Handbook of instrumental techniques for materials, chemical and biosciences research

This Handbook contains a collection of articles describing instrumental techniques used for Materials, Chemical and Biosciences research that are available at the Scientific and Technological Centers of theUniversity of Barcelona (CCiTUB). The CCiTUB are a group of facilities of the UB that provide both the research community and industry with ready access to a wide range of major instrumentation.Together with the latest equipment and technology, the CCiTUB provide expertise in addressing the methodological research needs of the user community and they also collaborate in R+D+i Projectswith industry. CCiTUB specialists include technical and Ph.D.-level professional staff members who are actively engaged in methodological research. Detailed information on the centers’ resources andactivities can be found at the CCiTUB website www.ccit.ub.edu ...

Systems Genetics of Metabolism: The Use of the BXD Murine Reference Panel for Multiscalar Integration of Traits.

Metabolic homeostasis is achieved by complex molecular and cellular networks that differ significantly among individuals and are difficult to model with genetically engineered lines of mice optimized to study single gene function. Here, we systematically acquired metabolic phenotypes by using the EUMODIC EMPReSS protocols across a large panel of isogenic but diverse strains of mice (BXD type) to study the genetic control of metabolism. We generated and analyzed 140 classical phenotypes and deposited these in an open-access web service for systems genetics (www.genenetwork.org). Heritability, influence of sex, and genetic modifiers of traits were examined singly and jointly by using quantitative-trait locus (QTL) and expression QTL-mapping methods. Traits and networks were linked to loci encompassing both known variants and novel candidate genes, including alkaline phosphatase (ALPL), here linked to hypophosphatasia. The assembled and curated phenotypes provide key resources and exemplars that can be used to dissect complex metabolic traits and disorders.

Identification of Laboratory Techniques to Optimize Superpave HMA Surface Friction Characteristics, TR-450, 2010

Wet pavement friction is known to be one of the most important roadway safety parameters. In this research, frictional properties of flexible (asphalt) pavements were investigated. As a part of this study, a laboratory device to polish asphalt specimens was refined and a procedure to evaluate mixture frictional properties was proposed. Following this procedure, 46 different Superpave mixtures, one stone matrix asphalt (SMA) mixture and one porous friction course (PFC) mixture were tested. In addition, 23 different asphalt and two concrete field sections were also tested for friction and noise. The results of both field and laboratory measurements were used to develop an International Friction Index (IFI)-based protocol for measurement of the frictional characteristics of asphalt pavements for laboratory friction measurements. Based on the results of the study, it appears the content of high friction aggregate should be 20% or more of the total aggregate blend when used with other, polish susceptible coarse aggregates; the frictional properties increased substantially as the friction aggregate content increased above 20%. Both steel slag and quartzite were found to improve the frictional properties of the blend, though steel slag had a lower polishing rate. In general, mixes containing soft limestone demonstrated lower friction values than comparable mixes with hard limestone or dolomite. Larger nominal maximum aggregate size mixes had better overall frictional performance than smaller sized mixes. In addition, mixes with higher fineness moduli generally had higher macrotexture and friction.

GPS to LRM: Integration of Spatial Point Features with Linear Referencing Methods, 2001

Global positioning systems (GPS) offer a cost-effective and efficient method to input and update transportation data. The spatial location of objects provided by GPS is easily integrated into geographic information systems (GIS). The storage, manipulation, and analysis of spatial data are also relatively simple in a GIS. However, many data storage and reporting methods at transportation agencies rely on linear referencing methods (LRMs); consequently, GPS data must be able to link with linear referencing. Unfortunately, the two systems are fundamentally incompatible in the way data are collected, integrated, and manipulated. In order for the spatial data collected using GPS to be integrated into a linear referencing system or shared among LRMs, a number of issues need to be addressed. This report documents and evaluates several of those issues and offers recommendations. In order to evaluate the issues associated with integrating GPS data with a LRM, a pilot study was created. To perform the pilot study, point features, a linear datum, and a spatial representation of a LRM were created for six test roadway segments that were located within the boundaries of the pilot study conducted by the Iowa Department of Transportation linear referencing system project team. Various issues in integrating point features with a LRM or between LRMs are discussed and recommendations provided. The accuracy of the GPS is discussed, including issues such as point features mapping to the wrong segment. Another topic is the loss of spatial information that occurs when a three-dimensional or two-dimensional spatial point feature is converted to a one-dimensional representation on a LRM. Recommendations such as storing point features as spatial objects if necessary or preserving information such as coordinates and elevation are suggested. The lack of spatial accuracy characteristic of most cartography, on which LRM are often based, is another topic discussed. The associated issues include linear and horizontal offset error. The final topic discussed is some of the issues in transferring point feature data between LRMs.

Stage-specific integration of maternal and embryonic peroxisome proliferator-activated receptor delta signaling is critical to pregnancy success.

Successful pregnancy depends on well coordinated developmental events involving both maternal and embryonic components. Although a host of signaling pathways participate in implantation, decidualization, and placentation, whether there is a common molecular link that coordinates these processes remains unknown. By exploiting genetic, molecular, pharmacological, and physiological approaches, we show here that the nuclear transcription factor peroxisome proliferator-activated receptor (PPAR) delta plays a central role at various stages of pregnancy, whereas maternal PPARdelta is critical to implantation and decidualization, and embryonic PPARdelta is vital for placentation. Using trophoblast stem cells, we further elucidate that a reciprocal relationship between PPARdelta-AKT and leukemia inhibitory factor-STAT3 signaling pathways serves as a cell lineage sensor to direct trophoblast cell fates during placentation. This novel finding of stage-specific integration of maternal and embryonic PPARdelta signaling provides evidence that PPARdelta is a molecular link that coordinates implantation, decidualization, and placentation crucial to pregnancy success. This study is clinically relevant because deferral of on time implantation leads to spontaneous pregnancy loss, and defective trophoblast invasion is one cause of preeclampsia in humans.

What matters for predicting spatial distributions of trees: techniques, data, or species' characteristics?

Data characteristics and species traits are expected to influence the accuracy with which species' distributions can be modeled and predicted. We compare 10 modeling techniques in terms of predictive power and sensitivity to location error, change in map resolution, and sample size, and assess whether some species traits can explain variation in model performance. We focused on 30 native tree species in Switzerland and used presence-only data to model current distribution, which we evaluated against independent presence-absence data. While there are important differences between the predictive performance of modeling methods, the variance in model performance is greater among species than among techniques. Within the range of data perturbations in this study, some extrinsic parameters of data affect model performance more than others: location error and sample size reduced performance of many techniques, whereas grain had little effect on most techniques. No technique can rescue species that are difficult to predict. The predictive power of species-distribution models can partly be predicted from a series of species characteristics and traits based on growth rate, elevational distribution range, and maximum elevation. Slow-growing species or species with narrow and specialized niches tend to be better modeled. The Swiss presence-only tree data produce models that are reliable enough to be useful in planning and management applications.

Integration of Notch 1 and calcineurin/NFAT signaling pathways in keratinocyte growth and differentiation control.

The Notch and Calcineurin/NFAT pathways have both been implicated in control of keratinocyte differentiation. Induction of the p21(WAF1/Cip1) gene by Notch 1 activation in differentiating keratinocytes is associated with direct targeting of the RBP-Jkappa protein to the p21 promoter. We show here that Notch 1 activation functions also through a second Calcineurin-dependent mechanism acting on the p21 TATA box-proximal region. Increased Calcineurin/NFAT activity by Notch signaling involves downregulation of Calcipressin, an endogenous Calcineurin inhibitor, through a HES-1-dependent mechanism. Besides control of the p21 gene, Calcineurin contributes significantly to the transcriptional response of keratinocytes to Notch 1 activation, both in vitro and in vivo. In fact, deletion of the Calcineurin B1 gene in the skin results in a cyclic alopecia phenotype, associated with altered expression of Notch-responsive genes involved in hair follicle structure and/or adhesion to the surrounding mesenchyme. Thus, an important interconnection exists between Notch 1 and Calcineurin-NFAT pathways in keratinocyte growth/differentiation control.

Integration of a 3D rendering engine with a physics simulator

The goal of this project is the integration of a set of technologies (graphics, physical simulation, input), with the azm of assembling an application framework in phyton. In this research, a set of key introductory concepts are presented in adoption of a deep study of the state of the art of 3D applications. Phyton is selected an justified as the programing language due to the features and advantages that it offers in front of other languages. Finally the design and implementation of the framework is presented in the last chapter with some client application examples.

Evolution of Genetic Techniques: Past, Present, and Beyond.

Genetics is the study of heredity, which means the study of genes and factors related to all aspects of genes. The scientific history of genetics began with the works of Gregor Mendel in the mid-19th century. Prior to Mendel, genetics was primarily theoretical whilst, after Mendel, the science of genetics was broadened to include experimental genetics. Developments in all fields of genetics and genetic technology in the first half of the 20th century provided a basis for the later developments. In the second half of the 20th century, the molecular background of genetics has become more understandable. Rapid technological advancements, followed by the completion of Human Genome Project, have contributed a great deal to the knowledge of genetic factors and their impact on human life and diseases. Currently, more than 1800 disease genes have been identified, more than 2000 genetic tests have become available, and in conjunction with this at least 350 biotechnology-based products have been released onto the market. Novel technologies, particularly next generation sequencing, have dramatically accelerated the pace of biological research, while at the same time increasing expectations. In this paper, a brief summary of genetic history with short explanations of most popular genetic techniques is given.

Assessment of dissolution techniques for the analysis of ceramic samples by plasma spectrometry

In this study, 13 ceramic samples were subjected to dissolution using three different procedures: (a) acid attack in open PTFE vessels with a mixture of HF-HClO4, (b) fusion of the sample with lithium metaborate and (c) microwave digestion in PTFE bombs. The samples used in the study had been previously analyzed by neutron activation analysis (NAA), X-ray fluorescence (XRF) and X-ray diffraction (XRD) and they cover a wide range of ceramics fired in different atmospheres and temperatures as well as different mineralogical and chemical compositions. The effectiveness of each procedure is evaluated in terms of its ability to dissolve the various mineralogical phases of the samples, of the number of elements that can be determined and of the time needed for the whole scheme of analysis to be completed.

Integration of Economics into Life Cycle Assessment in the Finnish Pulp and Paper Industry

Taloudellisen laskennan yhdistäminen elinkaariarviointiin (LCA) on alkanut kiinnostaa eri teollisuuden aloja maailmanlaajuisesti viime aikoina. Useat LCA-tietokoneohjelmat sisältävät kustannuslaskentaominaisuuksia ja yksittäiset projektit ovat yhdistäneet ympäristö- ja talouslaskentamenetelmiä. Tässä projektissa tutkitaan näiden yhdistelmien soveltuvuutta suomalaiselle sellu- ja paperiteollisuudelle, sekä kustannuslaskentaominaisuuden lisäämistä KCL:n LCA-ohjelmaan, KCL-ECO 3.0:aan. Kaikki tutkimuksen aikana löytyneet menetelmät, jotka yhdistävät LCA:n ja taloudellista laskentaa, on esitelty tässä työssä. Monet näistä käyttävät elinkaarikustannusarviointia (LCCA). Periaatteessa elinkaari määritellään eri tavalla LCCA:ssa ja LCA:ssa, mikä luo haasteita näiden menetelmien yhdistämiselle. Sopiva elinkaari tulee määritellä laskennan tavoitteiden mukaisesti. Työssä esitellään suositusmenetelmä, joka lähtee suomalaisen sellu- ja paperiteollisuuden erikoispiirteistä. Perusvaatimuksena on yhteensopivuus tavanomaisesti paperin LCA:ssa käytetyn elinkaaren kanssa. Menetelmän yhdistäminen KCL-ECO 3.0:aan on käsitelty yksityiskohtaisesti.

Assessment of meshing techniques for fatigue analysis of load carrying welded joints using the effective notch approach

The effective notch stress approach for the fatigue strength assessment of welded structures as included in the Fatigue Design Recommendation of the IIW requires the numerical analysis of the elastic notch stress in the weld toe and weld root which is fictitiously rounded with a radius of 1mm. The goal of this thesis work was to consider alternate meshing strategies when using the effective notch stress approach to assess the fatigue strength of load carrying partial penetration fillet-welded cruciform joints. In order to establish guidelines for modeling the joint and evaluating the results, various two-dimensional (2D) finite element analyses were carried out by systematically varying the thickness of the plates, the weld throat thickness, the degree of bending, and the shape and location of the modeled effective notch. To extend the scope of this work, studies were also carried out on the influence of

Synaptic Integration of Adult-Born Hippocampal Neurons Is Locally Controlled by Astrocytes.

Adult neurogenesis is regulated by the neurogenic niche, through mechanisms that remain poorly defined. Here, we investigated whether niche-constituting astrocytes influence the maturation of adult-born hippocampal neurons using two independent transgenic approaches to block vesicular release from astrocytes. In these models, adult-born neurons but not mature neurons showed reduced glutamatergic synaptic input and dendritic spine density that was accompanied with lower functional integration and cell survival. By taking advantage of the mosaic expression of transgenes in astrocytes, we found that spine density was reduced exclusively in segments intersecting blocked astrocytes, revealing an extrinsic, local control of spine formation. Defects in NMDA receptor (NMDAR)-mediated synaptic transmission and dendrite maturation were partially restored by exogenous D-serine, whose extracellular level was decreased in transgenic models. Together, these results reveal a critical role for adult astrocytes in local dendritic spine maturation, which is necessary for the NMDAR-dependent functional integration of newborn neurons.