Doppler ultrasonography principles and methods of evaluation of the reproductive tract in mares

Background: Doppler ultrasonography is a non-invasive real time pulse-wave technique recently used for the transrectal study of the reproductive system hemodynamics in large animals. This technic is based in the Doppler Effect Principle that proposes the change in frequency of a wave for an observer (red blood cells) moving relative to the source of the respective wave (ultrasonic transducer). This method had showed to be effective and useful for the evaluation of the in vivo equine reproductive tract increasing the diagnostic, monitoring, and predictive capabilities of theriogenology in mares. However, an accurate and truthful ultrasonic exam requires the previous knowledge of the Doppler ultrasonography principles. Review: In recent years, the capabilities of ultrasound flow imaging have increased enormously. The current Doppler ultrasound machines offer three methods of evaluation that may be used simultaneously (triplex mode). In B-mode ultrasound, a linear array of transducers simultaneously scans a plane through the tissue that can be viewed as a two-dimensional gray-scale image on screen. This mode is primarily used to identify anatomically a structure for its posterior evaluation using colored ultrasound modes (Color or Spectral modes). Colored ultrasound images of flow, whether Color or Spectral modes, are essentially obtained from measurements of moving red cells. In Color mode, velocity information is presented as a color coded overlay on top of a B-mode image, while Pulsed Wave Doppler provides a measure of the changing velocity throughout the cardiac cycle and the distribution of velocities in the sample volume represented by a spectral graphic. Color images conception varies according to the Doppler Frequency that is the difference between the frequency of received echoes by moving blood red cells and wave frequency transmitted by the transducer. To produce an adequate spectral graphic it is important determine the position and size of the simple gate. Furthermore, blood flow velocity measurement is influence by the intersection angle between ultrasonic pulses and the direction of moving blood-red cells (Doppler angle). Objectively colored ultrasound exam may be done on large arteries of the reproductive tract, as uterine and ovary arteries, or directly on the target tissue (follicle, for example). Mesovarium and mesometrium attachment arteries also can be used for spectral evaluation of the equine reproductive system. Subjectively analysis of the ovarian and uterine vascular perfusion must be done directly on the corpus luteum, follicular wall and uterus (endometrium and myometrium associated), respectively. Power-flow imaging has greater sensitivity to weak blood flow and independent of the Doppler angle, improving the evaluation of vessels with small diameters and slow blood flow. Conclusion: Doppler ultrasonography principles, methods of evaluation and reproductive system anatomy have been described. This knowledge is essential for the competent equipment acquisition and precise collection and analysis of colored ultrasound images. Otherwise, the reporting of inconsistent and not reproducible findings may result in the discredit of Doppler technology ahead of the scientific veterinary community.

Technique to combine images produced by different propagation modes of guided waves for damage detection and contrast improvement in plate-like structures

This paper describes an image compounding technique based on the use of different apodization functions, the evaluation of the signals phases and information from the interaction of different propagation modes of Lamb waves with defects for enhanced damage detection, resolution and contrast. A 16 elements linear array is attached to a 1 mm thickness isotropic aluminum plate with artificial defects. The array can excite the fundamental A0 and S0 modes at the frequencies of 100 kHz and 360 kHz, respectively. For each mode two synthetic aperture (SA) images with uniform and Blackman apodization and one image of Coherence Factor Map (CFM) are obtained. The specific interaction between each propagation mode and the defects and the characteristics of acoustic radiation patterns due to different apodization functions result in images with different resolution and contrast. From the phase information one of the SA images is selected at each pixel to compound the final image. The SA images are multiplied by the CFM image to improve contrast and for the dispersive A0 mode it is used a technique for dispersion compensation. There is a contrast improvement of 47.5 dB, reducing the dead zone and improving resolution and damage detection. © 2012 IEEE.

Preliminary assessment of the quantitative relationships between testicular tissue composition and ultrasonographic image attributes in the ram

This study examined the relationships between gross chemical composition and ultrasonographic characteristics of the ram testes. Ten testes from sexually mature Karakul rams were scanned ex situ with an 8-MHz linear-array transducer, in a transverse and longitudinal plane. All ultrasonograms were saved as digital images and subjected to computerized analyses. Crude protein content was determined by the Kjeldahl method, moisture was determined with an oven-drying method, and fat was measured by the Soxhlet extraction of dried samples. Mean pixel values (r = -0.64, P = 0.04), pixel heterogeneity (standard deviation of pixel values; r = -0.64, P = 0.04) and maximum pixel intensity (r = -0.76, P = 0.01) were all negatively correlated with parenchymal protein content. Pixel heterogeneity correlated directly with extractable lipids (r = 0.66, P = 0.02). The quantitative correlations between echotextural and biochemical parameters found in the present experiment confirm the utility of ultrasonographic imaging combined with computer-assisted image analysis for determining changes in testicular histophysiology. © 2013 Elsevier Ltd. All rights reserved.

Lamb mode diversity imaging for non-destructive testing of plate-like structures

Several Lamb wave modes can be coupled to a particular structure, depending on its geometry and transducer used to generate the guided waves. Each Lamb mode interacts in a particular form with different types of defects, like notches, delamination, surface defects, resulting in different information which can be used to improve damage detection and characterization. An image compounding technique that uses the information obtained from different propagation modes of Lamb waves for non-destructive testing of plate-like structures is proposed. A linear array consisting of 16 piezoelectric elements is attached to a 1 mm thickness aluminum plate, coupling the fundamental A0 and S0 modes at the frequencies of 100 kHz and 360 kHz, respectively. For each mode two images are obtained from amplitude and phase information: one image using the Total Focusing Method (TFM) and one phase image obtained from the Sign Coherence Factor (SCF). Each TFM image is multiplied by the SCF image of the respective mode to improve contrast and reduce side and grating lobes effects. The high dispersive characteristic of the A0 mode is compensated for adequate defect detection. The information in the SCF images is used to select one of the TFM mode images, at each pixel, to obtain the compounded image. As a result, dead zone is reduced, resolution and contrast are improved, enhancing damage detection when compared to the use of only one mode. © 2013 Elsevier Ltd.

Low frequency of human papillomavirus detection in prostate tissue from individuals from Northern Brazil

The presence of human papillomavirus (HPV) was evaluated in 65 samples of prostate tumours and six samples of prostates with benign prostatic hyperplasia from individuals from Northern Brazil. We used a highly sensitive test, the Linear Array HPV Genotyping Test, to detect 37 high and low-risk HPV types. In this study, only 3% of tumour samples showed HPV infection. Our findings support the conclusion that, despite the high incidence of HPV infection in the geographic regions studied, HPV was not associated with a higher risk of prostate cancer. To our knowledge, this is the first study evaluating the frequency of HPV detection in prostatic tissue of individuals from Brazil.

Comprehensive genome methylation and whole genome expression analysis in penile carcinoma: Uncovering new molecular markers

Background: Penile carcinoma (PeCa) is frequently associated with high morbidity rates. Unlikely of the vast majority of tumors, there is no molecular markers described that are able to assist in diagnosis and prognosis or with potential to be therapeutic targets in PeCa. Patients and methods: DNA methylation status (244K Human DNA Methylation Microarray platform, Agilent Technologies) and large-scale expression analysis (4x44K Whole Human Genome Microarray, Agilent Technologies) were performed in 35 and 37 PeCa, respectively. Quantitative bisulfite pyrosequencing (qBP) and RT-qPCR were used to validate the findings in 93 samples. HPV status was assessed using the Linear Array HPV Genotyping kit (Roche Molecular Diagnostics, CA, USA). Results: Methylome analysis revealed 171 hypermethylated and 449 hypomethylated CpGs sites and the transcriptome profiling showed 2986 down- and 2817 over-expressed genes. HPV positivity was found in 32.7% of the cases, mainly the HPV16. The integrative analysis in 32 PeCa revealed a panel of 96 genes with inverse correlation between methylation and gene expression levels. The CpG hypermetlylation and gene downexpression, was confirmed for TWIST1, RSOP2, SOX3, SOX17, CD133, OTX2, HOXA3 and MEIS. In addition, BIRC5, DNMT1 and DNMT3B presented low levels of methylation and overexpression. The comparison of the results with clinical findings revealed that LIN28A, NKX2.2, NKX2.3, LHX5, BDNF, FOXA1 and CDX2 were associated with poor prognosis features. Conclusion: Putative prognostic markers were detected revealing that DNA methylation modulates the expression of several genes in PeCa. These data may prove instrumental for biomarker discovery in clinics and molecular epidemiology of PeCa.

Análise integrada entre dados de expressão global de transcritos codificadores e de miRNAs em carcinomas de células escamosas de laringe

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Human papillomavirus genotypes distribution in 175 invasive cervical cancer cases from Brazil

Abstract Background Invasive cervical cancer is the second most common malignant tumor affecting Brazilian women. Knowledge on Human Papillomavirus (HPV) genotypes in invasive cervical cancer cases is crucial to guide the introduction and further evaluate the impact of new preventive strategies based on HPV. We aimed to provide updated comprehensive data about the HPV types’ distribution in patients with invasive cervical cancer. Methods Fresh tumor tissue samples of histologically confirmed invasive cervical cancer were collected from 175 women attending two cancer reference hospitals from São Paulo State: ICESP and Hospital de Câncer de Barretos. HPV detection and genotyping were performed by the Linear Array HPV Genotyping Test (Roche Molecular Diagnostics, Pleasanton,USA). Results 170 out of 172 valid samples (99%) were HPV DNA positive. The most frequent types were HPV16 (77.6%), HPV18 (12.3%), HPV31 (8.8%), HPV33 (7.1%) and HPV35 (5.9%). Most infections (75%) were caused by individual HPV types. Women with adenocarcinoma were not younger than those with squamous cell carcinoma, as well, as women infected with HPV33 were older than those infected by other HPV types. Some differences between results obtained in the two hospitals were observed: higher overall prevalence of HPV16, absence of single infection by HPV31 and HPV45 was verified in HC-Barretos in comparison to ICESP patients. Conclusions To our knowledge, this is one of the largest studies made with fresh tumor tissues of invasive cervical cancer cases in Brazil. This study depicted a distinct HPV genotype distribution between two centers that may reflect the local epidemiology of HPV transmission among these populations. Due to the impact of these findings on cervical cancer preventive strategies, extension of this investigation to routine screening populations is warranted.

Lamb mode diversity imaging fornon-destructivetesting of plate-likestructures

Several Lamb wave modes can be coupled to a particular structure, depending on its geometry and transducer used to generate the guided waves. Each Lamb mode interacts in a particular form with different types of defects, like notches, delamination, surface defects, resulting in different information which can be used to improve damage detection and characterization. An image compounding technique that uses the information obtained from different propagation modes of Lamb waves for non-destructive testing of plate-like structures is proposed. A linear array consisting of 16 piezoelectric elements is attached to a 1 mm thickness aluminum plate, coupling the fundamental A0 and SO modes at the frequencies of 100 kHz and 360 kHz, respectively. For each mode two images are obtained from amplitude and phase information: one image using the Total Focusing Method (TFM) and one phase image obtained from the Sign Coherence Factor (SCF). Each TFM image is multiplied by the SCF image of the respective mode to improve contrast and reduce side and grating lobes effects. The high dispersive characteristic of the A0 mode is compensated for adequate defect detection. The information in the SCF images is used to select one of the TFM mode images, at each pixel, to obtain the compounded image. As a result, dead zone is reduced, resolution and contrast are improved, enhancing damage detection when compared to the use of only one mode. (C) 2013 Elsevier Ltd. All rights reserved. (AU)

Application of FTIR microscopy to cultural heritage materials

Research in art conservation has been developed from the early 1950s, giving a significant contribution to the conservation-restoration of cultural heritage artefacts. In fact, only through a profound knowledge about the nature and conditions of constituent materials, suitable decisions on the conservation and restoration measures can thus be adopted and preservation practices enhanced. The study of ancient artworks is particularly challenging as they can be considered as heterogeneous and multilayered systems where numerous interactions between the different components as well as degradation and ageing phenomena take place. However, difficulties to physically separate the different layers due to their thickness (1-200 µm) can result in the inaccurate attribution of the identified compounds to a specific layer. Therefore, details can only be analysed when the sample preparation method leaves the layer structure intact, as for example the preparation of embedding cross sections in synthetic resins. Hence, spatially resolved analytical techniques are required not only to exactly characterize the nature of the compounds but also to obtain precise chemical and physical information about ongoing changes. This thesis focuses on the application of FTIR microspectroscopic techniques for cultural heritage materials. The first section is aimed at introducing the use of FTIR microscopy in conservation science with a particular attention to the sampling criteria and sample preparation methods. The second section is aimed at evaluating and validating the use of different FTIR microscopic analytical methods applied to the study of different art conservation issues which may be encountered dealing with cultural heritage artefacts: the characterisation of the artistic execution technique (chapter II-1), the studies on degradation phenomena (chapter II-2) and finally the evaluation of protective treatments (chapter II-3). The third and last section is divided into three chapters which underline recent developments in FTIR spectroscopy for the characterisation of paint cross sections and in particular thin organic layers: a newly developed preparation method with embedding systems in infrared transparent salts (chapter III-1), the new opportunities offered by macro-ATR imaging spectroscopy (chapter III-2) and the possibilities achieved with the different FTIR microspectroscopic techniques nowadays available (chapter III-3). In chapter II-1, FTIR microspectroscopy as molecular analysis, is presented in an integrated approach with other analytical techniques. The proposed sequence is optimized in function of the limited quantity of sample available and this methodology permits to identify the painting materials and characterise the adopted execution technique and state of conservation. Chapter II-2 describes the characterisation of the degradation products with FTIR microscopy since the investigation on the ageing processes encountered in old artefacts represents one of the most important issues in conservation research. Metal carboxylates resulting from the interaction between pigments and binding media are characterized using synthesised metal palmitates and their production is detected on copper-, zinc-, manganese- and lead- (associated with lead carbonate) based pigments dispersed either in oil or egg tempera. Moreover, significant effects seem to be obtained with iron and cobalt (acceleration of the triglycerides hydrolysis). For the first time on sienna and umber paints, manganese carboxylates are also observed. Finally in chapter II-3, FTIR microscopy is combined with further elemental analyses to characterise and estimate the performances and stability of newly developed treatments, which should better fit conservation-restoration problems. In the second part, in chapter III-1, an innovative embedding system in potassium bromide is reported focusing on the characterisation and localisation of organic substances in cross sections. Not only the identification but also the distribution of proteinaceous, lipidic or resinaceous materials, are evidenced directly on different paint cross sections, especially in thin layers of the order of 10 µm. Chapter III-2 describes the use of a conventional diamond ATR accessory coupled with a focal plane array to obtain chemical images of multi-layered paint cross sections. A rapid and simple identification of the different compounds is achieved without the use of any infrared microscope objectives. Finally, the latest FTIR techniques available are highlighted in chapter III-3 in a comparative study for the characterisation of paint cross sections. Results in terms of spatial resolution, data quality and chemical information obtained are presented and in particular, a new FTIR microscope equipped with a linear array detector, which permits reducing the spatial resolution limit to approximately 5 µm, provides very promising results and may represent a good alternative to either mapping or imaging systems.

The scintillating fiber focal plane detector for the use of Kaos as a double arm spectrometer

The upgrade of the Mainz Mikrotron (MAMI) electron accelerator facility in 2007 which raised the beam energy up to 1.5,GeV, gives the opportunity to study strangeness production channels through electromagnetic process. The Kaon Spectrometer (KAOS) managed by the A1 Collaboration, enables the efficient detection of the kaons associated with strangeness electroproduction. Used as a single arm spectrometer, it can be combined with the existing high-resolution spectrometers for exclusive measurements in the kinematic domain accessible to them.rnrnFor studying hypernuclear production in the ^A Z(e,e'K^+) _Lambda ^A(Z-1) reaction, the detection of electrons at very forward angles is needed. Therefore, the use of KAOS as a double-arm spectrometer for detection of kaons and the electrons at the same time is mandatory. Thus, the electron arm should be provided with a new detector package, with high counting rate capability and high granularity for a good spatial resolution. To this end, a new state-of-the-art scintillating fiber hodoscope has been developed as an electron detector.rnrnThe hodoscope is made of two planes with a total of 18432 scintillating double-clad fibers of 0.83 mm diameter. Each plane is formed by 72 modules. Each module is formed from a 60deg slanted multi-layer bundle, where 4 fibers of a tilted column are connected to a common read out. The read-out is made with 32 channels of linear array multianode photomultipliers. Signal processing makes use of newly developed double-threshold discriminators. The discriminated signal is sent in parallel to dead-time free time-to-digital modules and to logic modules for triggering purposes.rnrnTwo fiber modules were tested with a carbon beam at GSI, showing a time resolution of 220 ps (FWHM) and a position residual of 270 microm m (FWHM) with a detection efficiency epsilon>99%.rnrnThe characterization of the spectrometer arm has been achieved through simulations calculating the transfer matrix of track parameters from the fiber detector focal plane to the primary vertex. This transfer matrix has been calculated to first order using beam transport optics and has been checked by quasielastic scattering off a carbon target, where the full kinematics is determined by measuring the recoil proton momentum. The reconstruction accuracy for the emission parameters at the quasielastic vertex was found to be on the order of 0.3 % in first test realized.rnrnThe design, construction process, commissioning, testing and characterization of the fiber hodoscope are presented in this work which has been developed at the Institut für Kernphysik of the Johannes Gutenberg - Universität Mainz.

The equine DNAH3 gene: SNP discovery and exclusion of an involvement in recurrent airway obstruction (RAO) in European Warmblood horses

Recurrent airway obstruction is one of the most common airway diseases affecting mature horses. Increased bronchoalveolar mucus, neutrophil accumulation in airways, and airway obstruction are the main features of this disease. Mucociliary clearance is a key component of pulmonary defense mechanisms. Cilia are the motile part of this system and a complex linear array of dynein motors is responsible for their motility by moving along the microtubules in the axonemes of cilia and flagella. We previously detected a QTL for RAO on ECA 13 in a half-sib family of European Warmblood horses. The gene encoding DNAH3 is located in the peak of the detected QTL and encodes a dynein subunit. Therefore, we analysed this gene as a positional and functional candidate gene for RAO. In a mutation analysis of all 62 exons we detected 53 new polymorphisms including 7 non-synonymous variants. We performed an association study using 38 polymorphisms in a cohort of 422 animals. However, after correction for multiple testing we did not detect a significant association of any of these polymorphisms with RAO (P>0.05). Therefore, it seems unlikely that variants at the DNAH3 gene are responsible for the RAO QTL in European Warmblood horses.

Elemental and Lead Isotopic Data of Copper Finds from the Singen Cemetery, Germany – a Methodological Approach to Investigate Early Bronze Age Trade Networks

We report a trace element - Pb isotope analytical (LIA) database on the "Singen Copper", a peculiar type of copper found in the North Alpine realm, from its type locality, the Early Bronze Age Singen Cemetery (Germany). What distinguishes “Singen Copper” from other coeval copper types? (i) is it a discrete metal lot with a uniform provenance (if so, can its provenance be constrained)? (ii) was it manufactured by a special, unique metallurgical process that can be discriminated from others? Trace element concentrations can give clues on the ore types that were mined, but they can be modified (more or less intentionally) by metallurgical operations. A more robust indicator are the ratios of chemically similar elements (e.g. Co/Ni, Bi/Sb, etc.), since they should remain nearly constant during metallurgical operations, and are expected to behave homogeneously in each mineral of a given mining area, but their partition amongst the different mineral species is known to cause strong inter-element fractionations. We tested the trace element ratio pattern predicted by geochemical arguments on the Brixlegg mining area. Brixlegg itself is not compatible with the Singen Copper objects, and we only report it because it is a rare instance of a mining area for which sufficient trace element analyses are available in the literature. We observe that As/Sb in fahlerz varies by a factor 1.8 above/below median; As/Sb in enargite varies by a factor of 2.5 with a 10 times higher median. Most of the 102 analyzed metal objects from Singen are Sb-Ni-rich, corresponding to “antimony-nickel copper” of the literature. Other trace element concentrations vary by > 100 times, ratios by factors > 50. Pb isotopic compositions are all significantly different from each other. They do not form a single linear array and require > 3 ore batches that certainly do not derive from one single mining area. Our data suggest a heterogeneous provenance of “Singen copper”. Archaeological information limits the scope to Central European sources. LIA requires a diverse supply network from many mining localities, including possibly Brittany. Trace element ratios show more heterogeneity than LIA; this can be explained either by deliberate selection of one particular ore mineral (from very many sources) or by processing of assorted ore minerals from a smaller number of sources, with the unintentional effect that the quality of the copper would not be constant, as the metallurgical properties of alloys would vary with trace element concentrations.

Isotope ratios and trace element concentrations of basalts from DSDP Leg 15 sites (Appendix 1)

Formation of the Cretaceous Caribbean plateau, including the komatiites of Gorgona, has been linked to the currently active Galápagos hotspot. We use Hf-Nd isotopes and trace element data to characterise both the Caribbean plateau and the Galápagos hotspot, and to investigate the relationship between them. Four geochemical components are identified in the Galápagos mantle plume: two 'enriched' components with epsilon-Hf and epsilon-Nd similar to enriched components observed in other mantle plumes, one moderately enriched component with high Nb/Y, and a fourth component which most likely represents depleted MORB source mantle. The Caribbean plateau basalt data form a linear array in Hf-Nd isotope space, consistent with mixing between two mantle components. Combined Hf-Nd-Pb-Sr-He isotope and trace element data from this study and the literature suggest that the more enriched Caribbean end member corresponds to one or both of the enriched components identified on Galápagos. Likewise, the depleted end member of the array is geochemically indistinguishable from MORB and corresponds to the depleted component of the Galápagos system. Enriched basalts from Gorgona partially overlap with the Caribbean plateau array in epsilon-Hf vs. epsilon-Nd, whereas depleted basalts, picrites and komatiites from Gorgona have a high epsilon-Hf for a given epsilon-Nd, defining a high-epsilon-Hf depleted end member that is not observed elsewhere within the Caribbean plateau sequences. This component is similar, however, in terms of Hf-Nd-Pb-He isotopes and trace elements to the depleted plume component recognised in basalts from Iceland and along the Reykjanes Ridge. We suggest that the Caribbean plateau represents the initial outpourings of the ancestral Galápagos plume. Absence of a moderately enriched, high Nb/Y component in the older Caribbean plateau (but found today on the island of Floreana) is either due to changing source compositions of the plume over its 90 Ma history, or is an artifact of limited sampling. The high-epsilon-Hf depleted component sampled by the Gorgona komatiites and depleted basalts is unique to Gorgona and is not found in the Caribbean plateau. This may be an indication of the scale of heterogeneity of the Caribbean plateau system; alternatively Gorgona may represent a separate oceanic plateau derived from a completely different Pacific plume, such as the Sala y Gomez.

Study of the II Network as the Compound Slot Equivalent Circuit Model

A combination of Method of Moments (MoM) and compound slot Equivalent Circuit Model for linear array design is presented in this document. From the S Matrix of the single element, the more suitable network for its characterization is analyzed and selected. Then according to the radiation requirements of the desired array, the elements are designed and then properly connected by means of Forward Matching Procedure (FMP), which takes into account impedance matters in order to keep the input matched at the designing frequency. Comparison between HFSS simulations and MoM-FMP results are also presented. First part of this work was introduced in (1)(2) but a summary is included here to make the understanding easier.