Cellular source and mechanisms of high transcriptome complexity in the Mammalian testis.

Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexity in major mammalian organs have been scarce. Here, using extensive RNA-seq data, we show that transcription of the genome is substantially more widespread in the testis than in other organs across representative mammals. Furthermore, we reveal that meiotic spermatocytes and especially postmeiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding and long noncoding RNA genes but also poorly conserves intergenic sequences, suggesting that it may not be of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data suggest that this prevalent transcription, which most likely promoted the birth of new genes during evolution, is facilitated by an overall permissive chromatin in these germ cells that results from extensive chromatin remodeling.

Investigation of high-resolution functional magnetic resonance imaging by means of surface and array radiofrequency coils at 7 T.

In this investigation, high-resolution, 1x1x1-mm(3) functional magnetic resonance imaging (fMRI) at 7 T is performed using a multichannel array head coil and a surface coil approach. Scan geometry was optimized for each coil separately to exploit the strengths of both coils. Acquisitions with the surface coil focused on partial brain coverage, while whole-brain coverage fMRI experiments were performed with the array head coil. BOLD sensitivity in the occipital lobe was found to be higher with the surface coil than with the head array, suggesting that restriction of signal detection to the area of interest may be beneficial for localized activation studies. Performing independent component analysis (ICA) decomposition of the fMRI data, we consistently detected BOLD signal changes and resting state networks. In the surface coil data, a small negative BOLD response could be detected in these resting state network areas. Also in the data acquired with the surface coil, two distinct components of the positive BOLD signal were consistently observed. These two components were tentatively assigned to tissue and venous signal changes.

Assessment of high hydrostatic pressure and starter culture on the quality properties of low-acid fermented sausages

The addition of starter culture and high pressure processing after ripening improved the microbial quality of low-acid fermented sausages (fuet and chorizo). The use of Lactobacillus sakei CTC6626 and Staphylococcus xylosus CTC6013 as starter culture significantly reduced Enterobacteriaceae and Enterococcus levels in the finished sausages. Moreover, the addition of starter culture produced sausages of similar quality to traditional low-acid fermented sausages. Slightly lower pH values and higher cohesiveness were obtained for both fuet and chorizo with starter culture. Sensory analysis showed no differences between lots of chorizo whereas starter fuet was more acid and gummy. High pressure induced an additional reduction of Enterobacteriaceae in non-starter sausages. An increase of textural properties was observed after pressurization. No other differences were observed between non-treated and pressurized sausages.

Consumer acceptance of high pressure processed beef-based chilled ready meals: The mediating role of food-related lifestyle factors

The aim of this research was to investigate the effects of high pressure processing (HPP) on consumer acceptance for chilled ready meals manufactured using a low-value beef cut. Three hundred consumers evaluated chilled ready meals subjected to 4 pressure treatments and a non-treated control monadically on a 9-point scale for liking for beef tenderness and juiciness, overall flavour, overall liking, and purchase intent. Data were also collected on consumers' food consumption patterns, their attitudes towards food by means of the reduced food-related lifestyle (FRL) instrument, and socio-demographics. The results indicated that a pressure treatment of 200 MPa was acceptable to most consumers. K-means cluster analysis identified 4 consumer groups with similar preferences, and the optimal pressure treatments acceptable to specific consumer groups were identified for those firms that would wish to target attitudinally differentiated consumer segments

Quantitative integration of high-resolution hydrogeophysical data through Monte-Carlo-type conditional simulations

Geophysical techniques can help to bridge the inherent gap with regard to spatial resolution and the range of coverage that plagues classical hydrological methods. This has lead to the emergence of the new and rapidly growing field of hydrogeophysics. Given the differing sensitivities of various geophysical techniques to hydrologically relevant parameters and their inherent trade-off between resolution and range the fundamental usefulness of multi-method hydrogeophysical surveys for reducing uncertainties in data analysis and interpretation is widely accepted. A major challenge arising from such endeavors is the quantitative integration of the resulting vast and diverse database in order to obtain a unified model of the probed subsurface region that is internally consistent with all available data. To address this problem, we have developed a strategy towards hydrogeophysical data integration based on Monte-Carlo-type conditional stochastic simulation that we consider to be particularly suitable for local-scale studies characterized by high-resolution and high-quality datasets. Monte-Carlo-based optimization techniques are flexible and versatile, allow for accounting for a wide variety of data and constraints of differing resolution and hardness and thus have the potential of providing, in a geostatistical sense, highly detailed and realistic models of the pertinent target parameter distributions. Compared to more conventional approaches of this kind, our approach provides significant advancements in the way that the larger-scale deterministic information resolved by the hydrogeophysical data can be accounted for, which represents an inherently problematic, and as of yet unresolved, aspect of Monte-Carlo-type conditional simulation techniques. We present the results of applying our algorithm to the integration of porosity log and tomographic crosshole georadar data to generate stochastic realizations of the local-scale porosity structure. Our procedure is first tested on pertinent synthetic data and then applied to corresponding field data collected at the Boise Hydrogeophysical Research Site near Boise, Idaho, USA.

Development of Quality Standards for Inclusion of High Recycled Asphalt Pavement Content in Asphalt Mixtures – Phase II, TR-658, 2015

To conserve natural resources and energy, the amount of recycled asphalt pavement has been steadily increasing in the construction of asphalt pavements. The objective of this study is to develop quality standards for inclusion of high RAP content. To determine if the higher percentage of RAP materials can be used on Iowa’s state highways, three test sections with target amounts of RAP materials of 30%, 35% and 40% by weight were constructed on Highway 6 in Iowa City. To meet Superpave mix design requirements for mixtures with high RAP contents, it was necessary to fractionate the RAP materials. Three test sections with actual RAP materials of 30.0%, 35.5% and 39.2% by weight were constructed and the average field densities from the cores were measured as 95.3%, 94.0%, and 94.3%, respectively. Field mixtures were compacted in the laboratory to evaluate moisture sensitivity using a Hamburg Wheel Tracking Device. After 20,000 passes, rut depths were less than 3mm for mixtures obtained from three test sections. The binder was extracted from the field mixtures from each test section and tested to identify the effects of RAP materials on the performance grade of the virgin binder. Based on Dynamic Shear Rheometer and Bending Beam Rheometer tests, the virgin binders (PG 64-28) from test sections with 30.0%, 35.5% and 39.2% RAP materials were stiffened to PG 76-22, PG 76-16, and PG 82-16, respectively. The Semi-Circular Bending (SCB) test was performed on laboratory compacted field mixtures with RAP amounts of 30.0%, 35.5% and 39.2% at two different temperatures of -18 and -30 °C. As the test temperature decreased, the fracture energy decreased and the stiffness increased. As the RAP amount increased, the stiffness increased and the fracture energy decreased. Finally, a condition survey of the test sections was conducted to evaluate their short-term pavement performance and the reflective transverse cracking did not increase as RAP amount was increased from 30.0% to 39.2%.

Blunting the response to endotoxin in healthy sujects : effects of various dose of intravenous fish oil

Enjeux et contexte La recherche de cette dernière décennie sur les acides gras n-3 PUFA contenus dans l'huile de poisson a montré que ceux-ci, et particulièrement l'ΕΡΑ et le DHA, avaient des propriétés anti¬inflammatoires et anti arythmiques puissantes, potentiellement utiles chez les septiques et « cardiaques ». Les mécanismes sous-jacents sont nombreux, incluant l'incorporation des acides gras dans les membranes de phopholipides, la réduction de la production de médiateurs pro-inflammatoires (prostaglandines, leukotrienes, thromboxane), l'augmentation de la production de résolvines et protectines dérivées du DHA, et la régulation de voies de signalisation cellulaire. Cependant, les doses de n-3 PUFA utilisées dans les études cliniques et chez le sujet sain avant le travail de Yann-Karim Pittet étaient nettement supérieures aux doses nutritionnelles de l'ordre de 5-8 g/j par voie orale ou 1 g/kg par voie intraveineuse. De plus, la voie entérale avait la réputation de nécessiter plusieurs jours à semaines de traitement avant d'aboutir à une incorporation d'acides gras membranaire suffisante pour avoir un impact clinique; quant au temps minimal requis pour obtenir cet effet par voie IV, il était inconnu. Depuis, le développement d'émulsions lipidiques intraveineuses destinées à la nutrition parentérale a permis d'imaginer l'administration de prétraitements IV rapides. Pour les étudier, notre laboratoire a développé un modèle d'endotoxine (LPS d'E.Coli) qui mime les réponses physiologique, endocrinienne et biologique du sepsis chez le sujet sain, utilisant des doses de 2 ng/kg IV. Les réponses sont totalement réversibles en 8 heures. Dans le but de réduire à la fois la dose de lipides et le temps de perfusion, ce travail a étudié l'influence de 3 doses dégressives de n-3 PUFA sur les réponses à l'endotoxine, et sur l'incorporation membranaire de ces acides gras. Méthodes Etude prospective chez 3 groupes consécutifs de sujets sains soumis à un challenge d'endotoxine. Intervention : perfusions d'huile de poisson (0.5 et 0.2 g/kg de n-3 PUFA, Omegaven® 10%) ou placebo, administrées en 3 heures ou en 1 heure, soit le jour avant ou le jour-même du test d'endotoxine. Mesures : variables physiologiques (T°, fc, tension artérielle, calorimétrie indirecte) Laboratoire - prises de sang à T0, 60, 120 et 360 min après l'injection de LPS: TNF-α, hs-CRP, hormones de stress, composition en acides gras des membranes plaquettaires. Statistiques Les résultats ont été rapportés en moyennes et écarts types. Des aires sous la courbe (AUC) ont été calculées avec la méthode des parallélépipèdes pour toutes les variables déterminées de manière répétée. L'effet du temps a été exploré par des two-way ANOVA pour mesures répétées. Les comparaisons post-hoc ont été réalisées avec des tests de Dunnett's ou de Scheffe. Les modifications de composition membranaires ainsi que les AUC ont été analysées par des tests non-paramétriques (Kruskal-Wallis). Résultats Après LPS, la température, les concentrations d'ACTH et TNF-α ont augmenté dans les 3 groupes. Ces réponse ont été significativement atténuées (p<0.0001) par l'huile de poisson comparé à ce que nous avions observé dans le groupe contrôle de Pluess et al (ICM 2007). Les concentrations les plus faibles d'ACTH, de TNF-α, et les AUC les plus basses des températures, ont été observées après une dose unique de 0.2 g/kg de n-3 PUFA administrée 1 heure avant le LPS. Par contre, l'incorporation membranaire d'EPA est dose-dépendante. Conclusions Sachant que la réponse à l'endotoxine est reproductible, cette étude montre que 3 doses différentes d'huile de poisson atténuent de manière différente cette réponse. La perfusion de 0.2 g/kg administrée juste avant l'endotoxine s'est avérée la plus efficace à atténuer la réponse fébrile, les cytokines et les hormones de stress, suggérant une capture de l'endotoxine par l'émulsion lipidique qui se surajoute aux effets systémiques et membranaires.

In-vivo performance of high-density collagen gel tubes for urethral regeneration in a rabbit model.

Congenital malformations or injuries of the urethra can be treated using existing autologous tissue, but these procedures are sometimes associated with severe complications. Therefore, tissue engineering may be advantageous for generating urethral grafts. We evaluated engineered high-density collagen gel tubes as urethral grafts in 16 male New Zealand white rabbits. The constructs were either acellular or seeded with autologous smooth muscle cells, isolated from an open bladder biopsy. After the formation of a urethral defect by excision, the tissue-engineered grafts were interposed between the remaining urethral ends. No catheter was placed postoperatively. The animals were evaluated at 1 or 3 months by contrast urethrography and histological examination. Comparing the graft caliber to the control urethra at 3 months, a larger caliber was found in the cell-seeded grafts (96.6% of the normal caliber) than in the acellular grafts (42.3%). Histology of acellular and cell-seeded grafts did not show any sign of inflammation, and spontaneous regrowth of urothelium could be demonstrated in all grafts. Urethral fistulae, sometimes associated with stenosis, were observed, which might be prevented by urethral catheter application. High-density collagen gel tubes may be clinically useful as an effective treatment of congenital and acquired urethral pathologies.

Assessing the impact of high-pressure processing on selected physical and biochemical attributes of white cabbage (Brassica oleracea L. var. capitata alba)

The aim of this study was to investigate the effect of combined pressure/temperature treatments (200, 400 and 600 MPa, at 20 and 40 °C) on key physical and chemical characteristics of white cabbage (Brassica oleracea L. var. capitata alba). Thermal treatment (blanching) was also investigated and compared with high-pressure processing (HPP). HPP at 400 MPa and 20–40 °C caused significantly larger colour changes compared to any other pressure or thermal treatment. All pressure treatments induced a softening effect, whereas blanching did not significantly alter texture. Both blanching and pressure treatments resulted in a reduction in the levels of ascorbic acid, effect that was less pronounced for blanching and HPP at 600 MPa and 20–40 °C. HPP at 600 MPa resulted in significantly higher total phenol content, total antioxidant capacity and total isothiocyanate content compared to blanching. In summary, the colour and texture of white cabbage were better preserved by blanching. However, HPP at 600 MPa resulted in significantly higher levels of phytochemical compounds. The results of this study suggest that HPP may represent an attractive technology to process vegetable-based food products that better maintains important aspects related to the content of health-promoting compounds. This may be of particular relevance to the food industry sector involved in the development of convenient novel food products with excellent functional properties

Investigation of High Density Polyethylene Pipe for Highway Applications, HR-373, Phase 1, 1996

In the past, culvert pipes were made only of corrugated metal or reinforced concrete. In recent years, several manufacturers have made pipe of lightweight plastic - for example, high density polyethylene (HDPE) - which is considered to be viscoelastic in its structural behavior. It appears that there are several highway applications in which HDPE pipe would be an economically favorable alternative. However, the newness of plastic pipe requires the evaluation of its performance, integrity, and durability; A review of the Iowa Department of Transportation Standard Specifications for Highway and Bridge Construction reveals limited information on the use of plastic pipe for state projects. The objective of this study was to review and evaluate the use of HDPE pipe in roadway applications. Structural performance, soil-structure interaction, and the sensitivity of the pipe to installation was investigated. Comprehensive computerized literature searches were undertaken to define the state-of-the-art in the design and use of HDPE pipe in highway applications. A questionnaire was developed and sent to all Iowa county engineers to learn of their use of HDPE pipe. Responses indicated that the majority of county engineers were aware of the product but were not confident in its ability to perform as well as conventional materials. Counties currently using HDPE pipe in general only use it in driveway crossings. Originally, we intended to survey states as to their usage of HDPE pipe. However, a few weeks after initiation of the project, it was learned that the Tennessee DOT was in the process of making a similar survey of state DOT's. Results of the Tennessee survey of states have been obtained and included in this report. In an effort to develop more confidence in the pipe's performance parameters, this research included laboratory tests to determine the ring and flexural stiffness of HDPE pipe provided by various manufacturers. Parallel plate tests verified all specimens were in compliance with ASTM specifications. Flexural testing revealed that pipe profile had a significant effect on the longitudinal stiffness and that strength could not be accurately predicted on the basis of diameter alone. Realizing that the soil around a buried HDPE pipe contributes to the pipe stiffness, the research team completed a limited series of tests on buried 3 ft-diameter HDPE pipe. The tests simulated the effects of truck wheel loads above the pipe and were conducted with two feet of cover. These tests indicated that the type and quality of backfill significantly influences the performance of HDPE pipe. The tests revealed that the soil envelope does significantly affect the performance of HDPE pipe in situ, and after a certain point, no additional strength is realized by increasing the quality of the backfill.

Investigation of High Performance Concrete Pavement, MLR-05-01, 2006

The Iowa DOT has been using blended cements in ternary mixes since 1999. Use of these supplementary cementitious materials gives concrete with higher strengths and much lower permeability. Use of these materials has been incorporated for use in High Performance Concrete (HPC) decks to achieve lower permeability and thus long term performance. Since we have been using these materials in paving, it would be informative to determine what concrete pavement properties are enhanced as related to high performance concrete. The air void system was excellent at a spacing factor of 0.0047 in (0.120 mm). AVA spacing factor results are much higher than the hardened air void analysis. Although only 3 samples were tested between the image analysis air content and the RapidAir457, there is pretty good agreement between those test methods. Air void analysis indicates that excessive vibration was not required to place the concrete. Vibration was well within the specification limits with an average of 6683 vpm’s with a standard deviation of 461. Overall ride of the project was very good. The average smoothness for the project was 2.1 in/mile (33.8 mm/km). The International Roughness Index (IRI) was 81 in/mi (1.29 m/km). The compressive strength was 6260 psi (43.2 MPa) at 28 days and 6830 (47.1 MPa) at 56 days. The modulus of rupture by third point loading (MOR-TPL) tested at 28 days was 660 psi (4.55 MPa). The AASHTO T277 rapid chloride permeability results at 28 days using the Virginia cure method correlate fairly well with the 56 and 90 day results with standard curing. The Virginia cure method 28 day results were 2475 coulombs and the standard cure 56 and 90 day test results were 2180 and 2118, respectively.

Evaluation of High-Slump Concrete for Bridge Deck Overlays, TR-427, 2005

The Iowa Method for bridge deck overlays has been very successful in Iowa since its adoption in the 1970s. This method involves removal of deteriorated portions of a bridge deck followed by placement of a layer of dense (Type O) Portland Cement Concrete (PCC). The challenge encountered with this type of bridge deck overlay is that the PCC must be mixed on-site, brought to the placement area and placed with specialized equipment. This adds considerably to the cost and limits contractor selection, because not all contractors have the capability or equipment required. If it is possible for a ready-mix supplier to manufacture and deliver a dense PCC to the grade, then any competent bridge deck contractor would be able to complete the job. However, Type O concrete mixes are very stiff and generally cannot be transported and placed with ready-mix type trucks. This is where a “super-plasticizer” comes in to use. Addition of this admixture provides a substantial increase in the workability of the concrete – to the extent that it can be delivered to the site and placed on the deck directly out of a ready-mix truck. The objective of this research was to determine the feasibility of placing a deck overly of this type on county bridges within the limits of county budgets and workforce/contractor availability.

Field Instrumentation, Testing, and Long-Term Monitoring of High-Mast Lighting Towers in the State of Iowa, TR-518, 2006

As a result of the collapse of a 140 foot high-mast lighting tower in Sioux City, Iowa in November of 2003, a thorough investigation into the behavior and design of these tall, yet relatively flexible structures was undertaken. Extensive work regarding the root cause of this failure was carried out by Robert Dexter of The University of Minnesota. Furthermore, a statewide inspection of all the high-mast towers in Iowa revealed fatigue cracks and loose anchor bolts on other existing structures. The current study was proposed to examine the static and dynamic behavior of a variety of towers in the State of Iowa utilizing field testing, specifically long-term monitoring and load testing. This report presents the results and conclusions from this project. The field work for this project was divided into two phases. Phase 1 of the project was conducted in October 2004 and focused on the dynamic properties of ten different towers in Clear Lake, Ames, and Des Moines, Iowa. Of those ten, two were also instrumented to obtain stress distributions at various details and were included in a 12 month long-term monitoring study. Phase 2 of this investigation was conducted in May of 2005, in Sioux City, Iowa, and focused on determining the static and dynamic behavior of a tower similar to the one that collapsed in November 2003. Identical tests were performed on a similar tower which was retrofitted with a more substantial replacement bottom section in order to assess the effect of the retrofit. A third tower with different details was dynamically load tested to determine its dynamic characteristics, similar to the Phase 1 testing. Based on the dynamic load tests, the modal frequencies of the towers fall within the same range. Also, the damping ratios are significantly lower in the higher modes than the values suggested in the AASHTO and CAN/CSA specifications. The comparatively higher damping ratios in the first mode may be due to aerodynamic damping. These low damping ratios in combination with poor fatigue details contribute to the accumulation of a large number of damage-causing cycles. As predicted, the stresses in the original Sioux City tower are much greater than the stresses in the retrofitted towers at Sioux City. Additionally, it was found that poor installation practices which often lead to loose anchor bolts and out-of-level leveling nuts can cause high localized stresses in the towers, which can accelerate fatigue damage.