The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).

Blood flow and oxygen delivery to human brain during functional activity: Theoretical modeling and experimental data

Coupling of cerebral blood flow (CBF) and cerebral metabolic rate for oxygen (CMRO2) in physiologically activated brain states remains the subject of debates. Recently it was suggested that CBF is tightly coupled to oxidative metabolism in a nonlinear fashion. As part of this hypothesis, mathematical models of oxygen delivery to the brain have been described in which disproportionately large increases in CBF are necessary to sustain even small increases in CMRO2 during activation. We have explored the coupling of CBF and oxygen delivery by using two complementary methods. First, a more complex mathematical model was tested that differs from those recently described in that no assumptions were made regarding tissue oxygen level. Second, [15O] water CBF positron emission tomography (PET) studies in nine healthy subjects were conducted during states of visual activation and hypoxia to examine the relationship of CBF and oxygen delivery. In contrast to previous reports, our model showed adequate tissue levels of oxygen could be maintained without the need for increased CBF or oxygen delivery. Similarly, the PET studies demonstrated that the regional increase in CBF during visual activation was not affected by hypoxia. These findings strongly indicate that the increase in CBF associated with physiological activation is regulated by factors other than local requirements in oxygen.

NOMAD: a versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design.

Molecular analysis of complex modular structures, such as promoter regions or multi-domain proteins, often requires the creation of families of experimental DNA constructs having altered composition, order, or spacing of individual modules. Generally, creation of every individual construct of such a family uses a specific combination of restriction sites. However, convenient sites are not always available and the alternatives, such as chemical resynthesis of the experimental constructs or engineering of different restriction sites onto the ends of DNA fragments, are costly and time consuming. A general cloning strategy (nucleic acid ordered assembly with directionality, NOMAD; WWW resource locator http:@Lmb1.bios.uic.edu/NOMAD/NOMAD.htm l) is proposed that overcomes these limitations. Use of NOMAD ensures that the production of experimental constructs is no longer the rate-limiting step in applications that require combinatorial rearrangement of DNA fragments. NOMAD manipulates DNA fragments in the form of "modules" having a standardized cohesive end structure. Specially designed "assembly vectors" allow for sequential and directional insertion of any number of modules in an arbitrary predetermined order, using the ability of type IIS restriction enzymes to cut DNA outside of their recognition sequences. Studies of regulatory regions in DNA, such as promoters, replication origins, and RNA processing signals, construction of chimeric proteins, and creation of new cloning vehicles, are among the applications that will benefit from using NOMAD.

Mutational analysis and molecular modeling of the nonapeptide hormone binding domains of the [Arg8]vasotocin receptor.

To identify determinants that form nonapeptide hormone binding domains of the white sucker Catostomus commersoni [Arg8]vasotocin receptor, chimeric constructs encoding parts of the vasotocin receptor and parts of the isotocin receptor have been analyzed by [(3,5-3H)Tyr2, Arg8]vasotocin binding to membranes of human embryonic kidney cells previously transfected with the different cDNA constructs and by functional expression studies in Xenopus laevis oocytes injected with mutant cRNAs. The results indicate that the N terminus and a region spanning the second extracellular loop and its flanking transmembrane segments, which contains a number of amino acid residues that are conserved throughout the nonapeptide receptor family, contribute to the affinity of the receptor for its ligand. Nonapeptide selectivity, however, is mainly defined by transmembrane region VI and the third extracellular loop. These results are complemented by a molecular model of the vasotocin receptor obtained by aligning its sequence with those of other G-protein coupled receptors as well as that of bacteriorhodopsin. The model indicates that amino acid residues of transmembrane regions II-VII that are located close to the extracellular surface also contribute to the binding of vasotocin.

Human plectin: organization of the gene, sequence analysis, and chromosome localization (8q24).

Plectin, a 500-kDa intermediate filament binding protein, has been proposed to provide mechanical strength to cells and tissues by acting as a cross-linking element of the cytoskeleton. To set the basis for future studies on gene regulation, tissue-specific expression, and pathological conditions involving this protein, we have cloned the human plectin gene, determined its coding sequence, and established its genomic organization. The coding sequence contains 32 exons that extend over 32 kb of the human genome. Most of the introns reside within a region encoding the globular N-terminal domain of the molecule, whereas the entire central rod domain and the entire C-terminal globular domain were found to be encoded by single exons of remarkable length, >3 kb and >6 kb, respectively. Overall, the organization of the human plectin gene was strikingly similar to that of human bullous pemphigoid antigen 1 (BPAG1), confirming that both proteins belong to the same gene family. Comparison of the deduced protein sequences for human and rat plectin revealed that they were 93% identical. By using fluorescence in situ hybridization, we have mapped the plectin gene to the long arm of chromosome 8 within the telomeric region. This gene locus (8q24) has previously been implicated in the human blistering skin disease epidermolysis bullosa simplex Ogna. Detailed knowledge of the structure of the plectin gene and its chromosome localization will aid in the elucidation of whether this or any other pathological conditions are linked to alterations in the plectin gene.

Effects of receptor dimerization on the interaction between the class I major histocompatibility complex-related Fc receptor and IgG.

The neonatal Fc receptor (FcRn) transports maternal IgG from ingested milk in the gut to the bloodstream of newborn mammals. An FcRn dimer was observed in crystals of the receptor alone and of an FcRn-Fc complex, but its biological relevance was unknown. Here we use surface plasmon resonance-based biosensor assays to assess the role of FcRn dimerization in IgG binding. We find high-affinity IgG binding when FcRn is immobilized on a biosensor chip in an orientation facilitating dimerization but not when its orientation disrupts dimerization. This result supports a model in which IgG-induced dimerization of FcRn is relevant for signaling the cell to initiate endocytosis of the IgG-FcRn complex.

Examining the Impact of Child Psychologists' Stigmatization of Parents on Treatment Outcomes Through a Developmental Lens

The purpose of this paper is to examine how child psychologists' specialized training inhuman development may make them more prone to stigmatize the parents of their young clients. The stigmatization of parents may lead to fewer parents seeking treatment for their children and to poorer treatment outcomes for those who work with a child psychologist. The process of stigmatization is summarized to provide context for the method through which parents receive stigma. A commonly used theory of child development, Erik Erikson's stages of ego development, is outlined to provide background on how child psychologists may interpret and evaluate a child'sdevelopment. Child psychologists' may identify parenting practices that seem to hinder or stunt children's emotional development, which would make the psychologist more aptto stigmatize and isolate parents from the treatment process. To demonstrate the unique ways in which a child psychologist may stigmatize parents of children at different developmental stages two case studies are included. Finally, a theoretical model of treatment is described that may be more inclusive, and less stigmatizing of parents. This model outlines how the parents' concerns about and observations of their children should be validated and reflected in the treatment process. This treatment modality would allow for child psychologists to more actively involve parents in treatment and provide more education and support around their children's unique emotional development needs. Through this treatment model and child psychologists' awareness of and attempts to reduce the stigmatization of parents, treatment outcomes for young clients may improve.

Cross-Disciplinary Collaboration Behavior of Practitioners in the Treatment of Anxiety Disorders

Current research on the collaborative behaviors of conventional and alternative health care providers for the treatment of anxiety is lacking. While there are multiple studies looking at alternative health care integration into primary care, none of them look at anxiety specifically. The purpose of this paper is to provide a preliminary exploration of possible barriers to collaboration between conventional and alternative health care providers for the treatment of anxiety. Quantitative data on collaboration behavior patterns were obtained with an anonymous survey. Data from the surveys were analyzed using a chi-square analysis. Along with these numerical data narrative data from the survey and interviews were collected in order to assess beliefs about the barriers to collaboration from different health care providers. The results indicate that conventional providers collaborate the least with alternative providers and alternative providers collaborate the least with conventional providers. The descriptive results regarding the barriers to collaboration from the study illustrated a common theme, specifically, the lack of education of conventional providers on alternative health care practices on anxiety. This is an exploratory study: therefore it would be beneficial for future researchers to look deeper into the beliefs of health care providers on the barriers to collaboration, possibly identifying the specific barriers to collaboration for each type of healthcare provider.

Anaerobic Digestion Project Working Guide: A Case Study Analysis and Procedural Summary of Anaerobic Digester Projects for the United States Agricultural Sector

Renewable energy such as biomass has given markets, including dairy farms, an effective approach to reducing the costs of sustaining a profitable business. Anaerobic digestion systems offer dairy farms a very effective way to reduce manure odor, comply with soil and water pollution regulations, manufacture compost for general market sales, produce irrigation capacity and generate on-site electricity as well as the ability to sell excess electricity back to the local utilities. This project defines anaerobic digestion technologies and practices, analyzes case studies and presents a step-by-step anaerobic digestion project startup checklist. The result is an anaerobic digestion project working guide that acts as a tool to aid dairy farmers in their own potential anaerobic digestion project.

Evaluating the robustness of EmotiBlog for sentiment analysis and opinion mining

Preliminary research demonstrated the EmotiBlog annotated corpus relevance as a Machine Learning resource to detect subjective data. In this paper we compare EmotiBlog with the JRC Quotes corpus in order to check the robustness of its annotation. We concentrate on its coarse-grained labels and carry out a deep Machine Learning experimentation also with the inclusion of lexical resources. The results obtained show a similarity with the ones obtained with the JRC Quotes corpus demonstrating the EmotiBlog validity as a resource for the SA task.

Kinetic Analysis and Pollutant Evolution During Thermal Degradation of Printed Circuit Boards Considering the Effect of Metals

Paper submitted to the 7th International Symposium on Feedstock Recycling of Polymeric Materials (7th ISFR 2013), New Delhi, India, 23-26 October 2013.

Convergence analysis and validation of low cost distance metrics for computational cost reduction of the Iterative Closest Point algorithm

The Iterative Closest Point algorithm (ICP) is commonly used in engineering applications to solve the rigid registration problem of partially overlapped point sets which are pre-aligned with a coarse estimate of their relative positions. This iterative algorithm is applied in many areas such as the medicine for volumetric reconstruction of tomography data, in robotics to reconstruct surfaces or scenes using range sensor information, in industrial systems for quality control of manufactured objects or even in biology to study the structure and folding of proteins. One of the algorithm’s main problems is its high computational complexity (quadratic in the number of points with the non-optimized original variant) in a context where high density point sets, acquired by high resolution scanners, are processed. Many variants have been proposed in the literature whose goal is the performance improvement either by reducing the number of points or the required iterations or even enhancing the complexity of the most expensive phase: the closest neighbor search. In spite of decreasing its complexity, some of the variants tend to have a negative impact on the final registration precision or the convergence domain thus limiting the possible application scenarios. The goal of this work is the improvement of the algorithm’s computational cost so that a wider range of computationally demanding problems from among the ones described before can be addressed. For that purpose, an experimental and mathematical convergence analysis and validation of point-to-point distance metrics has been performed taking into account those distances with lower computational cost than the Euclidean one, which is used as the de facto standard for the algorithm’s implementations in the literature. In that analysis, the functioning of the algorithm in diverse topological spaces, characterized by different metrics, has been studied to check the convergence, efficacy and cost of the method in order to determine the one which offers the best results. Given that the distance calculation represents a significant part of the whole set of computations performed by the algorithm, it is expected that any reduction of that operation affects significantly and positively the overall performance of the method. As a result, a performance improvement has been achieved by the application of those reduced cost metrics whose quality in terms of convergence and error has been analyzed and validated experimentally as comparable with respect to the Euclidean distance using a heterogeneous set of objects, scenarios and initial situations.

The outburst decay of the low magnetic field magnetar SWIFT J1822.3−1606: phase-resolved analysis and evidence for a variable cyclotron feature

We study the timing and spectral properties of the low-magnetic field, transient magnetar SWIFT J1822.3−1606 as it approached quiescence. We coherently phase-connect the observations over a time-span of ∼500 d since the discovery of SWIFT J1822.3−1606 following the Swift-Burst Alert Telescope (BAT) trigger on 2011 July 14, and carried out a detailed pulse phase spectroscopy along the outburst decay. We follow the spectral evolution of different pulse phase intervals and find a phase and energy-variable spectral feature, which we interpret as proton cyclotron resonant scattering of soft photon from currents circulating in a strong (≳1014 G) small-scale component of the magnetic field near the neutron star surface, superimposed to the much weaker (∼3 × 1013 G) magnetic field. We discuss also the implications of the pulse-resolved spectral analysis for the emission regions on the surface of the cooling magnetar.

Comparative analysis of constructive solutions for thermal insulation by using computer applications in building rehabilitation in Mediterranean climate. The Spanish case

The new Spanish legislation in Energy Saving, similar to European regulation, provides new technical requirements to adequate technical solutions used in integral rehabilitation of existing buildings. The aim of this paper is to present, analyze and discuss the main thermal insulation constructive solutions best suited to a Mediterranean climate, and conclude on their suitability under the legislation in Energy Saving. The proposed methodology is based on the most usual constructive solutions in integral rehabilitation of buildings by analyzing their outstanding design features, by studying its construction details and then by applying the software provided by the Spanish legislation of energy efficiency in buildings. The results of the study evaluate and classify several solutions for façade rehabilitation according to energy efficiency criteria and their suitability for this type of weather, verifying the necessity of using software applications in energy saving for the proper design of constructive solutions in building rehabilitation.