Estimation of the correlation structure of crustal velocity heterogeneity from seismic reflection data

Numerous sources of evidence point to the fact that heterogeneity within the Earth's deep crystalline crust is complex and hence may be best described through stochastic rather than deterministic approaches. As seismic reflection imaging arguably offers the best means of sampling deep crustal rocks in situ, much interest has been expressed in using such data to characterize the stochastic nature of crustal heterogeneity. Previous work on this problem has shown that the spatial statistics of seismic reflection data are indeed related to those of the underlying heterogeneous seismic velocity distribution. As of yet, however, the nature of this relationship has remained elusive due to the fact that most of the work was either strictly empirical or based on incorrect methodological approaches. Here, we introduce a conceptual model, based on the assumption of weak scattering, that allows us to quantitatively link the second-order statistics of a 2-D seismic velocity distribution with those of the corresponding processed and depth-migrated seismic reflection image. We then perform a sensitivity study in order to investigate what information regarding the stochastic model parameters describing crustal velocity heterogeneity might potentially be recovered from the statistics of a seismic reflection image using this model. Finally, we present a Monte Carlo inversion strategy to estimate these parameters and we show examples of its application at two different source frequencies and using two different sets of prior information. Our results indicate that the inverse problem is inherently non-unique and that many different combinations of the vertical and lateral correlation lengths describing the velocity heterogeneity can yield seismic images with the same 2-D autocorrelation structure. The ratio of all of these possible combinations of vertical and lateral correlation lengths, however, remains roughly constant which indicates that, without additional prior information, the aspect ratio is the only parameter describing the stochastic seismic velocity structure that can be reliably recovered.

Integrated methodologies to study human transcriptional regulation from functional genomics data

Abstract : The human body is composed of a huge number of cells acting together in a concerted manner. The current understanding is that proteins perform most of the necessary activities in keeping a cell alive. The DNA, on the other hand, stores the information on how to produce the different proteins in the genome. Regulating gene transcription is the first important step that can thus affect the life of a cell, modify its functions and its responses to the environment. Regulation is a complex operation that involves specialized proteins, the transcription factors. Transcription factors (TFs) can bind to DNA and activate the processes leading to the expression of genes into new proteins. Errors in this process may lead to diseases. In particular, some transcription factors have been associated with a lethal pathological state, commonly known as cancer, associated with uncontrolled cellular proliferation, invasiveness of healthy tissues and abnormal responses to stimuli. Understanding cancer-related regulatory programs is a difficult task, often involving several TFs interacting together and influencing each other's activity. This Thesis presents new computational methodologies to study gene regulation. In addition we present applications of our methods to the understanding of cancer-related regulatory programs. The understanding of transcriptional regulation is a major challenge. We address this difficult question combining computational approaches with large collections of heterogeneous experimental data. In detail, we design signal processing tools to recover transcription factors binding sites on the DNA from genome-wide surveys like chromatin immunoprecipitation assays on tiling arrays (ChIP-chip). We then use the localization about the binding of TFs to explain expression levels of regulated genes. In this way we identify a regulatory synergy between two TFs, the oncogene C-MYC and SP1. C-MYC and SP1 bind preferentially at promoters and when SP1 binds next to C-NIYC on the DNA, the nearby gene is strongly expressed. The association between the two TFs at promoters is reflected by the binding sites conservation across mammals, by the permissive underlying chromatin states 'it represents an important control mechanism involved in cellular proliferation, thereby involved in cancer. Secondly, we identify the characteristics of TF estrogen receptor alpha (hERa) target genes and we study the influence of hERa in regulating transcription. hERa, upon hormone estrogen signaling, binds to DNA to regulate transcription of its targets in concert with its co-factors. To overcome the scarce experimental data about the binding sites of other TFs that may interact with hERa, we conduct in silico analysis of the sequences underlying the ChIP sites using the collection of position weight matrices (PWMs) of hERa partners, TFs FOXA1 and SP1. We combine ChIP-chip and ChIP-paired-end-diTags (ChIP-pet) data about hERa binding on DNA with the sequence information to explain gene expression levels in a large collection of cancer tissue samples and also on studies about the response of cells to estrogen. We confirm that hERa binding sites are distributed anywhere on the genome. However, we distinguish between binding sites near promoters and binding sites along the transcripts. The first group shows weak binding of hERa and high occurrence of SP1 motifs, in particular near estrogen responsive genes. The second group shows strong binding of hERa and significant correlation between the number of binding sites along a gene and the strength of gene induction in presence of estrogen. Some binding sites of the second group also show presence of FOXA1, but the role of this TF still needs to be investigated. Different mechanisms have been proposed to explain hERa-mediated induction of gene expression. Our work supports the model of hERa activating gene expression from distal binding sites by interacting with promoter bound TFs, like SP1. hERa has been associated with survival rates of breast cancer patients, though explanatory models are still incomplete: this result is important to better understand how hERa can control gene expression. Thirdly, we address the difficult question of regulatory network inference. We tackle this problem analyzing time-series of biological measurements such as quantification of mRNA levels or protein concentrations. Our approach uses the well-established penalized linear regression models where we impose sparseness on the connectivity of the regulatory network. We extend this method enforcing the coherence of the regulatory dependencies: a TF must coherently behave as an activator, or a repressor on all its targets. This requirement is implemented as constraints on the signs of the regressed coefficients in the penalized linear regression model. Our approach is better at reconstructing meaningful biological networks than previous methods based on penalized regression. The method is tested on the DREAM2 challenge of reconstructing a five-genes/TFs regulatory network obtaining the best performance in the "undirected signed excitatory" category. Thus, these bioinformatics methods, which are reliable, interpretable and fast enough to cover large biological dataset, have enabled us to better understand gene regulation in humans.

Spatial correlations and cross sections of clusters in the A + B -> 0 reaction

We consider the distribution of cross sections of clusters and the density-density correlation functions for the A+B¿0 reaction. We solve the reaction-diffusion equations numerically for random initial distributions of reactants. When both reactant species have the same diffusion coefficients the distribution of cross sections and the correlation functions scale with the diffusion length and obey superuniversal laws (independent of dimension). For different diffusion coefficients the correlation functions still scale, but the scaling functions depend on the dimension and on the diffusion coefficients. Furthermore, we display explicitly the peculiarities of the cluster-size distribution in one dimension.

Geostatistical inversion of seismic and GPR reflection images: what can we actually resolve?

Estimation of the spatial statistics of subsurface velocity heterogeneity from surface-based geophysical reflection survey data is a problem of significant interest in seismic and ground-penetrating radar (GPR) research. A method to effectively address this problem has been recently presented, but our knowledge regarding the resolution of the estimated parameters is still inadequate. Here we examine this issue using an analytical approach that is based on the realistic assumption that the subsurface velocity structure can be characterized as a band-limited scale-invariant medium. Our work importantly confirms recent numerical findings that the inversion of seismic or GPR reflection data for the geostatistical properties of the probed subsurface region is sensitive to the aspect ratio of the velocity heterogeneity and to the decay of its power spectrum, but not to the individual values of the horizontal and vertical correlation lengths.

Nonlinear Pile Behavior in Integral Abutment Bridges, HR-227, Part 1, 1982

The highway departments of all fifty states were contacted to find the extent of application of integral abutment bridges, to survey the different guidelines used for analysis and design of integral abutment bridges, and to assess the performance of such bridges through the years. The variation in design assumptions and length limitations among the various states in their approach to the use of integral abutments is discussed. The problems associated with lateral displacements at the abutment, and the solutions developed by the different states for most of the ill effects of abutment movements are summarized in the report. An algorithm based on a state-of-the-art nonlinear finite element procedure was developed and used to study piling stresses and pile-soil interaction in integral abutment bridges. The finite element idealization consists of beam-column elements with geometric and material nonlinearities for the pile and nonlinear springs for the soil. An idealized soil model (modified Ramberg-Osgood model) was introduced in this investigation to obtain the tangent stiffness of the nonlinear spring elements. Several numerical examples are presented in order to establish the reliability of the finite element model and the computer software developed. Three problems with analytical solutions were first solved and compared with theoretical solutions. A 40 ft H pile (HP 10 X 42) in six typical Iowa soils was then analyzed by first applying a horizontal displacement (to simulate bridge motion) and no rotation at the top and then applying a vertical load V incrementally until failure occurred. Based on the numerical results, the failure mechanisms were generalized to be of two types: (a) lateral type failure and (b) vertical type failure. It appears that most piles in Iowa soils (sand, soft clay and stiff clay) failed when the applied vertical load reached the ultimate soil frictional resistance (vertical type failure). In very stiff clays, however, the lateral type failure occurs before vertical type failure because the soil is sufficiently stiff to force a plastic hinge to form in the pile as the specified lateral displacement is applied. Preliminary results from this investigation showed that the vertical load-carrying capacity of H piles is not significantly affected by lateral displacements of 2 inches in soft clay, stiff clay, loose sand, medium sand and dense sand. However, in very stiff clay (average blow count of 50 from standard penetration tests), it was found that the vertical load carrying capacity of the H pile is reduced by about 50 percent for 2 inches of lateral displacement and by about 20 percent for lateral displacement of 1 inch. On the basis of the preliminary results of this investigation, the 265-feet length limitation in Iowa for integral abutment concrete bridges appears to be very conservative.

Correlation of Locally-Based Performance of Asphalts with their Physicochemical Parameters, Task 1 Report, HR-298, 1988

This is the first report of 6 tasks to be performed in an effort to establish locally-based quality and performance criteria for asphalts, and ultimately to develop performance-related specifications based on simple physicochemical methods. Three of the most promising chemical methods (high performance liquid chromatography (HPLC), thermal analysis, and X-ray diffraction were selected to analyze 4 different types of samples. The results will indicate the fundamental asphalt property variables that directly affect the field performance in Iowa. The details of the materials and procedures employed are described, and the results of the tests are presented.

Polyethylene wear in anatomic and reversed shoulder prostheses

Purpose: Polyethylene wear is a recurrent problem in joint arthroplasty. Small debris particles are also associated to inflammation reaction of the surrounding bone, eventually leading to the failure of the bound between the implant and the host bone, and implant loosening. The goal of this study was thus to estimate the volume of polyethylene wear of a reversed prosthesis, and compare it to an anatomic prosthesis, during one year of activities of daily living. Material and Methods: A numerical musculoskeletal model of the glenohumeral joint was used for this comparative study. The reversed (RP) and anatomic (AP) Aequalis prostheses were positioned in the numerical model. Eight levels of abduction were considered. Their daily frequency was estimated from in-vivo recorded data on healthy volunteers during activities of daily living. One year of use was simulated to predict the linear and volumetric wear. The volumetric wear was the difference of volume between the original and worn component. Results: With the AP, the contact pattern on the glenoid surface moved rapidly from the inferior to the superior side during the first 30 degrees of abduction, and then went back to the inferior side. With the RP, the contact pattern on the humeral cup surface remained at the inferior side. Contact pressure was 20 times lower with the RP than with the AP. One year of use produced a maximum linear wear of 0.2 mm with the AP, and 0.13 mm with the RP. However, the volumetric wear was 8.4 mm3 with the AP, but reached 44.6 mm3 with the RP. Conclusion: Polyethylene particles are a matter of concern with AP. Infiltration of these particles within the bone-implant interface can induce a implant loosening. This problem should not be underestimated with RP. It might be associated to a higher level of humeral stem loosening reported with RP. The long term survival of RP might be improved by using a highly cross-linked polyethylene, which has a better abrasion resistance but lower plastic resistance.

Copeptin is not associated with menstrual cycle hormone.

Background: Copeptin (CP), a derivate from the antidiuretic hormone (ADH) precursor pre-pro-vasopressin, stochiometrically mirrors ADH secretion. CP is increasingly evaluated as a diagnostic and prognostic biomarker in different diseases. It is therefore important to recognize possible confounding factors when interpreting CP levels. In healthy regularly menstruating women, there is a small but measurable physiological variability of hormones involved in fluid regulation. ADH plasma levels have been found to be lowest at menstruation, increasing during the follicular phase with a peak at ovulation and a drop in the luteal phase. We investigated the variability of CP during the menstrual cycle (MC) and its correlation to MC hormones. Methods: In total, 15 healthy women with regular MC (from 26 to 33 days) were included in this study. Ovulation was confirmed by progesterone (prog) levels on day 21 of the MC before entering the study and during the study. Blood collection was performed on days 3, 5, 8-16, 18, 21, 24 and 27 of their MC. Serums were assayed for prog, estradiol (E2), LH, and CP. Mixed linear regression analysis for repeated measures was performed to study the changes of CP, prog, E2 and LH during the MC, and to test the correlation of CP with sex hormones during the MC. Results: Mean MC length in all subjects was 28.5±2.2 d. E2, prog, and LH exhibited characteristic changes during the MC (all P< 0.05). All cycles were ovulatory (peak prog 54±15 nmol/l). CP levels did not change significantly throughout the MC, and were not associated with changes in prog, E2 or LH-levels (all P=ns). Conclusion: CP levels remain stable during the MC and are not influenced by changes in sex hormones. This implicates that it is not necessary to consider MC phases when using CP as a biomarker in premenopausal women.

Imazaquin sorption in surface and subsurface soil samples

The objective of this work was to study the sorption and desorption of imazaquin, in surface and subsurface soil samples from Brazil. Sorption and desorption steps were carried out using batch equilibration and high performance liquid chromatography analytical routines. The value of Kf,ads was positively correlated with clay content, and negatively correlated with pH of supernatant. Samples from Typic Haplustox, clayey soil profile having high clay content, provided higher Kf,ads values, and negative correlation with organic carbon, silt content, cation exchange capacity and pH.

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.

Associations between mood, anxiety or substance use disorders and inflammatory markers after adjustment for multiple covariates in a population-based study.

Inflammation is one possible mechanism underlying the associations between mental disorders and cardiovascular diseases (CVD). However, studies on mental disorders and inflammation have yielded inconsistent results and the majority did not adjust for potential confounding factors. We examined the associations of several pro-inflammatory cytokines (IL-1β, IL-6 and TNF-α) and high sensitive C-reactive protein (hsCRP) with lifetime and current mood, anxiety and substance use disorders (SUD), while adjusting for multiple covariates. The sample included 3719 subjects, randomly selected from the general population, who underwent thorough somatic and psychiatric evaluations. Psychiatric diagnoses were made with a semi-structured interview. Major depressive disorder was subtyped into "atypical", "melancholic", "combined atypical-melancholic" and "unspecified". Associations between inflammatory markers and psychiatric diagnoses were assessed using multiple linear and logistic regression models. Lifetime bipolar disorders and atypical depression were associated with increased levels of hsCRP, but not after multivariate adjustment. After multivariate adjustment, SUD remained associated with increased hsCRP levels in men (β = 0.13 (95% CI: 0.03,0.23)) but not in women. After multivariate adjustment, lifetime combined and unspecified depression were associated with decreased levels of IL-6 (β = -0.27 (-0.51,-0.02); β = -0.19 (-0.34,-0.05), respectively) and TNF-α (β = -0.16 (-0.30,-0.01); β = -0.10 (-0.19,-0.02), respectively), whereas current combined and unspecified depression were associated with decreased levels of hsCRP (β = -0.20 (-0.39,-0.02); β = -0.12 (-0.24,-0.01), respectively). Our data suggest that the significant associations between increased hsCRP levels and mood disorders are mainly attributable to the effects of comorbid disorders, medication as well as behavioral and physical CVRFs.

Hybrid turbo FEC/ARQ systems and distributed space-time coding for cooperative transmission

Cooperative transmission can be seen as a "virtual" MIMO system, where themultiple transmit antennas are in fact implemented distributed by the antennas both at the source and the relay terminal. Depending on the system design, diversity/multiplexing gainsare achievable. This design involves the definition of the type of retransmission (incrementalredundancy, repetition coding), the design of the distributed space-time codes, the errorcorrecting scheme, the operation of the relay (decode&forward or amplify&forward) and thenumber of antennas at each terminal. Proposed schemes are evaluated in different conditionsin combination with forward error correcting codes (FEC), both for linear and near-optimum(sphere decoder) receivers, for its possible implementation in downlink high speed packetservices of cellular networks. Results show the benefits of coded cooperation over directtransmission in terms of increased throughput. It is shown that multiplexing gains areobserved even if the mobile station features a single antenna, provided that cell wide reuse of the relay radio resource is possible.

Flight movement and spatial distribution of immunomarked thrips in onion, potato, and tomato

The objective of this work was to evaluate the spatial distribution of thrips in different crops, and the correlation between meterological parameters and the flight movements of this pest, using immunomarking. The experiment was conducted in cultivated areas, with tomato (Solanum lycopersicum), potato (Solanum tuberosum), and onion (Allium cepa); and non-cultivated areas, with weedy plants. The areas with tomato (100 days), potato (20 days), and weeds were sprayed with casein, albumin, and soy milk, respectively, to mark adult thrips; however, the areas with onion (50 days) and tomato (10 days) were not sprayed. Thrips were captured with georeferenced blue sticky traps, transferred into tubes, and identified by treatment area with the Elisa test. The dependence between the samples and the capture distance was determined using geostatistics. Meteorlogical parameters were correlated with thrips density in each area. The three protein types used for immunomarking were detected in different proportions in the thrips. There was a correlation between casein-marked thrips and wind speed. The thrips flew a maximum distance of 3.5 km and dispersed from the older (tomato) to the younger crops (potato). The immunomarking method is efficient to mark large quantities of thrips.

Transketolase-like 1 expression is modulated during Colorectal cancer progression and metastasis formation

Background Transketolase-like 1 (TKTL1) induces glucose degradation through anaerobic pathways, even in presence of oxygen, favoring the malignant aerobic glycolytic phenotype characteristic of tumor cells. As TKTL1 appears to be a valid biomarker for cancer prognosis, the aim of the current study was to correlate its expression with tumor stage, probability of tumor recurrence and survival, in a series of colorectal cancer patients. Methodolody/Principal Findings Tumor tissues from 63 patients diagnosed with colorectal cancer at different stages of progression were analyzed for TKTL1 by immunohistochemistry. Staining was quantified by computational image analysis, and correlations between enzyme expression, local growth, lymph-node involvement and metastasis were assessed. The highest values for TKTL1 expression were detected in the group of stage III tumors, which showed significant differences from the other groups (Kruskal-Wallis test, P = 0.000008). Deeper analyses of T, N and M classifications revealed a weak correlation between local tumor growth and enzyme expression (Mann-Whitney test, P = 0.029), a significant association of the enzyme expression with lymph-node involvement (Mann-Whitney test, P = 0.0014) and a significant decrease in TKTL1 expression associated with metastasis (Mann-Whitney test, P = 0.0004). Conclusions/Significance To our knowledge, few studies have explored the association between variations in TKTL1 expression in the primary tumor and metastasis formation. Here we report downregulation of enzyme expression when metastasis appears, and a correlation between enzyme expression and regional lymph-node involvement in colon cancer. This finding may improve our understanding of metastasis and lead to new and more efficient therapies against cancer.

Value added logistics in supply and demand chains. Smile. Part 1. eBusiness between global company and itslocal sme supplier network

VALOSADE (Value Added Logistics in Supply and Demand Chains) is the research project of Anita Lukka's VALORE (Value Added Logistics Research) research team inLappeenranta University of Technology. VALOSADE is included in ELO (Ebusiness logistics) technology program of Tekes (Finnish Technology Agency). SMILE (SME-sector, Internet applications and Logistical Efficiency) is one of four subprojects of VALOSADE. SMILE research focuses on case network that is composed of small and medium sized mechanical maintenance service providers and global wood processing customers. Basic principle of SMILE study is communication and ebusiness insupply and demand network. This first phase of research concentrates on creating backgrounds for SMILE study and for ebusiness solutions of maintenance case network. The focus is on general trends of ebusiness in supply chains and networksof different industries; total ebusiness system architecture of company networks; ebusiness strategy of company network; information value chain; different factors, which influence on ebusiness solution of company network; and the correlation between ebusiness and competitive advantage. Literature, interviews and benchmarking were used as research methods in this qualitative case study. Networks and end-to-end supply chains are the organizational structures, which can add value for end customer. Information is one of the key factors in these decentralized structures. Because of decentralization of business, information is produced and used in different companies and in different information systems. Information refinement services are needed to manage information flows in company networksbetween different systems. Furthermore, some new solutions like network information systems are utilised in optimising network performance and in standardizingnetwork common processes. Some cases have however indicated, that utilization of ebusiness in decentralized business model is not always a necessity, but value-add of ICT must be defined case-specifically. In the theory part of report, different ebusiness and architecture models are introduced. These models are compared to empirical case data in research results. The biggest difference between theory and empirical data is that models are mainly developed for large-scale companies - not for SMEs. This is due to that implemented network ebusiness solutions are mainly large company centered. Genuine SME network centred ebusiness models are quite rare, and the study in that area has been few in number. Business relationships between customer and their SME suppliers are nowadays concentrated more on collaborative tactical and strategic initiatives besides transaction based operational initiatives. However, ebusiness systems are further mainly based on exchange of operational transactional data. Collaborative ebusiness solutions are in planning or pilot phase in most case companies. Furthermore, many ebusiness solutions are nowadays between two participants, but network and end-to-end supply chain transparency and information systems are quite rare. Transaction volumes, data formats, the types of exchanged information, information criticality,type and duration of business relationship, internal information systems of partners, processes and operation models (e.g. different ordering models) differ among network companies, and furthermore companies are at different stages on networking and ebusiness readiness. Because of former factors, different customer-supplier combinations in network must utilise totally different ebusiness architectures, technologies, systems and standards.