bluuebunny/crossref_metadata_2025 huggingface dataset:
The relationship between pornography use and sexual behaviours among at-risk HIV-negative men who have sex with men
Authors: Eaton Lisa A. , Cain Demetria N. , Pope Howard , Garcia Jonathan , Cherry Chauncey
Published: October 2011

Objectives
Although pornography is widely available and frequently used among many adults in the USA, little is known about the relationship between pornography and risk factors for HIV transmission among men who have sex with men. Methods: Baseline assessments from a behavioural intervention trial for at-risk men who have sex with men were conducted in Atlanta, GA in 2009. Univariate and multivariate generalised linear models were used to assess the relationships between known risk factors for HIV infection, time spent viewing pornography, and sex behaviours. Results: One hundred forty-nine men reporting HIV-negative status and two or more unprotected anal sex partners in the past 6 months were enrolled in an intervention trial and completed survey assessments. Time spent viewing pornography was significantly associated with having more male sexual partners (B = 0.45, SE = 0.04, P < 0.001) and unprotected insertive anal sex acts (B = 0.28, SE = 0.04, P < 0.001). Moreover, increased substance use (drug use, B = 0.61, SE = 0.14, P < 0.001; alcohol use, B = 0.03, SE = 0.01, P < 0.01) and decreased perception of risk for HIV infection (B = –0.09, SE = 0.04, P < 0.05) were found to be significantly associated with greater time spent viewing pornography. Conclusions: This exploratory study is novel in that it sheds light on the associations between viewing pornography and sexual risk taking for HIV infection. Future studies in this area should focus on understanding how the content of pornography; in particular, the viewing of unprotected and protected sex acts, may affect sexual risk taking behaviour.
Regulation of tomato fruit ripening.
Authors: Pirrello J. , Regad F. , Latché A. , Pech J. C. , Bouzayen M.
Published: October 2011

Fruit ripening is a sophisticatedly orchestrated developmental process, unique to plants, that results in major physiological and metabolic changes, ultimately leading to fruit decay and seed dispersal. Because of their strong impact on fruit nutritional and sensory qualities, the ripening-associated changes have been a matter of sustained investigation aiming at unravelling the molecular and genetic basis of fruit ripening. Tomato rapidly emerged as the model of choice for fleshy fruit research and a wealth of genetic resources and genomics tools have been developed, providing new entries into the regulatory mechanisms involved in the triggering and coordination of the ripening process. Some of the key components participating in the control of tomato fruit ripening have been uncovered, but our knowledge of the network of signalling pathways engaged in this complex developmental process remains fragmentary. This review highlights the main advances and emphasizes issues still to be addressed using the rapidly developing 'omics' approaches.
Potential for engineering horticultural crops with high antioxidant capacity.
Authors: Shukla V. , Mattoo A. K.
Published: October 2011

Cellular oxidation index has emerged as an important determinant in defining the fate of a living cell and its susceptibility to disease. Oxidative stress targets include oxidation of DNA, protein and lipids; causing cellular oncogenesis, chronic diseases and premature senescence. The possibility that dietary intervention via nutrition-enriched food may significantly decrease incidence of diet-related diseases has catalysed scientific efforts to understand this relationship, which is fundamental to developing future strategies for stemming disease. Multiple and synergistic interactions among nutrients influence antiproliferative activity of a fruit compared with an isolated antioxidant. Nutritional molecules including vitamins (B, C, E and β-carotene), folates, lycopene, flavonoids, isothyocyanates, glucosinolates, polyphenols, glutathione and minerals contribute to the antioxidative capacity of vegetables, fruits, nuts and various herbs. The true potential of a supplemental antioxidant or crop nutrients in human health benefits is in their accessibility, bioavailability and biological potency. Studies on the absorption, metabolism and
in vivo
potency of phytonutrients have lagged behind and are only now beginning to provide some results. Also, it is important to bear in mind that the levels of phytonutrients present in horticultural crops are low and significantly influenced by genotype/cultivar, growth condition and developmental stage. In this regard, genetic engineering has become a refined tool to increase the antioxidant and nutrient capacity of economically important crops including fruits and vegetables to the levels favourable not only for a highly nutritional diet but also to enable in-depth studies on the relationships between diet, genetics and metabolism. Together with modern biotechnology, deciphering transcriptome-proteome-metabolome of the new transgenics should provide new knowledge to ease the concerns of the society and open the market for genetically engineered horticulture crops, as is seen by higher sales of Hawaii-grown transgenic papaya in the USA. Also, this knowledge will help us in developing precise strategies for redesigning metabolic pathways so that desired levels of a particular phytonutrient (antioxidant) in crops are achieved.
Functional genomic approaches to understand the biological pathways underpinning intramuscular fat in beef.
Authors: Pannier L. , Hamill R. M. , Mullen A. M. , Sweeney T.
Published: October 2011

Meat quality traits, such as intramuscular fat level, have a heritable component and are quantitative in nature, being influenced by many genes of variable individual effects. The identification of the genetic variation associated with meat quality is an important step towards the improvement of meat quality in livestock selection programmes and meat management systems. Functional genomic approaches relate the static information of variation in genomic regions and individual genes with the dynamic interplay of gene expression pathways and biological processes. Therefore, through the application of functional genomic tools, researchers are gaining deeper insights into the biological pathways underpinning meat quality. Knowledge gained from these approaches can be beneficial in defining and optimizing management systems for quality, providing assurance of meat quality and in tailoring quality to suit market needs.
Intragenic vectors for plant transformation within gene pools.
Authors: Barrell P. J. , Jacobs J. M. E. , Baldwin S. J. , Conner A. J.
Published: October 2011

The design of vectors for plant transformation has recently progressed to the development of intragenic systems. This involves identifying plant-derived DNA sequences similar to important vector components. The most useful approach involves adjoining two fragments from plant genomes to form sequences that have the functional equivalence of vector elements such as: T-DNA borders for
Agrobacterium
-mediated transformation, bacterial origins of replication and bacterial selectable elements. Such DNA fragments have been identified from a wide range of plant species, suggesting that intragenic vectors can be constructed from the genome of any plant species. Intragenic vectors provide a mechanism for the well-defined genetic improvement of plants with the entire DNA destined for transfer originating from within the gene pool already available to plant breeders. In this manner, genes can be introgressed into elite cultivars in a single step without linkage drag and, most importantly, without the incorporation of foreign DNA. The resulting genetically modified (GM) plants are non-transgenic, although they are derived using the tools of molecular biology and plant transformation. The genetic makeup of the resulting plants is equivalent to minor rearrangements or micro-translocations that could theoretically arise through natural or induced rearrangements of the endogenous genome. Given the public concerns over the deployment of GM crops in agriculture, especially for food crops, intragenic vector systems offer a more socially acceptable and responsible way forward for genetic engineering. It may especially help us to alleviate some of the ethical issues associated with the transfer of DNA across wide taxonomic boundaries. Plants derived from the use of intragenic vectors raise important issues concerning the definition, regulation and testing of GM plants. This review critically evaluates the progress toward the development and use of intragenic vectors and the implications of their use for the genetic improvement of crops.
A highly sensitive ammonia chemical sensor based on α-Fe2O3 nanoellipsoids
Authors: Abaker M , Umar Ahmad , Baskoutas S , Dar G N , Zaidi S A , Al-Sayari S A , Al-Hajry A , Kim S H , Hwang S W
Published: October 2011

This paper reports the facile synthesis of α-Fe2O3 nanoellipsoids by a low-temperature hydrothermal process and their effective utilization in the fabrication of a highly sensitive aqueous ammonia chemical sensor by the I–V technique. The as-synthesized α-Fe2O3 nanoellipsoids are characterized in terms of their morphological, structural and optical properties. The detailed structural and optical properties confirm a rhombohedral α-Fe2O3 structure and indirect (1.87 eV) and direct (2.15 eV) band gaps, respectively, for the synthesized nanoellipsoids. The fabricated aqueous ammonia sensor based on nanoellipsoids exhibits a very high and reproducible sensitivity of ∼4.678 µA cm−2 mM−1 and a detection limit of ∼0.04 nM with a correlation coefficient (R) of 0.995 in a short response time (10.0 s). The presented work demonstrates that simply synthesized iron oxide nanostructures can efficiently be used for the fabrication of reliable and reproducible chemical sensors.
Growth Sensitivity of Corynespora cassiicola to Thiophanate-methyl, Iprodione, and Fludioxonil
Authors: Clark Justin S. , Blythe Eugene K. , Copes Warren E. , Windham Alan S. , Bost Steve C. , Windham Mark T.
Published: October 2011

An African violet production facility has relied solely on thiophanate-methyl, a site-specific fungicide that possesses a high risk for pathogens to develop resistance, to manage a devastating Corynespora leaf spot problem. During a disease outbreak in September 2007, 325 isolates of C. cassiicola were collected and 40 isolates were randomly selected to determine the pathogen's sensitivity for mycelium growth on agar amended with various concentrations of thiophanate-methyl, iprodione, or fludioxonil. EC50 values, concentration resulting in a 50% reduction in mycelium growth, were determined and indicate a population that currently is sensitive to all three fungicides. Due to the high risk of the pathogen developing resistance to thiophanate-methyl and iprodione, a moderate risk for cross-sensitivity between iprodione and fludioxonil, and phytotoxicity and visual residue problems with protective fungicides such as chlorothalonil, a fungicide rotation is recommended with fludioxonil as the main chemical selection.

Accepted for publication 22 July 2011. Published 26 September 2011.
A human ventricular cell model for investigation of cardiac arrhythmias under hyperkalaemic conditions
Authors: Carro Jesús , Rodríguez José Félix , Laguna Pablo , Pueyo Esther
Published: October 2011

In this study, several modifications were introduced to a recently proposed human ventricular action potential (AP) model so as to render it suitable for the study of ventricular arrhythmias. These modifications were driven by new sets of experimental data available from the literature and the analysis of several well-established cellular arrhythmic risk biomarkers, namely AP duration at 90 per cent repolarization (APD
90
), AP triangulation, calcium dynamics, restitution properties, APD
90
adaptation to abrupt heart rate changes, and rate dependence of intracellular sodium and calcium concentrations. The proposed methodology represents a novel framework for the development of cardiac cell models. Five stimulation protocols were applied to the original model and the ventricular AP model developed here to compute the described arrhythmic risk biomarkers. In addition, those models were tested in a one-dimensional fibre in which hyperkalaemia was simulated by increasing the extracellular potassium concentration, [K
+
]
o
. The effective refractory period (ERP), conduction velocity (CV) and the occurrence of APD alternans were investigated. Results show that modifications improved model behaviour as verified by: (i) AP triangulation well within experimental limits (the difference between APD at 50 and 90 per cent repolarization being 78.1 ms); (ii) APD
90
rate adaptation dynamics characterized by fast and slow time constants within physiological ranges (10.1 and 105.9 s); and (iii) maximum S1S2 restitution slope in accordance with experimental data (
S
S1S2
=1.0). In simulated tissues under hyperkalaemic conditions, APD
90
progressively shortened with the degree of hyperkalaemia, whereas ERP increased once a threshold in [K
+
]
o
was reached ([K
+
]
o
≈6 mM). CV decreased with [K
+
]
o
, and conduction was blocked for [K
+
]
o
>10.4 mM. APD
90
alternans were observed for [K
+
]
o
>9.8 mM. Those results adequately reproduce experimental observations. This study demonstrated the value of basing the development of AP models on the computation of arrhythmic risk biomarkers, as opposed to joining together independently derived ion channel descriptions to produce a whole-cell AP model, with the new framework providing a better picture of the model performance under a variety of stimulation conditions. On top of replicating experimental data at single-cell level, the model developed here was able to predict the occurrence of APD
90
alternans and areas of conduction block associated with high [K
+
]
o
in tissue, which is of relevance for the investigation of the arrhythmogenic substrate in ischaemic hearts.
Verification of cardiac tissue electrophysiology simulators using an
N
-version benchmark
Authors: Niederer Steven A. , Kerfoot Eric , Benson Alan P. , Bernabeu Miguel O. , Bernus Olivier , Bradley Chris , Cherry Elizabeth M. , Clayton Richard , Fenton Flavio H. , Garny Alan , Heidenreich Elvio , Land Sander , Maleckar Mary , Pathmanathan Pras , Plank Gernot , Rodríguez José F. , Roy Ishani , Sachse Frank B. , Seemann Gunnar , Skavhaug Ola , Smith Nic P.
Published: October 2011

Ongoing developments in cardiac modelling have resulted, in particular, in the development of advanced and increasingly complex computational frameworks for simulating cardiac tissue electrophysiology. The goal of these simulations is often to represent the detailed physiology and pathologies of the heart using codes that exploit the computational potential of high-performance computing architectures. These developments have rapidly progressed the simulation capacity of cardiac virtual physiological human style models; however, they have also made it increasingly challenging to verify that a given code provides a faithful representation of the purported governing equations and corresponding solution techniques. This study provides the first cardiac tissue electrophysiology simulation benchmark to allow these codes to be verified. The benchmark was successfully evaluated on 11 simulation platforms to generate a consensus gold-standard converged solution. The benchmark definition in combination with the gold-standard solution can now be used to verify new simulation codes and numerical methods in the future.
Active tactile exploration for adaptive locomotion in the stick insect
Authors: Schütz Christoph , Dürr Volker
Published: October 2011

Insects carry a pair of actively movable feelers that supply the animal with a range of multimodal information. The antennae of the stick insectCarausius morosusare straight and of nearly the same length as the legs, making them ideal probes for near-range exploration. Indeed, stick insects, like many other insects, use antennal contact information for the adaptive control of locomotion, for example, in climbing. Moreover, the active exploratory movement pattern of the antennae is context-dependent. The first objective of the present study is to reveal the significance of antennal contact information for the efficient initiation of climbing. This is done by means of kinematic analysis of freely walking animals as they undergo a tactually elicited transition from walking to climbing. The main findings are that fast, tactually elicited re-targeting movements may occur during an ongoing swing movement, and that the height of the last antennal contact prior to leg contact largely predicts the height of the first leg contact. The second objective is to understand the context-dependent adaptation of the antennal movement pattern in response to tactile contact. We show that the cycle frequency of both antennal joints increases after obstacle contact. Furthermore, inter-joint coupling switches distinctly upon tactile contact, revealing a simple mechanism for context-dependent adaptation.
Haptic object perception: spatial dimensionality and relation to vision
Authors: Klatzky Roberta L. , Lederman Susan J.
Published: October 2011

Enabled by the remarkable dexterity of the human hand, specialized haptic exploration is a hallmark of object perception by touch. Haptic exploration normally takes place in a spatial world that is three-dimensional; nevertheless, stimuli of reduced spatial dimensionality are also used to display spatial information. This paper examines the consequences of full (three-dimensional) versus reduced (two-dimensional) spatial dimensionality for object processing by touch, particularly in comparison with vision. We begin with perceptual recognition of common human-made artefacts, then extend our discussion of spatial dimensionality in touch and vision to include faces, drawing from research on haptic recognition of facial identity and emotional expressions. Faces have often been characterized as constituting a specialized input for human perception. We find that contrary to vision, haptic processing of common objects is impaired by reduced spatial dimensionality, whereas haptic face processing is not. We interpret these results in terms of fundamental differences in object perception across the modalities, particularly the special role of manual exploration in extracting a three-dimensional structure.
Active vibrissal sensing in rodents and marsupials
Authors: Mitchinson Ben , Grant Robyn A. , Arkley Kendra , Rankov Vladan , Perkon Igor , Prescott Tony J.
Published: October 2011

In rats, the long facial whiskers (mystacial macrovibrissae) are repetitively and rapidly swept back and forth during exploration in a behaviour known as ‘whisking’. In this paper, we summarize previous evidence from rats, and present new data for rat, mouse and the marsupial grey short-tailed opossum (
Monodelphis domestica
) showing that whisking in all three species is actively controlled both with respect to movement of the animal's body and relative to environmental structure. Using automatic whisker tracking, and Fourier analysis, we first show that the whisking motion of the mystacial vibrissae, in the horizontal plane, can be approximated as a blend of two sinusoids at the fundamental frequency (mean 8.5, 11.3 and 7.3 Hz in rat, mouse and opossum, respectively) and its second harmonic. The oscillation at the second harmonic is particularly strong in mouse (around 22 Hz) consistent with previous reports of fast whisking in that species. In all three species, we found evidence of asymmetric whisking during head turning and following unilateral object contacts consistent with active control of whisker movement. We propose that the presence of active vibrissal touch in both rodents and marsupials suggests that this behavioural capacity emerged at an early stage in the evolution of therian mammals.
Whisking and whisker kinematics during a texture classification task
Authors: Zuo Yanfang , Perkon Igor , Diamond Mathew E.
Published: October 2011

Rats explore objects by rhythmically whisking with their vibrissae. The goal of the present study is to learn more about the motor output used by rats to acquire texture information as well as the whisker motion evoked by texture contact. We trained four rats to discriminate between different grooved textures and used high-speed video to characterize whisker motion during the task. The variance in whisking parameters among subjects was notable. After whisker trimming, the animals changed their behaviour in ways that appear consistent with an optimization of whisker movement to compensate for lost information. These results lead to the intriguing notion that the rats use an information-seeking ‘cognitive’ motor strategy, instead of a rigid motor programme. Distinct stick/slip events occurred during texture palpation and their frequency increased in relation to the spatial frequency of the grooves. The results allow a preliminary assessment of three candidate texture-coding mechanisms—the number of grooves encountered during each touch, the temporal difference between groove contacts and the spatial pattern of groove contacts across the whiskers.
Radial distance determination in the rat vibrissal system and the effects of Weber's law
Authors: Solomon Joseph H. , Hartmann Mitra J. Z.
Published: October 2011

Rats rhythmically tap and brush their vibrissae (whiskers) against objects to tactually explore the environment. To extract a complex feature such as the contour of an object, the rat must at least implicitly estimate
radial object distance
, that is, the distance from the base of the vibrissa to the point of object contact. Radial object distance cannot be directly measured, however, because there are no mechanoreceptors along the vibrissa. Instead, the mechanical signals generated by the vibrissa's interaction with the environment must be transmitted to mechanoreceptors near the vibrissa base. The first part of this paper surveys the different mechanical methods by which the rat could determine radial object distance. Two novel methods are highlighted: one based on measurement of bending moment and axial force at the vibrissa base, and a second based on measurement of how far the vibrissa rotates beyond initial contact. The second part of the paper discusses the application of Weber's law to two methods for radial distance determination. In both cases, Weber's law predicts that the rat will have greatest sensing resolution close to the vibrissa tip. These predictions could be tested with behavioural experiments that measure the perceptual acuity of the rat.
Active touch sensing
Authors: Prescott Tony J. , Diamond Mathew E. , Wing Alan M.
Published: October 2011

Active sensing systems are purposive and information-seeking sensory systems. Active sensing usually entails sensor movement, but more fundamentally, it involves control of the sensor apparatus, in whatever manner best suits the task, so as to maximize information gain. In animals, active sensing is perhaps most evident in the modality of touch. In this theme issue, we look at active touch across a broad range of species from insects, terrestrial and marine mammals, through to humans. In addition to analysing natural touch, we also consider how engineering is beginning to exploit physical analogues of these biological systems so as to endow robots with rich tactile sensing capabilities. The different contributions show not only the varieties of active touch—antennae, whiskers and fingertips—but also their commonalities. They explore how active touch sensing has evolved in different animal lineages, how it serves to provide rapid and reliable cues for controlling ongoing behaviour, and even how it can disintegrate when our brains begin to fail. They demonstrate that research on active touch offers a means both to understand this essential and primary sensory modality, and to investigate how animals, including man, combine movement with sensing so as to make sense of, and act effectively in, the world.
Human perception of shape from touch
Authors: Kappers Astrid M. L.
Published: October 2011

In this paper, I focus on the role of active touch in three aspects of shape perception and discrimination studies. First an overview is given of curvature discrimination experiments. The most prominent result is that first-order stimulus information (that is, the difference in attitude or slope over the stimulus) is the dominant factor determining the curvature threshold. Secondly, I compare touch under bimanual and two-finger performance with unimanual and one-finger performance. Consistently, bimanual or two-finger performance turned out to be worse. The most likely explanation for the former finding is that a loss of accuracy during intermanual comparisons is owing to interhemispheric relay. Thirdly, I address the presence of strong after-effects after just briefly touching a shape. These after-effects have been measured and studied in various conditions (such as, static, dynamic, transfer to other hand or finger). Combination of the results of these studies leads to the insight that there are possibly different classes of after-effect: a strong after-effect, caused by immediate contact with the stimulus, that does only partially transfer to the other hand, and one much less strong after-effect, caused by moving over the stimulus for a certain period, which shows a full transfer to other fingers.
Immunofluorescence Localization of Nuclear Proteins: Figure 1.
Authors: Spector David L.
Published: October 2011

Many nuclear proteins have been successfully localized using immunofluorescence microscopy. These proteins span all nuclear domains, including the nuclear envelope, nuclear lamina, nucleolus, chromatin-associated proteins, and proteins associated with RNA metabolism and nuclear bodies. This article describes a general method for localizing nuclear proteins. Cells grown on coverslips are fixed in either formaldehyde or methanol and permeabilized in Triton X-100. Incubating the cells with primary antibody and fluorescently conjugated secondary antibody allows visualization of the target antigen.
Injection of Recombinant Adenovirus for Delivery of Genetically Encoded Calcium Indicators into Astrocytes of the Cerebellar Cortex: Figure 1.
Authors: Kuhn Bernd , Hoogland Tycho M. , Wang Samuel S.-H.
Published: October 2011

The cerebellar cortex contains two astrocyte types: the Bergmann glia of the molecular layer and the velate protoplasmic astrocytes of the granule cell layer. In vivo, these cell types generate both subcellular calcium transients and trans-glial calcium waves. This protocol outlines a method for in vivo calcium imaging in cerebellar astrocytes, using the injection of a replication-incompetent recombinant adenovirus for gene transfer of the fluorescent calcium indicator protein (FCIP) G-CaMP2. The adenovirus contains a cytomegalovirus (CMV) immediate-early (IE) promoter which confines expression of G-CaMP2 to astrocytes. Expression is sufficiently high to allow calcium signals to be recorded in Bergmann glial processes as well as the processes and somata of velate protoplasmic astrocytes. To obtain structural information, G-CaMP2 fused with the brighter chromophore DsRed allows three-dimensional (3D) reconstruction of cells. G-CaMP2 expression lasts for at least 3 wk, enabling long-term functional imaging in both anesthetized and awake animals.
Creating 3D Digital Replicas of Ascidian Embryos from Stacks of Confocal Images
Authors: Robin François B. , Dauga Delphine , Tassy Olivier , Sobral Daniel , Daian Fabrice , Lemaire Patrick
Published: October 2011

During embryonic development, cell behaviors that are tightly coordinated both spatially and temporally integrate at the tissue level and drive embryonic morphogenesis. Over the past 20 years, advances in imaging techniques, in particular, the development of confocal imaging, have opened a new world in biology, not only giving us access to a wealth of information, but also creating new challenges. It is sometimes difficult to make the best use of the recordings of the complex, inherently three-dimensional (3D) processes we now can observe. In particular, these data are often not directly suitable for even simple but conceptually fundamental quantifications. This article describes a process whereby image stacks gathered from live or fixed ascidian embryos are digitalized and segmented to produce 3D embryo replicas. These replicas can then be interfaced via a 3D Virtual Embryo module to a model organism database (Aniseed) that allows one to relate the geometrical properties of cells and cell contacts to additional parameters such as cell lineage, cell fates, or the underlying genetic program. Such an integrated system can serve several general purposes. First, it makes it possible to quantify and better understand the dynamics of cell behaviors during embryonic development, including, for instance, the automatic detection of asymmetric cell divisions or the evolution of cell contacts. Second, the 3D Virtual Embryo software proposes a panel of mathematical shape descriptors to precisely quantify cellular geometries and generate a 3D identity card for each embryonic cell. Such reconstructions open the door to a detailed 3D simulation of morphogenesis.
DADIMODO: a program for refining the structure of multidomain proteins and complexes against small-angle scattering data and NMR-derived restraints
Authors: Evrard Guillaume , Mareuil Fabien , Bontems Francois , Sizun Christina , Perez Javier
Published: October 2011

DADIMODOis a program for refining atomic models of multidomain proteins or complexes against small-angle X-ray scattering data. Interdomain distance and orientational restraints, such as those derived from NMR measurements, can be included in the optimization process. While domain structures are mainly kept rigid, flexible regions can be user defined. Stepwise generic conformational changes, specified by the user, are applied cyclically in a stochastic optimization algorithm that performs a search in the protein conformation space. The convergence for this genetic algorithm is driven by an adaptable selection pressure. The algorithmic structure guarantees that a physically acceptable full atomic model of the structure is present at all stages of the optimization. A graphical user interface ensures user-friendly handling.
Moving crystal assembly for handling small bulk samples
Authors: Levin Eduard , Treninkov Igor , Polyakov Sergei
Published: October 2011

The conventional zero-background holder technique has been adapted for handling small bulk samples by adding one-axis mobility to a single-crystal wafer using a Newport optical stage. Experiments showed that ana-plane (11{\overline 2}0) sapphire crystal with a surface-to-crystal-plane angle of ∼3° can be used as a zero-background holder. Such a crystal is a viable alternative to the commercial Rigaku product and shows better performance in the intermediate angle range (2θ = 60–110° for Cu Kα radiation). It has also been demonstrated that the proposed scheme of hardware stacking is operational.
Misleading results of likelihood‐based phylogenetic analyses in the presence of missing data
Authors: Simmons Mark P.
Published: October 2011

The amount of missing data in many contemporary phylogenetic analyses has substantially increased relative to previous norms, particularly in supermatrix studies that compile characters from multiple previous analyses. In such cases the missing data are non‐randomly distributed and usually present in all partitions (i.e. groups of characters) sampled. Parametric methods often provide greater resolution and support than parsimony in such cases, yet this may be caused by extrapolation of branch lengths from one partition to another. In this study I use contrived and simulated examples to demonstrate that likelihood, even when applied to simple matrices with little or no homoplasy, homogeneous evolution across groups of characters, perfect model fit, and hundreds or thousands of variable characters, can provide strong support for incorrect topologies when the matrices have non‐random distributions of missing data distributed across all partitions. I do so using a systematic exploration of alternative seven‐taxon tree topologies and distributions of missing data in two partitions to demonstrate that these likelihood‐based artefacts may occur frequently and are not shared by parsimony. I also demonstrate that Bayesian Markov chain Monte Carlo analysis is more robust to these artefacts than is likelihood.

© The Willi Hennig Society 2011.
Growth, yield and nitrogen performance of faba bean intercrops with oat and triticale at varying seeding ratios
Authors: Dordas C. A. , Lithourgidis A. S.
Published: October 2011

Intercropping of grain legumes with cereals may offer several advantages over sole crops for forage production and is commonly used, particularly in low‐input agriculture. Faba bean (Vicia faba L.), oat (Avena sativa L.) and triticale (×Triticosecale Wittmack) sole crops as well as the intercrops of faba bean with each of the above cereals, in three seeding ratios (75:25, 50:50 and 25:75), were compared for dry‐matter (DM) yield, nitrogen (N) concentration, chlorophyll content, growth rate and plant height in a 2‐year field experiment. Triticale sole crop and faba bean intercrops with triticale provided higher DM yield than faba bean sole crop and the intercrops of faba bean with oat. Growth rates of faba bean, oat and triticale in mixtures were lower than those in sole crops. Faba bean plants were taller in the intercrops than in the sole crop at 3 weeks after tillering (WAT), whereas at 6 WAT, the trend was different as faba bean plants in the sole crop were taller than in the intercrops. N concentration was higher for the cereals when faba bean was included in the mixture. Crude protein (CP) concentration was the highest in faba bean sole crop followed by the faba bean intercrops with oat. However, triticale sole crop and faba bean mixtures with triticale provided higher CP yield than all other crops because of their highest DM yield. Thus, mixtures of faba beans with triticale could be a promising alternative for increased forage production because of their capacity for high DM and protein yields.
Effects of sowing date and nitrogen fertilizer on forage yield, nitrogen‐ and water‐use efficiency and nutritive value of an annual triple‐crop complementary forage rotation
Authors: Islam M. R. , Garcia S. C.
Published: October 2011

Complementary forage rotation (CFR) systems based on non‐limiting inputs of fertilizer nitrogen (N) (∼600 kg N ha−1) are perceived as uneconomic. An experiment was carried out in Australia to investigate the effects of rates and timing of N fertilizer and sowing date on yield, nutrient‐use efficiency and nutritive value of a triple‐crop (maize, forage rape, field peas) CFR system. Treatments were early‐ and late‐sown maize grown with 0 or 135 kg fertilizer N ha−1 pre‐sowing (N1) and 0, 79 or 158 kg N ha−1 post‐sowing (N2). Forage rape was sown with 0 or 230 kg N ha−1 (N3) and field peas without N. Application of fertilizer N at N1, N2 and N3 increased CFR yield from 28·5 to 48·8 t dry matter (DM) ha−1 and irrigation water‐use efficiency (IWUE) from 3·4 to 6·1 t DM per megalitre. Increase in yield and IWUE of CFR occurs at the expense of nitrogen‐use efficiency (NUE) as applications of N at N1, N2 and N3 decreased NUE of CFR from 524 to 91 kg DM kg−1 N. Nutritive value, particularly metabolizable energy content of all forages, was similar among N treatments, and interactions between treatments were minimal. Results indicate that increase in NUE of CFR may occur at the expense of reduced yield, but increased IWUE need not compromise the yield of this CFR system.
Upregulation of Polymeric Immunoglobulin Receptor Expression by the Heat‐Inactivated Potential Probiotic Bifidobacterium bifidum OLB6378 in a Mouse Intestinal Explant Model
Authors: Nakamura Y. , Terahara M. , Iwamoto T. , Yamada K. , Asano M. , Kakuta S. , Iwakura Y. , Totsuka M.
Published: October 2011

We determined whether a potential probiotic bacterium, Bifidobacterium bifidum OLB6378 (BB6378), exerts beneficial effects on the mucosal immune system in a mouse intestinal explant model. The addition of heat‐inactivated BB6378 to intestinal explants prepared from embryonic day 18 BALB/c mice increased the expression of polymeric immunoglobulin receptor (pIgR) mRNA by two‐ to fivefold. These effects were observed on ileal and colonic explants but not on jejunal explants, suggesting that the BB6378‐induced pIgR upregulation is site‐specific within the mouse intestine. The upregulation of pIgR protein expression in colonic explants was also detected after 24 h of culture. The results of DNA microarray analysis of ileal and colonic samples indicated that BB6378 increased the gene expression of interleukin (IL)‐1α and IL‐1β, and IL‐1α content in colonic explants was significantly increased after 20 h of culture with BB6378. We then examined the involvement of endogenously induced IL‐1α in pIgR mRNA upregulation by using IL‐1α knockout (KO) mice. Contrary to our expectations, pIgR mRNA expression was equally upregulated by BB6378 in colonic explants from BALB/c and IL‐1α KO mice. Conversely, we examined the involvement of Toll‐like receptors in pIgR mRNA upregulation by using MyD88 KO mice. The upregulation of pIgR was completely suppressed in the explants derived from MyD88 KO mice. Taken together, we conclude that in a mouse intestinal explant model, the heat‐inactivated potential probiotic BB6378 increases intestinal pIgR expression in a site‐specific manner and that the upregulation of pIgR could be explained by a direct microbial effect on the epithelium via Toll‐like receptors.
[18F]fallypride PET measurement of striatal and extrastriatal dopamine D2/3 receptor availability in recently abstinent alcoholics
Authors: Rominger Axel , Cumming Paul , Xiong Guoming , Koller Gabriele , Böning Guido , Wulff Melanie , Zwergal Andreas , Förster Stefan , Reilhac Anthonin , Munk Ole , Soyka Michael , Wängler Björn , Bartenstein Peter , la Fougère Christian , Pogarell Oliver
Published: October 2011

Positron emission tomography (PET) shows reduced binding of the dopamine D2/3 antagonist [11C]raclopride in striatum of withdrawn psychostimulant abusers, but not consistently in patients with alcohol dependence (AD). We make first use of the high affinity ligand [18F]fallypride to obtain serial measures of D2/3 receptor availability in striatal and extrastriatal regions of AD patients undergoing detoxification. Seventeen patients (mean age 44 ± 5y) with AD and 14 age‐matched healthy volunteers participated. Each patient underwent [18F]fallypride PET upon hospital admission, and again 1–2 weeks later; two patients achieving abstinence, and two with substantial harm reduction had additional PET follow‐up at 1 year. Dynamic 180‐minute PET recordings were used for volume of interest (VOI)‐based and voxel‐wise analysis of [18F]fallypride binding potential (BPND). Mean baseline BPND in striatum of the AD patients (15.7 ± 3.6) was unaltered during short‐term follow‐up, and did not differ from that in healthy controls (16.8 ± 3.0); however, BPND was 10–20% lower in thalamus, hippocampus, and insular and temporal cortex of the AD patients (P < 0.05). Age‐dependent declines in BPND were very small in controls, but more pronounced and widespread in the AD group. Striatal and thalamic BPND increased by 30% in four patients with long‐term abstinence or reduced alcohol consumption. VOI‐based [18F]fallypride PET analyses revealed group differences in D2/3 receptor availability primarily in extra‐striatal regions. Age‐related loss of dopamine D2/3 receptors was more pronounced in AD patients. Receptor availability was unaltered by acute withdrawal, but increased in the subgroup of patients with long‐term follow‐up, suggesting reversibility of receptor changes.
Tetrathyridiosis and Tubulopapillary Carcinoma Occurring Simultaneously in the Mammary Gland of a Cat
Authors: Avci H , Toplu N
Published: October 2011

Contents

This report describes a case of tubulopapillary carcinoma and concomitant tetrathyridiosis in a 5‐year‐old female cross‐breed cat. A mass was located at right inguinal mammary gland and measured 5.5 × 5 × 3 cm in size with multilobulated to solid appearance. The cut surface of the mass had a centrally located large cyst (approximately 3 cm in diameter) surrounded by other smaller cysts. Histologically, the mass was diagnosed as tubulopapillary mammary carcinoma, intensely positive for AE1/AE3 cytokeratins. The cyst found at post‐mortem examination was tetrathyridia of Mesocestoides species surrounded by inflammatory cells and a loose fibrous capsule. To the authors’ best knowledge, this is the first description of a tubulopapillary carcinoma and tetrathyridiosis found simultaneously in the mammary gland of a cat.
Animal‐Level Factors Affecting Ovarian Function in Bos indicus Heifers Treated to Synchronize Ovulation with Intravaginal Progesterone‐Releasing Devices and Oestradiol Benzoate
Authors: Butler SAA , Phillips NJ , Boe‐Hansen GB , Bo GA , Burns BM , Dawson K , McGowan MR
Published: October 2011

Contents

The primary objective of this study was to investigate the impact of animal‐level factors including energy balance and environmental/management stress, on the ovarian function of Bos indicus heifers treated to synchronize ovulation. Two‐year‐old Brahman (BN) (n = 30) and BN‐cross (n = 34) heifers were randomly allocated to three intravaginal progesterone‐releasing device (IPRD) treatment groups: (i) standard‐dose IPRD [Cue‐Mate® (CM) 1.56 g; n = 17]; (ii) half‐dose IPRD [0.78 g progesterone (P4); CM 0.78 g; n = 15]; (iii) half‐dose IPRD + 300 IU equine chorionic gonadotrophin at IPRD removal (CM 0.78 g + G; n = 14); (iv) and a control group, 2× PGF2α [500 μg prostaglandin F2α (PGF2α)] on Day −16 and −2 (n = 18). Intravaginal progesterone‐releasing device‐treated heifers received 250 μg PGF2α at IPRD insertion (Day −10) and IPRD removal (Day −2) and 1 mg oestradiol benzoate on Day −10 and −1. Heifers were managed in a small feedlot and fed a defined ration. Ovarian function was evaluated by ultrasonography and plasma P4 throughout the synchronized and return cycles. Energy balance was evaluated using plasma insulin‐like growth factor 1 (IGF‐I) and glucose concentrations. The impact of environmental stressors was evaluated using plasma cortisol concentration. Heifers that had normal ovarian function had significantly higher IGF‐I concentrations at commencement of the experiment (p = 0.008) and significantly higher plasma glucose concentrations at Day −2 (p = 0.040) and Day 4 (p = 0.043), than heifers with abnormal ovarian function. There was no difference between the mean pre‐ovulatory cortisol concentrations of heifers that ovulated or did not ovulate. However, heifers that ovulated had higher cortisol concentrations at Day 4 (p = 0.056) and 6 (p = 0.026) after ovulation than heifers that did not ovulate.
Effect of Incorporation of Additives in Tris‐Based Egg Yolk Extender on Buffalo (Bubalus bubalis) Sperm Tyrosine Phosphorylation During Cryopreservation
Authors: Kumar R , Atreja SK
Published: October 2011

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Phosphorylation of tyrosine residues on sperm protein is a known indicator of capacitation and a major intracellular signalling event. There is evidence that sperm cryopreservation promotes tyrosine phosphorylation and is associated with reduced fertility of spermatozoa. Under this study, cryoprotective role of different additives namely taurine, trehalose, catalase and 4‐bromophenacyl bromide on buffalo sperm quality was evaluated. Buffalo semen was cryopreserved in tris‐based egg yolk extender supplemented with additives like taurine (50 mm) or trehalose (100 mm) or 4‐bromophenacyl bromide (200 μm) or catalase (100 U/ml) and used for assessment of levels of tyrosine phosphorylation in frozen‐thawed spermatozoa. The results obtained were compared with the level of protein tyrosine phosphorylation of semen cryopreserved in tris‐based egg yolk extender without additives. Proteins were extracted from a total number of nine ejaculates from three individual buffalo bulls chosen at random and analysed for tyrosine phospho‐proteins using SDS–PAGE followed by immunoblotting. Monoclonal anti‐phosphotyrosine antibody (Clone pT‐154) was used as primary antibody followed by treatment with HRP‐conjugated secondary antibody. Signals were detected on X‐ray film using chemiluminescence. Nine proteins (p20, p30, p32, p38, p49, p56, p59, p72 and p86) were found to be tyrosine phosphorylated in cryopreserved spermatozoa. Supplementation of additives significantly (p<0.05) reduced the level of protein tyrosine phosphorylation in spermatozoa. Moreover, this study showed improved (p<0.05) post‐thaw motility, viability and membrane integrity of spermatozoa on addition of these additives. The results obtained clearly indicate reduced level of capacitation like changes on supplementation of additives in terms of protein tyrosine phosphorylation.
Molecular phylogeny of Potamotrygonocotyle (Monogenea, Monocotylidae) challenges the validity of some of its species
Authors: Fehlauer‐Ale Karin H. , Littlewood D. Timothy J.
Published: October 2011

Fehlauer‐Ale, K. H. & Littlewood, D. T. J. (2011). Molecular phylogeny of Potamotrygonocotyle (Monogenea, Monocotylidae) challenges the validity of some of its species. —Zoologica Scripta, 40, 638–658.

The marine‐derived stingrays Potamotrygonidae are the only chondrichthyans landlocked to freshwaters of Central and South America. The family includes approximately 22 described species organized in four genera widely distributed across the main Atlantic and Caribbean continental drainages. Investigations into the parasite fauna of potamotrygonids have mainly focused on cestodes, with a few studies addressing the biodiversity of monogeneans. Potamotrygonocotyle (Monogenea, Monocotylidae) is composed of 12 species, exclusively found in the gills of species of Potamotrygonidae. This study presents molecular phylogenetic analyses of this group of monogeneans distributed throughout La Plata and Amazonas basins, with the purpose of readdressing the phylogeny of Monocotylidae based on 28S rDNA sequences and of unravelling the phylogeny of its species using data from mitochondrial gene cytochrome c oxidase subunit I and nuclear gene internal transcribed spacer 1. The phylogenetic status of the five tested monocotylid subfamilies and most of their internal relationships are concordant with the results of a previous study, and the monophyletic status of Potamotrygonocotyle based on molecular data is corroborated for the first time. However, the placement of the genus within Monocotylidae is not resolved, as its sister‐group relationship with Neoheterocotyle and Troglocephalus is uncertain. Investigations into the relationships within Potamotrygonocotyle support the monophyletic status of nine nominal species and suggest the existence of cryptic lineages for the remaining three. Molecular analyses reveal distinct sister‐groups relationships in comparison with a previously published phylogeny for the genus based on morphological data. Finally, the surveys of this study expand the known distribution range of some members of Potamotrygonocotyle.