expression is now a popular computational analysis in biology. In general, the amount of expression can be measured by high‐throughput techniques over thousands of genes simultaneously. The expression dataset can be a large table (or matrix) with numerical values, each being specified by one gene and one sample, and needs computational methods to be analyzed. This review starts with surveying techniques of clustering genes by expression, classifying them into three types: hierarchical, partitional, and subspace clustering. Major methods of hierarchical and partitional clustering as well as a variety of algorithms for subspace clustering are extensively reviewed. Techniques for clustering over expression, however, are now well matured and their performance is limited due to the inevitable noisiness of the high‐throughput nature of expression data. We then extend the scope of this review further to clustering genes with recently emerging data, gene networks, and show graph partitioning approaches, such as spectral methods, for clustering genes by a network. Furthermore, advanced approaches of gene clustering now combine gene networks with expression. This setting corresponds to so‐called semi‐supervised clustering in machine learning, and approaches under this problem setting will be widely reviewed, classifying those approaches into three types. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 496–511 DOI: 10.1002/widm.41

This article is categorized under:

Algorithmic Development > Biological Data Mining

Application Areas > Science and Technology

Technologies > Machine Learning
Nanotechnology in interventional cardiology
Authors: Cyrus Tillmann , Wickline Samuel A. , Lanza Gregory M.
Published: July 2011

High‐grade atherosclerotic stenoses are reduced to zero or minimal residual stenosis grades by a single or a series of balloon angioplasties. Currently, stents are implanted to prevent immediate vascular recoil and elution of an antimitotic drug from the stent struts minimizes restenosis. An unwanted side‐effect of this drug elution is delayed re‐endothelialization which requires treatment with two anti‐platelet drugs, in many cases for a minimum of 1 year to prevent acute in‐stent thrombosis. Advances in stent design and drug elution technology, now in its fourth generation, have not abated this issue. Nanotechnology‐based local drug delivery has the potential to achieve restenosis prevention while not impeding endothelial healing. Molecularly targeted drugs can be aimed to specifically bind to epitopes in the injured media and adventitia. Thus, endothelial healing may progress unhindered. To prevent restenosis, this technology may be used with bare metal or biodegradable stents. In this article novel nanoparticulate agents will be compared regarding their potential to deliver drugs to molecular targets within the vascular wall. Potential molecular targets, targeting mechanisms, drug‐delivery propensities, and biocompatibility will be reviewed. WIREs Nanomed Nanobiotechnol 2012, 4:82–95. doi: 10.1002/wnan.154

This article is categorized under:

Therapeutic Approaches and Drug Discovery > Emerging Technologies

Diagnostic Tools > In Vivo Nanodiagnostics and Imaging

Therapeutic Approaches and Drug Discovery > Nanomedicine for Cardiovascular Disease
Clinical Significance of the B7‐H4 Coregulatory Molecule as a Novel Prognostic Marker in Gastric Cancer
Authors: Arigami Takaaki , Uenosono Yoshikazu , Ishigami Sumiya , Hagihara Takahiko , Haraguchi Naoto , Natsugoe Shoji
Published: July 2011

Background

The B7‐H4 coregulatory molecule is a member of the B7 family of molecules, which regulate the T‐cell‐mediated immune response through CD28 receptors. Recently, B7‐H4 has been reported to be a negative regulator of the immune response in patients with several malignant diseases. However, few reports have investigated the clinical significance of B7‐H4 expression in patients with gastric cancer. In the present study, we analyzed B7‐H4 expression and the relationship between its expression and clinicopathological factors including prognosis in gastric cancer.

Methods

B7‐H4 expression in gastric cancer cell lines and clinical gastric cancer specimens was initially assessed with the reverse transcription‐polymerase chain reaction (RT‐PCR). Moreover, B7‐H4 and CD3 expression in 120 resected specimens from gastric cancer patients were evaluated by immunohistochemistry (IHC).

Results

B7‐H4 expression was identified in the gastric cancer cell lines and clinical tumor tissues by RT‐PCR. B7‐H4 expression was high in 25.8% (31/120) of resected tumor specimens. B7‐H4 expression significantly correlated with tumor stage (P = 0.04). The 5‐year survival rate was significantly lower in patients with high B7‐H4 expression than in those with low B7‐H4 expression (P = 0.001). Multivariate analysis demonstrated that B7‐H4 expression was an independent prognostic factor (P = 0.035). Immunohistochemical analysis of CD3 expression showed that B7‐H4 expression was inversely correlated with the number of tumor infiltrating T lymphocytes (P < 0.001).

Conclusions

The B7‐H4 coregulatory molecule is a novel prognostic marker related to the T‐cell‐mediated immune response, and its pathway may be a molecular target for controlling tumor progression in patients with gastric cancer.
Acute Ethanol Intoxication and the Trauma Patient: Hemodynamic Pitfalls
Authors: Bilello John , McCray Victor , Davis James , Jackson LaScienya , Danos Leigh Ann
Published: July 2011

Many trauma patients are acutely intoxicated with alcohol. Animal studies have demonstrated that acute alcohol intoxication inhibits the normal release of epinephrine, norepinephrine, and vasopressin in response to acute hemorrhage. Ethanol also increases nitric oxide release and inhibits antidiuretic hormone secretion. This article studies the effects of alcohol intoxication (measured by blood alcohol level, BAL) on the presentation and resuscitation of trauma patients with blunt hepatic injuries. A retrospective registry and chart review was conducted of all patients who presented with blunt liver injuries at an ACS‐verified, level I trauma center. Data collected included admission BAL, systolic blood pressure, hematocrit, International Normalized Ratio (INR), liver injury grade, Injury Severity Score (ISS), intravenous fluid and blood product requirements, base deficit, and mortality. From September 2002 to May 2008, 723 patients were admitted with blunt hepatic injuries. Admission BAL was obtained in 569 patients, with 149 having levels >0.08%. Intoxicated patients were more likely to be hypotensive on admission (p = 0.01) despite a lower liver injury grade and no significant difference in ISS. There was no significant difference in the percent of intoxicated patients requiring blood transfusion. However, when blood was given, intoxicated patients required significantly more units of packed red blood cells (PRBC) than their nonintoxicated counterparts (p = 0.01). Intoxicated patients also required more intravenous fluid during their resuscitation (p = 0.002). Alcohol intoxication may impair the ability of blunt trauma patients to compensate for acute blood loss, making them more likely to be hypotensive on admission and increasing their PRBC and intravenous fluid requirements. All trauma patients should have BAL drawn upon admission and their resuscitation should be performed with an understanding of the physiologic alterations associated with acute alcohol intoxication.
Random UV-C mutagenesis ofScheffersomyces(formerlyPichia)stipitisNRRL Y-7124 to improve anaerobic growth on lignocellulosic sugars
Authors: Hughes Stephen R , Gibbons William R , Bang Sookie S , Pinkelman Rebecca , Bischoff Kenneth M , Slininger Patricia J , Qureshi Nasib , Kurtzman Cletus P , Liu Siqing , Saha Badal C , Jackson John S , Cotta Michael A , Rich Joseph O , Javers Jeremy E
Published: July 2011

Scheffersomyces (formerly Pichia) stipitis NRRL Y-7124 was mutagenized using UV-C irradiation to produce yeast strains for anaerobic conversion of lignocellulosic sugars to ethanol. UV-C irradiation potentially produces large numbers of random mutations broadly and uniformly over the whole genome to generate unique strains. Wild-type cultures of S. stipitis NRRL Y-7124 were subjected to UV-C (234 nm) irradiation targeted at approximately 40% cell survival. When surviving cells were selected in sufficient numbers via automated plating strategies and cultured anaerobically on xylose medium for 5 months at 28°C, five novel mutagenized S. stipitis strains were obtained. Variable number tandem repeat analysis revealed that mutations had occurred in the genome, which may have produced genes that allowed the anaerobic utilization of xylose. The mutagenized strains were capable of growing anaerobically on xylose/glucose substrate with higher ethanol production during 250- to 500-h growth than a Saccharomyces cerevisiae yeast strain that is the standard for industrial fuel ethanol production. The S. stipitis strains resulting from this intense multigene mutagenesis strategy have potential application in industrial fuel ethanol production from lignocellulosic hydrolysates.
Combined methylmalonic acidemia and homocystinuria, cblC type. II. Complications, pathophysiology, and outcomes
Authors: Carrillo‐Carrasco Nuria , Venditti Charles P.
Published: July 2011

Combined methylmalonic acidemia and homocystinuria, cblC type, is stated to be the most common inborn error of intracellular cobalamin metabolism. The disorder can display a wide spectrum of clinical manifestations, spanning the prenatal period through late adulthood. While increased homocysteine concentrations and impaired methyl group metabolism may contribute to disease‐related complications, the characteristic macular and retinal degeneration seen in many affected patients appears to be unique to cblC disease. The early detection of cblC disease by newborn screening mandates a careful assessment of therapeutic approaches and provides a new opportunity to improve the outcome of affected patients. The following article reviews the current knowledge on the complications, pathophysiology, and outcome of cblC disease in an effort to better guide clinical practice and future therapeutic trials.
Natural history of alkaptonuria revisited: analyses based on scoring systems
Authors: Ranganath Lakshminarayan R. , Cox Trevor F.
Published: July 2011

Increased circulating homogentisic acid in body fluids occurs in alkaptonuria (AKU) due to lack of enzyme homogentisate dioxygenase leading in turn to conversion of HGA to a pigmented melanin‐like polymer, known as ochronosis. The tissue damage in AKU is due to ochronosis. A potential treatment, a drug called nitisinone, to decrease formation of HGA is available. However, deploying nitisinone effectively requires its administration at the most optimal time in the natural history. AKU has a long apparent latent period before overt ochronosis develops. The rate of change of ochronosis and its consequences over time following its recognition has not been fully described in any quantitative manner. Two potential tools are described that were used to quantitate disease burden in AKU. One tool describes scoring the clinical features that includes clinical assessments, investigations and questionnaires in 15 patients with AKU. The second tool describes a scoring system that only includes items obtained from questionnaires in 44 people with AKU. Analysis of the data reveals distinct phases of the disease, a pre‐ochronotic phase and an ochronotic phase. The ochronotic phase appears to demonstrate an earlier slower progression followed by a rapidly progressive phase. The rate of change of the disease will have implications for monitoring the course of the disease as well as decide on the most appropriate time that treatment should be started for it to be effective either in prevention or arrest of the disease.
Attitudes and Beliefs of African‐Americans Toward Genetics, Genetic Testing, and Sickle Cell Disease Education and Awareness
Authors: Long Katie A. , Thomas Stephen B. , Grubs Robin E. , Gettig Elizabeth A. , Krishnamurti Lakshmanan
Published: July 2011

Research among African‐Americans indicates this population perceives sickle cell (SCD) to be a serious disease and sickle cell trait (SCT) screening an important intervention. However, studies have consistently demonstrated a lower than desired uptake of SCD education, inadequate knowledge regarding personal and family trait status, and a low perceived susceptibility of giving birth to a child with the disease. We examined general attitudes and beliefs regarding genetics and genetic testing including prenatal testing and newborn screening; we used this information as the foundation to more specifically assess attitudes and beliefs regarding SCD and perceived barriers to SCD education and awareness. Thirty‐five African‐American adult men and women participated in one of four focus groups. Thematic analysis identified that both prenatal testing and newborn screening are acceptable forms of genetic testing. Based largely on their personal experiences, participants possessed an understanding of the natural progression of SCD but had a limited understanding of the inheritance and probable risk of giving birth to a child with the disease. Barriers to education and greater awareness of SCD were classified as personal, familial, and societal. Community based interventions focused on sharing the stories of individuals with first‐hand experiences with SCD should be considered.
Probabilistic Projections of the Total Fertility Rate for All Countries
Authors: Alkema Leontine , Raftery Adrian E. , Gerland Patrick , Clark Samuel J. , Pelletier François , Buettner Thomas , Heilig Gerhard K.
Published: July 2011

We describe a Bayesian projection model to produce country-specific projections of the total fertility rate (TFR) for all countries. The model decomposes the evolution of TFR into three phases: pre-transition high fertility, the fertility transition, and post-transition low fertility. The model for the fertility decline builds on the United Nations Population Division’s current deterministic projection methodology, which assumes that fertility will eventually fall below replacement level. It models the decline in TFR as the sum of two logistic functions that depend on the current TFR level, and a random term. A Bayesian hierarchical model is used to project future TFR based on both the country’s TFR history and the pattern of all countries. It is estimated from United Nations estimates of past TFR in all countries using a Markov chain Monte Carlo algorithm. The post-transition low fertility phase is modeled using an autoregressive model, in which long-term TFR projections converge toward and oscillate around replacement level. The method is evaluated using out-of-sample projections for the period since 1980 and the period since 1995, and is found to be well calibrated.