bluuebunny/crossref_metadata_2025 huggingface dataset:
Liparid and macrourid fishes of the hadal zone:in situobservations of activity and feeding behaviour
Authors: Jamieson A.J , Fujii T , Solan M , Matsumoto A.K , Bagley P.M , Priede I.G
Published: January 2009

Using baited camera landers, the first images of living fishes were recorded in the hadal zone (6000–11 000 m) in the Pacific Ocean. The widespread abyssal macrouridCoryphaenoides yaquinaewas observed at a new depth record of approximately 7000 m in the Japan Trench. Two endemic species of liparid were observed at similar depths:Pseudoliparis amblystomopsisin the Japan Trench andNotoliparis kermadecensisin the Kermadec Trench. From these observations, we have documented swimming and feeding behaviour of these species and derived the first estimates of hadal fish abundance. The liparids intercepted bait within 100–200 min but were observed to preferentially feed on scavenging amphipods.Notoliparis kermadecensisact as top predators in the hadal food web, exhibiting up to nine suction-feeding events per minute. Both species showed distinctive swimming gaits:P. amblystomopsis(mean length 22.5 cm) displayed a mean tail-beat frequency of 0.47 Hz and mean caudal : pectoral frequency ratio of 0.76, whereasN. kermadecensis(mean length 31.5 cm) displayed respective values of 1.04 and 2.08 Hz. Despite living at extreme depths, these endemic liparids exhibit similar activity levels compared with shallow-water liparids.
How much do genetic covariances alter the rate of adaptation?
Authors: Agrawal Aneil F , Stinchcombe John R
Published: January 2009

Genetically correlated traits do not evolve independently, and the covariances between traits affect the rate at which a population adapts to a specified selection regime. To measure the impact of genetic covariances on the rate of adaptation, we compare the rate fitness increases given the observed

G

matrix to the expected rate if all the covariances in the

G

matrix are set to zero. Using data from the literature, we estimate the effect of genetic covariances in real populations. We find no net tendency for covariances to constrain the rate of adaptation, though the quality and heterogeneity of the data limit the certainty of this result. There are some examples in which covariances strongly constrain the rate of adaptation but these are balanced by counter examples in which covariances facilitate the rate of adaptation; in many cases, covariances have little or no effect. We also discuss how our metric can be used to identify traits or suites of traits whose genetic covariances to other traits have a particularly large impact on the rate of adaptation.
Reproductive competition in the bumble-beeBombus terrestris:do workers advertise sterility?
Authors: Amsalem Etya , Twele Robert , Francke Wittko , Hefetz Abraham
Published: January 2009

Reproductive competition in social insects is generally mediated through specific fertility pheromones. By analysing Dufour's gland secretion in queens and workers ofBombus terrestrisunder varying social conditions, we demonstrate here that the volatile constituents of the secretion exhibit a context-dependent composition. The secretion of egg-laying queens is composed of a series of aliphatic hydrocarbons (alkanes and alkenes), while that of sterile workers contains in addition octyl esters, dominated by octyl hexadecanoate and octyl oleate. These esters disappear in workers with developed ovaries, whether queenright (QR) or queenless (QL), rendering their secretion queen-like. This constitutes an unusual case in which the sterile caste, rather than the fertile one, possesses extra components. Individually isolated (socially deprived) workers developed ovaries successfully, but failed to oviposit, and still possessed the octyl esters. Thus, whereas social interactions are not needed in order to develop ovaries, they appear essential for oviposition and compositional changes in Dufour's gland secretion (ester disappearance). The apparent link between high ester levels and an inability to lay eggs lends credence to the hypothesis that these esters signal functional sterility. We hypothesize that by producing a sterility-specific secretion, workers signal that ‘I am out of the competition’, and therefore are not attacked, either by the queen or by the reproductive workers. This enables proper colony function and brood care, in particular sexual brood, even under the chaotic conditions of the competition phase.
The genomic architecture of segmental duplications and associated copy number variants in dogs
Authors: Nicholas Thomas J. , Cheng Ze , Ventura Mario , Mealey Katrina , Eichler Evan E. , Akey Joshua M.
Published: January 2009

Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated copy number variants (CNVs) in the modern domesticated dog,Canis familiaris, which exhibits considerable morphological, physiological, and behavioral variation. Through computational analyses of the publicly available canine reference sequence, we estimate that segmental duplications comprise ∼4.21% of the canine genome. Segmental duplications overlap 841 genes and are significantly enriched for specific biological functions such as immunity and defense and KRAB box transcription factors. We designed high-density tiling arrays spanning all predicted segmental duplications and performed aCGH in a panel of 17 breeds and a gray wolf. In total, we identified 3583 CNVs, ∼68% of which were found in two or more samples that map to 678 unique regions. CNVs span 429 genes that are involved in a wide variety of biological processes such as olfaction, immunity, and gene regulation. Our results provide insight into mechanisms of canine genome evolution and generate a valuable resource for future evolutionary and phenotypic studies.
Compromised Virus-Induced Gene Silencing in RDR6-Deficient Plants
Authors: Vaistij Fabián E. , Jones Louise
Published: January 2009

RNA silencing in plants serves as a potent antiviral defense mechanism through the action of small interfering RNAs (siRNAs), which direct RNA degradation. siRNAs can be derived directly from the viral genome or via the action of host-encoded RNA-dependent RNA polymerases (RDRs). Plant genomes encode multiple RDRs, and it has been demonstrated that plants defective for RDR6 hyperaccumulate several classes of virus. In this study, we compared the effectiveness of virus-induced gene silencing (VIGS) and RNA-directed DNA methylation (RdDM) in wild-type and RDR6-deficient Nicotiana benthamiana plants. For the potexvirus Potato virus X (PVX) and the potyvirus Plum pox virus (PPV), the efficiency of both VIGS and RdDM were compromised in RDR6-defective plants despite accumulating high levels of viral siRNAs similar to infection of wild-type plants. The reduced efficiency of VIGS and RdDM was unrelated to the size class of siRNA produced and, at least for PVX, was not dependent on the presence of the virus-encoded silencing suppressor protein, 25K. We suggest that primary siRNAs produced from PVX and PPV in the absence of RDR6 may not be good effectors of silencing and that RDR6 is required to produce secondary siRNAs that drive a more effective antiviral response.
Cell Culture-Induced Gradual and Frequent Epigenetic Reprogramming of Invertedly Repeated Tobacco Transgene Epialleles
Authors: Krizova Katerina , Fojtova Miloslava , Depicker Ann , Kovarik Ales
Published: January 2009

Using a two-component transgene system involving two epiallelic variants of the invertedly repeated transgenes in locus 1 (Lo1) and a homologous single-copy transgene locus 2 (Lo2), we have studied the stability of the methylation patterns and trans-silencing interactions in cell culture and regenerated tobacco (Nicotiana tabacum) plants. The posttranscriptionally silenced (PTGS) epiallele of the Lo1 trans-silences and trans-methylates the target Lo2 in a hybrid (Lo1/Lo2 line), while its transcriptionally silenced variant (Lo1E) does not. This pattern was stable over several generations in plants. However, in early Lo1E/Lo2 callus, decreased transgene expression and partial loss of Lo1E promoter methylation compared with leaf tissue in the parental plant were observed. Analysis of small RNA species and coding region methylation suggested that the transgenes were silenced by a PTGS mechanism. The Lo1/Lo2 line remained silenced, but the nonmethylated Lo1 promoter acquired partial methylation in later callus stages. These data indicate that a cell culture process has brought both epialleles to a similar epigenetic ground. Bisulfite sequencing of the 35S promoter within the Lo1 silencer revealed molecules with no, intermediate, and high levels of methylation, demonstrating, to our knowledge for the first time, cell-to-cell methylation diversity of callus. Regenerated plants showed high interindividual but low intraindividual epigenetic variability, indicating that the callus-induced epiallelic variants were transmitted to plants and became fixed. We propose that epigenetic changes associated with dedifferentiation might influence regulatory pathways mediated by trans-PTGS processes.
The Proteome of Seed Development in the Model Legume Lotus japonicus
Authors: Dam Svend , Laursen Brian S. , Ørnfelt Jane H. , Jochimsen Bjarne , Stærfeldt Hans Henrik , Friis Carsten , Nielsen Kasper , Goffard Nicolas , Besenbacher Søren , Krusell Lene , Sato Shusei , Tabata Satoshi , Thøgersen Ida B. , Enghild Jan J. , Stougaard Jens
Published: January 2009

We have characterized the development of seeds in the model legume Lotus japonicus. Like soybean (Glycine max) and pea (Pisum sativum), Lotus develops straight seed pods and each pod contains approximately 20 seeds that reach maturity within 40 days. Histological sections show the characteristic three developmental phases of legume seeds and the presence of embryo, endosperm, and seed coat in desiccated seeds. Furthermore, protein, oil, starch, phytic acid, and ash contents were determined, and this indicates that the composition of mature Lotus seed is more similar to soybean than to pea. In a first attempt to determine the seed proteome, both a two-dimensional polyacrylamide gel electrophoresis approach and a gel-based liquid chromatography-mass spectrometry approach were used. Globulins were analyzed by two-dimensional polyacrylamide gel electrophoresis, and five legumins, LLP1 to LLP5, and two convicilins, LCP1 and LCP2, were identified by matrix-assisted laser desorption ionization quadrupole/time-of-flight mass spectrometry. For two distinct developmental phases, seed filling and desiccation, a gel-based liquid chromatography-mass spectrometry approach was used, and 665 and 181 unique proteins corresponding to gene accession numbers were identified for the two phases, respectively. All of the proteome data, including the experimental data and mass spectrometry spectra peaks, were collected in a database that is available to the scientific community via a Web interface (http://www.cbs.dtu.dk/cgi-bin/lotus/db.cgi). This database establishes the basis for relating physiology, biochemistry, and regulation of seed development in Lotus. Together with a new Web interface (http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress4legumes/) collecting all protein identifications for Lotus, Medicago, and soybean seed proteomes, this database is a valuable resource for comparative seed proteomics and pathway analysis within and beyond the legume family.
System Potentials, a Novel Electrical Long-Distance Apoplastic Signal in Plants, Induced by Wounding
Authors: Zimmermann Matthias R. , Maischak Heiko , Mithöfer Axel , Boland Wilhelm , Felle Hubert H.
Published: January 2009

Systemic signaling was investigated in both a dicot (Vicia faba) and a monocot (Hordeum vulgare) plant. Stimuli were applied to one leaf (S-leaf), and apoplastic responses were monitored on a distant leaf (target; T-leaf) with microelectrodes positioned in substomatal cavities of open stomata. Leaves that had been injured by cutting and to which a variety of cations were subsequently added caused voltage transients at the T-leaf, which are neither action potentials nor variation potentials: with respect to the cell interior, the initial polarity of these voltage transients is hyperpolarizing; they do not obey the all-or-none rule but depend on both the concentration and the type of substance added and propagate at 5 to 10 cm min−1. This response is thought to be due to the stimulation of the plasma membrane H+-ATPase, a notion supported by the action of fusicoccin, which also causes such voltage transients to appear on the T-leaf, whereas orthovanadate prevents their propagation. Moreover, apoplastic ion flux analysis reveals that, in contrast to action or variation potentials, all of the investigated ion movements (Ca2+, K+, H+, and Cl−) occur after the voltage change begins. We suggest that these wound-induced “system potentials” represent a new type of electrical long-distance signaling in higher plants.
Synthesis of Hydrated Aluminum Sulfate from Kaolin by Microwave Extraction
Authors: Park Seong Soo , Hwang Eun Hee , Kim Byoung Chan , Park Hee Chan
Published: January 2009

The feasibility of extracting alumina from kaolin via a microwave extraction process was investigated by comparing reaction times, reaction temperatures, and acid concentrations under microwave treatment with the same factors under conventional thermal extraction. The maximum amount of alumina extracted from kaolin under conventional processing at 90°C for 240 min with 1M H2SO4 was 99.9%; the same amount of alumina was extracted under microwave processing at 90°C for 120 min with 1M H2SO4.
Reactivity of Aluminum Nitride Powder in Dilute Inorganic Acids
Authors: Krnel Kristoffer , Kosmac̆ Tomaz̆
Published: January 2009

The reactivity of AlN powder in diluted inorganic acids was studied by measuring the pH and temperature during its hydrolysis. At very low starting pH (pH ∼1) no reaction was observed, regardless of the acid used. In contrast, in a less acidic environment, i.e., at higher pH values (pH ∼3), the reaction was fast enough to reveal the influence of different acids on the hydrolysis reaction. Monoprotonic acids which are completely dissociated (HCl, HF, HNO3), and form water‐soluble salts with aluminum, did not influence the hydrolysis reactions. In the presence of incompletely dissociated diprotonic H2SO4 and H2CO3 acids which form water‐soluble salts with aluminum, the reaction was hindered but not prevented. In the presence of phosphoric acid the hydrolysis was prevented at room temperature, presumably because of the formation of insoluble phosphates on the powder surface. At elevated temperatures their solubility was substantial, and the reactivity of AlN powder in a diluted hot phosphoric acid was reestablished. In the presence of silicic acid the reaction was suppressed at both room and elevated temperatures, which was also ascribed to the formation of insoluble silicates. The adsorption of silicate anions onto the powder surface was confirmed by chemical analysis and zeta potential measurement. Using DRIFT measurements, however, the presence of Si–O bonds on the powder could not be unambiguously confirmed, since the characteristic wavelengths for these bonds are in the region of very strong Al–N stretching frequencies.
Sol–Gel Preparation of Lead Zirconate Titanate Powders and Ceramics: Effect of Alkoxide Stabilizers and Lead Precursors
Authors: Wu Aiying , Vilarinho Paula M. , Salvado Isabel M. Miranda , Baptista João L.
Published: January 2009

Lead zirconate titanate (PZT) (52/48) powders were prepared by a sol–gel process, using different raw materials to introduce the lead component together with several solvents and chemical modifying agents. A study of the effect of these variables on crystallization behavior was conducted to determine the best conditions for preparing monophasic submicrometer‐sized PZT perovskite powders in the morphotropic region. In the present work, well‐crystallized, submicrometer‐sized single‐phase perovskite PZT powders were obtained after heat treatment at 600°C for 1 h. The dependence of this crystallization temperature on the preparation conditions was observed. The sol–gel‐derived submicrometer‐sized PZT powders were sintered to ∼96% of relative density after 2 h at 950°–970°C. The sintered ceramics exhibited a dielectric permittivity of 1000, a piezoelectric coefficient of 135 pC·N−1, a remanent polarization of 20 μC·cm−2, and a coercive field of 10.6 kV·cm−1.
Mimicking Nanometer Atomic Processes on a Micrometer Scale via Electrophoretic Deposition
Authors: Sarkar Partho , De Debnath , Yamashita Kimihiro , Nicholson Patrick S. , Umegaki Takao
Published: January 2009

The process of submonolayer formation during the electrophoretic deposition (EPD) of colloidal films of micrometer‐sized (diameter ∼ 0.5 μm) silica particles on a silicon wafer has been observed as a function of deposition time. The process of nucleation and growth of the silica monolayer is compared with that of atomic film growth (10000 times smaller scale) via molecular‐beam epitaxy (MBE), and for the first time, a striking similarity between the two growth processes is observed. Likewise in the atomic growth process via MBE, the entire nucleation, growth, and aggregation process during EPD of silica particles can be broadly classified into two regions. At low surface coverage when silica particles are deposited outside of clusters, diffuse randomly, and stick to a cluster on touching them, the mechanism of growth in this region follows diffusion‐limited aggregation (DLA) and the fractal dimension of the two‐dimensional clusters is found to be close to 1.65. Later on, as the clusters grow in size, deposition of particles inside the clusters become important and clusters become more and more compact, resulting in a dense, close‐packed, and homogeneous monolayer. This region is termed a consolidation region, and a change in fractal dimension from 1.65 toward 2 with increasing surface coverage has been observed.
Low‐Fire Processing of ZrO2–SnO2–TiO2 Ceramics
Authors: Jean Jau‐Ho , Lin Shih‐Chun
Published: January 2009

Effects of a liquid‐phase‐sintering aid, BaCuO2+ CuO (BCC), on densification and microwave dielectric properties of (Zr0.8Sn0.2)TiO4 (ZST) ceramics have been investigated. The densification kinetics of ZST are greatly enhanced with the presence of 2.5–5 wt% BCC, but become retarded when the amount of BCC increases further. At a given BCC content, moreover, slower densification kinetics are observed with a larger particle size of ZST. The above results are attributed to a chemical reaction taking place at the interface of BCC/ZST during firing. The ZST dissolves into BCC, forming crystalline phases of ZrO2, SnO2, CuO, and BaTi8O16 which reduce the amount of BCC flux available for liquid‐phase sintering. The crystallization kinetics become more significant, compared with densification kinetics, with increasing the amount of BCC and the particle sizes of ZST. For samples with 2.5–5 wt% BCC, a high relative sintered density is obtained at 1000°C and the resulting microwave ceramics have a dielectric constant and a value of Q at 7 GHz in the ranges of 35–38 and 2800–5000, respectively.
Thermal Stability of Low‐Oxygen Silicon Carbide Fiber (Hi‐Nicalon) Subjected to Selected Oxidation Treatment
Authors: Shimoo Toshio , Toyoda Fumihiko , Okamura Kiyohito
Published: January 2009

Low‐oxygen silicon carbide fibers (Hi‐Nicalon) were oxidized at temperatures from 1073 to 1773 K under an oxygen partial pressure of 0.25 atm. The strength of the unoxidized core was practically unaffected by the oxidation temperatures. The strength of the as‐oxidized fibers with an SiO2 film decreased markedly with increasing oxidation temperature. When exposed subsequently to 1773 K in argon, the fibers with a SiO2 film of 0.3–0.5 μm thickness had the best thermal stability.
Mechanical Properties of La1‐xSrxCo0.2Fe0.8O3 Mixed‐Conducting Perovskites Made by the Combustion Synthesis Technique
Authors: Chou Yeong‐Shyung , Stevenson Jeffrey W. , Armstrong Timothy R. , Pederson Larry R.
Published: January 2009

This paper examined the room‐temperature mechanical properties of a mixed‐conducting perovskite La1–xSrxCo0.2Fe0.8O3 (x= 0.2–0.8). Powders were made by the combustion synthesis technique and sintered at 1250°C in air. Sintered density, crystal phase, and grain size were characterized. Young's and shear moduli, microhardness, indentation fracture toughness, and biaxial flexure strength were determined. The Young's and shear moduli slightly increased with increasing strontium content. Young's modulus of 151–188 GPa and shear modulus of 57–75 GPa were measured. Biaxial flexure strength of ∼160 MPa was measured for lower strontium content batches. Strength greatly decreased to ∼40 MPa at higher strontium concentrations (x= 0.6–0.8) because of the formation of extensive cracking. Indentation toughness showed a higher value (∼1.5 MPa·m1/2) for low strontium (x= 0.2) content and a lower value (∼1.1 MPa·m1/2) for the other batches (x= 0.4–0.8). Materials with fine and coarse grain size were also tested at various indent loads and showed no dependence of toughness on crack size. In addition, fractography was used to characterize the critical flaw and fracture mode.
Rate of Strength Decrease of Fiber‐Reinforced Ceramic‐Matrix Composites during Fatigue
Authors: Sørensen Bent F. , Holmes John W. , Vanswijgenhoven Eddy L.
Published: January 2009

An experimental investigation was performed to study the rate at which strength‐controlling fatigue damage evolves in a ceramic‐matrix composite. Tensile specimens of a unidirectional SiC‐fiber‐reinforced calcium aluminosilicate matrix composite were cycled to failure or to a preselected number of cycles under similar loading histories. The residual strength of the precycled specimens was found to be similar to that of virgin specimens. Microstructural investigations showed that the fracture surfaces of the specimens cycled to failure had a central region where fiber pullout was negligible. It is proposed that frictional heating (due to interfacial sliding) is the cause of fatigue failure. High interfacial temperatures are assumed to cause the formation of a strong interface bond, leading to internal embrittlement.
Controlling and Testing the Fracture Strength of Silicon on the Mesoscale
Authors: Chen Kuo‐Shen , Ayon Arturo , Spearing S. Mark
Published: January 2009

Strength characterizations and supporting analysis of mesoscale biaxial flexure and radiused hub flexure single‐crystal silicon specimens are presented. The Weibull reference strengths of planar biaxial flexure specimens were found to lie in the range 1.2 to 4.6 GPa. The local strength at stress concentrations was obtained by testing radiused hub flexure specimens. For the case of deep reactive ion‐etched specimens the strength at fillet radii was found to be significantly lower than that measured on planar specimens. This result prompted the introduction of an additional isotropic etch after the deep reactive ion etch step to recover the strength in such regions. The mechanical test results reported herein have important implications for the development of highly stressed microfabricated structures. The sensitivity of the mechanical strength to etching technique must be accounted for in the structural design cycle, particularly with regard to the selection of fabrication processes. The scatter of data measured in the mechanical tests clearly illustrated the need to use a probabilistic design approach. Weibull statistics may be the appropriate means to describe the data, although a simple two‐parameter Weibull model only provides a moderately good fit to the experimental data reported in this study.
Preliminary Observations on Phase Relations in the “V2O3–FeO” and V2O3–TiO2 Systems from 1400°C to 1600°C in Reducing Atmospheres
Authors: Coetsee Theresa , Pistorius Chris
Published: January 2009

Phase relations within the “V2O3–FeO” and V2O3–TiO2 oxide systems were determined using the quench technique. Experimental conditions were as follows: partial oxygen pressures of 3.02 × 10−10, 2.99 × 10−9, and 2.31 × 10−8 atm at 1400°, 1500°, and 1600°C, respectively. Analysis techniques that were used to determine the phase relations within the reacted samples included X‐ray diffractometry, electron probe microanalysis (energy‐dispersive spectroscopy and wavelength‐dispersive spectroscopy), and optical microscopy. The solid‐solution phases M2O3, M3O5, and higher Magneli phases (MnO2n−1, where M = V, Ti) were identified in the V2O3–TiO2 system. In the “V2O3–FeO” system, the solid‐solution phases M2O3 and M3O4 (where M = V, Ti), as well as liquid, were identified.
Formation of Core/Rim Structures in Ti(C,N)‐WC‐Ni Cermets via a Dissolution and Precipitation Process
Authors: Ahn Sun‐Yong , Kang Shinhoo
Published: January 2009

The core/rim structures of compounds in the Ti(C,N)‐xWC‐20Ni system have been investigated to determine the effect of WC and nitrogen content on the microstructure of the system. In addition, the relative dissolution rate of WC to Ti(C,N) in the system was studied by analyzing the rim compositions. Variations in the WC content had a much‐lesser influence, as an additive, on the general microstructure than that of other carbides that have been used in previous studies. However, the nitrogen content in Ti(C1−XNX) had a significant effect on its microstructure. The composition of the rim structure was determined by the ratio of solutes that were dissolved in the liquid binder, under the given processing conditions. The dissolution rate of WC was ∼2 and 5 times faster than that of Ti(C,N) in the system at temperatures of 1300° and 1510°C, respectively. The results have been interpreted in terms of phase stability and precipitation phenomena.
Influence of Air Compressibility on the Permeability Evaluation of Refractory Castables
Authors: Innocentini Murilo D. M. , Pardo Arturo R. F. , Pandolfelli Victor C.
Published: January 2009

Air compressibility is important in attaining an accurate quantification of the permeability parameters for refractory castables. Nevertheless, this effect is often neglected in the permeability equations that are found in ceramics literature. The consequences of omitting the compressibility effect in two of the main permeability equations are highlighted and discussed. The permeability to air flow of high‐Al2O3 ultra‐low‐cement refractory castables has been quantified by Darcy's law according to U.S. ASTM C577–96 and European PRE‐16th permeability methods, which propose distinct approaches for air compressibility. Forchheimer's equation, which establishes a more realistic dependence between fluid pressure and fluid velocity, also has been used to obtain the permeability constants k1 and k2. Results show that equations proposed by the ASTM and the PRE methods may yield very distinct values of Darcian permeability k1 for the same sample. Forchheimer's equation for compressible fluids provides the best fitting with experimental data.
Cytological features of chromophobe renal cell carcinoma, classic type. A report of nine cases
Authors: Tejerina E. , González‐Peramato P. , Jiménez‐Heffernan J. A. , Vicandi B. , Serrano A. , López‐Ferrer P. , Viguer J. M.
Published: January 2009

Objective:  To review our experience with nine cases of chromophobe renal cell carcinoma (ChRCC), classic type. The cytological descriptions of this entity are still rare, and information concerning the diagnostic value of cytology is needed.

Methods:  Nine cases of ChRCC evaluated using fine needle aspiration (n = 6) or intraoperative scrape cytology (n = 3) were selected. Expression of vimentin was evaluated in four cases using immunocytochemistry, which was performed on alcohol‐fixed material. In all cases a complete pathological study was available.

Results:  The neoplastic cells were arranged mainly as single cells and small, discohesive, monolayered groups. A polymorphous cellular population was identified, with coexisting large, small and intermediate‐sized cells. The large neoplastic cells showed clear, flocculent cytoplasm with small, eccentric nuclei and frequent binucleation. Dense, homogeneous cytoplasm was most commonly seen in smaller cells. Clear cytoplasmic spaces resembling perinuclear halos were frequently observed, best appreciated in cells with more dense cytoplasm. Binucleation and a marginal nuclear location were commonly seen. Necrosis, basement membrane or other stromal material were absent. Vimentin was not expressed in the four cases analysed. Precise cytological recognition was possible in the last five cases.

Conclusions:  There is increasing evidence that a cytological diagnosis of ChRCC is possible. In our experience the histopathological features of ChRCC were well reflected in cytological samples, allowing specific recognition. In our cases the main differential diagnosis considered was clear cell carcinoma. Cytology can be especially helpful in the evaluation of intraoperative samples.
European guidelines for clinical management of abnormal cervical cytology, Part 2
Authors: Jordan J. , Martin‐Hirsch P. , Arbyn M. , Schenck U. , Baldauf J.‐J. , Da Silva D. , Anttila A. , Nieminen P. , Prendiville W.
Published: January 2009

The current paper presents the second part of chapter 6 of the second edition of the European Guidelines for Quality Assurance in Cervical Cancer Screening. The first part of the same chapter was published in a previous issue (Cytopathology 2008;19:342–54). This part provides guidance on how to manage and treat women with histologically confirmed cervical intraepithelial neoplasia. The paper describes the characteristics, indications and possible complications of excisional and ablative treatment methods. The three options to monitor the outcome after treatment (repeat cytology, HPV testing and colposcopy) are discussed. Specific recommendations for particular clinical situations are provided: pregnancy, immuno‐suppression, HIV infection, post‐menopause, adolescence and cyto‐colpo‐histological disparity. The paper ends with recommendations for quality assurance in patient management and some general advice on how to communicate screening, diagnosis and treatment results to the woman concerned. Finally, a data collection form is attached.
Effect ofMucuna prurienson oxidative stress mediated damage in aged rat sperm
Authors: Suresh Sekar , Prithiviraj Elumalai , Prakash Seppan
Published: January 2009

Mucuna pruriensLinn., a leguminous plant, has been recognized as an aphrodisiac and spermatogenic agent. Protective efficacy ofM. prurienson reactive oxygen species (ROS)‐induced pathophysiological alterations in structural and functional integrity of epididymal sperm in aged Wister albino rat was analysed. Animals were grouped as groups I, II, III and IV, i.e. young (control), aged, aged treated with ethanolic extract (200 mg/kg b.w.) ofM. pruriensand young rats treated withM. pruriens, respectively. At the end of the experimental period, i.e. after 60 days animals were sacrificed, epididymal sperm were collected and subjected to count, viability, motility, morphology and morphometric analysis. Enzymatic and non‐enzymatic antioxidants, ROS, lipid peroxidation (LPO), DNA damage, chromosomal integrity and mitochondrial membrane potential were estimated. Results obtained from the aged animals showed significant reduction in sperm count, viability and motility, increased morphological damage and an increase in the number of sperm with cytoplasmic remnant, and these alterations were significantly reversed inM. prurienstreated group. Significant increase in LPO, HO˙ and H2O2production and significant decline in the levels of the enzymatic and non‐enzymatic antioxidants were observed in the aged animals. Supplementation ofM. prurienssignificantly reduced ROS and LPO production and significant increase in both enzymatic and non‐enzymatic antioxidant levels. There were significant DNA damage, loss of chromosomal integrity and increase in mitochondrial membrane permeability in aged rat sperm. This was significantly reduced in group III. Present observation indicates the antioxidant enhancing property, free radical quenching ability and spermatogenic efficacy of theM. pruriens. Collectively, sperm damage in ageing was significantly reduced by quenching ROS, improving antioxidant defence system and mitochondrial function.
Gauging the effects of sampling failure in biogeographical analysis
Authors: Turner Alan H. , Smith Nathan D. , Callery John A.
Published: January 2009

Aim  Various methods are employed to recover patterns of area relationships in extinct and extant clades. The fidelity of these patterns can be adversely affected by sampling error in the form of missing data. Here we use simulation studies to evaluate the sensitivity of an analytical biogeographical method, namely tree reconciliation analysis (TRA), to this form of sampling failure.

Location  Simulation study.

Methods  To approximate varying degrees of taxonomic sampling failure within phylogenies varying in size and in redundancy of biogeographical signal, we applied sequential pruning protocols to artificial taxon–area cladograms displaying congruent patterns of area relationships. Initial trials assumed equal probability of sampling failure among all areas. Additional trials assigned weighted probabilities to each of the areas in order to explore the effects of uneven geographical sampling. Pruned taxon–area cladograms were then analysed with TRA to determine if the optimal area cladograms recovered match the original biogeographical signal, or if they represent false, ambiguous or uninformative signals.

Results  The results indicate a period of consistently accurate recovery of the true biogeographical signal, followed by a nonlinear decrease in signal recovery as more taxa are pruned. At high levels of sampling failure, false biogeographical signals are more likely to be recovered than the true signal. However, randomization testing for statistical significance greatly decreases the chance of accepting false signals. The primary inflection of the signal recovery curve, and its steepness and slope depend upon taxon–area cladogram size and area redundancy, as well as on the evenness of sampling. Uneven sampling across geographical areas is found to have serious deleterious effects on TRA, with the accuracy of recovery of biogeographical signal varying by an order of magnitude or more across different sampling regimes.

Main conclusions  These simulations reiterate the importance of taxon sampling in biogeographical analysis, and attest to the importance of considering geographical, as well as overall, sampling failure when interpreting the robustness of biogeographical signals. In addition to randomization testing for significance, we suggest the use of randomized sequential taxon deletions and the construction of signal decay curves as a means to assess the robustness of biogeographical signals for empirical data sets.
Can herbarium records be used to map alien species invasion and native species expansion over the past 100 years?
Authors: Crawford Priscilla H. C. , Hoagland Bruce W.
Published: January 2009

Aim  To determine if the temporal and spatial pattern of alien plant invasion and native plant expansion can be observed using 100 years of herbarium data from Oklahoma, USA, and to eliminate herbarium collection biases in such analyses.

Location  Oklahoma, USA.

Methods  Using herbarium records from the Oklahoma Vascular Plants Database from 1903 to 2004, we reconstructed the spatial and temporal collection history of two alien invasive taxa (Lonicera japonica and Tamarix spp.) and three native expansive species (Ambrosia psilostachya, Amphiachyris dracunculoides and Juniperus virginiana). To compare the overall collecting trend, groups of native non‐expansive taxa were selected as counterparts. We recorded the year of the first collection in each township in Oklahoma for all taxa. The cumulative number of occupied townships was log‐transformed, plotted against time and modelled with linear regression. The slope of the linear regression represented collection trend over time for the non‐expansive counterpart group. However, for the invasive and expansive species, the regression slope represented the collection effort plus the invasion or expansion rate. We calculated the proportion of invasive and expansive species to non‐expansive species by dividing the cumulative number of townships for each invasive or expansive species by the cumulative number of townships occupied by the counterpart group (proportion curve).

Results  Maps of the collection records of invasive and expansive taxa illustrated no discernible spatial invasion or expansion pattern. The slopes of the linear regression for alien invasive taxa were significantly steeper than those of their associated native non‐expansive counterparts, indicating an increase in abundance. Juniperus virginiana, L. japonica and Tamarix spp. exhibited one or more periods during which they were collected at a disproportionately higher rate than their native non‐expansive counterparts.

Main conclusions  Patterns of species invasion and expansion in Oklahoma were detected using techniques developed for regions with longer collecting plant histories. The proportion curve analysis eliminated some biases inherent in herbarium data by reducing the effect of collecting effort. Both the regression model and proportion curve analyses illustrate the temporal invasion patterns of alien invasive species. The native species did not show a clear expansion pattern. The information found in recently established herbaria may not be sensitive enough to detect the increase in abundance of native species.
Enrolment and response rates in a longitudinal birth cohort
Authors: Golding Jean , Birmingham Karen
Published: January 2009

For the scientific credibility of study results, longitudinal cohort studies need to invest time, money and creative thought in establishing and maintaining the maximum number of study participants. Although success depends to a large extent on the resources available, much can be achieved by establishing a culture of integrity and enthusiasm among study staff that is conveyed to participants at all times. In this paper we outline various strategies that can be included in order to maximise the response rates.
Mapping of pachytene bivalents of female codling moth Cydia pomonella (Linnaeus) (Lep., Tortricidae)
Authors: Makee H. , Tafesh N. , Harrown H.
Published: January 2009

Spread pachytene nuclei of codling moth Cydia pomonella (Linnaeus) (Lep., Tortricidae) females of a Syrian strain (SY) were used to investigate chromomere patterns of chromosome bivalents and determine their length. The karyotype of female codling moths consists of 28 chromosome bivalents, of which seven are clearly distinguishable using chromosome length and the number and size of the chromomeres in the pachytene stage. One autosome bivalent has two nucleolar organizing regions (NORs) that are located at the opposite ends of the chromosome and appear as distinct structural landmarks. In female codling moths, the WZ sex chromosome bivalent was easily identified in pachytene oocytes according to the heterochromatic thread of the W chromosome. This study contributed to the knowledge and identification of pachytene chromosomes of female codling moths.
Effects of lipopolysaccharide on platelet‐derived growth factor isoform and receptor expression in cultured rat common bile duct fibroblasts and cholangiocytes
Authors: Kim Tae‐Hyeon , Moon Jong Ho , Savard Christopher E , Kuver Rahul , Lee Sum P
Published: January 2009

Background and Aim:  Little is known about the role of platelet‐derived growth factor (PDGF) in biliary fibrosis in the setting of bacterial colonization of the biliary tree. We therefore sought to investigate whether exposure to bacterial lipopolysaccharide (LPS) alters PDGF isoform and receptor expression in cultured rat common bile duct fibroblasts (CBDF) and normal rat cholangiocytes (NRC).

Methods:  Collagen content in cells and media was assessed by colorimetric assay and gel electrophoresis. mRNA levels of PDGF‐A and ‐B, and PDGF‐Receptors (PDGF‐R) α and β were measured by relative quantitative real‐time PCR. Protein levels of PDGF‐AA, AB and BB were measured by ELISA, and PDGF‐Rα and PDGF‐Rβ by Western blot.

Results:  In CBDF, LPS increased total soluble collagen synthesis and secretion. PDGF‐Rα and β mRNA and protein were also increased by LPS treatment in CBDF. Lipopolysaccharide treatment elicited an increase in PDGF‐A and ‐B mRNA levels in CBDF. In NRC, levels of PDGF‐A mRNA increased in a dose‐dependent fashion following LPS treatment, whereas PDGF‐B mRNA showed no response. PDGF‐AA secretion was higher by CBDF than by NRC. PDGF‐BB levels were also higher in CBDF than in NRC. While PDGF‐BB levels did not respond to LPS treatment in CBDF, there was a dose‐dependent response of this isoform to LPS in NRC. Intracellular and secreted PDGF‐AB increased with LPS treatment in NRC.

Conclusions:  These results support a model in which chronic bacterial colonization of the biliary tree induces fibrosis through PDGF‐dependent mechanisms.
Immunophenotyping of interstitial infiltrate does not distinguish between BK virus nephropathy and acute cellular rejection
Authors: ROGERS NATASHA M , RUSS GRAEME R , COOPER JOHN , COATES P TOBY
Published: January 2009

Introduction:  BK virus nephropathy (BKVN) is a significant cause of late renal allograft loss. It is characterized histologically by an interstitial nephritis that can be difficult to distinguish from acute cellular rejection (ACR). We investigated whether immunophenotyping of the infiltrate would aid this distinction.

Methods:  Ten cases of biopsy‐proven BKVN, following renal transplantation, were identified from a single transplant centre. The infection was confirmed by renal biopsy and staining for SV‐40 T‐antigen. Biopsies from 20 consecutive patients with ACR were identified and used as controls. There was no evidence of BK infection serologically or histologically in these patients. Immunohistochemical staining with anti‐CD20, perforin and granzyme B was performed on remaining tissue samples.

Results:  Clustered B cells were demonstrated in both BKVN and ACR. Hence, the CD20‐stained component within the interstitial infiltrate was not useful in distinguishing these biopsies. Perforin‐stained slides demonstrated fewer cytotoxic T cells in the biopsies with BK virus (average 2.4 ± 1.4 cells per 100 lymphocytes per field) compared with those samples with acute rejection (8.6 ± 5.7 cells per 100 lymphocytes, P < 0.0001). No significant difference in granzyme B staining was detected between ACR and BKVN.

Conclusion:  Clustered B cells and granzyme B staining did not differentiate between ACR and BKVN. However, ACR cellular infiltrate was rich in perforin positive cells suggesting that perforin staining may be a useful marker to discriminate between these conditions.
Urinary levels of epidermal growth factor, interleukin‐6 and monocyte chemoattractant protein‐1 may act as predictor markers of renal function outcome in immunoglobulin A nephropathy
Authors: STANGOU MARIA , ALEXOPOULOS EFSTATHIOS , PAPAGIANNI AIKATERINI , PANTZAKI AFRODITI , BANTIS CHRISTOS , DOVAS SPIROS , ECONOMIDOU DOMNIKI , LEONTSINI MARIA , MEMMOS DIMITRIOS
Published: January 2009

Aim:  Urinary cytokine excretion may reflect histological changes in immunoglobulin A nephropathy (IgAN), and their measurement can give information about disease outcome.

Methods:  Thirty‐three IgAN patients were prospectively followed for 5.6 ± 3.1 years. Urinary levels of monocyte chemoattractant protein‐1 (MCP‐1), interleukin (IL)‐6 and epidermal growth factor (EGF) were measured at diagnosis and repeated 1 year later for IL‐6 and EGF.

Results:  Urinary MCP‐1 and IL‐6 levels were increased significantly, while EGF excretion reduced in IgAN patients, compared to controls. IL‐6 urinary levels showed significant positive correlation with chronic histological lesions. Patients were classified into five groups, according to the Haas classification system. MCP‐1 and IL‐6 urinary levels were increased, whereas EGF levels were reduced in the progression of staging. EGF urinary excretion was a strong predictor factor of disease outcome, significantly correlated with creatinine clearance at time of diagnosis (r = 0.5, P = 0.005), and at the end of follow up (r = 0.6, P = 0.001). Urinary EGF levels measured a year later could predict long‐term outcome better, and a cut of 0.05 pg/mg urine creatinine levels could distinguish between progressors and non‐progressors.

Conclusion:  Urinary MCP‐1, IL‐6 and EGF levels may represent histology in IgAN. EGF excretion can be a predictive marker and its serial measurements may give information about disease outcome and the effect of treatment.
Increased urinary excretion of orosomucoid is a risk predictor of diabetic nephropathy
Authors: JIANG HONGJUAN , GUAN GUANGJU , ZHANG RUI , LIU GANG , LIU HAIYING , HOU XIANGHUA , CHENG JING
Published: January 2009

Aim:  Identification of the risk predictor of diabetic nephropathy (DN) remains a major challenge currently. Thus, proteomic approaches to identify DN‐related biomarker were performed.

Methods:  A comparative proteomic approach of 2‐D gel electrophoresis (2‐DE) and mass spectrometry to identify biomarkers in urine samples from 12 DN patients (six type 1 and six type 2 diabetic patients) and six healthy controls. Then, the urinary level of identified protein biomarker was detected by immunoturbidimetry assay in urine samples from 90 type 1 and type 2 diabetic patients with normo‐, micro‐ and macroalbuminuria (n = 30 in each group), and 30 healthy controls.

Results:  A novel DN‐related protein, orosomucoid (α1‐acid glycoprotein), was identified by proteomic method. Its abundance was highly upregulated (>eightfold) in DN patients. The data of immunoturbidimetry assay showed urinary orosomucoid excretion rate (UOER) was gradually increased in the normo‐, micro‐ and macroalbuminuria group versus control (0.71 ± 0.41, 1.93 ± 0.68, 2.88 ± 0.94 vs 0.39 ± 0.28 ug/min, P < 0.05). The result indicated that UOER increased in early stage of DN and gradually increased with the development of DN. Also, Pearson's correlation analysis indicated UOER was positively correlated with urinary albumin excretion rate, serum creatinine and C‐reactive protein (r = 0.830, 0.787 and 0.360, respectively; P < 0.05). Multivariate logistic regression analysis also showed that increased UOER was an independent risk factor for DN (odds ratio = 3.10, P < 0.0001).

Conclusion:  Urinary orosomucoid is a DN‐related biomarker, which is associated with the development and progression of DN. Furthermore, increased UOER is an independent risk factor of DN.
Review article: How cells sense oxygen: Lessons from and for the kidney
Authors: GLEADLE JONATHAN M
Published: January 2009

The kidney has contributed two critical insights to an understanding of the mechanism by which all mammalian cells sense oxygen. The first followed from the detailed characterization of the regulation of expression of erythropoietin by oxygen and led to the discovery of the hypoxically regulated transcription factor, HIF (hypoxia‐inducible factor). The second insight developed from the exploration of the molecular pathogenesis of von Hippel Lindau disease protein whose mutation is characterized by the development of renal cancers. The essential role for the von Hippel Lindau disease protein in the oxygen‐dependent degradation of HIF led directly to the discovery of the oxygen sensing mechanism that regulates HIF by oxygen‐dependent peptidyl hydroxylation. This understanding now generates novel therapeutic possibilities and is providing insights into the mechanisms of other renal diseases.