bluuebunny/crossref_metadata_2025 huggingface dataset:
Breast carcinomas with borderline (2+) HER2 immunohistochemistry: percentage of cells with complete membrane staining for HER2 and the frequency of HER2 amplification: Table 1
Authors: Lee Andrew H S , Key Heather P , Bell Jane A , Hodi Zsolt , Ellis Ian O
Published: March 2011

Aim

HER2 status is vital for selecting breast cancer patients for trastuzumab treatment. One recommended approach is to assess immunohistochemical staining and then perform in situ hybridisation on those tumours with a borderline (2+) immunohistochemical result. This audit aimed to assess the value of the percentage of immunohistochemical staining in 2+ tumours in selecting tumours for in-situ hybridisation.

Methods

HER2 immunohistochemistry and in situ hybridisation was performed according to UK guidelines. The percentage of complete membrane staining of invasive carcinoma cells for HER2 was recorded as part of routine reporting.

Results

191 (11%) of 1735 invasive carcinomas were scored as 3+. 419 (24%) were scored as 2+. 57 of 413 2+ carcinomas (14%) were amplified (ratio of HER2 to chromosome 17≥2.0). The frequency of amplification was related to the percentage of complete membrane staining: eight of 149 (5%) with 10–19% membrane staining, 11 of 93 (12%) with 20–29% staining, 26 of 150 (17%) with 30–79% staining and 12 of 21 (57%) with 80–100% staining.

Conclusions

This audit suggests that increasing the threshold for 2+ from 10% to 20% complete membrane staining would reduce the number of in-situ hybridisation tests by 36%, but reduce the detection of amplified tumours by 14%.
Filamentous bacteria masquerading as fungi: a diagnostic pitfall in direct smear interpretation with report of two cases
Authors: Sutton Brian J , Parsons Amy C , Palavecino Elizabeth L
Published: March 2011

Bacteria, particularly Gram-negative bacilli, can develop abnormal morphology after the administration of subinhibitory concentrations of antibacterial agents. Filamentation is a common response in which bacteria replicate but incompletely divide, leading to long slender chains that resemble fungal hyphae. Pathologists are frequently consulted to examine direct smears of body fluids, which often contain microorganisms. Antibiotic-related filamentous morphology may resemble fungal hyphae and this potential misinterpretation can lead to inappropriate treatment for presumed fungal infections. Two cases are described in which direct smears of body fluids were examined by on-call pathology residents who misinterpreted filamentous bacteria as fungal organisms, with one case leading to the initiation of antifungal medication. Although well-established within the field of microbiology, many residents and practising pathologists are less familiar with antibiotic-related bacterial morphology, as it may not be routinely encountered. It is important for pathologists to be aware of this phenomenon in order to avoid misinterpretation.
EpCAM expression in primary tumour tissues and metastases: an immunohistochemical analysis
Authors: Spizzo Gilbert , Fong Dominic , Wurm Martin , Ensinger Christian , Obrist Peter , Hofer Carina , Mazzoleni Guido , Gastl Guenther , Went Philip
Published: March 2011

Aims

Epithelial cell adhesion molecule (EpCAM) is a cell surface protein with oncogenic features that is expressed on healthy human epithelia and corresponding malignant tumours. EpCAM expression frequently correlates with more aggressive tumour behaviour and new EpCAM-specific therapeutic agents have recently been approved for clinical use in patients with cancer. However, no consensus exists on how and when to evaluate EpCAM expression in patients with cancer.

Material and methods

EpCAM expression was assessed by a well-established immunohistochemical staining protocol in 2291 primary tumour tissues and in 108 metastases using the EpCAM-specific antibody clone VU1D9. A total immunostaining score was calculated as the product of a proportion score and an intensity score. Four expression subgroups (no, weak, moderate and intense) were defined. As described previously, the term ‘EpCAM overexpression’ was reserved for tissues showing a total immunostaining score >4.

Results

EpCAM was highly expressed in most tumours of gastrointestinal origin and in some carcinomas of the genitourinary tract. However, hepatocellular carcinomas, clear cell renal cell cancer, urothelial cancer and squamous cell cancers were frequently EpCAM negative. EpCAM expression in breast cancer depended on the histological subtype; lobular histology usually showed no or weak expression. Most metastases were EpCAM positive and they frequently reflected the expression phenotype of the primary tumour.

Conclusion

EpCAM expression was detected on adenocarcinomas of various primary sites. If EpCAM-specific antibodies are intended to be used in patients with cancer, we recommend prior immunohistochemical evaluation of EpCAM expression, particularly in patients with renal cell cancer, hepatocellular carcinoma, urothelial carcinoma, breast cancer and squamous cell carcinomas.
Eocene rotation of the Coast Plutonic Complex and Intermontane Belt: paleomagnetism of Eocene plutons along the Klondike Highway
Authors: Symons David T.A. , Kawasaki Kazuo
Published: March 2011

Paleomagnetic results are reported for the ∼59 Ma Skagway, ∼54 Ma Fraser, ∼53 Ma Summit Lake, and ∼48 Ma Clifton felsic plutons of the eastern Coast Plutonic Complex (CPC) that outcrop along the south Klondike Highway in Alaska and British Columbia. Thermal and alternating field step demagnetizing methods yielded stable characteristic remanent magnetization (ChRM) directions for all 29 sites of normal, reversed, and mixed polarity. The ChRM resides in single or pseudosingle domain magnetite and (or) pyrrhotite that is shown to be primary by contact tests with the ∼47 Ma vertical White Pass mafic dikes. Paleopoles from six 56 to 50 Ma (mean 52 ± 2 Ma) Intermontane Belt – Yukon–Tanana terrane (IMB–YTT) units that cannot be explained by tectonic tilt are compared with nine clustered 59 to 46 Ma (mean 52 ± 4 Ma) eastern CPC paleopoles. Both paleopole populations show nonsignificant poleward (northward) translation relative to North America (IMB–YTT, 3.7° ± 5.3°N; CPC, 4.3° ± 6.4°S; overall, 1.2° ± 4.9°S), indicating that northward translation of the accreted terranes ended by ∼58 Ma. Conversely, both populations show clockwise (CW) rotation that is either highly significant or substantial (IMB–YTT, 19.3° ± 10.5 °CW; CPC, 7.1° ± 16.1 °CW; overall 12.8° ± 10.9 °CW). The results are best explained by tectonic rotation from ∼50 to ∼45 Ma of the IMB–YTT as a thin-skin on top of North America during emplacement and co-incident rotation of the massive Eocene plutons of the eastern CPC along the North American margin.
Size matters in Triticeae polyploids: larger genomes have higher remodeling
Authors: Bento Miguel , Gustafson J. Perry , Viegas Wanda , Silva Manuela
Published: March 2011

Polyploidization is one of the major driving forces in plant evolution and is extremely relevant to speciation and diversity creation. Polyploidization leads to a myriad of genetic and epigenetic alterations that ultimately generate plants and species with increased genome plasticity. Polyploids are the result of the fusion of two or more genomes into the same nucleus and can be classified as allopolyploids (different genomes) or autopolyploids (same genome). Triticeae synthetic allopolyploid species are excellent models to study polyploids evolution, particularly the wheat–rye hybrid triticale, which includes various ploidy levels and genome combinations. In this review, we reanalyze data concerning genomic analysis of octoploid and hexaploid triticale and different synthetic wheat hybrids, in comparison with other polyploid species. This analysis reveals high levels of genomic restructuring events in triticale and wheat hybrids, namely major parental band disappearance and the appearance of novel bands. Furthermore, the data shows that restructuring depends on parental genomes, ploidy level, and sequence type (repetitive, low copy, and (or) coding); is markedly different after wide hybridization or genome doubling; and affects preferentially the larger parental genome. The shared role of genetic and epigenetic modifications in parental genome size homogenization, diploidization establishment, and stabilization of polyploid species is discussed.
On the bias of recombination fractions, Kosambi's and Haldane's distances based on frequencies of gametes
Authors: Huehn Manfred
Published: March 2011

The estimation of recombination frequencies is a crucial step in genetic mapping. For the construction of linkage maps, nonadditive recombination fractions must be transformed into additive map distances. Two of the most commonly used transformations are Kosambi’s and Haldane’s mapping functions. This paper reports on the calculation of the bias associated with estimation of recombination fractions, Kosambi’s distances, and Haldane’s distances. I calculated absolute and relative biases numerically for a wide range of recombination fractions and sample sizes. I assumed that the ratio of recombinant gametes to the total number of gametes can be adequately represented by a binomial function. I found that the bias in recombination fraction estimates is negative, i.e., the estimator is an underestimate. However, significant values were only obtained when recombination fractions were large and sample sizes were small. The relevant estimates of recombination fractions were, therefore, nearly unbiased. Haldane’s and Kosambi’s distances were found to be strongly biased, with positive bias for the most interesting values of recombination fractions and sample sizes. The bias of Kosambi’s distance was considerably smaller than the bias of Haldane’s distance.
Genetic maps of SSR and SRAP markers in diploid orchardgrass (Dactylis glomerataL.) using the pseudo-testcross strategy
Authors: Xie Wengang , Zhang Xinquan , Cai Hongwei , Huang Linkai , Peng Yan , Ma Xiao
Published: March 2011

Orchardgrass ( Dactylis glomerata L.) is one of the most important cool-season forage grasses commonly grown throughout the temperate regions of the world. The objective of this work was to construct a diploid (2n = 2x = 14) orchardgrass genetic linkage map useful as a framework for basic genetic studies and plant breeding. A combination of simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular markers were used for map construction. The linkage relationships among 164 SSRs and 108 SRAPs, assayed in a pseudo-testcross F1segregating population generated from a cross between two diploid parents, were used to construct male (01996) and female (YA02-103) parental genetic maps. The paternal genetic map contains 90 markers (57 SSRs and 33 SRAPs) over 9 linkage groups (LGs), and the maternal genetic map is composed of 87 markers (54 SSRs and 33 SRAPs) assembled over 10 LGs. The total map distance of the male map is 866.7 centimorgans (cM), representing 81% genome coverage, whereas the female map spans 772.0 cM, representing 75% coverage. The mean map distance between markers is 9.6 cM in the male map and 8.9 cM in the female map. About 14% of the markers remained unassigned. The level of segregation distortion observed in this cross was 15%. Homology between the two maps was established between five LGs of the male map and five LGs of the female map using 10 bridging markers. The information presented in this study establishes a foundation for extending genetic mapping in this species, serves as a framework for mapping quantitative trait loci (QTLs), and provides basic information for future molecular breeding studies.
Identification of novel α-gliadin genes
Authors: Qi Peng-Fei , Wei Yu-Ming , Chen Qing , Ouellet Thérèse , Ai Jia , Chen Guo-Yue , Li Wei , Zheng You-Liang
Published: March 2011

Ten novel α-gliadin genes (Gli-ta, Gli-turg1, Gli-turg2, Gli-turg3, Gli-turg4, Gli-turg5, Gli-turg6, Gli-cs1, Gli-cs2, and Gli-cs3) with unique characteristics were isolated from wheat ( Triticum aestivum L.), among which Gli-cs1, Gli-cs2, Gli-cs3, and Gli-turg6 were pseudogenes. Gli-cs3 and nine other sequences were much larger and smaller, respectively, than the typical α-gliadins. This variation was caused by insertion or deletion of the unique domain I and a polyglutamine region, possibly the result of illegitimate recombination. Consequently, Gli-cs3 contained 10 cysteine residues, whereas there were 2 cysteine residues only in the other nine sequences. Gli-ta/Gli-ta-like α-gliadin genes are normally expressed during the development of seeds. SDS–PAGE analysis showed that in-vitro-expressed Gli-ta could form intermolecular disulphide bonds and could be chain extenders. A protein band similar in size to Gli-ta has been observed in seed extracts, and mass spectrometry results confirm that the band contains small molecular mass α-gliadins, which is a characteristic of the novel α-gliadins. Mass spectrometry results also indicated that the two cysteine residues of Gli-ta/Gli-ta-like proteins participated in the formation of intermolecular disulphide bonds in vivo.
The effects of conformally invariant Maxwell source on the magnetic wormhole solutions in Gauss–Bonnet gravity
Authors: Hendi S. H.
Published: March 2011

In this paper we introduce a new class of nonsingular higher dimensional conformally invariant magnetic solutions that may be interpreted as traversable wormholes, which could be supported by matter not violating the weak energy conditions. The electromagnetic source is chosen in which the expression of the Maxwell field does not depend on the dimension and its value coincides with the Reissner–Nordström solution in four dimensions. We generalize this class of solutions to the case of rotating solutions and show that the rotating wormhole solutions have a net electric charge that is proportional to the magnitude of the rotation parameter, while the static wormhole has no net electric charge. Finally, we use the counterterm method and compute the conserved quantities of these spacetimes.
Pion production in relativistic nucleus–nucleus collisions
Authors: Abdelsalam A. , El–Nagdy M. S. , Badawy B. M.
Published: March 2011

An experimental study on the production of pions is reviewed, covering pion spectra and multiplicity distributions. Emphasis is placed on progress in characterizing the conditions of nuclear matter by employing particle production observables. Further, the information derived from the Hagedorn temperature of the system emitting pions is critically examined, along with a discussion of the sources responsible for pion emission in the reaction, as revealed by particle spectra and yields.
Bright and dark solitons for a generalized Korteweg-de Vries–modified Korteweg-de Vries equation with high-order nonlinear terms and time-dependent coefficients
Authors: Triki Houria , Wazwaz Abdul-Majid
Published: March 2011

We consider a generalized Korteweg-de Vries–modified Korteweg-de Vries (KdV–mKdV) equation with high-order nonlinear terms and time-dependent coefficients. Bright and dark soliton solutions are obtained by means of the solitary wave ansatz method. The physical parameters in the soliton solutions are obtained as functions of the varying model coefficients. Parametric conditions for the existence of envelope solitons are given. In view of the analysis, we see that the method used is an efficient way to construct exact soliton solutions for such a generalized version of the KdV–mKdV equation with time-dependent coefficients and high-order nonlinear terms.
Energy scales in a holographic black hole and conductivity at finite momentum
Authors: Basu Pallab
Published: March 2011

In this work we discuss the low temperature (T) behavior of gauge field correlators with finite momentum (k) in a AdS4 black hole background. At low temperature, a substantial nonzero conductivity is only possible for a frequency range ω > ωg = k. This tallies with the simple fact that at least an amount of energy ωg is needed to create an excitation of momentum k. Due to the existence of this “gap”, one may expect that at the zero frequency limit the real part of momentum-dependent conductivity falls exponentially with 1/T. Using analytic methods, we found a exp(–ωc/T) falloff of the real part of conductivity with inverse temperature. Interestingly, ωg ≠ ωc. From the above results, we speculate that the “degrees of freedom”, say carriers, different than quasiparticle excitation determines conductivity at the low temperature and the low-frequency limit. Here ωc < ωg, and we may calculate their ratios analytically. We also discuss similar issues at a finite chemical potential. The situation is rather different for an extremal blackhole. A zero temperature extremal blackhole does not show a sharp gap for the finite momentum excitations, and the real part of the conductivity is always nonzero for any nonzero frequency ω. However, the real part of the conductivity goes to zero at the ω → 0 limit. Not surprisingly, we find a power-law decay with temperature for the same quantity, as the extremal limit is approached.
The renormalization group and the effective action
Authors: McKeon D. G.C.
Published: March 2011

The renormalization group is used to sum the leading-log (LL) contributions to the effective action for a large constant external gauge field in terms of the one-loop renormalization group (RG) function β, the next-to-leading-log (NLL) contributions in terms of the two-loop RG function, etc. The log-independent pieces are not determined by the RG equation, but can be fixed by considering the anomaly in the trace of the energy-momentum tensor. Similar considerations can be applied to the effective potential V for a scalar field [Formula: see text]; here the log-independent pieces are fixed by the condition [Formula: see text].
Local density approximation description of electronic properties of wurtzite cadmium sulfide (w-CdS)
Authors: Ekuma E. C. , Franklin L. , Zhao G. L. , Wang J. T. , Bagayoko D.
Published: March 2011

We present calculated, electronic, and related properties of wurtzite cadmium sulfide (w-CdS). Our ab initio, nonrelativistic calculations employ a local density functional approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). Following the Bagayoko, Zhao, and Williams (BZW) method, we solved self-consistently both the Kohn–Sham equation and the equation giving the ground-state density in terms of the wave functions of the occupied states. Our calculated, direct band gap of 2.47 eV at the Γ point is in excellent agreement with experiment. So are the calculated density of states and the electron effective mass. In particular, our results reproduce the peaks in the conduction band density of states, within experimental uncertainties.
Propagation of ion-acoustic solitary waves in a relativistic electron-positron-ion plasma
Authors: Saberian E. , Esfandyari-Kalejahi A. , Akbari-Moghanjoughi M.
Published: March 2011

The propagation of large amplitude ion-acoustic solitary waves (IASWs) in a fully relativistic plasma consisting of cold ions and ultra-relativistic hot electrons and positrons is investigated using the Sagdeev pseudopotential method in a relativistic hydrodynamics model. The effects of streaming speed of the plasma fluid, thermal energy, positron density, and positron temperature on large amplitude IASWs are studied by analysis of the pseudopotential structure. It is found that in regions in which the streaming speed of the plasma fluid is larger than that of the solitary wave, by increasing the streaming speed of the plasma fluid, the depth and width of the potential well increase, resulting in narrower solitons with larger amplitude. This behavior is opposite to the case where the streaming speed of the plasma fluid is less than that of the solitary wave. On the other hand, an increase in the thermal energy results in wider solitons with smaller amplitude, because the depth and width of the potential well decrease in that case. Additionally, the maximum soliton amplitude increases and the width becomes narrower as a result of an increase in positron density. It is shown that varying the positron temperature does not have a considerable effect on the width and amplitude of IASWs. The existence of stationary soliton-like arbitary amplitude waves is also predicted in fully relativistic electron-positron-ion (EPI) plasmas. The effects of streaming speed of the plasma fluid, thermal energy, positron density, and positron temperature on these kinds of solitons are the same for large amplitude IASWs.
Heat transfer over an unsteady stretching surface in a micropolar fluid in the presence of magnetic field and thermal radiation
Authors: Aldawody D. A. , Elbashbeshy E. M.A.
Published: March 2011

The effects of thermal radiation and magnetic field on flow and heat transfer over an unsteady stretching surface in a micropolar fluid are studied. The governing partial differential equations are transformed into a system of ordinary differential equations containing the material parameter K, magnetic parameter M, radiation parameter R, and Prandtl number Pr. These equations are solved numerically by applying a shooting technique, using the Runge–Kutta method. Comparison of the numerical results is made with previously published results under the special cases, and the results are found to be in good agreement. Effects of the material parameter K, magnetic parameter M, radiation parameter R, and Prandtl number Pr on the flow and heat transfer are studied.
Field monitoring of an unsaturated saprolitic hillslope
Authors: Leung A. K. , Sun H. W. , Millis S.W. , Pappin J.W. , Ng C. W.W. , Wong H. N.
Published: March 2011

To advance the understanding of the rainfall-induced landslide triggering mechanism, a comprehensive field monitoring programme was implemented in a saprolitic hillslope in Hong Kong. The instrumentation covered the measurements of the two stress-state variables (i.e., net normal stress and matric suction) and their effects. The monitoring results, including pore-water pressure (PWP), volumetric water content, subsurface total horizontal stress, horizontal displacement, and rainfall intensity, are reported. Most instruments recorded reliable and good quality data, which have strong correlation among each other. The site-specific infiltration and deformation characteristics of the hillslope subjected to heavy rainstorms are investigated. Shallow transient perched groundwater tables were believed to be developed at colluvial deposits on the top 3 m, where PWPs up to 20 kPa were typically measured. The main groundwater table probably rose by 6 m when the hillslope was subjected to rainfall intensity of 133.5 mm/h. It is possible that cross-slope groundwater flowed along a shallow, dipped decomposed rock stratum at the central portion of the landslide body. Besides, two distinct types of slope movements were generally observed, namely the “cantilever” and the “deep-seated” mode. Rupture surfaces have possibly been developed at 5 m below ground or deeper, resulting in a multiple translational- and rotational-slide type of failure.
Ground movements above tunnels: a method for calculating volume loss
Authors: Palmer Andrew C. , Mair Robert J.
Published: March 2011

Excavation of a tunnel induces small movements at the surface of the ground above. Those movements are often estimated by empirical methods. This paper presents a simple derivation of formulas for elastic ground, based on the reciprocal theorem. It confirms that the effect of removal of the weight of the soil in the tunnel is not negligible.
Modelling the applied vertical stress and settlement relationship of shallow foundations in saturated and unsaturated sands
Authors: Oh Won Taek , Vanapalli Sai K.
Published: March 2011

The bearing capacity and settlement of foundations are determined experimentally or modelled numerically based on conventional soil mechanics for saturated soils. In both methods, bearing capacity and settlement are estimated based on the applied vertical stress versus surface settlement relationship. These methods are also conventionally used for soils that are in an unsaturated condition, ignoring the contribution of matric suction. In this study, a methodology is proposed to estimate the bearing capacity and settlement of shallow foundations in unsaturated sands by predicting the applied vertical stress versus surface settlement relationship. The proposed method requires soil parameters obtained under only saturated conditions (i.e., effective cohesion, effective internal friction angle, and modulus of subgrade reaction from model footing test) along with the soil-water characteristic curve (SWCC). In addition, finite element analyses are undertaken to simulate the applied vertical stress versus surface settlement relationship for unsaturated sands. The proposed method and finite element analyses are performed using an elastic – perfectly plastic model. The predicted bearing capacities and settlements from the proposed method and finite element analyses are compared with published model footing test results. There is good agreement between measured and predicted results.
Development of a Vs30(NEHRP) map for the city of Ottawa, Ontario, Canada
Authors: Motazedian D. , Hunter J. A. , Pugin A. , Crow H.
Published: March 2011

Four different seismic methods were used extensively to evaluate the shear wave velocity of soils and rock in the city of Ottawa, Canada, from which the travel-time weighted average shear wave velocity (Vs) from surface to 30 m in depth (Vs30) and the fundamental frequency (F0) were computed. Three main geological or geotechnical units were identified with distinct shear wave velocities: these consist of very loose thick post-glacial fine-grained sands, silts, and clays (Vs <150 m/s, thickness up to 110 m), firm glacial sediments (Vs ∼580 m/s, thickness ∼3 m), and very firm bedrock (Vs ∼1750–3550 m/s). The seismic methods applied were downhole interval Vs measurements at 15 borehole sites, seismic refraction–reflection profile measurements for 686 sites, high-resolution shear wave reflection “landstreamer” profiling for 25 km in total, and horizontal-to-vertical spectral ratio (HVSR) of ambient seismic noise to evaluate the fundamental frequency for ∼400 sites. Most of these methods are able to distinguish the very high shear wave impedance of and depth to bedrock. Sparse earthquake recordings show that the soil amplification is large for weak motion when the soil behaves linearly.
Effect of anchor width on pullout capacity of strip anchors in sand
Authors: Khatri Vishwas N. , Kumar Jyant
Published: March 2011

By incorporating the variation of peak soil friction angle ([Formula: see text]) with mean principal stress (σm), the effect of anchor width (B) on vertical uplift resistance of a strip anchor plate has been examined. The anchor was embedded horizontally in a granular medium. The analysis was performed using lower bound finite element limit analysis and linear programming. An iterative procedure, proposed recently by the authors, was implemented to incorporate the variation of [Formula: see text] with σm. It is noted that for a given embedment ratio, with a decrease in anchor width (B), (i) the uplift factor (Fγ) increases continuously and (ii) the average ultimate uplift pressure (qu) decreases quite significantly. The scale effect becomes more pronounced at greater embedment ratios.
Photophysical aspects of 6-methylcoumarin–cucurbit[8]uril host–guest complexes
Authors: Pemberton Barry C. , Kumarasamy Elango , Jockusch Steffen , Srivastava D. K. , Sivaguru J.
Published: March 2011

Photophysical measurements of 6-methylcoumarin (1) encapsulated within cucurbit[8]uril (CB[8]) indicate a pronounced red shift in the fluorescence maximum with an increase in the emission quantum yield and fluorescence lifetime. In addition, at 77 K, there is observable phosphorescence upon encapsulation within CB[8]. The photophysical measurements add credibility to our previously proposed dynamic nature of the CB–coumarin complex in solution. The dynamic nature of the CB[8]–coumarin host–guest complex in water is critical to a CB acting as a supramolecular catalytic nanoreaction vessel to facilitate the photodimerization of coumarins leading to syn dimers.
Photoinduced charge separation in microporous and mesoporous materials
Authors: Koodali Ranjit T.
Published: March 2011

A review of photoinduced charge separation of organic molecules in microporous and mesoporous materials is presented. In particular, the photoionization of N-alkylphenothiazine (PCn), N,N,N′,N′-tetramethylbenzidine (TMB), and porphyrin in microporous materials, such as zeolites, aluminophosphates (AlPOs), silicoaluminophosphates (SAPOs), and mesoporous materials, such as MCM-41, MCM-48, and SBA-15, is discussed.
Zirconium oxide nanoparticles coated on sepiolite by sol–gel process — Their application as a solvent-free catalyst for condensation reactions
Authors: Letaief Sadok , Liu Yun , Detellier Christian
Published: March 2011

An inorganic nanocomposite made of zirconia nanoparticles coated on the external surfaces of the fibrous clay mineral sepiolite was prepared by using the sol–gel process under soft conditions using zirconium(IV) propoxide in 1-propanol as the precursor. The resulting materials were characterized by X-ray diffraction (XRD), thermal gravimetric analyses (TGA) and differential thermal analyses (DTA), microporosimetry, 29Si magic-angle spinning (MAS) nuclear magnetic resonance (NMR), and high-resolution transmission electron microscopy (HR-TEM). The organic material from the precursor was fully removed after calcination at 450 °C, concurrently with the crystallization of the cubic phase of zirconium oxide. The coordinated water molecules of sepiolite were fully removed and its symmetrical layered structure was folded after calcination at 650 °C, as observed by XRD and 29Si cross-polarization (CP) / MAS NMR. The arrangement of the nanoparticles of zirconium oxide on the sepiolite external surfaces maintains a fibrous morphology for the nanocomposite. This material was applied as a catalyst for the Knoevenagel condensation reaction of benzaldehyde and malononitrile under solvent-free conditions. Strongly improved yields of reaction, attributed to larger catalytically active surfaces, were obtained compared with either the sepiolite clay mineral or the zirconium oxide tested individually.
p-Hydroxyphenacyl photoremovable protecting groups — Robust photochemistry despite substituent diversity
Authors: Givens Richard S. , Stensrud Kenneth , Conrad Peter G. , Yousef Abraham L. , Perera Chamani , Senadheera Sanjeewa N. , Heger Dominik , Wirz Jakob
Published: March 2011

A broadly based investigation of the effects of a diverse array of substituents on the photochemical rearrangement of p-hydroxyphenacyl esters has demonstrated that common substituents such as F, MeO, CN, CO2R, CONH2, and CH3have little effect on the rate and quantum efficiencies for the photo-Favorskii rearrangement and the release of the acid leaving group or on the lifetimes of the reactive triplet state. A decrease in the quantum yields across all substituents was observed for the release and rearrangement when the photolyses were carried out in buffered aqueous media at pHs that exceeded the ground-state pKaof the chromophore where the conjugate base is the predominant form. Otherwise, substituents have only a very modest effect on the photoreaction of these robust chromophores.
A Förster resonance energy transfer (FRET) approach for enhancing fluorescence contrast in phase-separated membranes
Authors: Carter Ramirez Daniel M. , Ding Jason , Guan Jack , Vobornik Dusan , Carnini Anna , Ogilvie William W. , Jakubek Zygmunt J. , Johnston Linda J.
Published: March 2011

The partitioning of the dye-labeled lipid probe, NBD-DHPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl) (ammonium salt)), was examined by fluorescence microscopy in phase-separated lipid bilayers with mixtures of coexisting liquid-ordered and fluid phases. This probe shows slightly higher fluorescence intensity in the ordered domains but undergoes a contrast reversal to give a more strongly fluorescent fluid phase in the presence of >0.2% Texas red-DHPE (TR-DHPE). The change in contrast is shown to result from Förster resonance energy transfer between the NBD donor and TR acceptor in the fluid phase, which has a TR concentration that is approximately 3 times higher than in the domains. An alternate approach using a nitroxide-substituted lipid that partitions into the fluid phase as a quencher, was also examined as a means to enhance the contrast; however, the quencher modified the behaviour of the bilayer. The energy transfer method for enhancing the contrast between ordered and fluid phases was used to examine the morphology of enzyme-treated bilayers.
Comparison of photoenolization and alcohol release from alkyl-substituted benzoyl benzoic esters
Authors: Muthukrishnan Sivaramakrishnan , Pace Tamara C.S. , Li Qian , Seok Brian , de Jong Gerdien , Bohne Cornelia , Gudmundsdottir Anna D.
Published: March 2011

Photolysis of 1B in argon-saturated solutions yields 4B and releases methanol. Laser flash photolysis of 1B shows formation of biradical 2B, which has a lifetime of ~50 ns and a λmax at 330 nm. Biradical 2B undergoes an intersystem crossing to form photoenols E-3B and Z-3B with a λmax at 390 nm. Laser flash photolysis shows that the lifetimes of E-3B and Z-3B are affected by the solvent. Density functional theory calculations demonstrate that the transition-state barrier for a 1,5-H atom shift from Z-3B to regenerate 1B is affected by the ortho-alkyl substituents, whereas the stereoelectronics of the alkyl substituent affect the transition-state barrier of E-3B as it undergoes electrocyclic ring closure to form 4B. The photoreactivity of 1B was compared with its analogous methyl and isopropyl derivatives 1A and 1C, respectively, to better estimate the effect of the alkyl substituent on reactivity.
Locked nucleic acid hairpin detection of UV-induced DNA damage
Authors: El-Yazbi Amira , Loppnow Glen R.
Published: March 2011

The exposure of DNA to radiation and chemical insults leads to damage and disease. Thus, detection and understanding of DNA damage is important for elucidating molecular mechanisms of disease. However, current methods of DNA damage detection are either time-consuming, destroy the sample, or are too specific to be used for generic detection of damage. In this paper, we examine the sensitivity of different locked nucleic acid (LNA) hairpin probes for detecting UV-induced oligonucleotide damage to LNA composition, target concentration, and ionic strength. We also compare the selectivity of the LNA hairpin probe with a DNA molecular beacon (MB) hairpin probe for detecting DNA damage. Our results show that the selectivity of the LNA hairpin probe to UV-induced nucleic acid damage increases with increasing ionic strength of the buffer and decreases with increasing target concentration and with increasing LNA ratio.
Increased plasma level of asymmetric dimethylarginine in hypertensive rats facilitates platelet aggregation: role of plasma tissue factor
Authors: Li Dai , Guo Ren , Chen Qing-Quan , Hu Chang-Ping , Chen Xiang
Published: March 2011

This study was designed to explore the role of asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide synthesis, in platelet aggregation in hypertension and its possible mechanisms. Spontaneously hypertensive rats (SHR) and l-NAME-induced hypertensive rats were orally administered with l-arginine (1 g/(kg·day) for 14 days. Systolic blood pressure, platelet aggregation, and plasma tissue factor (TF) level and activity were measured. The plasma concentration of ADMA in SHR was determined. In vitro, platelet-rich plasma isolated from Wistar rats was prepared in order to observe the effect of exogenous ADMA on platelet aggregation and TF level and (or) activity in platelet-rich plasma. In both types of hypertensive rats, systolic blood pressure, platelet aggregation, and the level and activity of plasma TF were elevated compared with corresponding control animals. Plasma ADMA level was also increased in SHR. Treatment with l-arginine, a competitor of ADMA, lowered blood pressure and inhibited platelet aggregation concomitantly with a decrease in plasma TF level and activity in both types of hypertensive rats. We also found that exogenous ADMA promoted platelet aggregation and increased TF level and (or) activity in platelet-rich plasma, an effect that was inhibited by pretreatment with l-arginine. Importantly, the enhanced platelet aggregation induced by exogenous ADMA was reduced by pretreatment with anti-TF antibody. The results suggest that endogenous ADMA may be involved in platelet hyperaggregation status in hypertension, and the facilitation of platelet aggregation by ADMA is related to upregulation of the level and activity of plasma TF.
A germacranolide sesquiterpene lactone suppressed inducible nitric oxide synthase by downregulating NF-κB activity
Authors: Lee Hwa Jin , Jung Hyeyoun , Kwon Junhye , Li Hua , Lee Da Yeon , Lim Hyo Jin , Kim Mi-Ran , Moon Dong-Cheul , Ryu Jae-Ha
Published: March 2011

A germacranolide sesquiterpene lactone, 2α,5-epoxy-5,10-dihydroxy-6α-angeloyloxy-9β-(3-methylbutyloxy)-germacran-8α,12-olide (EDAG), isolated from Carpesium triste var. manshuricum , showed inhibitory activity in the production of nitric oxide (NO) and the expression of inducible nitric oxide synthase (iNOS) mRNA and protein in LPS-activated macrophage cells. Molecular analysis reveals that these suppressive effects are correlated with the inhibition of NF-κB activation by EDAG. Immunoblotting showed that EDAG suppressed the LPS-induced degradation of I-κBα and decreased nuclear translocation of p65. Futhermore, EDAG showed reduced phosphorylation of ERK1/2 and p38 MAPK, whereas activation of JNK was not changed. These data suggest, at least in part, that EDAG utilizes the signal cascades of ERK1/2, p38 MAPK, and NF-κB for the suppression of iNOS gene expression.
Rutaecarpine prevents hypoxia–reoxygenation-induced myocardial cell apoptosis via inhibition of NADPH oxidases
Authors: Bao Mei-Hua , Dai Wen , Li Yuan-Jian , Hu Chang-Ping
Published: March 2011

It is proposed that myocardial cell apoptosis causes ventricular remodeling and heart failure. The aim of the present study was to determine the effects of rutaecarpine (Rut) on hypoxia–reoxygenation (H–R)-induced apoptosis in myocardial cell line H9c2, as well as the underlying mechanisms. Cultured H9c2 cells were exposed to hypoxia for 24 h, followed by 12 h reoxygenation. Rut (in concentrations of 0.1, 1, and 10 µmol/L) was added 1 h prior to H–R. Cell viability and lactate dehydrogenase were measured to evaluate the cell injuries. Apoptosis was evaluated by Hoechst 33258 staining and flow cytometry. NADPH oxidase activity was measured by assay kit; intracellular reactive oxygen species (ROS) generation was detected by 2′,7′-dichlorofluorescein diacetate; and Nox2, Nox4, and p47phox mRNA and protein expression were analyzed by real-time PCR and Western blotting, respectively. The results showed that H–R significantly decreased cell viability and increased the lactate dehydrogenase release, as well as the apoptotic rate, concomitantly with enhanced NADPH oxidase activity. H–R also upregulated mRNA and protein expressions of Nox2, Nox4, and p47phox and increased ROS production. Treatment with Rut markedly reversed these effects introduced by H–R. These results suggest that the protective effects of Rut against H–R-induced myocardial cell injury and apoptosis might, at least partly, be due to the inhibition of the NADPH oxidase – ROS pathway.
Acute renal response to rapid onset respiratory acidosis
Authors: Ramadoss Jayanth , Stewart Randolph H. , Cudd Timothy A.
Published: March 2011

Renal strong ion compensation to chronic respiratory acidosis has been established, but the nature of the response to acute respiratory acidosis is not well defined. We hypothesized that the response to acute respiratory acidosis in sheep is a rapid increase in the difference in renal fractional excretions of chloride and sodium (FeCl – FeNa). Inspired CO2 concentrations were increased for 1 h to significantly alter PaCO2 and pHa from 32 ± 1 mm Hg and 7.52 ± 0.02 to 74 ± 2 mm Hg and 7.22 ± 0.02, respectively. FeCl – FeNa increased significantly from 0.372 ± 0.206 to 1.240 ± 0.217% and returned to baseline at 2 h when PaCO2 and pHa were 37 ± 0.6 mm Hg and 7.49 ± 0.01, respectively. Arterial pH and FeCl – FeNa were significantly correlated. We conclude that the kidney responds rapidly to acute respiratory acidosis, within 30 min of onset, by differential reabsorption of sodium and chloride.
A fingernail clam (Sphaerium sp.) shows higher reproductive success in hypoxic waters
Authors: Joyner-Matos J. , Richardson H. , Sammeli T. , Chapman L. J.
Published: March 2011

Low dissolved O2, or hypoxia, is becoming increasingly prevalent in aquatic habitats and is considered to be stressful for aerobic organisms. However, hypoxia also can be beneficial by decreasing cellular stress, particularly that related to free radicals. Therefore, an animal’s ideal habitat may have the minimum O2necessary to sustain aerobic metabolism, with excess O2increasing the need to scavenge free radicals and repair free radical damage. Here we show that a natural population of small (<9 mm shell length) freshwater clams (genus Sphaerium Scopoli, 1777) lives along a dissolved O2gradient from extreme hypoxia to moderate hypoxia. We tested the hypothesis that clams living in extreme hypoxia would have higher reproductive success than clams that live in moderate hypoxia. Clam abundance was highest in water with very low dissolved O2, conditions previously demonstrated to decrease cellular stress. The internally brooding clams reproduced year-round and had higher reproductive output in extreme hypoxia than in moderate hypoxia. The findings demonstrate that the apparent cellular-level benefits of hypoxia may translate into increased fitness, especially for small organisms.
Spatial organization of Molina’s hog-nosed skunk (Conepatus chinga) in two landscapes of the Pampas grassland of Argentina
Authors: Castillo D. F. , Lucherini M. , Luengos Vidal E. M. , Manfredi C. , Casanave E. B.
Published: March 2011

We radio-tracked 16 individuals (6 males, 10 females) of the little known Molina’s hog-nosed skunk ( Conepatus chinga (Molina, 1782)) and compared home-range dynamics, movement rates, and densities between a protected area and a landscape fragmented by agriculture. The mean home-range size (95% fixed kernel) was 166.7 ha (SD = 107.5 ha), without significant differences between areas. Home-range size varied significantly between males (mean = 243.7 ha, SD = 76.5 ha) and females (mean = 120.4 ha, SD =77.6 ha). Overlap between home range and core area was extensive between and within sexes in the protected area and more limited in the cropland area. Mean distance traveled between two consecutive resting sites was 269.5 m (SD = 365 m) and did not differ between areas, although movements were greater for males than females. Distance moved was influenced by seasons, being greater during the cold period. Finally, density estimates were consistently greater at the protected area. We argue that home-range size in Molina’s hog-nosed skunks is an inherent species property, whereas population density and territoriality are more flexible parameters that could reflect how the ecosystem state was affected. In our study, the greater dispersion of food patches in the cropland area than in the protected area may be the major factor influencing these parameters.
Sperm morphology, ATP content, and analysis of motility in Atlantic halibut (Hippoglossus hippoglossus)
Authors: Alavi Sayyed Mohammad Hadi , Butts Ian A.E. , Hatef Azadeh , Mommens Maren , Trippel Edward A. , Litvak Matthew K. , Babiak Igor
Published: March 2011

Spermatozoon of Atlantic halibut ( Hippoglossus hippoglossus (L., 1758)) is uniflagellated, lacks an acrosome, and is differentiated into a head, midpiece, and flagellum. There are two to five mitochondria in the midpiece, as well as proximal and distal centrioles. The flagellum consisted of 9 + 2 microtubules surrounded by plasma membrane, which is extended at the proximal part of the flagellum owing to the presence of vacuoles. After sperm activation in seawater, sperm motility and velocity decreased from 98.4% ± 3.4% and 170.3 ± 8.9 µm·s–1at 15 s after sperm activation to 4.8% ± 4.7% and 9.2 ± 8.9 µm·s–1at 120 s after sperm activation, respectively. ATP content (nmol·L–1ATP per 108spermatozoa) significantly decreased at 60 s after sperm activation (5.9 ± 1.5) compared with at 0 and 30 s after sperm activation (14.9 ± 1.5 and 14.5 ± 1.5, respectively). Beating waves propagated along the full length of the flagellum after sperm activation, whereas waves were restricted to the proximal section during the latter motility period. Wave amplitude significantly decreased at 45 s after sperm activation, but wavelength did not differ. The present study showed associations among sperm morphology, ATP content, flagellar wave parameters, and sperm velocity, which could be used in comparative spermatology.
DIFFICULTIES IN THE USE OF DFA TO CHARACTERIZE PETROLEUM RESERVOIRS
Authors: RIBEIRO R. A. , MATA MARIA V. M. , COSTA K. C. O. , SILVA F. W. F. , LUCENA L. S. , FULCO U. L. , CORSO G.
Published: March 2011

In this work we have used the Detrended Fluctuation Analysis (DFA) technique to investigate an oil reservoir. The system we address here is situated at Bacia de Namorados, RJ, Brazil. The data corresponds to well logs of five geophysical variables: sonic, porosity, electrical resistivity, gamma ray and density measured in 56 wells. The objective of this work is to analyze the correlation or similarity among the DFA index of several geophysical quantities. We perform a linear correlation test to compare pairs of DFA indices of the geophysical quantities for the well logs. We have not found a major similarity among the five variables which indicates an absence of correlation for these variables. Therefore, we argue that the DFA index should be used with caution in the characterization of oil reservoirs. In this way we suggest to integrate the information of DFA of several physical quantities to adequately model this kind of system.
A NEW METHOD TO CALCULATE THE INCONCLUSIVE COEFFICIENTS IN THE QUANTUM STATE DISCRIMINATION
Authors: EVANGELISTA TATIANE , LAVOR CARLILE , RABELO WILSON R. M.
Published: March 2011

The problem of determining the state of a quantum system is a central task in any quantum information processing. However, there are limitations imposed by quantum mechanics on the possibilities to determine the state of a quantum system. For example, nonorthogonal states cannot be discriminated perfectly. In this paper, we propose a new method to calculate the inconclusive coefficients based on the solution of a quadratic system, replacing the determination of the roots of a polynomial of degree 8, used in an algorithm to quantum state discrimination previously defined in the literature. The new method simplifies the calculation of the inconclusive coefficients and can be extended very easily to any dimension. The method was written in Matlab and successfully applied to problems with different dimensions.
MULTIWALLED CARBON NANOTUBES AND NANOFIBERS: SIMILARITIES AND DIFFERENCES FROM STRUCTURAL, ELECTRONIC AND CHEMICAL CONCEPTS; CHEMICAL MODIFICATION FOR NEW MATERIALS DESIGN
Authors: SAVILOV SERGUEI , CHERKASOV NIKOLAI , KIRIKOVA MARINA , IVANOV ANTON , LUNIN VALERY
Published: March 2011

Present work points out the differences between possible tubular carbon structures: nanotubes and nanofibers, as well as describes ways of their modification for utilization for new materials design. For material characterization, XRD, XPS, Raman spectroscopy, thermal analysis, HRTEM and SEM, pore size distribution, EELS, elemental analysis and adiabatic bomb calorimetry were used. Heats of formation for nanotubes and nanofibers and their dependence on carboxylation extent as well as properties of the modified materials are also discussed. The perspectives of applications of modified carbon nanotubes in catalysis and polymers chemistry are given.