WorldWideScience

Sample records for relevant molecular systems

  1. Spectroscopic Studies of Molecular Systems relevant in Astrobiology

    Science.gov (United States)

    Fornaro, Teresa

    2016-01-01

    In the Astrobiology context, the study of the physico-chemical interactions involving "building blocks of life" in plausible prebiotic and space-like conditions is fundamental to shed light on the processes that led to emergence of life on Earth as well as to molecular chemical evolution in space. In this PhD Thesis, such issues have been addressed both experimentally and computationally by employing vibrational spectroscopy, which has shown to be an effective tool to investigate the variety of intermolecular interactions that play a key role in self-assembling mechanisms of nucleic acid components and their binding to mineral surfaces. In particular, in order to dissect the contributions of the different interactions to the overall spectroscopic signals and shed light on the intricate experimental data, feasible computational protocols have been developed for the characterization of the spectroscopic properties of such complex systems. This study has been carried out through a multi-step strategy, starting the investigation from the spectroscopic properties of the isolated nucleobases, then studying the perturbation induced by the interaction with another molecule (molecular dimers), towards condensed phases like the molecular solid, up to the case of nucleic acid components adsorbed on minerals. A proper modeling of these weakly bound molecular systems has required, firstly, a validation of dispersion-corrected Density Functional Theory methods for simulating anharmonic vibrational properties. The isolated nucleobases and some of their dimers have been used as benchmark set for identifying a general, reliable and effective computational procedure based on fully anharmonic quantum mechanical computations of the vibrational wavenumbers and infrared intensities within the generalized second order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective dispersion-corrected density functional B3LYP-D3, in conjunction with basis sets of

  2. Properties of aqueous systems relevant to the SCWR via molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kallikragas, D. [Trent Univ., Dept. of Chemistry, Peterborough, Ontario (Canada); Guzonas, D. [Canadian Nuclear Laboratories, Chalk River, Ontario (Canada); Svishchev, I., E-mail: isvishchev@trentu.ca [Trent Univ., Dept. of Chemistry, Peterborough, Ontario (Canada)

    2015-06-15

    Supercritical water (SCW) is the intended heat transfer fluid in the proposed GEN-IV supercritical water cooled reactor (SCWR). The oxidative environment poses challenges in choosing appropriate design materials and understanding the behaviour of SCW at the nanoscale within crevices of the passivation layer is needed for developing a control strategy to minimize corrosion. Molecular dynamics simulations have been employed to investigate molecular structure and diffusion of water and chloride in nanometer-spaced iron hydroxide surfaces. Results demonstrate that water is more likely to accumulate on the surface at low-density conditions. The effect of confinement on the water structure diminishes with as little as 20 Å of surface separation. Clustering and the accumulation of water at the surface imply that the SCWR will be most susceptible to pitting corrosion and stress corrosion cracking. A parameterized equation is provided that gives the diffusion coefficients of {sub O2}, H{sub 2}, and OH radical in high temperature and SCW. (author)

  3. Gregory Bateson's relevance to current molecular biology

    DEFF Research Database (Denmark)

    Bruni, Luis Emilio

    2008-01-01

    in a developmental pathway. Being a central figure in the development of cybernetic theory he collaborated with a range of researchers from the life sciences who were innovating their own disciplines by introducing cybernetic concepts in their particular fields and disciplines. In the light of this, it should...... not come as a surprise today to realize how the general ideas that he was postulating for the study of communication systems in biology fit so well with the astonishing findings of current molecular biology, for example in the field of cellular signal transduction networks. I guess this is the case due...

  4. [Relevance of big data for molecular diagnostics].

    Science.gov (United States)

    Bonin-Andresen, M; Smiljanovic, B; Stuhlmüller, B; Sörensen, T; Grützkau, A; Häupl, T

    2018-04-01

    Big data analysis raises the expectation that computerized algorithms may extract new knowledge from otherwise unmanageable vast data sets. What are the algorithms behind the big data discussion? In principle, high throughput technologies in molecular research already introduced big data and the development and application of analysis tools into the field of rheumatology some 15 years ago. This includes especially omics technologies, such as genomics, transcriptomics and cytomics. Some basic methods of data analysis are provided along with the technology, however, functional analysis and interpretation requires adaptation of existing or development of new software tools. For these steps, structuring and evaluating according to the biological context is extremely important and not only a mathematical problem. This aspect has to be considered much more for molecular big data than for those analyzed in health economy or epidemiology. Molecular data are structured in a first order determined by the applied technology and present quantitative characteristics that follow the principles of their biological nature. These biological dependencies have to be integrated into software solutions, which may require networks of molecular big data of the same or even different technologies in order to achieve cross-technology confirmation. More and more extensive recording of molecular processes also in individual patients are generating personal big data and require new strategies for management in order to develop data-driven individualized interpretation concepts. With this perspective in mind, translation of information derived from molecular big data will also require new specifications for education and professional competence.

  5. Synergetics of molecular systems

    CERN Document Server

    Lupichev, Lev N; Kadantsev, Vasiliy N

    2014-01-01

    Synergetics is the quantitative study of multicomponent systems that exhibit nonlinear dynamics and cooperativity. This book specifically considers basic models of the nonlinear dynamics of molecular systems and discusses relevant applications in biological physics and the polymer sciences.Emphasis is placed on specific solutions to the dynamical equations that correspond to the coherent formation of spatial-temporal structures, such as solitons, kinks and breathers, in particular. The emergence of these patterns in molecular structures provides a variety of information on their structural pro

  6. Electron and molecular ion collisions relevant to divertor plasma

    International Nuclear Information System (INIS)

    Takagi, H.

    2005-01-01

    We introduce the concept of the multi-channel quantum defect theory (MQDT) and show the outline of the MQDT newly extended to include the dissociative states. We investigate some molecular processes relevant to the divertor plasma by using the MQDT: the dissociative recombination, dissociative excitation, and rotation-vibrational transition in the hydrogen molecular ion and electron collisions. (author)

  7. Resveratrol and Calcium Signaling: Molecular Mechanisms and Clinical Relevance

    Directory of Open Access Journals (Sweden)

    Audrey E. McCalley

    2014-06-01

    Full Text Available Resveratrol is a naturally occurring compound contributing to cellular defense mechanisms in plants. Its use as a nutritional component and/or supplement in a number of diseases, disorders, and syndromes such as chronic diseases of the central nervous system, cancer, inflammatory diseases, diabetes, and cardiovascular diseases has prompted great interest in the underlying molecular mechanisms of action. The present review focuses on resveratrol, specifically its isomer trans-resveratrol, and its effects on intracellular calcium signaling mechanisms. As resveratrol’s mechanisms of action are likely pleiotropic, its effects and interactions with key signaling proteins controlling cellular calcium homeostasis are reviewed and discussed. The clinical relevance of resveratrol’s actions on excitable cells, transformed or cancer cells, immune cells and retinal pigment epithelial cells are contrasted with a review of the molecular mechanisms affecting calcium signaling proteins on the plasma membrane, cytoplasm, endoplasmic reticulum, and mitochondria. The present review emphasizes the correlation between molecular mechanisms of action that have recently been identified for resveratrol and their clinical implications.

  8. Profiling and functional data on the developing olfactory/GnRH system reveal cellular and molecular pathways essential for this process and potentially relevant for the Kallmann syndrome

    Directory of Open Access Journals (Sweden)

    Giulia eGaraffo

    2013-12-01

    Full Text Available During embryonic development, immature neurons in the olfactory epithelium (OE extend axons through the nasal mesenchyme, to contact projection neurons in the olfactory bulb. Axon navigation is accompanied by migration of the GnRH+ neurons, which enter the anterior forebrain and home in the septo-hypothalamic area. This process can be interrupted at various points and lead to the onset of the Kallmann syndrome (KS, a disorder characterized by anosmia and central hypogonadotropic hypogonadism. Several genes has been identified in human and mice that cause KS or a KS-like phenotype. In mice a set of transcription factors appears to be required for olfactory connectivity and GnRH neuron migration; thus we explored the transcriptional network underlying this developmental process by profiling the OE and the adjacent mesenchyme at three embryonic ages. We also profiled the OE from embryos null for Dlx5, a homeogene that causes a KS-like phenotype when deleted. We identified 20 interesting genes belonging to the following categories: 1 transmembrane adhesion/receptor, 2 axon-glia interaction, 3 scaffold/adapter for signalling, 4 synaptic proteins. We tested some of them in zebrafish embryos: the depletion of five (of six Dlx5 targets affected axonal extension and targeting, while three (of three affected GnRH neuron position and neurite organization. Thus, we confirmed the importance of cell-cell and cell-matrix interactions and identified new molecules needed for olfactory connection and GnRH neuron migration. Using available and newly generated data, we predicted/prioritized putative KS-disease genes, by building conserved co-expression networks with all known disease genes in human and mouse. The results show the overall validity of approaches based on high-throughput data and predictive bioinformatics to identify genes potentially relevant for the molecular pathogenesis of KS. A number of candidate will be discussed, that should be tested in

  9. Molecular subtypes of glioblastoma are relevant to lower grade glioma.

    Directory of Open Access Journals (Sweden)

    Xiaowei Guan

    Full Text Available Gliomas are the most common primary malignant brain tumors in adults with great heterogeneity in histopathology and clinical course. The intent was to evaluate the relevance of known glioblastoma (GBM expression and methylation based subtypes to grade II and III gliomas (ie. lower grade gliomas.Gene expression array, single nucleotide polymorphism (SNP array and clinical data were obtained for 228 GBMs and 176 grade II/II gliomas (GII/III from the publically available Rembrandt dataset. Two additional datasets with IDH1 mutation status were utilized as validation datasets (one publicly available dataset and one newly generated dataset from MD Anderson. Unsupervised clustering was performed and compared to gene expression subtypes assigned using the Verhaak et al 840-gene classifier. The glioma-CpG Island Methylator Phenotype (G-CIMP was assigned using prediction models by Fine et al.Unsupervised clustering by gene expression aligned with the Verhaak 840-gene subtype group assignments. GII/IIIs were preferentially assigned to the proneural subtype with IDH1 mutation and G-CIMP. GBMs were evenly distributed among the four subtypes. Proneural, IDH1 mutant, G-CIMP GII/III s had significantly better survival than other molecular subtypes. Only 6% of GBMs were proneural and had either IDH1 mutation or G-CIMP but these tumors had significantly better survival than other GBMs. Copy number changes in chromosomes 1p and 19q were associated with GII/IIIs, while these changes in CDKN2A, PTEN and EGFR were more commonly associated with GBMs.GBM gene-expression and methylation based subtypes are relevant for GII/III s and associate with overall survival differences. A better understanding of the association between these subtypes and GII/IIIs could further knowledge regarding prognosis and mechanisms of glioma progression.

  10. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  11. Clinical Relevance of Prognostic and Predictive Molecular Markers in Gliomas.

    Science.gov (United States)

    Siegal, Tali

    2016-01-01

    Sorting and grading of glial tumors by the WHO classification provide clinicians with guidance as to the predicted course of the disease and choice of treatment. Nonetheless, histologically identical tumors may have very different outcome and response to treatment. Molecular markers that carry both diagnostic and prognostic information add useful tools to traditional classification by redefining tumor subtypes within each WHO category. Therefore, molecular markers have become an integral part of tumor assessment in modern neuro-oncology and biomarker status now guides clinical decisions in some subtypes of gliomas. The routine assessment of IDH status improves histological diagnostic accuracy by differentiating diffuse glioma from reactive gliosis. It carries a favorable prognostic implication for all glial tumors and it is predictive for chemotherapeutic response in anaplastic oligodendrogliomas with codeletion of 1p/19q chromosomes. Glial tumors that contain chromosomal codeletion of 1p/19q are defined as tumors of oligodendroglial lineage and have favorable prognosis. MGMT promoter methylation is a favorable prognostic marker in astrocytic high-grade gliomas and it is predictive for chemotherapeutic response in anaplastic gliomas with wild-type IDH1/2 and in glioblastoma of the elderly. The clinical implication of other molecular markers of gliomas like mutations of EGFR and ATRX genes and BRAF fusion or point mutation is highlighted. The potential of molecular biomarker-based classification to guide future therapeutic approach is discussed and accentuated.

  12. Vitamin E-drug interactions: molecular basis and clinical relevance.

    Science.gov (United States)

    Podszun, Maren; Frank, Jan

    2014-12-01

    Vitamin E (α-, β-, γ- and δ-tocopherol and -tocotrienol) is an essential factor in the human diet and regularly taken as a dietary supplement by many people, who act under the assumption that it may be good for their health and can do no harm. With the publication of meta-analyses reporting increased mortality in persons taking vitamin E supplements, the safety of the micronutrient was questioned and interactions with prescription drugs were suggested as one potentially underlying mechanism. Here, we review the evidence in the scientific literature for adverse vitamin E-drug interactions and discuss the potential of each of the eight vitamin E congeners to alter the activity of drugs. In summary, there is no evidence from animal models or randomised controlled human trials to suggest that the intake of tocopherols and tocotrienols at nutritionally relevant doses may cause adverse nutrient-drug interactions. Consumption of high-dose vitamin E supplements ( ≥  300 mg/d), however, may lead to interactions with the drugs aspirin, warfarin, tamoxifen and cyclosporine A that may alter their activities. For the majority of drugs, however, interactions with vitamin E, even at high doses, have not been observed and are thus unlikely.

  13. Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling

    International Nuclear Information System (INIS)

    Tawara, H.

    1997-01-01

    This issue is the collection of the paper presented status on atomic and molecular data relevant to fusion plasma diagnostics and modeling. The 10 of the presented papers are indexed individually. (J.P.N.)

  14. Review of relevant studies of isolated systems

    DEFF Research Database (Denmark)

    Hansen, L.H.; Lundsager, P.

    2001-01-01

    The report presents the results of a review of studies relating to integration of wind energy in isolated power supply systems, based on a systematic literature survey. The purpose of the study is to develop a methodology consisting of a set of guidelinesfor wind energy projects in isolated energy...... systems and a set of tools and models that are operational on an engineering level. The review is based on a literature search in the ETDE Energy Database with a main search covering the period 7/88 to 6/97 andsupplemented by partial update periods. A few newer references have been included in the review...... have been organised according to the following keywords: methods & guides, economics, concept ofapplication, system solutions, case studies, financial programmes, dedicated software tools. None of the found references presents methods or tools that contradict the philosophy of Risø's methodology...

  15. Stratification and prognostic relevance of Jass’s molecular classification of colorectal cancer

    OpenAIRE

    Inti eZlobec; Inti eZlobec; Michel P Bihl; Anja eFoerster; Alex eRufle; Luigi eTerracciano; Alessandro eLugli; Alessandro eLugli

    2012-01-01

    Background: The current proposed model of colorectal tumorigenesis is based primarily on CpG island methylator phenotype (CIMP), microsatellite instability (MSI), KRAS, BRAF, and methylation status of 0-6-Methylguanine DNA Methyltransferase (MGMT) and classifies tumors into 5 subgroups. The aim of this study is to validate this molecular classification and test its prognostic relevance. Methods: 302 patients were included in this study. Molecular analysis was performed for 5 CIMP-related pro...

  16. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

    Directory of Open Access Journals (Sweden)

    Xinxin Peng

    2018-04-01

    Full Text Available Summary: Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression patterns of seven major metabolic processes and assessed their clinical relevance. Our metabolic expression subtypes correlated extensively with clinical outcome: subtypes with upregulated carbohydrate, nucleotide, and vitamin/cofactor metabolism most consistently correlated with worse prognosis, whereas subtypes with upregulated lipid metabolism showed the opposite. Metabolic subtypes correlated with diverse somatic drivers but exhibited effects convergent on cancer hallmark pathways and were modulated by highly recurrent master regulators across cancer types. As a proof-of-concept example, we demonstrated that knockdown of SNAI1 or RUNX1—master regulators of carbohydrate metabolic subtypes—modulates metabolic activity and drug sensitivity. Our study provides a system-level view of metabolic heterogeneity within and across cancer types and identifies pathway cross-talk, suggesting related prognostic, therapeutic, and predictive utility. : Peng et al. analyze a cohort of 9,125 TCGA samples across 33 cancer types to characterize tumor subtypes based on the expression of seven metabolic pathways. They find metabolic expression subtypes are associated with patient survivals and suggest the therapeutic and predictive relevance of subtype-related master regulators. Keywords: The Cancer Genome Atlas, tumor subtypes, prognostic markers, somatic drivers, master regulator, therapeutic targets, drug sensitivity, carbohydrate metabolism

  17. Synthesis and Surface-Specific Analysis of Molecular Constituents Relevant to Biogenic Secondary Organic Aerosol Material

    Science.gov (United States)

    Be, A. G.; Upshur, M. A.; Chase, H. M.; Geiger, F.; Thomson, R. J.

    2017-12-01

    Secondary organic aerosol (SOA) particles formed from the oxidation of biogenic volatile organic compounds (BVOCs) remain a principal, yet elusive, class of airborne particulate matter that impacts the Earth's radiation budget. Given the characteristic molecular complexity comprising biogenic SOA particles, chemical information selective to the gas-aerosol interface may be valuable in the investigation of such systems, as surface considerations likely dictate the phenomena driving particle evolution mechanisms and climate effects. In particular, cloud activation processes may be parameterized using the surface tension depression that coincides with partitioning of surface-active organic species to the gas-droplet interface. However, the extent to which surface chemical processes, such as cloud droplet condensation, are influenced by the chemical structure and reactivity of individual surface-active molecules in SOA particles is largely unknown. We seek to study terpene-derived organic species relevant to the surfaces of biogenic SOA particles via synthesis of putative oxidation products followed by analysis using surface-selective physicochemical measurements. Using dynamic surface tension measurements, considerable differences are observed in the surface tension depression of aqueous pendant droplets that contain synthetically prepared ozonolysis products derived from abundant terpene precursors. Furthermore, sum frequency generation spectroscopy is utilized for comparison of the surface vibrational spectral responses of synthesized reference compounds with those observed for laboratory aerosol toward probing the surface composition of SOA material. Such ongoing findings highlight the underlying importance of molecular structure and reactivity when considering the surface chemistry of biogenic terpene-derived atmospheric aerosols.

  18. Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma

    International Nuclear Information System (INIS)

    Janky, Rekin’s; Binda, Maria Mercedes; Allemeersch, Joke; Van den broeck, Anke; Govaere, Olivier; Swinnen, Johannes V.; Roskams, Tania; Aerts, Stein; Topal, Baki

    2016-01-01

    Pancreatic cancer is poorly characterized at genetic and non-genetic levels. The current study evaluates in a large cohort of patients the prognostic relevance of molecular subtypes and key transcription factors in pancreatic ductal adenocarcinoma (PDAC). We performed gene expression analysis of whole-tumor tissue obtained from 118 surgically resected PDAC and 13 histologically normal pancreatic tissue samples. Cox regression models were used to study the effect on survival of molecular subtypes and 16 clinicopathological prognostic factors. In order to better understand the biology of PDAC we used iRegulon to identify transcription factors (TFs) as master regulators of PDAC and its subtypes. We confirmed the PDAssign gene signature as classifier of PDAC in molecular subtypes with prognostic relevance. We found molecular subtypes, but not clinicopathological factors, as independent predictors of survival. Regulatory network analysis predicted that HNF1A/B are among thousand TFs the top enriched master regulators of the genes expressed in the normal pancreatic tissue compared to the PDAC regulatory network. On immunohistochemistry staining of PDAC samples, we observed low expression of HNF1B in well differentiated towards no expression in poorly differentiated PDAC samples. We predicted IRF/STAT, AP-1, and ETS-family members as key transcription factors in gene signatures downstream of mutated KRAS. PDAC can be classified in molecular subtypes that independently predict survival. HNF1A/B seem to be good candidates as master regulators of pancreatic differentiation, which at the protein level loses its expression in malignant ductal cells of the pancreas, suggesting its putative role as tumor suppressor in pancreatic cancer. The study was registered at ClinicalTrials.gov under the number NCT01116791 (May 3, 2010). The online version of this article (doi:10.1186/s12885-016-2540-6) contains supplementary material, which is available to authorized users

  19. An antilock molecular braking system.

    Science.gov (United States)

    Sun, Wei-Ting; Huang, Shou-Ling; Yao, Hsuan-Hsiao; Chen, I-Chia; Lin, Ying-Chih; Yang, Jye-Shane

    2012-08-17

    A light-driven molecular brake displaying an antilock function is constructed by introducing a nonradiative photoinduced electron transfer (PET) decay channel to compete with the trans (brake-off) → cis (brake-on) photoisomerization. A fast release of the brake can be achieved by deactivating the PET process through addition of protons. The cycle of irradiation-protonation-irradiation-deprotonation conducts the brake function and mimics the antilock braking system (ABS) of vehicles.

  20. System for selecting relevant information for decision support.

    Science.gov (United States)

    Kalina, Jan; Seidl, Libor; Zvára, Karel; Grünfeldová, Hana; Slovák, Dalibor; Zvárová, Jana

    2013-01-01

    We implemented a prototype of a decision support system called SIR which has a form of a web-based classification service for diagnostic decision support. The system has the ability to select the most relevant variables and to learn a classification rule, which is guaranteed to be suitable also for high-dimensional measurements. The classification system can be useful for clinicians in primary care to support their decision-making tasks with relevant information extracted from any available clinical study. The implemented prototype was tested on a sample of patients in a cardiological study and performs an information extraction from a high-dimensional set containing both clinical and gene expression data.

  1. Information theory of molecular systems

    CERN Document Server

    Nalewajski, Roman F

    2006-01-01

    As well as providing a unified outlook on physics, Information Theory (IT) has numerous applications in chemistry and biology owing to its ability to provide a measure of the entropy/information contained within probability distributions and criteria of their information ""distance"" (similarity) and independence. Information Theory of Molecular Systems applies standard IT to classical problems in the theory of electronic structure and chemical reactivity. The book starts by introducing the basic concepts of modern electronic structure/reactivity theory based upon the Density Functional Theory

  2. Molecular simulation of the thermophysical properties and phase behaviour of impure CO2 relevant to CCS.

    Science.gov (United States)

    Cresswell, Alexander J; Wheatley, Richard J; Wilkinson, Richard D; Graham, Richard S

    2016-10-20

    Impurities from the CCS chain can greatly influence the physical properties of CO 2 . This has important design, safety and cost implications for the compression, transport and storage of CO 2 . There is an urgent need to understand and predict the properties of impure CO 2 to assist with CCS implementation. However, CCS presents demanding modelling requirements. A suitable model must both accurately and robustly predict CO 2 phase behaviour over a wide range of temperatures and pressures, and maintain that predictive power for CO 2 mixtures with numerous, mutually interacting chemical species. A promising technique to address this task is molecular simulation. It offers a molecular approach, with foundations in firmly established physical principles, along with the potential to predict the wide range of physical properties required for CCS. The quality of predictions from molecular simulation depends on accurate force-fields to describe the interactions between CO 2 and other molecules. Unfortunately, there is currently no universally applicable method to obtain force-fields suitable for molecular simulation. In this paper we present two methods of obtaining force-fields: the first being semi-empirical and the second using ab initio quantum-chemical calculations. In the first approach we optimise the impurity force-field against measurements of the phase and pressure-volume behaviour of CO 2 binary mixtures with N 2 , O 2 , Ar and H 2 . A gradient-free optimiser allows us to use the simulation itself as the underlying model. This leads to accurate and robust predictions under conditions relevant to CCS. In the second approach we use quantum-chemical calculations to produce ab initio evaluations of the interactions between CO 2 and relevant impurities, taking N 2 as an exemplar. We use a modest number of these calculations to train a machine-learning algorithm, known as a Gaussian process, to describe these data. The resulting model is then able to accurately

  3. Molecular epidemiology of mastitis pathogens of dairy cattle and comparative relevance to humans.

    Science.gov (United States)

    Zadoks, Ruth N; Middleton, John R; McDougall, Scott; Katholm, Jorgen; Schukken, Ynte H

    2011-12-01

    Mastitis, inflammation of the mammary gland, can be caused by a wide range of organisms, including gram-negative and gram-positive bacteria, mycoplasmas and algae. Many microbial species that are common causes of bovine mastitis, such as Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae and Staphylococcus aureus also occur as commensals or pathogens of humans whereas other causative species, such as Streptococcus uberis, Streptococcus dysgalactiae subsp. dysgalactiae or Staphylococcus chromogenes, are almost exclusively found in animals. A wide range of molecular typing methods have been used in the past two decades to investigate the epidemiology of bovine mastitis at the subspecies level. These include comparative typing methods that are based on electrophoretic banding patterns, library typing methods that are based on the sequence of selected genes, virulence gene arrays and whole genome sequencing projects. The strain distribution of mastitis pathogens has been investigated within individual animals and across animals, herds, countries and host species, with consideration of the mammary gland, other animal or human body sites, and environmental sources. Molecular epidemiological studies have contributed considerably to our understanding of sources, transmission routes, and prognosis for many bovine mastitis pathogens and to our understanding of mechanisms of host-adaptation and disease causation. In this review, we summarize knowledge gleaned from two decades of molecular epidemiological studies of mastitis pathogens in dairy cattle and discuss aspects of comparative relevance to human medicine.

  4. [The G-DRG System 2009--relevant changes for rheumatology].

    Science.gov (United States)

    Fiori, W; Liedtke-Dyong, A; Lakomek, H-J; Buscham, K; Lehmann, H; Liman, W; Fuchs, A-K; Bessler, F; Roeder, N

    2010-05-01

    The following article presents the major general and specific changes in the G-DRG system, in the classification systems for diagnoses and procedures as well as for the billing process for 2010. Since the G-DRG system is primarily a tool for the redistribution of resources, every hospital needs to analyze the economic effects of the changes by applying the G-DRG transition-grouper to its own cases. Depending on their clinical focus, rheumatological departments may experience positive or negative consequences from the adjustments. In addition, relevant current case law is considered.

  5. Developments in entanglement theory and applications to relevant physical systems

    OpenAIRE

    Lamata Manuel, Lucas

    2007-01-01

    This Thesis is devoted to the analysis of entanglement in relevant physical systems. Entanglement is the conducting theme of this research, though I do not dedicate to a single topic, but consider a wide scope of physical situations. I have followed mainly three lines of research for this Thesis, with a series of different works each, which are, Entanglement and Relativistic Quantum Theory, Continuous-variable entanglement, and Multipartite entanglement.

  6. Stratification and Prognostic Relevance of Jass’s Molecular Classification of Colorectal Cancer

    International Nuclear Information System (INIS)

    Zlobec, Inti; Bihl, Michel P.; Foerster, Anja; Rufle, Alex; Terracciano, Luigi; Lugli, Alessandro

    2012-01-01

    Background: The current proposed model of colorectal tumorigenesis is based primarily on CpG island methylator phenotype (CIMP), microsatellite instability (MSI), KRAS, BRAF, and methylation status of 0-6-Methylguanine DNA Methyltransferase (MGMT) and classifies tumors into five subgroups. The aim of this study is to validate this molecular classification and test its prognostic relevance. Methods: Three hundred two patients were included in this study. Molecular analysis was performed for five CIMP-related promoters (CRABP1, MLH1, p16INK4a, CACNA1G, NEUROG1), MGMT, MSI, KRAS, and BRAF. Methylation in at least 4 promoters or in one to three promoters was considered CIMP-high and CIMP-low (CIMP-H/L), respectively. Results: CIMP-H, CIMP-L, and CIMP-negative were found in 7.1, 43, and 49.9% cases, respectively. One hundred twenty-three tumors (41%) could not be classified into any one of the proposed molecular subgroups, including 107 CIMP-L, 14 CIMP-H, and two CIMP-negative cases. The 10 year survival rate for CIMP-high patients [22.6% (95%CI: 7–43)] was significantly lower than for CIMP-L or CIMP-negative (p = 0.0295). Only the combined analysis of BRAF and CIMP (negative versus L/H) led to distinct prognostic subgroups. Conclusion: Although CIMP status has an effect on outcome, our results underline the need for standardized definitions of low- and high-level CIMP, which clearly hinders an effective prognostic and molecular classification of colorectal cancer.

  7. Stratification and Prognostic Relevance of Jass’s Molecular Classification of Colorectal Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Zlobec, Inti [Institute of Pathology, University of Bern, Bern (Switzerland); Institute for Pathology, University Hospital Basel, Basel (Switzerland); Bihl, Michel P.; Foerster, Anja; Rufle, Alex; Terracciano, Luigi [Institute for Pathology, University Hospital Basel, Basel (Switzerland); Lugli, Alessandro, E-mail: inti.zlobec@pathology.unibe.ch [Institute of Pathology, University of Bern, Bern (Switzerland); Institute for Pathology, University Hospital Basel, Basel (Switzerland)

    2012-02-27

    Background: The current proposed model of colorectal tumorigenesis is based primarily on CpG island methylator phenotype (CIMP), microsatellite instability (MSI), KRAS, BRAF, and methylation status of 0-6-Methylguanine DNA Methyltransferase (MGMT) and classifies tumors into five subgroups. The aim of this study is to validate this molecular classification and test its prognostic relevance. Methods: Three hundred two patients were included in this study. Molecular analysis was performed for five CIMP-related promoters (CRABP1, MLH1, p16INK4a, CACNA1G, NEUROG1), MGMT, MSI, KRAS, and BRAF. Methylation in at least 4 promoters or in one to three promoters was considered CIMP-high and CIMP-low (CIMP-H/L), respectively. Results: CIMP-H, CIMP-L, and CIMP-negative were found in 7.1, 43, and 49.9% cases, respectively. One hundred twenty-three tumors (41%) could not be classified into any one of the proposed molecular subgroups, including 107 CIMP-L, 14 CIMP-H, and two CIMP-negative cases. The 10 year survival rate for CIMP-high patients [22.6% (95%CI: 7–43)] was significantly lower than for CIMP-L or CIMP-negative (p = 0.0295). Only the combined analysis of BRAF and CIMP (negative versus L/H) led to distinct prognostic subgroups. Conclusion: Although CIMP status has an effect on outcome, our results underline the need for standardized definitions of low- and high-level CIMP, which clearly hinders an effective prognostic and molecular classification of colorectal cancer.

  8. Stratification and prognostic relevance of Jass’s molecular classification of colorectal cancer

    Directory of Open Access Journals (Sweden)

    Inti eZlobec

    2012-02-01

    Full Text Available Background: The current proposed model of colorectal tumorigenesis is based primarily on CpG island methylator phenotype (CIMP, microsatellite instability (MSI, KRAS, BRAF, and methylation status of 0-6-Methylguanine DNA Methyltransferase (MGMT and classifies tumors into 5 subgroups. The aim of this study is to validate this molecular classification and test its prognostic relevance. Methods: 302 patients were included in this study. Molecular analysis was performed for 5 CIMP-related promoters (CRABP1, MLH1, p16INK4a, CACNA1G, NEUROG1, MGMT, MSI, KRAS and BRAF. Tumors were CIMP-high or CIMP-low if ≥4 and 1-3 promoters were methylated, respectively. Results: CIMP-high, CIMP-low and CIMP–negative were found in 7.1%, 43% and 49.9% cases, respectively. 123 tumors (41% could not be classified into any one of the proposed molecular subgroups, including 107 CIMP-low, 14 CIMP-high and 2 CIMP-negative cases. The 10-year survival rate for CIMP-high patients (22.6% (95%CI: 7-43 was significantly lower than for CIMP-low or CIMP-negative (p=0.0295. Only the combined analysis of BRAF and CIMP (negative versus low/high led to distinct prognostic subgroups. Conclusion: Although CIMP status has an effect on outcome, our results underline the need for standardized definitions of low- and high-level CIMP, which clearly hinders an effective prognostic and molecular classification of colorectal cancer.

  9. Molecular interpretation of ACTH-β-endorphin coaggregation: relevance to secretory granule biogenesis.

    Directory of Open Access Journals (Sweden)

    Srivastav Ranganathan

    Full Text Available Peptide/protein hormones could be stored as non-toxic amyloid-like structures in pituitary secretory granules. ACTH and β-endorphin are two of the important peptide hormones that get co-stored in the pituitary secretory granules. Here, we study molecular interactions between ACTH and β-endorphin and their colocalization in the form of amyloid aggregates. Although ACTH is known to be a part of ACTH-β-endorphin aggregate, ACTH alone cannot aggregate into amyloid under various plausible conditions. Using all atom molecular dynamics simulation we investigate the early molecular interaction events in the ACTH-β-endorphin system, β-endorphin-only system and ACTH-only system. We find that β-endorphin and ACTH formed an interacting unit, whereas negligible interactions were observed between ACTH molecules in ACTH-only system. Our data suggest that ACTH is not only involved in interaction with β-endorphin but also enhances the stability of mixed oligomers of the entire system.

  10. Advances on the molecular characterization, clinical relevance, and detection methods of Gadiform parvalbumin allergens.

    Science.gov (United States)

    Fernandes, Telmo J R; Costa, Joana; Carrapatoso, Isabel; Oliveira, Maria Beatriz P P; Mafra, Isabel

    2017-10-13

    Gadiform order includes several fish families, from which Gadidae and Merlucciidae are part of, comprising the most commercially important and highly appreciated fish species, such as cod, pollock, haddock, and hake. Parvalbumins, classified as calcium-binding proteins, are considered the main components involved in the majority of fish allergies. Nine and thirteen parvalbumins were identified in different fish species from Gadidae and Merlucciidae families, respectively. This review intends to describe their molecular characterization and the clinical relevance, as well as the prevalence of fish allergy. In addition, the main protein- and DNA-based methods to detect fish allergens are fully reviewed owing to their importance in the safeguard of sensitized/allergic individuals.

  11. Sphingosine kinase 1 is a relevant molecular target in gastric cancer

    DEFF Research Database (Denmark)

    Fuereder, Thorsten; Hoeflmayer, Doris; Jaeger-Lansky, Agnes

    2011-01-01

    Sphingosine kinase 1 (Sphk1), a lipid kinase implicated in cell transformation and tumor growth, is overexpressed in gastric cancer and is linked with a poor prognosis. The biological relevance of Sphk1 expression in gastric cancer is unclear. Here, we studied the functional significance of Sphk1...... as a novel molecular target for gastric cancer by using an antisense oligonucleotide approach in vitro and in vivo. Gastric cancer cell lines (MKN28 and N87) were treated with Sphk1 with locked nucleic acid-antisense oligonucleotides (LNA-ASO). Sphk1 target regulation, cell growth, and apoptosis were...... assessed for single-agent Sphk1 LNA-ASO and for combinations with doxorubicin. Athymic nude mice xenografted with gastric cancer cells were treated with Sphk1 LNA and assessed for tumor growth and Sphk1 target regulation, in vivo. In vitro, nanomolar concentrations of Sphk1 LNA-ASO induced an approximately...

  12. The Systemic Theory of Living Systems and Relevance to CAM

    Directory of Open Access Journals (Sweden)

    José A. Olalde Rangel

    2005-01-01

    Full Text Available The Systemic Theory of Living Systems is being published in several parts in eCAM. The theory is axiomatic. It originates from the phenomenological idea that physiological health is based on three factors: integrity of its structure or organization, O, functional organic energy reserve, E, and level of active biological intelligence, I. From the theory is derived a treatment strategy called Systemic Medicine (SM. This is based on identifying and prescribing phytomedicines and/or other medications that strengthen each factor. Energy-stimulating phytomedicines increase available energy and decrease total entropy of an open biological system by providing negative entropy. The same occurs with phytomedicines that act as biological intelligence modulators. They should be used as the first line of treatment in all ailments, since all pathologies, by definition, imply a higher than normal organic entropy. SM postulates that the state of health, H, of an individual, is effectively equal to the product of the strength of each factor H = O × E × I. SM observes that when all three factors are brought back to ideal levels, patients' conditions begin the recovery to normal health.

  13. [G-DRG system 2009: relevant changes for rheumatology].

    Science.gov (United States)

    Fiori, W; Liedtke-Dyong, A; Lakomek, H-J; Buscham, K; Lehmann, H; Liman, W; Fuchs, A-K; Bessler, F; Roeder, N

    2009-08-01

    The following article presents the main general and specific changes in the G-DRG (German diagnosis-related groups) system in terms of the classification systems for diagnoses and procedures as well as the billing process for 2009. Of fundamental relevance is the national weighting of the G-DRG I97Z (complex rheumatologic treatment), which up to now had to be negotiated individually by each hospital. Emphasis is also put on case auditing by the health insurers. Being primarily a tool for redistribution of resources, every hospital has to analyze the economic effects of the 2009 G-DRG system by applying the G-DRG transition grouper to its own cases. Depending on their clinical focus rheumatological departments may experience positive or negative consequences from the development. The strain imposed on hospitals by inadequate refunding of rising costs has to be assessed separately from the effects of redistribution by the G-DRG system.

  14. Tuning Piezo ion channels to detect molecular-scale movements relevant for fine touch

    Science.gov (United States)

    Poole, Kate; Herget, Regina; Lapatsina, Liudmila; Ngo, Ha-Duong; Lewin, Gary R.

    2014-01-01

    In sensory neurons, mechanotransduction is sensitive, fast and requires mechanosensitive ion channels. Here we develop a new method to directly monitor mechanotransduction at defined regions of the cell-substrate interface. We show that molecular-scale (~13 nm) displacements are sufficient to gate mechanosensitive currents in mouse touch receptors. Using neurons from knockout mice, we show that displacement thresholds increase by one order of magnitude in the absence of stomatin-like protein 3 (STOML3). Piezo1 is the founding member of a class of mammalian stretch-activated ion channels, and we show that STOML3, but not other stomatin-domain proteins, brings the activation threshold for Piezo1 and Piezo2 currents down to ~10 nm. Structure–function experiments localize the Piezo modulatory activity of STOML3 to the stomatin domain, and higher-order scaffolds are a prerequisite for function. STOML3 is the first potent modulator of Piezo channels that tunes the sensitivity of mechanically gated channels to detect molecular-scale stimuli relevant for fine touch. PMID:24662763

  15. Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies.

    Directory of Open Access Journals (Sweden)

    Benedikt Frieg

    2016-02-01

    Full Text Available Glutamine synthetase (GS catalyzes ATP-dependent ligation of ammonia and glutamate to glutamine. Two mutations of human GS (R324C and R341C were connected to congenital glutamine deficiency with severe brain malformations resulting in neonatal death. Another GS mutation (R324S was identified in a neurologically compromised patient. However, the molecular mechanisms underlying the impairment of GS activity by these mutations have remained elusive. Molecular dynamics simulations, free energy calculations, and rigidity analyses suggest that all three mutations influence the first step of GS catalytic cycle. The R324S and R324C mutations deteriorate GS catalytic activity due to loss of direct interactions with ATP. As to R324S, indirect, water-mediated interactions reduce this effect, which may explain the suggested higher GS residual activity. The R341C mutation weakens ATP binding by destabilizing the interacting residue R340 in the apo state of GS. Additionally, the mutation is predicted to result in a significant destabilization of helix H8, which should negatively affect glutamate binding. This prediction was tested in HEK293 cells overexpressing GS by dot-blot analysis: Structural stability of H8 was impaired through mutation of amino acids interacting with R341, as indicated by a loss of masking of an epitope in the glutamate binding pocket for a monoclonal anti-GS antibody by L-methionine-S-sulfoximine; in contrast, cells transfected with wild type GS showed the masking. Our analyses reveal complex molecular effects underlying impaired GS catalytic activity in three clinically relevant mutants. Our findings could stimulate the development of ATP binding-enhancing molecules by which the R324S mutant can be repaired extrinsically.

  16. Modulation of the mirror system by social relevance.

    Science.gov (United States)

    Kilner, James M; Marchant, Jennifer L; Frith, Chris D

    2006-09-01

    When we observe the actions of others, certain areas of the brain are activated in a similar manner as to when we perform the same actions ourselves. This 'mirror system' includes areas in the ventral premotor cortex and the inferior parietal lobule. Experimental studies suggest that action observation automatically elicits activity in the observer, which precisely mirrors the activity observed. In this case we would expect this activity to be independent of observer's viewpoint. Here we use whole-head magnetoencephalography (MEG) to record cortical activity of human subjects whilst they watched a series of videos of an actor making a movement recorded from different viewpoints. We show that one cortical response to action observation (oscillatory activity in the 7-12 Hz frequency range) is modulated by the relationship between the observer and the actor. We suggest that this modulation reflects a mechanism that filters information into the 'mirror system', allowing only socially relevant information to pass.

  17. The endocannabinoid system and its relevance for nutrition

    DEFF Research Database (Denmark)

    Maccarrone, Mauro; Gasperi, Valeria; Catani, Maria Valeria

    2010-01-01

    Endocannabinoids bind to cannabinoid, vanilloid, and peroxisome proliferator-activated receptors. The biological actions of these polyunsaturated lipids are controlled by key agents responsible for their synthesis, transport and degradation, which together form an endocannabinoid system (ECS......). In the past few years, evidence has been accumulated for a role of the ECS in regulating food intake and energy balance, both centrally and peripherally. In addition, up-regulation of the ECS in the gastrointestinal tract has a potential impact on inflammatory bowel diseases. In this review, the main features...... of the ECS are summarized in order to put in better focus our current knowledge of the nutritional relevance of endocannabinoid signaling and of its role in obesity, cardiovascular pathologies, and gastrointestinal diseases. The central and peripheral pathways that underlie these effects are discussed...

  18. Neural systems supporting and affecting economically relevant behavior

    Directory of Open Access Journals (Sweden)

    Braeutigam S

    2012-05-01

    Full Text Available Sven BraeutigamOxford Centre for Human Brain Activity, University of Oxford, Oxford, United KingdomAbstract: For about a hundred years, theorists and traders alike have tried to unravel and understand the mechanisms and hidden rules underlying and perhaps determining economically relevant behavior. This review focuses on recent developments in neuroeconomics, where the emphasis is placed on two directions of research: first, research exploiting common experiences of urban inhabitants in industrialized societies to provide experimental paradigms with a broader real-life content; second, research based on behavioral genetics, which provides an additional dimension for experimental control and manipulation. In addition, possible limitations of state-of-the-art neuroeconomics research are addressed. It is argued that observations of neuronal systems involved in economic behavior converge to some extent across the technologies and paradigms used. Conceptually, the data available as of today raise the possibility that neuroeconomic research might provide evidence at the neuronal level for the existence of multiple systems of thought and for the importance of conflict. Methodologically, Bayesian approaches in particular may play an important role in identifying mechanisms and establishing causality between patterns of neural activity and economic behavior.Keywords: neuroeconomics, behavioral genetics, decision-making, consumer behavior, neural system

  19. From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses.

    Directory of Open Access Journals (Sweden)

    Rafael Sanjuán

    Full Text Available Although evolution is a multifactorial process, theory posits that the speed of molecular evolution should be directly determined by the rate at which spontaneous mutations appear. To what extent these two biochemical and population-scale processes are related in nature, however, is largely unknown. Viruses are an ideal system for addressing this question because their evolution is fast enough to be observed in real time, and experimentally-determined mutation rates are abundant. This article provides statistically supported evidence that the mutation rate determines molecular evolution across all types of viruses. Properties of the viral genome such as its size and chemical composition are identified as major determinants of these rates. Furthermore, a quantitative analysis reveals that, as expected, evolution rates increase linearly with mutation rates for slowly mutating viruses. However, this relationship plateaus for fast mutating viruses. A model is proposed in which deleterious mutations impose an evolutionary speed limit and set an extinction threshold in nature. The model is consistent with data from replication kinetics, selection strength and chemical mutagenesis studies.

  20. Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement.

    Science.gov (United States)

    Harfouche, Antoine; Meilan, Richard; Altman, Arie

    2014-11-01

    Abiotic stresses, such as drought, salinity and cold, are the major environmental stresses that adversely affect tree growth and, thus, forest productivity, and play a major role in determining the geographic distribution of tree species. Tree responses and tolerance to abiotic stress are complex biological processes that are best analyzed at a systems level using genetic, genomic, metabolomic and phenomic approaches. This will expedite the dissection of stress-sensing and signaling networks to further support efficient genetic improvement programs. Enormous genetic diversity for stress tolerance exists within some forest-tree species, and due to advances in sequencing technologies the molecular genetic basis for this diversity has been rapidly unfolding in recent years. In addition, the use of emerging phenotyping technologies extends the suite of traits that can be measured and will provide us with a better understanding of stress tolerance. The elucidation of abiotic stress-tolerance mechanisms will allow for effective pyramiding of multiple tolerances in a single tree through genetic engineering. Here we review recent progress in the dissection of the molecular basis of abiotic stress tolerance in forest trees, with special emphasis on Populus, Pinus, Picea, Eucalyptus and Quercus spp. We also outline practices that will enable the deployment of trees engineered for abiotic stress tolerance to land owners. Finally, recommendations for future work are discussed. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Atomic and molecular data for H2O, CO and CO2 relevant to edge plasma impurities

    International Nuclear Information System (INIS)

    Tawara, Hiro.

    1992-10-01

    The present status of atomic and molecular data under electron impact involving the most relevant plasma impurity species (H 2 O, CO and CO 2 ) has been surveyed and some data have been compiled and evaluated. The emphasis is the cross sections for ionization, dissociation, excitation, photon emission and recombination processes. (author)

  2. Divergence time estimates of mammals from molecular clocks and fossils: relevance of new fossil finds from India.

    Science.gov (United States)

    Prasad, G V R

    2009-11-01

    This paper presents a brief review of recent advances in the classification of mammals at higher levels using fossils and molecular clocks. It also discusses latest fossil discoveries from the Cretaceous - Eocene (66-55 m.y.) rocks of India and their relevance to our current understanding of placental mammal origins and diversifications.

  3. Relevance of a molecular tumour board (MTB) for patients' enrolment in clinical trials: experience of the Institut Curie.

    Science.gov (United States)

    Basse, Clémence; Morel, Claire; Alt, Marie; Sablin, Marie Paule; Franck, Coralie; Pierron, Gaëlle; Callens, Céline; Melaabi, Samia; Masliah-Planchon, Julien; Bataillon, Guillaume; Gardrat, Sophie; Lavigne, Marion; Bonsang, Benjamin; Vaflard, Pauline; Pons Tostivint, Elvire; Dubot, Coraline; Loirat, Delphine; Marous, Miguelle; Geiss, Romain; Clément, Nathalie; Schleiermacher, Gudrun; Kamoun, Choumouss; Girard, Elodie; Ardin, Maude; Benoist, Camille; Bernard, Virginie; Mariani, Odette; Rouzier, Roman; Tresca, Patricia; Servois, Vincent; Vincent-Salomon, Anne; Bieche, Ivan; Le Tourneau, Christophe; Kamal, Maud

    2018-01-01

    High throughput molecular screening techniques allow the identification of multiple molecular alterations, some of which are actionable and can be targeted by molecularly targeted agents (MTA). We aimed at evaluating the relevance of using this approach in the frame of Institut Curie Molecular Tumor Board (MTB) to guide patients with cancer to clinical trials with MTAs. We included all patients presented at Institut Curie MTB from 4 October 2014 to 31 October 2017. The following information was extracted from the chart: decision to perform tumour profiling, types of molecular analyses, samples used, molecular alterations identified and those which are actionable, and inclusion in a clinical trial with matched MTA. 736 patients were presented at the MTB. Molecular analyses were performed in 442 patients (60%). Techniques used included next-generation sequencing, comparative genomic hybridisation array and/or other techniques including immunohistochemistry in 78%, 51% and 58% of patients, respectively. Analyses were performed on a fresh frozen biopsy in 91 patients (21%), on archival tissue (fixed or frozen) in 326 patients (74%) and on both archival and fresh frozen biopsy in 25 patients (6%). At least one molecular alteration was identified in 280 analysed patients (63%). An actionable molecular alteration was identified in 207 analysed patients (47%). Forty-five analysed patients (10%) were enrolled in a clinical trial with matched MTA and 29 additional patients were oriented and included in a clinical trial based on a molecular alteration identified prior to the MTB analysis. Median time between date of specimen reception and molecular results was 28 days (range: 5-168). The implementation of an MTB at Institut Curie enabled the inclusion of 10% of patients into a clinical trial with matched therapy.

  4. Molecular motor assembly of a biomimetic system

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Active biological molecules and functional structures can be fabricated into a bio-mimetic system by using molecular assembly method. Such materials can be used for the drug delivery, disease diagnosis and therapy, and new nanodevice construction.

  5. Electron-nuclear dynamics of molecular systems

    International Nuclear Information System (INIS)

    Diz, A.; Oehrn, Y.

    1994-01-01

    The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

  6. Molecular Dynamics Insights into Water-Parylene C Interface: Relevance of Oxygen Plasma Treatment for Biocompatibility

    Czech Academy of Sciences Publication Activity Database

    Golda-Cepa, M.; Kulig, W.; Cwiklik, Lukasz; Kotarba, A.

    2017-01-01

    Roč. 9, č. 19 (2017), s. 16685-16693 ISSN 1944-8244 R&D Projects: GA ČR(CZ) GA17-06792S Institutional support: RVO:61388955 Keywords : molecular dynamics * contact angle * surface free energy * parylene C * biomaterials oxygen plasma Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 7.504, year: 2016

  7. Molecular Dynamics Insights into Water-Parylene C Interface: Relevance of Oxygen Plasma Treatment for Biocompatibility

    Czech Academy of Sciences Publication Activity Database

    Golda-Cepa, M.; Kulig, W.; Cwiklik, Lukasz; Kotarba, A.

    2017-01-01

    Roč. 9, č. 19 (2017), s. 16685-16693 ISSN 1944-8244 Institutional support: RVO:61388963 Keywords : molecular dynamics * contact angle * surface free energy * parylene C * biomaterials oxygen plasma Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 7.504, year: 2016

  8. Molecular techniques for the identification and detection of microorganisms relevant for the food industry

    NARCIS (Netherlands)

    Klijn, N.

    1996-01-01

    The research described in this thesis concerns the development and application in food microbiology of molecular identification and detection techniques based on 16S rRNA sequences. The technologies developed were applied to study the microbial ecology of two groups of bacteria, namely

  9. Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.

    Science.gov (United States)

    Okaty, Benjamin W; Freret, Morgan E; Rood, Benjamin D; Brust, Rachael D; Hennessy, Morgan L; deBairos, Danielle; Kim, Jun Chul; Cook, Melloni N; Dymecki, Susan M

    2015-11-18

    Serotonergic (5HT) neurons modulate diverse behaviors and physiology and are implicated in distinct clinical disorders. Corresponding diversity in 5HT neuronal phenotypes is becoming apparent and is likely rooted in molecular differences, yet a comprehensive approach characterizing molecular variation across the 5HT system is lacking, as is concomitant linkage to cellular phenotypes. Here we combine intersectional fate mapping, neuron sorting, and genome-wide RNA-seq to deconstruct the mouse 5HT system at multiple levels of granularity-from anatomy, to genetic sublineages, to single neurons. Our unbiased analyses reveal principles underlying system organization, 5HT neuron subtypes, constellations of differentially expressed genes distinguishing subtypes, and predictions of subtype-specific functions. Using electrophysiology, subtype-specific neuron silencing, and conditional gene knockout, we show that these molecularly defined 5HT neuron subtypes are functionally distinct. Collectively, this resource classifies molecular diversity across the 5HT system and discovers sertonergic subtypes, markers, organizing principles, and subtype-specific functions with potential disease relevance. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. [The G-DRG system 2008. Relevant changes for rheumatology].

    Science.gov (United States)

    Fiori, W; Lakomek, H-J; Buscham, K; Lehmann, H; Liman, W; Fuchs, A-K; Hülsemann, J L; Roeder, N

    2008-05-01

    The G-DRG system 2008 once again brings many changes to rheumatological departments in Germany. The following article presents the main general and specific changes in the G-DRG system, as well as in the classification systems for diagnoses and procedures and in invoicing for 2008. Since the G-DRG system is only a tool for the redistribution of resources, every hospital needs to analyze the economic effects of the system by applying the G-DRG transition grouper to its own cases. Depending on their clinical focus, rheumatological departments may experience positive or negative effects from the system's application. The strain placed on hospitals by the inadequate funding of increased costs needs to be assessed separately from the effects of redistribution by the G-DRG system.

  11. Relevant Costs for Decision in an Effective Controlling System

    Directory of Open Access Journals (Sweden)

    Mihaela TULVINSCHI

    2010-05-01

    Full Text Available Controlling is considered a leading concept in the sense of coordination, planning, control and automation, in order to produce the synthesis necessary in decision making. The purpose of article is to highlight the link between a dynamic accounting system and an effective controlling system. The research method used is based on the idea that the cost analysis in an efficient controlling system involves obtaining accounting information from within the entity which management then uses in decision making. In conclusion, we emphasize that an effective controlling system must provide managers the tools to meet their informational needs.

  12. Canada's health care system: A relevant approach for South Africa ...

    African Journals Online (AJOL)

    Background. While countries such as the USA, South Africa and China debate health reforms to improve access to care while rationalising costs, Canada's health care system has emerged as a notable option. In the USA, meaningful discussion of the advantages and disadvantages of the Canadian system has been ...

  13. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  14. Mapping healthcare systems: a policy relevant analytic tool.

    Science.gov (United States)

    Sekhri Feachem, Neelam; Afshar, Ariana; Pruett, Cristina; Avanceña, Anton L V

    2017-07-01

    In the past decade, an international consensus on the value of well-functioning systems has driven considerable health systems research. This research falls into two broad categories. The first provides conceptual frameworks that take complex healthcare systems and create simplified constructs of interactions and functions. The second focuses on granular inputs and outputs. This paper presents a novel translational mapping tool - the University of California, San Francisco mapping tool (the Tool) - which bridges the gap between these two areas of research, creating a platform for multi-country comparative analysis. Using the Murray-Frenk framework, we create a macro-level representation of a country's structure, focusing on how it finances and delivers healthcare. The map visually depicts the fundamental policy questions in healthcare system design: funding sources and amount spent through each source, purchasers, populations covered, provider categories; and the relationship between these entities. We use the Tool to provide a macro-level comparative analysis of the structure of India's and Thailand's healthcare systems. As part of the systems strengthening arsenal, the Tool can stimulate debate about the merits and consequences of different healthcare systems structural designs, using a common framework that fosters multi-country comparative analyses. © The Author 2017. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene.

  15. Automated systems to identify relevant documents in product risk management

    Science.gov (United States)

    2012-01-01

    Background Product risk management involves critical assessment of the risks and benefits of health products circulating in the market. One of the important sources of safety information is the primary literature, especially for newer products which regulatory authorities have relatively little experience with. Although the primary literature provides vast and diverse information, only a small proportion of which is useful for product risk assessment work. Hence, the aim of this study is to explore the possibility of using text mining to automate the identification of useful articles, which will reduce the time taken for literature search and hence improving work efficiency. In this study, term-frequency inverse document-frequency values were computed for predictors extracted from the titles and abstracts of articles related to three tumour necrosis factors-alpha blockers. A general automated system was developed using only general predictors and was tested for its generalizability using articles related to four other drug classes. Several specific automated systems were developed using both general and specific predictors and training sets of different sizes in order to determine the minimum number of articles required for developing such systems. Results The general automated system had an area under the curve value of 0.731 and was able to rank 34.6% and 46.2% of the total number of 'useful' articles among the first 10% and 20% of the articles presented to the evaluators when tested on the generalizability set. However, its use may be limited by the subjective definition of useful articles. For the specific automated system, it was found that only 20 articles were required to develop a specific automated system with a prediction performance (AUC 0.748) that was better than that of general automated system. Conclusions Specific automated systems can be developed rapidly and avoid problems caused by subjective definition of useful articles. Thus the efficiency of

  16. Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis: a model for "active" disease.

    Science.gov (United States)

    Peng, Ruoqi; Sridhar, Sriram; Tyagi, Gaurav; Phillips, Jonathan E; Garrido, Rosario; Harris, Paul; Burns, Lisa; Renteria, Lorena; Woods, John; Chen, Leena; Allard, John; Ravindran, Palanikumar; Bitter, Hans; Liang, Zhenmin; Hogaboam, Cory M; Kitson, Chris; Budd, David C; Fine, Jay S; Bauer, Carla M T; Stevenson, Christopher S

    2013-01-01

    The preclinical model of bleomycin-induced lung fibrosis, used to investigate mechanisms related to idiopathic pulmonary fibrosis (IPF), has incorrectly predicted efficacy for several candidate compounds suggesting that it may be of limited value. As an attempt to improve the predictive nature of this model, integrative bioinformatic approaches were used to compare molecular alterations in the lungs of bleomycin-treated mice and patients with IPF. Using gene set enrichment analysis we show for the first time that genes differentially expressed during the fibrotic phase of the single challenge bleomycin model were significantly enriched in the expression profiles of IPF patients. The genes that contributed most to the enrichment were largely involved in mitosis, growth factor, and matrix signaling. Interestingly, these same mitotic processes were increased in the expression profiles of fibroblasts isolated from rapidly progressing, but not slowly progressing, IPF patients relative to control subjects. The data also indicated that TGFβ was not the sole mediator responsible for the changes observed in this model since the ALK-5 inhibitor SB525334 effectively attenuated some but not all of the fibrosis associated with this model. Although some would suggest that repetitive bleomycin injuries may more effectively model IPF-like changes, our data do not support this conclusion. Together, these data highlight that a single bleomycin instillation effectively replicates several of the specific pathogenic molecular changes associated with IPF, and may be best used as a model for patients with active disease.

  17. Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis: a model for "active" disease.

    Directory of Open Access Journals (Sweden)

    Ruoqi Peng

    Full Text Available The preclinical model of bleomycin-induced lung fibrosis, used to investigate mechanisms related to idiopathic pulmonary fibrosis (IPF, has incorrectly predicted efficacy for several candidate compounds suggesting that it may be of limited value. As an attempt to improve the predictive nature of this model, integrative bioinformatic approaches were used to compare molecular alterations in the lungs of bleomycin-treated mice and patients with IPF. Using gene set enrichment analysis we show for the first time that genes differentially expressed during the fibrotic phase of the single challenge bleomycin model were significantly enriched in the expression profiles of IPF patients. The genes that contributed most to the enrichment were largely involved in mitosis, growth factor, and matrix signaling. Interestingly, these same mitotic processes were increased in the expression profiles of fibroblasts isolated from rapidly progressing, but not slowly progressing, IPF patients relative to control subjects. The data also indicated that TGFβ was not the sole mediator responsible for the changes observed in this model since the ALK-5 inhibitor SB525334 effectively attenuated some but not all of the fibrosis associated with this model. Although some would suggest that repetitive bleomycin injuries may more effectively model IPF-like changes, our data do not support this conclusion. Together, these data highlight that a single bleomycin instillation effectively replicates several of the specific pathogenic molecular changes associated with IPF, and may be best used as a model for patients with active disease.

  18. Towards a barrier height benchmark set for biologically relevant systems.

    Science.gov (United States)

    Kromann, Jimmy C; Christensen, Anders S; Cui, Qiang; Jensen, Jan H

    2016-01-01

    We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10-15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4-5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems, geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model, the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set

  19. Towards a barrier height benchmark set for biologically relevant systems

    Directory of Open Access Journals (Sweden)

    Jimmy C. Kromann

    2016-05-01

    Full Text Available We have collected computed barrier heights and reaction energies (and associated model structures for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p[LANL2DZ]//B3LYP/6-31G(d,p level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10–15 kcal/mol, while DFTB results in a MAD that is significantly lower (6 kcal/mol. The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4–5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p. For the remaining systems, geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model, the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and

  20. Dynamic regulation of neurotransmitter specification: Relevance to nervous system homeostasis

    Science.gov (United States)

    Borodinsky, Laura N.; Belgacem, Yesser Hadj; Swapna, Immani; Sequerra, Eduardo Bouth

    2013-01-01

    During nervous system development the neurotransmitter identity changes and coexpression of several neurotransmitters is a rather generalized feature of developing neurons. In the mature nervous system, different physiological and pathological circumstances recreate this phenomenon. The rules of neurotransmitter respecification are multiple. Among them, the goal of assuring balanced excitability appears as an important driving force for the modifications in neurotransmitter phenotype expression. The functional consequences of these dynamic revisions in neurotransmitter identity span a varied range, from fine-tuning the developing neural circuit to modifications in addictive and locomotor behaviors. Current challenges include determining the mechanisms underlying neurotransmitter phenotype respecification and how they intersect with genetic programs of neuronal specialization. PMID:23270605

  1. Imaging the glutamatergic system in vivo - relevance to schizophrenia

    Energy Technology Data Exchange (ETDEWEB)

    Bressan, R.A.; Pilowsky, L.S. [Inst. of Psychiatry, London (United Kingdom); Inst. of Nuclear Medicine, University College of London Medical School (United Kingdom)

    2000-11-01

    Schizophrenia is a devastating psychiatric illness. Its pathophysiology is not fully clarified. Animal data, in vitro and indirect in vivo imaging support glutamatergic N-methyl-D-aspartate (NMDA) receptor hypofunction in the disorder. A lack of suitable ligands has obstructed direct evaluation of the NMDA receptor hypofunction hypothesis of schizophrenia. Many research groups are working towards developing appropriate single-photon emission tomography and positron emission tomography ligands for the NMDA receptor. This paper briefly presents evidence for links between glutamatergic system dysfunction and schizophrenia. It reviews the radioligands to evaluate glutamatergic receptors in vivo and discusses issues in developing novel ligands for the glutamatergic system. (orig.)

  2. Imaging the glutamatergic system in vivo - relevance to schizophrenia

    International Nuclear Information System (INIS)

    Bressan, R.A.; Pilowsky, L.S.

    2000-01-01

    Schizophrenia is a devastating psychiatric illness. Its pathophysiology is not fully clarified. Animal data, in vitro and indirect in vivo imaging support glutamatergic N-methyl-D-aspartate (NMDA) receptor hypofunction in the disorder. A lack of suitable ligands has obstructed direct evaluation of the NMDA receptor hypofunction hypothesis of schizophrenia. Many research groups are working towards developing appropriate single-photon emission tomography and positron emission tomography ligands for the NMDA receptor. This paper briefly presents evidence for links between glutamatergic system dysfunction and schizophrenia. It reviews the radioligands to evaluate glutamatergic receptors in vivo and discusses issues in developing novel ligands for the glutamatergic system. (orig.)

  3. ORIGINAL ARTICLES Canada's health care system: A relevant ...

    African Journals Online (AJOL)

    Canada's universal health care system, named Medicare, was fully in place. While this universal .... through lotteries and 'sin taxes' on alcohol and cigarettes. Since 2004, the federal portion of ..... Himmelstein DU, Thorne D, Warren E, Woolhandler S. Medical bankruptcy in the United. States, 2007: results of a national study.

  4. Development of nuclear power standards and relevant system in China

    International Nuclear Information System (INIS)

    Cao Shudong

    2008-01-01

    By analyzing the history of nuclear power development and the status of nuclear power codes and standards in China, the significance and necessity to quicken the development of nuclear power standards system in China are pointed out, and the guiding ideology, development thoughts, working doctrine and development objectives are put forward in this paper. (authors)

  5. The endocannabinoid system and appetite: relevance for food reward

    NARCIS (Netherlands)

    Jager, G.; Witkamp, R.F.

    2014-01-01

    Mounting evidence substantiates the central role of the endocannabinoid system (ECS) in the modulation of both homeostatic and hedonic elements of appetite and food intake. Conversely, feeding status and dietary patterns directly influence activity of the ECS. Following a general introduction on the

  6. System for Selection of Relevant Information for Decision Support

    Czech Academy of Sciences Publication Activity Database

    Kalina, Jan; Seidl, L.; Zvára, K.; Grünfeldová, H.; Slovák, Dalibor; Zvárová, Jana

    2013-01-01

    Roč. 1, č. 1 (2013), s. 46-46 ISSN 1805-8698. [EFMI 2013 Special Topic Conference. 17.04.2013-19.04.2013, Prague] Institutional support: RVO:67985807 Keywords : decision support system * web-service * information extraction * high-dimension * gene expressions Subject RIV: IN - Informatics, Computer Science

  7. Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

    Science.gov (United States)

    Lee, Roy E; Henricks, Walter H; Sirintrapun, Sahussapont J

    2016-03-01

    Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

  8. [Influence of reverse osmosis concentrate on physicochemical parameters of Sini decoction material system and their relevance].

    Science.gov (United States)

    Jin, Tang-Hui; Zhang, Liu-Hong; Zhu, Hua-Xu; Guo, Li-Wei; Li, Bo; Lu, Ming-Ming

    2014-04-01

    By studying the process of reverse osmosis system for traditional Chinese medicine materials physicochemical parameters affecting the osmotic pressure of its relevance, new compound system reverse osmosis process design methods were explored. Three concentrations materials for high, middle and low were dubbed with Sini decoction as a model drug, and pretreated by 50 thousand relative molecular weight cut-off ultrafiltration membrane. The viscosity, turbidity, conductivity, salinity, TDS, pH value and osmotic pressure of each sample were determined after the reverse osmosis to study the physical and chemical parameters between their respective correlations with the osmotic pressure, and characterized by HPLC chromatograms showing changes before and after the main chemical composition of samples of reverse osmosis. Conductivity-osmotic pressure, salinity-osmotic pressure of the linear correlation coefficient, TDS-osmotic pressure between the three sets of parameters were 0.963 8, 0.932 7, 0.973 7, respectively. Reverse osmosis concentrate and its characteristic spectrum ultrafiltrate HPLC similarity were up to 0. 968 or more, except the low concentrations. There is a significant correlation between the three physicochemical parameters (conductivity, salinity, TDS) and osmotic pressure of each sample system, and there is also significant linear correlation between salinity, conductivity, TDS. The original chemical composition of Sini decoction material concentrate was completely remained after the process of reverse osmosis.

  9. A molecular hybrid polyoxometalate-organometallic moieties and its relevance to supercapacitors in physiological electrolytes

    Science.gov (United States)

    Chinnathambi, Selvaraj; Ammam, Malika

    2015-06-01

    Supercapacitors operating in physiological electrolytes are of great relevance for both their environmentally friendly aspect as well as the possibility to be employed for powering implantable microelectronic devices using directly biological fluids as electrolytes. Polyoxometalate (POMs) have been proven to be useful for supercapacitors in acidic media. However, in neutral pH, POMs are usually not stable. One relevant alternative is to stabilize POMs by pairing them with organic moieties to form hybrids. In this study, we combined K6P2Mo18O62·12H2O (P2Mo18) with Ru(bpy)3Cl2.6H2O (Ru(bpy)). The synthesis was carried out with and without the mild reducing agent KI. The hybrids were characterized by CHN analysis, TEM, FT-IR, XRD, TGA and cyclic voltammetry. CHN elemental analysis revealed that one mole [P2Mo18O62]6- is paired with 3 mol [Ru(bpy)3]2+ to form [Ru(bpy)3]3PMo18O62·nH2O. With KI present, [P2Mo18O62]6- is linked to 3.33 mol to yield [Ru(bpy)3]3.33PMo18O62·mH2O. Excess of Ru(bpy) in [Ru(bpy)3]3.33PMo18O62·mH2O was further confirmed by TEM, FT-IR, XRD, TGA and cyclic voltammetry. In turn, hybrid composition is found to strongly influence the supercapacitor behavior. The hybrid rich in Ru(bpy) is found to perform better for supercapacitors in physiological electrolytes. 125 F g-1 and 68 F g-1 are the capacitance values obtained with [Ru(bpy)3]3.33PMo18O62·mH2O and [Ru(bpy)3]3PMo18O62·nH2O, respectively. In terms of specific energy densities, 3.5 Wh kg-1 and 2 Wh kg-1 were obtained for both hybrid simultaneously. The difference in supercapacitor performance between both hybrids is also noticed in impedance spectroscopy which showed that [Ru(bpy)3]3.33PMo18O62·mH2O has lower electron transfer resistance if compared to [Ru(bpy)3]3PMo18O62·nH2O. Finally, if compared of parent K6P2Mo18O62·12H2O, the stability of both hybrids is found to be highly improved.

  10. High sensitivity optical molecular imaging system

    Science.gov (United States)

    An, Yu; Yuan, Gao; Huang, Chao; Jiang, Shixin; Zhang, Peng; Wang, Kun; Tian, Jie

    2018-02-01

    Optical Molecular Imaging (OMI) has the advantages of high sensitivity, low cost and ease of use. By labeling the regions of interest with fluorescent or bioluminescence probes, OMI can noninvasively obtain the distribution of the probes in vivo, which play the key role in cancer research, pharmacokinetics and other biological studies. In preclinical and clinical application, the image depth, resolution and sensitivity are the key factors for researchers to use OMI. In this paper, we report a high sensitivity optical molecular imaging system developed by our group, which can improve the imaging depth in phantom to nearly 5cm, high resolution at 2cm depth, and high image sensitivity. To validate the performance of the system, special designed phantom experiments and weak light detection experiment were implemented. The results shows that cooperated with high performance electron-multiplying charge coupled device (EMCCD) camera, precision design of light path system and high efficient image techniques, our OMI system can simultaneously collect the light-emitted signals generated by fluorescence molecular imaging, bioluminescence imaging, Cherenkov luminance and other optical imaging modality, and observe the internal distribution of light-emitting agents fast and accurately.

  11. The endocannabinoid system and appetite: relevance for food reward.

    Science.gov (United States)

    Jager, Gerry; Witkamp, Renger F

    2014-06-01

    Mounting evidence substantiates the central role of the endocannabinoid system (ECS) in the modulation of both homeostatic and hedonic elements of appetite and food intake. Conversely, feeding status and dietary patterns directly influence activity of the ECS. Following a general introduction on the functioning of the ECS, the present review specifically addresses its role in the modulation of hedonic eating. Humans possess strong motivational systems triggered by rewarding aspects of food. Food reward is comprised of two components: one appetitive (orienting towards food); the other consummatory (hedonic evaluation), also referred to as 'wanting' and 'liking', respectively. Endocannabinoid tone seems to influence both the motivation to feed and the hedonic value of foods, probably by modifying palatability. Human physiology underlying hedonic eating is still not fully understood. A better understanding of the role of the ECS in the rewarding value of specific foods or diets could offer new possibilities to optimise the balance between energy and nutrient intake for different target groups. These groups include the obese and overweight, and potentially individuals suffering from malnutrition. Examples for the latter group are patients with disease-related anorexia, as well as the growing population of frail elderly suffering from persistent loss of food enjoyment and appetite resulting in malnutrition and involuntary weight loss. It has become clear that the psychobiology of food hedonics is extremely complex and the clinical failure of CB1 inverse agonists including rimonabant (Accomplia®) has shown that 'quick wins' in this field are unlikely.

  12. Toxic effects of pesticide mixtures at a molecular level: Their relevance to human health

    International Nuclear Information System (INIS)

    Hernández, Antonio F.; Parrón, Tesifón; Tsatsakis, Aristidis M.; Requena, Mar; Alarcón, Raquel; López-Guarnido, Olga

    2013-01-01

    Highlights: ► Toxic effects of pesticide mixtures can be independent, dose addition or interaction. ► Metabolic interactions involve inhibition or induction of detoxifying enzymes. ► Organophosphates can potentiate pyrethroid, carbaryl and triazine toxicity. ► Synergism occurs when two active pesticides elicit greater than additive toxicity. ► Endocrine disruptors have the potential for additivity rather than synergism. - Abstract: Pesticides almost always occur in mixtures with other ones. The toxicological effects of low-dose pesticide mixtures on the human health are largely unknown, although there are growing concerns about their safety. The combined toxicological effects of two or more components of a pesticide mixture can take one of three forms: independent, dose addition or interaction. Not all mixtures of pesticides with similar chemical structures produce additive effects; thus, if they act on multiple sites their mixtures may produce different toxic effects. The additive approach also fails when evaluating mixtures that involve a secondary chemical that changes the toxicokinetics of the pesticide as a result of its increased activation or decreased detoxification, which is followed by an enhanced or reduced toxicity, respectively. This review addresses a number of toxicological interactions of pesticide mixtures at a molecular level. Examples of such interactions include the postulated mechanisms for the potentiation of pyrethroid, carbaryl and triazine herbicides toxicity by organophosphates; how the toxicity of some organophosphates can be potentiated by other organophosphates or by previous exposure to organochlorines; the synergism between pyrethroid and carbamate compounds and the antagonism between triazine herbicides and prochloraz. Particular interactions are also addressed, such as those of pesticides acting as endocrine disruptors, the cumulative toxicity of organophosphates and organochlorines resulting in estrogenic effects and the

  13. An Exploration of Molecular Correlates Relevant to Radiation Combined Skin-Burn Trauma.

    Directory of Open Access Journals (Sweden)

    Aminul Islam

    Full Text Available Exposure to high dose radiation in combination with physical injuries such as burn or wound trauma can produce a more harmful set of medical complications requiring specialist interventions. Currently these interventions are unavailable as are the precise biomarkers needed to help both accurately assess and treat such conditions. In the present study, we tried to identify and explore the possible role of serum exosome microRNA (miRNA signatures as potential biomarkers for radiation combined burn injury (RCBI.Female B6D2F1/J mice were assigned to four experimental groups (n = 6: sham control (SHAM, burn injury (BURN, radiation injury (RI and combined radiation skin burn injury (CI. We performed serum multiplex cytokine analysis and serum exosome miRNA expression profiling to determine novel miRNA signatures and important biological pathways associated with radiation combined skin-burn trauma.Serum cytokines, IL-5 and MCP-1, were significantly induced only in CI mice (p<0.05. From 890 differentially expressed miRNAs identified, microarray analysis showed 47 distinct miRNA seed sequences significantly associated with CI mice compared to SHAM control mice (fold change ≥ 1.2, p<0.05. Furthermore, only two major miRNA seed sequences (miR-690 and miR-223 were validated to be differentially expressed for CI mice specifically (fold change ≥ 1.5, p<0.05.Serum exosome miRNA signature data of adult mice, following RCBI, provides new insights into the molecular and biochemical pathways associated with radiation combined skin-burn trauma in vivo.

  14. Relevance of the formal red meat classification system to the South ...

    African Journals Online (AJOL)

    Relevance of the formal red meat classification system to the South African ... to market information make them less willing to sell their animals through the formal market. ... Keywords: Communal farmers, marketing system, meat industry ...

  15. Computational methods for the description of pharmacologically relevant platinum complexes - molecular structure and bond dissociation

    Czech Academy of Sciences Publication Activity Database

    Kokoschka, Malte; Galgonek, Jakub; Vondrášek, Jiří; Hobza, Pavel

    2016-01-01

    Roč. 18, č. 5 (2016), s. 4051-4062 ISSN 1463-9076 Institutional support: RVO:61388963 Keywords : hybrid density functionals * many-electron systems * auxiliary basis sets Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.123, year: 2016

  16. Molecular dynamics simulations of interactions between hydrogen and fusion-relevant materials

    International Nuclear Information System (INIS)

    Rooij, Dagmar de

    2010-01-01

    In a thermonuclear reactor fusion between hydrogen isotopes takes place, producing helium and energy. The so-called divertor is the part of the fusion reactor vessel where the plasma is neutralized in order to exhaust the helium. The surface plates of the divertor are subjected to high heat loads and high fluxes of energetic hydrogen and helium. In the next generation fusion device - the tokamak ITER - the expected conditions at the plates are particle fluxes exceeding 10 24 per second and square metre, particle energies ranging from 1 to 100 eV and an average heat load of 10 MW per square metre. Two materials have been identified as candidates for the ITER divertor plates: carbon and tungsten. Since there are currently no fusion devices that can create these harsh conditions, it is unknown how the materials will behave in terms of erosion and hydrogen retention. To gain more insight in the physical processes under these conditions molecular dynamics simulations have been conducted. Since diamond has been proposed as possible plasma facing material, we have studied erosion and hydrogen retention in diamond and amorphous hydrogenated carbon (a-C:H). As in experiments, diamond shows a lower erosion yield than a-C:H, however the hydrogen retention in diamond is much larger than in a-C:H and also hardly depending on the substrate temperature. This implies that simple heating of the surface is not sufficient to retrieve the hydrogen from diamond material, whereas a-C:H readily releases the retained hydrogen. So, in spite of the higher erosion yield carbon material other than diamond seems more suitable. Experiments suggest that the erosion yield of carbon material decreases with increasing flux. This was studied in our simulations. The results show no flux dependency, suggesting that the observed reduction is not a material property but is caused by external factors as, for example, redeposition of the erosion products. Our study of the redeposition showed that the

  17. Nuclear molecular structure in heavy mass systems

    International Nuclear Information System (INIS)

    Arctaedius, T.; Bargholtz, C.

    1989-04-01

    A study is made of nuclear molecular configurations involving one heavy mass partner. The stability of these configurations to mass flow and to fission is investigated as well as their population in fusion reactions. It is concluded that shell effects in combination with the effects of angular momentum may be important in stabilizing certain configurations. A possible relation of these configurations to the so called superdeformed states is pointed out. The spectrum of rotational and vibrational trasitions within molecular configurations is investigated. For sufficiently mass-asymmetric systems the engergies of vibrational transitions are comparable to the neutron separation energy. Gamma radiation from such transitions may then be observable above the background of statistical transitions. The gamma spectrum and the directional distribution of the radioation following fusion reactions with 12 C and 16 O are calculated. (authors)

  18. Molecular Simulation of Reacting Systems; TOPICAL

    International Nuclear Information System (INIS)

    THOMPSON, AIDAN P.

    2002-01-01

    The final report for a Laboratory Directed Research and Development project entitled, Molecular Simulation of Reacting Systems is presented. It describes efforts to incorporate chemical reaction events into the LAMMPS massively parallel molecular dynamics code. This was accomplished using a scheme in which several classes of reactions are allowed to occur in a probabilistic fashion at specified times during the MD simulation. Three classes of reaction were implemented: addition, chain transfer and scission. A fully parallel implementation was achieved using a checkerboarding scheme, which avoids conflicts due to reactions occurring on neighboring processors. The observed chemical evolution is independent of the number of processors used. The code was applied to two test applications: irreversible linear polymerization and thermal degradation chemistry

  19. Molecular ecology of anaerobic reactor systems

    DEFF Research Database (Denmark)

    Hofman-Bang, H. Jacob Peider; Zheng, D.; Westermann, Peter

    2003-01-01

    Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible for these ......Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible...... to the abundance of each microbe in anaerobic reactor systems by rRNA probing. This chapter focuses on various molecular techniques employed and problems encountered when elucidating the microbial ecology of anaerobic reactor systems. Methods such as quantitative dot blot/fluorescence in-situ probing using various...

  20. Microelectromechanical systems integrating molecular spin crossover actuators

    Energy Technology Data Exchange (ETDEWEB)

    Manrique-Juarez, Maria D. [LCC, CNRS and Université de Toulouse, UPS, INP, F-31077 Toulouse (France); LAAS, CNRS and Université de Toulouse, INSA, UPS, F-31077 Toulouse (France); Rat, Sylvain; Salmon, Lionel; Molnár, Gábor; Bousseksou, Azzedine, E-mail: liviu.nicu@laas.fr, E-mail: azzedine.bousseksou@lcc-toulouse.fr [LCC, CNRS and Université de Toulouse, UPS, INP, F-31077 Toulouse (France); Mathieu, Fabrice; Saya, Daisuke; Séguy, Isabelle; Leïchlé, Thierry; Nicu, Liviu, E-mail: liviu.nicu@laas.fr, E-mail: azzedine.bousseksou@lcc-toulouse.fr [LAAS, CNRS and Université de Toulouse, INSA, UPS, F-31077 Toulouse (France)

    2016-08-08

    Silicon MEMS cantilevers coated with a 200 nm thin layer of the molecular spin crossover complex [Fe(H{sub 2}B(pz){sub 2}){sub 2}(phen)] (H{sub 2}B(pz){sub 2} = dihydrobis(pyrazolyl)borate and phen = 1,10-phenantroline) were actuated using an external magnetic field and their resonance frequency was tracked by means of integrated piezoresistive detection. The light-induced spin-state switching of the molecules from the ground low spin to the metastable high spin state at 10 K led to a well-reproducible shift of the cantilever's resonance frequency (Δf{sub r} = −0.52 Hz). Control experiments at different temperatures using coated as well as uncoated devices along with simple calculations support the assignment of this effect to the spin transition. This latter translates into changes in mechanical behavior of the cantilever due to the strong spin-state/lattice coupling. A guideline for the optimization of device parameters is proposed so as to efficiently harness molecular scale movements for large-scale mechanical work, thus paving the road for nanoelectromechanical systems (NEMS) actuators based on molecular materials.

  1. The Optical Bichromatic Force in Molecular Systems

    Science.gov (United States)

    Aldridge, Leland; Galica, Scott; Eyler, E. E.

    2015-05-01

    The optical bichromatic force has been demonstrated to be useful for slowing atomic beams much more rapidly than radiative forces. Through numerical simulations, we examine several aspects of applying the bichromatic force to molecular beams. One is the unavoidable existence of out-of-system radiative decay, requiring one or more repumping beams. We find that the average deceleration varies strongly with the repumping intensity, but when using optimal parameters, the force approaches the limiting value allowed by population statistics. Another consideration is the effect of fine and hyperfine structure. We examine a simplified multlevel model based on the B X transition in calcium monofluoride. To circumvent optical pumping into coherent dark states, we include two possible schemes: (1) a skewed dc magnetic field, and (2) rapid optical polarization switching. Our results indicate that the bichromatic force remains a viable option for creating large forces in molecular beams, with a reduction in the peak force by approximately an order of magnitude compared to a two-level atom, but little effect on the velocity range over which the force is effective. We also describe our progress towards experimental tests of the bichromatic force on a molecular beam of CaF. Supported by the National Science Foundation.

  2. Molecular marker systems for Oenothera genetics.

    Science.gov (United States)

    Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

    2008-11-01

    The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

  3. Prospective molecular profiling of canine cancers provides a clinically relevant comparative model for evaluating personalized medicine (PMed) trials.

    Science.gov (United States)

    Paoloni, Melissa; Webb, Craig; Mazcko, Christina; Cherba, David; Hendricks, William; Lana, Susan; Ehrhart, E J; Charles, Brad; Fehling, Heather; Kumar, Leena; Vail, David; Henson, Michael; Childress, Michael; Kitchell, Barbara; Kingsley, Christopher; Kim, Seungchan; Neff, Mark; Davis, Barbara; Khanna, Chand; Trent, Jeffrey

    2014-01-01

    Molecularly-guided trials (i.e. PMed) now seek to aid clinical decision-making by matching cancer targets with therapeutic options. Progress has been hampered by the lack of cancer models that account for individual-to-individual heterogeneity within and across cancer types. Naturally occurring cancers in pet animals are heterogeneous and thus provide an opportunity to answer questions about these PMed strategies and optimize translation to human patients. In order to realize this opportunity, it is now necessary to demonstrate the feasibility of conducting molecularly-guided analysis of tumors from dogs with naturally occurring cancer in a clinically relevant setting. A proof-of-concept study was conducted by the Comparative Oncology Trials Consortium (COTC) to determine if tumor collection, prospective molecular profiling, and PMed report generation within 1 week was feasible in dogs. Thirty-one dogs with cancers of varying histologies were enrolled. Twenty-four of 31 samples (77%) successfully met all predefined QA/QC criteria and were analyzed via Affymetrix gene expression profiling. A subsequent bioinformatics workflow transformed genomic data into a personalized drug report. Average turnaround from biopsy to report generation was 116 hours (4.8 days). Unsupervised clustering of canine tumor expression data clustered by cancer type, but supervised clustering of tumors based on the personalized drug report clustered by drug class rather than cancer type. Collection and turnaround of high quality canine tumor samples, centralized pathology, analyte generation, array hybridization, and bioinformatic analyses matching gene expression to therapeutic options is achievable in a practical clinical window (strategies may aid cancer drug development.

  4. Prospective molecular profiling of canine cancers provides a clinically relevant comparative model for evaluating personalized medicine (PMed trials.

    Directory of Open Access Journals (Sweden)

    Melissa Paoloni

    Full Text Available Molecularly-guided trials (i.e. PMed now seek to aid clinical decision-making by matching cancer targets with therapeutic options. Progress has been hampered by the lack of cancer models that account for individual-to-individual heterogeneity within and across cancer types. Naturally occurring cancers in pet animals are heterogeneous and thus provide an opportunity to answer questions about these PMed strategies and optimize translation to human patients. In order to realize this opportunity, it is now necessary to demonstrate the feasibility of conducting molecularly-guided analysis of tumors from dogs with naturally occurring cancer in a clinically relevant setting.A proof-of-concept study was conducted by the Comparative Oncology Trials Consortium (COTC to determine if tumor collection, prospective molecular profiling, and PMed report generation within 1 week was feasible in dogs. Thirty-one dogs with cancers of varying histologies were enrolled. Twenty-four of 31 samples (77% successfully met all predefined QA/QC criteria and were analyzed via Affymetrix gene expression profiling. A subsequent bioinformatics workflow transformed genomic data into a personalized drug report. Average turnaround from biopsy to report generation was 116 hours (4.8 days. Unsupervised clustering of canine tumor expression data clustered by cancer type, but supervised clustering of tumors based on the personalized drug report clustered by drug class rather than cancer type.Collection and turnaround of high quality canine tumor samples, centralized pathology, analyte generation, array hybridization, and bioinformatic analyses matching gene expression to therapeutic options is achievable in a practical clinical window (<1 week. Clustering data show robust signatures by cancer type but also showed patient-to-patient heterogeneity in drug predictions. This lends further support to the inclusion of a heterogeneous population of dogs with cancer into the preclinical

  5. Functional relevance for associations between genetic variants and systemic lupus erythematosus.

    Directory of Open Access Journals (Sweden)

    Fei-Yan Deng

    Full Text Available Systemic lupus erythematosus (SLE is a serious prototype autoimmune disease characterized by chronic inflammation, auto-antibody production and multi-organ damage. Recent association studies have identified a long list of loci that were associated with SLE with relatively high statistical power. However, most of them only established the statistical associations of genetic markers and SLE at the DNA level without supporting evidence of functional relevance. Here, using publically available datasets, we performed integrative analyses (gene relationship across implicated loci analysis, differential gene expression analysis and functional annotation clustering analysis and combined with expression quantitative trait loci (eQTLs results to dissect functional mechanisms underlying the associations for SLE. We found that 14 SNPs, which were significantly associated with SLE in previous studies, have cis-regulation effects on four eQTL genes (HLA-DQA1, HLA-DQB1, HLA-DQB2, and IRF5 that were also differentially expressed in SLE-related cell groups. The functional evidence, taken together, suggested the functional mechanisms underlying the associations of 14 SNPs and SLE. The study may serve as an example of mining publically available datasets and results in validation of significant disease-association results. Utilization of public data resources for integrative analyses may provide novel insights into the molecular genetic mechanisms underlying human diseases.

  6. Creation of reliable relevance judgments in information retrieval systems evaluation experimentation through crowdsourcing: a review.

    Science.gov (United States)

    Samimi, Parnia; Ravana, Sri Devi

    2014-01-01

    Test collection is used to evaluate the information retrieval systems in laboratory-based evaluation experimentation. In a classic setting, generating relevance judgments involves human assessors and is a costly and time consuming task. Researchers and practitioners are still being challenged in performing reliable and low-cost evaluation of retrieval systems. Crowdsourcing as a novel method of data acquisition is broadly used in many research fields. It has been proven that crowdsourcing is an inexpensive and quick solution as well as a reliable alternative for creating relevance judgments. One of the crowdsourcing applications in IR is to judge relevancy of query document pair. In order to have a successful crowdsourcing experiment, the relevance judgment tasks should be designed precisely to emphasize quality control. This paper is intended to explore different factors that have an influence on the accuracy of relevance judgments accomplished by workers and how to intensify the reliability of judgments in crowdsourcing experiment.

  7. Molecular Imaging with Activatable Reporter Systems

    Directory of Open Access Journals (Sweden)

    Gang Niu, Xiaoyuan Chen

    2012-01-01

    Full Text Available Molecular imaging is a newly emerged multiple disciplinary field that aims to visualize, characterize and quantitatively measure biological processes at cellular and molecular levels in humans and other living systems. A reporter gene is a piece of DNA encoding reporter protein, which presents as a readily measurable phenotype that can be distinguished easily from the background of endogenous protein. After being transferred into cells of organ systems (transgenes, the reporter gene can be utilized to visualize transcriptional and posttranscriptional regulation of gene expression, protein-protein interactions, or trafficking of proteins or cells in living subjects. Herein, we review previous classification of reporter genes and regroup the reporter gene based imaging as basic, inducible and activatable, based on the regulation of reporter gene transcription and post-translational modification of reporter proteins. We then focus on activatable reporters, in which the signal can be activated at the posttranslational level for visualizing protein-protein interactions, protein phosphorylation or tertiary structure changes. The applications of several types of activatable reporters will also be summarized. We conclude that activatable reporter imaging can benefit both basic biomedical research and drug development.

  8. Energy transformation in molecular electronic systems

    International Nuclear Information System (INIS)

    Kasha, M.

    1985-01-01

    Our new optical pumping spectroscopy (steady state, and double-laser pulse) allows the production and study of the unstable rare tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole (model for biological purines), 3-hydroxyflavone (model for plant flavones), lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worth of industrial development. The excited and highly reactive singlet molecular oxygen species 1 Δ/sub g/) has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of tris - dibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on π-electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved. 18 refs., 4 figs

  9. Systems Pharmacology in Small Molecular Drug Discovery

    Directory of Open Access Journals (Sweden)

    Wei Zhou

    2016-02-01

    Full Text Available Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity, target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level.

  10. Basic pathologies of neurodegenerative dementias and their relevance for state-of-the-art molecular imaging studies

    International Nuclear Information System (INIS)

    Drzezga, Alexander

    2008-01-01

    Rising life-expectancy in the modern society has resulted in a rapidly growing prevalence of dementia, particularly of Alzheimer's disease (AD). Dementia turns into one of the most common age-related disorders with deleterious consequences for the concerned patients and their relatives, as well as worrying effects on the socio-economic systems. These facts justify strengthened scientific efforts to identify the pathologic origin of dementing disorders, to improve diagnosis, and to interfere therapeutically with the disease progression. In the recent years, remarkable progress has been made concerning the identification of molecular mechanisms underlying the pathology of neurodegenerative disorders. Growing evidence indicates that a common basis of many neurodegenerative dementias can be found in increased production, misfolding and pathological aggregation of proteins, such as ss-amyloid, tau protein, a-synuclein, or the recently described ubiquitinated TDP-43. This progressive insight in pathological processes is paralleled by the development of new therapeutic approaches. However, the exact contribution or mechanism of different pathologies with regard to the development of disease is not yet sufficiently clear. Considerable overlap of pathologies has been documented in different types of clinically defined dementias post mortem, and it has been difficult to correlate post mortem histopathology data with disease-expression during life. Molecular imaging procedures may play a valuable role to circumvent this limitation. In general, methods of molecular imaging have recently experienced an impressive advance, with numerous new and improved technologies emerging. These exciting tools may play a key role in the future regarding the evaluation of pathomechanisms, preclinical evaluation of new diagnostic procedures in animal models, selection of patients for clinical trials, and therapy monitoring. In this overview, molecular key pathologies, which are currently

  11. Clinical aspects and relevance of molecular diagnosis in late mucocutaneous leishmaniasis patients in Paraná, Brazil

    Directory of Open Access Journals (Sweden)

    Andréa Thomaz-Soccol

    2011-06-01

    Full Text Available The aim of the present work was to study the clinical aspects and relevance of molecular diagnosis in late mucocutaneous leishmaniasis patients in Parana, Brazil. Twenty one suspected cases of mucocutaneous leishmaniasis (MCL in patients from the endemic areas of leishmaniasis were assessed. Different methods used in diagnosing the disease and the polymerase chain reaction (PCR technique were compared in order to establish the sensitivity of each method. Out of the 21 patients analyzed, 14.3% presented other etiologies such as vasculitis, syphilis, and paracoccidioidomycosis, with all tests negative for leishmaniasis. Out of the remaining 15 patients, 6.7% cases were confirmed for leishmaniasis by direct examination; 46.67% were positive for culture, which allowed isolating and identifying the parasite and - with the PCR technique - it was possible to diagnose 100% MCL patients for all the three repetitions of exams. The PCR optimized for the present work proved to be an auxiliary method for diagnosing leishmaniasis applicable in the patients carrying MCL due to Leishmania (Viannia braziliensis and did not need culture to be performed, resulting in a faster diagnosis.

  12. Control-relevant modeling and simulation of a SOFC-GT hybrid system

    Directory of Open Access Journals (Sweden)

    Rambabu Kandepu

    2006-07-01

    Full Text Available In this paper, control-relevant models of the most important components in a SOFC-GT hybrid system are described. Dynamic simulations are performed on the overall hybrid system. The model is used to develop a simple control structure, but the simulations show that more elaborate control is needed.

  13. Control-relevant modeling and simulation of a SOFC-GT hybrid system

    OpenAIRE

    Rambabu Kandepu; Lars Imsland; Christoph Stiller; Bjarne A. Foss; Vinay Kariwala

    2006-01-01

    In this paper, control-relevant models of the most important components in a SOFC-GT hybrid system are described. Dynamic simulations are performed on the overall hybrid system. The model is used to develop a simple control structure, but the simulations show that more elaborate control is needed.

  14. Perceived Relevance of an Introductory Information Systems Course to Prospective Business Students

    Directory of Open Access Journals (Sweden)

    Irene Govender

    2013-12-01

    Full Text Available The study is designed to examine students’ perceptions of the introductory Information Systems (IS course. It was an exploratory study in which 67 students participated. A quantitative approach was followed making use of questionnaires for the collection of data. Using the theory of reasoned action as a framework, the study explores the factors that influence non-IS major students’ perceived relevance of the IS introductory course. The analysis of collected data included descriptive and inferential statistics. Using multiple regression analysis, the results suggest that overall, the independent variables, relevance of the content, previous IT knowledge, relevance for professional practice, IT preference in courses and peers’ influence may account for 72% of the explanatory power for the dependent variable, perceived relevance of the IS course. In addition, the results have shown some strong predictors (IT preference and peers’ influence that influence students’ perceived relevance of the IS course. Practical work was found to be a strong mediating variable toward positive perceptions of IS. The results of this study suggest that students do indeed perceive the introductory IS course to be relevant and match their professional needs, but more practical work would enhance their learning. Implications for theory and practice are discussed as a result of the behavioural intention to perceive the IS course to be relevant and eventually to recruit more IS students.

  15. Computer modeling of properties of complex molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Kulkova, E.Yu. [Moscow State University of Technology “STANKIN”, Vadkovsky per., 1, Moscow 101472 (Russian Federation); Khrenova, M.G.; Polyakov, I.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); Nemukhin, A.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334 (Russian Federation)

    2015-03-10

    Large molecular aggregates present important examples of strongly nonhomogeneous systems. We apply combined quantum mechanics / molecular mechanics approaches that assume treatment of a part of the system by quantum-based methods and the rest of the system with conventional force fields. Herein we illustrate these computational approaches by two different examples: (1) large-scale molecular systems mimicking natural photosynthetic centers, and (2) components of prospective solar cells containing titan dioxide and organic dye molecules. We demonstrate that modern computational tools are capable to predict structures and spectra of such complex molecular aggregates.

  16. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

    Directory of Open Access Journals (Sweden)

    Lauren Boldon

    2015-02-01

    Full Text Available In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS experiments, molecular dynamics (MD simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

  17. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

    Science.gov (United States)

    Boldon, Lauren; Laliberte, Fallon; Liu, Li

    2015-01-01

    In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

  18. Molecular communications and nanonetworks from nature to practical systems

    CERN Document Server

    Atakan, Barış

    2014-01-01

    In this book, the concepts of molecular communications and nanonetworks are introduced. Throughout the book, the existing molecular communication paradigms are categorized into two main groups. The first group includes the Passive Molecular Communication (PMC) paradigms in which molecules freely diffuse to transfer information from a transmitter to a receiver. The second group includes the Active Molecular Communication (AMC) paradigms in which molecules are carried or guided by some mediators such as molecular motors, gap junction channels and bacteria. In the book, after briefly discussing why molecular communication is needed for the sophisticated nano and biotechnology applications, the existing molecular communication systems are first presented. Then, the principles of diffusion phenomena and molecular reception with absorbers and the ligand-receptor binding mechanism are introduced. Based on these principles, the communication theories and techniques are given for the PMC. Then, the physical dynamics o...

  19. Some New Theoretical Issues in Systems Thinking Relevant for Modelling Corporate Learning

    Science.gov (United States)

    Minati, Gianfranco

    2007-01-01

    Purpose: The purpose of this paper is to describe fundamental concepts and theoretical challenges with regard to systems, and to build on these in proposing new theoretical frameworks relevant to learning, for example in so-called learning organizations. Design/methodology/approach: The paper focuses on some crucial fundamental aspects introduced…

  20. Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems.

    Science.gov (United States)

    Fujita, Takatoshi; Mochizuki, Yuji

    2018-04-19

    We developed the fragment-based method for calculating nonlocal excitations in large molecular systems. This method is based on the multilayer fragment molecular orbital method and the configuration interaction single (CIS) wave function using localized molecular orbitals. The excited-state wave function for the whole system is described as a superposition of configuration state functions (CSFs) for intrafragment excitations and for interfragment charge-transfer excitations. The formulation and calculations of singlet excited-state Hamiltonian matrix elements in the fragment CSFs are presented in detail. The efficient approximation schemes for calculating the matrix elements are also presented. The computational efficiency and the accuracy were evaluated using the molecular dimers and molecular aggregates. We confirmed that absolute errors of 50 meV (relative to the conventional calculations) are achievable for the molecular systems in their equilibrium geometries. The perturbative electron correlation correction to the CIS excitation energies is also demonstrated. The present theory can compute a large number of excited states in large molecular systems; in addition, it allows for the systematic derivation of a model exciton Hamiltonian. These features are useful for studying excited-state dynamics in condensed molecular systems based on the ab initio electronic structure theory.

  1. Molecular Etiology of Hearing Impairment in Inner Mongolia: mutations in SLC26A4 gene and relevant phenotype analysis

    Directory of Open Access Journals (Sweden)

    Wu Bailin

    2008-11-01

    Full Text Available Abstract Background The molecular etiology of hearing impairment in Chinese has not been thoroughly investigated. Study of GJB2 gene revealed that 30.4% of the patients with hearing loss in Inner Mongolia carried GJB2 mutations. The SLC26A4 gene mutations and relevant phenotype are analyzed in this study. Methods One hundred and thirty-five deaf patients were included. The coding exons of SLC26A4 gene were sequence analyzed in 111 patients, not including 22 patients carrying bi-allelic GJB2 mutations or one patient carrying a known GJB2 dominant mutation as well as one patient with mtDNA 1555A>G mutation. All patients with SLC26A4 mutations or variants were subjected to high resolution temporal bone CT scan and those with confirmed enlarged vestibular aqueduct and/or other inner ear malformation were then given further ultrasound scan of thyroid and thyroid hormone assays. Results Twenty-six patients (19.26%, 26/135 were found carrying SLC26A4 mutation. Among them, 17 patients with bi-allelic SLC26A4 mutations were all confirmed to have EVA or other inner ear malformation by CT scan. Nine patients were heterozygous for one SLC26A4 mutation, including 3 confirmed to be EVA or EVA and Mondini dysplasia by CT scan. The most common mutation, IVS7-2A>G, accounted for 58.14% (25/43 of all SLC26A4 mutant alleles. The shape and function of thyroid were confirmed to be normal by thyroid ultrasound scan and thyroid hormone assays in 19 of the 20 patients with EVA or other inner ear malformation except one who had cystoid change in the right side of thyroid. No Pendred syndrome was diagnosed. Conclusion In Inner Mongolia, China, mutations in SLC26A4 gene account for about 12.6% (17/135 of the patients with hearing loss. Together with GJB2 (23/135, SLC26A4 are the two most commonly mutated genes causing deafness in this region. Pendred syndrome is not detected in this deaf population. We established a new strategy that detects SLC26A4 mutations prior to the

  2. Molecular Etiology of Hearing Impairment in Inner Mongolia: mutations in SLC26A4 gene and relevant phenotype analysis

    Science.gov (United States)

    Dai, Pu; Yuan, Yongyi; Huang, Deliang; Zhu, Xiuhui; Yu, Fei; Kang, Dongyang; Yuan, Huijun; Wu, Bailin; Han, Dongyi; Wong, Lee-Jun C

    2008-01-01

    Background The molecular etiology of hearing impairment in Chinese has not been thoroughly investigated. Study of GJB2 gene revealed that 30.4% of the patients with hearing loss in Inner Mongolia carried GJB2 mutations. The SLC26A4 gene mutations and relevant phenotype are analyzed in this study. Methods One hundred and thirty-five deaf patients were included. The coding exons of SLC26A4 gene were sequence analyzed in 111 patients, not including 22 patients carrying bi-allelic GJB2 mutations or one patient carrying a known GJB2 dominant mutation as well as one patient with mtDNA 1555A>G mutation. All patients with SLC26A4 mutations or variants were subjected to high resolution temporal bone CT scan and those with confirmed enlarged vestibular aqueduct and/or other inner ear malformation were then given further ultrasound scan of thyroid and thyroid hormone assays. Results Twenty-six patients (19.26%, 26/135) were found carrying SLC26A4 mutation. Among them, 17 patients with bi-allelic SLC26A4 mutations were all confirmed to have EVA or other inner ear malformation by CT scan. Nine patients were heterozygous for one SLC26A4 mutation, including 3 confirmed to be EVA or EVA and Mondini dysplasia by CT scan. The most common mutation, IVS7-2A>G, accounted for 58.14% (25/43) of all SLC26A4 mutant alleles. The shape and function of thyroid were confirmed to be normal by thyroid ultrasound scan and thyroid hormone assays in 19 of the 20 patients with EVA or other inner ear malformation except one who had cystoid change in the right side of thyroid. No Pendred syndrome was diagnosed. Conclusion In Inner Mongolia, China, mutations in SLC26A4 gene account for about 12.6% (17/135) of the patients with hearing loss. Together with GJB2 (23/135), SLC26A4 are the two most commonly mutated genes causing deafness in this region. Pendred syndrome is not detected in this deaf population. We established a new strategy that detects SLC26A4 mutations prior to the temporal bone CT scan to

  3. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

    Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

  4. Remote Laser Evaporative Molecular Absorption Spectroscopy Sensor System

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose a sensor system capable of remotely probing the molecular composition of cold solar system targets (asteroids, comets, planets, moons), such as from a...

  5. SULT1A3-Mediated Regiospecific 7-O-Sulfation of Flavonoids in Caco-2 Cells Can Be Explained by the Relevant Molecular Docking Studies

    Science.gov (United States)

    Meng, Shengnan; Wu, Baojian; Singh, Rashim; Yin, Taijun; Morrow, John Kenneth; Zhang, Shuxing; Hu, Ming

    2012-01-01

    Flavonoids are the polyphenolic compounds with various claimed health benefits, but the extensive metabolism by uridine-5'-diphospho-glucuronosyltransferases (UGTs) and sulfotransferases (SULTs) in liver and intestine led to poor oral bioavailabilities. The effects of structural changes on the sulfonation of flavonoids have not been systemically determined, although relevant effects of structural changes on the glucuronidation of flavonoids had. We performed the regiospecific sulfonation of sixteen flavonoids from five different subclasses of flavonoids, which are represented by apigenin (flavone), genistein (isoflavone), naringenin (flavanone), kaempherol (flavonol), and phloretin (chalcone). Additional studies were performed using 4 mono-hydroxyl flavonoids with –OH group at 3, 4’, 5 or 7 position, followed by 5 di-hydroxyl-flavonoids, and 2 tri-hydroxyl flavonoids by using expressed human SULT1A3 and Caco-2 cell lysates. We found that these compounds were exclusively sulfated at the 7-OH position by SULT1A3 and primarily sulfated at 7-OH position in Caco-2 cell lysates with minor amounts of 4’-O-sulfates formed as well. Sulfonation rates measured using SULT1A3 and Caco-2 cell lysates were highly correlated at substrate concentrations of 2.5 and 10 µM. Molecular docking studies provided structural explanations as to why sulfonation only occurred at the 7-OH position of flavones, flavonols and flavanones. In conclusion, molecular docking studies explain why SULT1A3 exclusively mediates sulfonation at the 7-OH position of flavones/flavonols, and correlation studies indicate that SULT1A3 is the main isoform responsible for flavonoid sulfonation in the Caco-2 cells. PMID:22352375

  6. Physical, Spatial, and Molecular Aspects of Extracellular Matrix of In Vivo Niches and Artificial Scaffolds Relevant to Stem Cells Research

    Directory of Open Access Journals (Sweden)

    Maria Akhmanova

    2015-01-01

    Full Text Available Extracellular matrix can influence stem cell choices, such as self-renewal, quiescence, migration, proliferation, phenotype maintenance, differentiation, or apoptosis. Three aspects of extracellular matrix were extensively studied during the last decade: physical properties, spatial presentation of adhesive epitopes, and molecular complexity. Over 15 different parameters have been shown to influence stem cell choices. Physical aspects include stiffness (or elasticity, viscoelasticity, pore size, porosity, amplitude and frequency of static and dynamic deformations applied to the matrix. Spatial aspects include scaffold dimensionality (2D or 3D and thickness; cell polarity; area, shape, and microscale topography of cell adhesion surface; epitope concentration, epitope clustering characteristics (number of epitopes per cluster, spacing between epitopes within cluster, spacing between separate clusters, cluster patterns, and level of disorder in epitope arrangement, and nanotopography. Biochemical characteristics of natural extracellular matrix molecules regard diversity and structural complexity of matrix molecules, affinity and specificity of epitope interaction with cell receptors, role of non-affinity domains, complexity of supramolecular organization, and co-signaling by growth factors or matrix epitopes. Synergy between several matrix aspects enables stem cells to retain their function in vivo and may be a key to generation of long-term, robust, and effective in vitro stem cell culture systems.

  7. Logic circuits based on molecular spider systems.

    Science.gov (United States)

    Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

    2016-08-01

    Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. Pathohistological classification systems in gastric cancer: diagnostic relevance and prognostic value.

    Science.gov (United States)

    Berlth, Felix; Bollschweiler, Elfriede; Drebber, Uta; Hoelscher, Arnulf H; Moenig, Stefan

    2014-05-21

    Several pathohistological classification systems exist for the diagnosis of gastric cancer. Many studies have investigated the correlation between the pathohistological characteristics in gastric cancer and patient characteristics, disease specific criteria and overall outcome. It is still controversial as to which classification system imparts the most reliable information, and therefore, the choice of system may vary in clinical routine. In addition to the most common classification systems, such as the Laurén and the World Health Organization (WHO) classifications, other authors have tried to characterize and classify gastric cancer based on the microscopic morphology and in reference to the clinical outcome of the patients. In more than 50 years of systematic classification of the pathohistological characteristics of gastric cancer, there is no sole classification system that is consistently used worldwide in diagnostics and research. However, several national guidelines for the treatment of gastric cancer refer to the Laurén or the WHO classifications regarding therapeutic decision-making, which underlines the importance of a reliable classification system for gastric cancer. The latest results from gastric cancer studies indicate that it might be useful to integrate DNA- and RNA-based features of gastric cancer into the classification systems to establish prognostic relevance. This article reviews the diagnostic relevance and the prognostic value of different pathohistological classification systems in gastric cancer.

  9. Molecular profiles to biology and pathways: a systems biology approach.

    Science.gov (United States)

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  10. Molecular signature and in vivo behavior of bone marrow endosteal and subendosteal stromal cell populations and their relevance to hematopoiesis

    Energy Technology Data Exchange (ETDEWEB)

    Balduino, Alex, E-mail: balduino@uva.edu.br [School of Dentistry, Veiga de Almeida University, Rio de Janeiro, RJ (Brazil); Mello-Coelho, Valeria [Biomedical Science Institute, Federal University of Rio de Janeiro, Rio de Janeiro, RJ (Brazil); National Institute on Aging, National Institute of Health, Baltimore, MD (United States); Wang, Zhou; Taichman, Russell S.; Krebsbach, Paul H. [Department of Periodontics, Prevention and Geriatrics, University of Michigan School of Dentistry, Ann Arbor, MI (United States); Weeraratna, Ashani T.; Becker, Kevin G. [National Institute on Aging, National Institute of Health, Baltimore, MD (United States); Mello, Wallace de [Instituto Oswaldo Cruz, Rio de Janeiro, RJ (Brazil); Taub, Dennis D. [National Institute on Aging, National Institute of Health, Baltimore, MD (United States); Borojevic, Radovan [Biomedical Science Institute, Federal University of Rio de Janeiro, Rio de Janeiro, RJ (Brazil)

    2012-11-15

    In the bone marrow cavity, hematopoietic stem cells (HSC) have been shown to reside in the endosteal and subendosteal perivascular niches, which play specific roles on HSC maintenance. Although cells with long-term ability to reconstitute full hematopoietic system can be isolated from both niches, several data support a heterogenous distribution regarding the cycling behavior of HSC. Whether this distinct behavior depends upon the role played by the stromal populations which distinctly create these two niches is a question that remains open. In the present report, we used our previously described in vivo assay to demonstrate that endosteal and subendosteal stromal populations are very distinct regarding skeletal lineage differentiation potential. This was further supported by a microarray-based analysis, which also demonstrated that these two stromal populations play distinct, albeit complementary, roles in HSC niche. Both stromal populations were preferentially isolated from the trabecular region and behave distinctly in vitro, as previously reported. Even though these two niches are organized in a very close range, in vivo assays and molecular analyses allowed us to identify endosteal stroma (F-OST) cells as fully committed osteoblasts and subendosteal stroma (F-RET) cells as uncommitted mesenchymal cells mainly represented by perivascular reticular cells expressing high levels of chemokine ligand, CXCL12. Interestingly, a number of cytokines and growth factors including interleukin-6 (IL-6), IL-7, IL-15, Hepatocyte growth factor (HGF) and stem cell factor (SCF) matrix metalloproteases (MMPs) were also found to be differentially expressed by F-OST and F-RET cells. Further microarray analyses indicated important mechanisms used by the two stromal compartments in order to create and coordinate the 'quiescent' and 'proliferative' niches in which hematopoietic stem cells and progenitors reside.

  11. Molecular signature and in vivo behavior of bone marrow endosteal and subendosteal stromal cell populations and their relevance to hematopoiesis

    International Nuclear Information System (INIS)

    Balduino, Alex; Mello-Coelho, Valeria; Wang, Zhou; Taichman, Russell S.; Krebsbach, Paul H.; Weeraratna, Ashani T.; Becker, Kevin G.; Mello, Wallace de; Taub, Dennis D.; Borojevic, Radovan

    2012-01-01

    In the bone marrow cavity, hematopoietic stem cells (HSC) have been shown to reside in the endosteal and subendosteal perivascular niches, which play specific roles on HSC maintenance. Although cells with long-term ability to reconstitute full hematopoietic system can be isolated from both niches, several data support a heterogenous distribution regarding the cycling behavior of HSC. Whether this distinct behavior depends upon the role played by the stromal populations which distinctly create these two niches is a question that remains open. In the present report, we used our previously described in vivo assay to demonstrate that endosteal and subendosteal stromal populations are very distinct regarding skeletal lineage differentiation potential. This was further supported by a microarray-based analysis, which also demonstrated that these two stromal populations play distinct, albeit complementary, roles in HSC niche. Both stromal populations were preferentially isolated from the trabecular region and behave distinctly in vitro, as previously reported. Even though these two niches are organized in a very close range, in vivo assays and molecular analyses allowed us to identify endosteal stroma (F-OST) cells as fully committed osteoblasts and subendosteal stroma (F-RET) cells as uncommitted mesenchymal cells mainly represented by perivascular reticular cells expressing high levels of chemokine ligand, CXCL12. Interestingly, a number of cytokines and growth factors including interleukin-6 (IL-6), IL-7, IL-15, Hepatocyte growth factor (HGF) and stem cell factor (SCF) matrix metalloproteases (MMPs) were also found to be differentially expressed by F-OST and F-RET cells. Further microarray analyses indicated important mechanisms used by the two stromal compartments in order to create and coordinate the “quiescent” and “proliferative” niches in which hematopoietic stem cells and progenitors reside.

  12. Developing predictive systems models to address complexity and relevance for ecological risk assessment.

    Science.gov (United States)

    Forbes, Valery E; Calow, Peter

    2013-07-01

    Ecological risk assessments (ERAs) are not used as well as they could be in risk management. Part of the problem is that they often lack ecological relevance; that is, they fail to grasp necessary ecological complexities. Adding realism and complexity can be difficult and costly. We argue that predictive systems models (PSMs) can provide a way of capturing complexity and ecological relevance cost-effectively. However, addressing complexity and ecological relevance is only part of the problem. Ecological risk assessments often fail to meet the needs of risk managers by not providing assessments that relate to protection goals and by expressing risk in ratios that cannot be weighed against the costs of interventions. Once more, PSMs can be designed to provide outputs in terms of value-relevant effects that are modulated against exposure and that can provide a better basis for decision making than arbitrary ratios or threshold values. Recent developments in the modeling and its potential for implementation by risk assessors and risk managers are beginning to demonstrate how PSMs can be practically applied in risk assessment and the advantages that doing so could have. Copyright © 2013 SETAC.

  13. Advances in study of molecular imaging reporte gene systems

    International Nuclear Information System (INIS)

    Wu Tao; An Rui

    2010-01-01

    The use of molecular imaging reporter gene systems has allowed gene therapy to move from the laboratory to the clinical application, which provides methodology to monitor the expression of therapeutic gene noninvasively and achieve quantitative outcome in vivo. Recently, the radionuclide reporter gene still is the focus many studies, but MRI and optical reporter gene have gradually played a important part in reporter gene systems. On the basis of combination of multi-subject, for example applied chemistry and molecular biology, more and more new modified reporter genes and molecular probes have spread out. This paper mainly introduces the advantages and disadvantages of reporter gene system and development trends. (authors)

  14. A New Molecular Surveillance System for Leishmaniasis

    Science.gov (United States)

    Pandey, Kishor; Pandey, Basu Dev; Mallik, Arun Kumar; Acharya, Jyoti; Kato, Kentaro; Kaneko, Osamu; Ferreira, Pedro Eduardo

    2014-01-01

    Abstract. Presently, global efforts are being made to control and eradicate the deadliest tropical diseases through the improvement of adequate interventions. A critical point for programs to succeed is the prompt and accurate diagnosis in endemic regions. Rapid diagnostic tests (RDTs) are being massively deployed and used to improve diagnosis in tropical countries. In the present report, we evaluated the hypothesis of, after use for diagnosis, the reuse of the Leishmania RDT kit as a DNA source, which can be used downstream as a molecular surveillance and/or quality control tool. As a proof of principle, a polymerase chain reaction-based method was used to detect Leishmania spp. minicircle kinetoplast DNA from leishmaniasis RDT kits. Our results show that Leishmania spp. DNA can be extracted from used RDTs and may constitute an important, reliable, and affordable tool to assist in future leishmaniasis molecular surveillance methods. PMID:24752687

  15. Development and Validation of a Scalable Next-Generation Sequencing System for Assessing Relevant Somatic Variants in Solid Tumors12

    Science.gov (United States)

    Hovelson, Daniel H.; McDaniel, Andrew S.; Cani, Andi K.; Johnson, Bryan; Rhodes, Kate; Williams, Paul D.; Bandla, Santhoshi; Bien, Geoffrey; Choppa, Paul; Hyland, Fiona; Gottimukkala, Rajesh; Liu, Guoying; Manivannan, Manimozhi; Schageman, Jeoffrey; Ballesteros-Villagrana, Efren; Grasso, Catherine S.; Quist, Michael J.; Yadati, Venkata; Amin, Anmol; Siddiqui, Javed; Betz, Bryan L.; Knudsen, Karen E.; Cooney, Kathleen A.; Feng, Felix Y.; Roh, Michael H.; Nelson, Peter S.; Liu, Chia-Jen; Beer, David G.; Wyngaard, Peter; Chinnaiyan, Arul M.; Sadis, Seth; Rhodes, Daniel R.; Tomlins, Scott A.

    2015-01-01

    Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with 95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts. PMID:25925381

  16. CESAR cost-efficient methods and processes for safety-relevant embedded systems

    CERN Document Server

    Wahl, Thomas

    2013-01-01

    The book summarizes the findings and contributions of the European ARTEMIS project, CESAR, for improving and enabling interoperability of methods, tools, and processes to meet the demands in embedded systems development across four domains - avionics, automotive, automation, and rail. The contributions give insight to an improved engineering and safety process life-cycle for the development of safety critical systems. They present new concept of engineering tools integration platform to improve the development of safety critical embedded systems and illustrate capacity of this framework for end-user instantiation to specific domain needs and processes. They also advance state-of-the-art in component-based development as well as component and system validation and verification, with tool support. And finally they describe industry relevant evaluated processes and methods especially designed for the embedded systems sector as well as easy adoptable common interoperability principles for software tool integratio...

  17. Knowledge-based driver assistance systems traffic situation description and situation feature relevance

    CERN Document Server

    Huelsen, Michael

    2014-01-01

    The comprehension of a traffic situation plays a major role in driving a vehicle. Interpretable information forms a basis for future projection, decision making and action performing, such as navigating, maneuvering and driving control. Michael Huelsen provides an ontology-based generic traffic situation description capable of supplying various advanced driver assistance systems with relevant information about the current traffic situation of a vehicle and its environment. These systems are enabled to perform reasonable actions and approach visionary goals such as injury and accident free driv

  18. The Relevance of the Renin-Angiotensin System in the Development of Drugs to Combat Preeclampsia

    Directory of Open Access Journals (Sweden)

    Norikazu Ueki

    2015-01-01

    Full Text Available Preeclampsia is a hypertensive disorder that occurs during pregnancy. It has an unknown etiology and affects approximately 5–8% of pregnancies worldwide. The pathophysiology of preeclampsia is not yet known, and preeclampsia has been called “a disease of theories.” The central symptom of preeclampsia is hypertension. However, the etiology of the hypertension is unknown. In this review, we analyze the molecular mechanisms of preeclampsia with a particular focus on the pathogenesis of the hypertension in preeclampsia and its association with the renin-angiotensin system. In addition, we propose potential alternative strategies to target the renin-angiotensin system, which is enhanced during pregnancy.

  19. Relevant Factors in The Post-Merger Systems Integration and Information Technology in Brazilian Banks

    Directory of Open Access Journals (Sweden)

    Marcel Ginotti Pires

    2017-01-01

    Full Text Available This article discusses the factors present in post-merger integration of Systems and Information Technology (SIT that lead to positive and negative results in mergers and acquisitions (M & A. The research comprised three of the largest acquiring banks in Brazil. We adopted two methods of research, qualitative, to operationalize the theoretical concepts and quantitative, to test the hypotheses. We interviewed six executives of banks that held relevant experience in M & A processes. Subsequently, we applied questionnaires to IT professionals who were involved in the SIT integration processes. The results showed that the quality and expertise of the integration teams and managing the integration were the most relevant factors in the processes, with positive results for increased efficiency and the increased capacity of SIT. Negative results were due to failures in exploiting learning opportunities, the loss of employees and the inexpressive record of integration procedures.

  20. Libretexts: a flexible online open system for disseminating educational materials relevant to geophysics at all levels

    Science.gov (United States)

    Halpern, J. B.

    2017-12-01

    Libretexts is an online open system for distributing educational materials with over 5 million page views per month. Covering geophysics, chemistry, physics and more it offers a platform for authors and users including faculty and students to access curated educational materials. Currently there are on line texts covering geology, geobiology, natural hazards and understanding the refusal to accept climate change as well as relevant materials in other sections on aquatic and atmospheric chemistry. In addition to "written" materials Libretexts provides access to simulations and demonstrations that are relevant. Most importantly the Libretext project welcomes new contributors. Faculty can use available materials to construct their own texts or supplementary materials in relatively short order. Since all material is covered by a Creative Commons Copyright, material can be added to as needed for teaching.

  1. DNA-Enabled Integrated Molecular Systems for Computation and Sensing

    Science.gov (United States)

    2014-05-21

    Computational devices can be chemically conjugated to different strands of DNA that are then self-assembled according to strict Watson − Crick binding rules... DNA -Enabled Integrated Molecular Systems for Computation and Sensing Craig LaBoda,† Heather Duschl,† and Chris L. Dwyer*,†,‡ †Department of...guided folding of DNA , inspired by nature, allows designs to manipulate molecular-scale processes unlike any other material system. Thus, DNA can be

  2. National critical incident reporting systems relevant to anaesthesia: a European survey.

    Science.gov (United States)

    Reed, S; Arnal, D; Frank, O; Gomez-Arnau, J I; Hansen, J; Lester, O; Mikkelsen, K L; Rhaiem, T; Rosenberg, P H; St Pierre, M; Schleppers, A; Staender, S; Smith, A F

    2014-03-01

    Critical incident reporting is a key tool in the promotion of patient safety in anaesthesia. We surveyed representatives of national incident reporting systems in six European countries, inviting information on scope and organization, and intelligence on factors determining success and failure. Some systems are government-run and nationally conceived; others started out as small, specialty-focused initiatives, which have since acquired a national reach. However, both national co-ordination and specialty enthusiasts seem to be necessary for an optimally functioning system. The role of reporting culture, definitional issues, and dissemination is discussed. We make recommendations for others intending to start new systems and speculate on the prospects for sharing patient safety lessons relevant to anaesthesia at European level.

  3. Aqueous Guanidinium-Carbonate Interactions by Molecular Dynamics and Neutron Scattering: Relevance to Ion-Protein Interactions

    Czech Academy of Sciences Publication Activity Database

    Vazdar, Mario; Jungwirth, Pavel; Mason, Philip E.

    2013-01-01

    Roč. 117, č. 6 (2013), s. 1844-1848 ISSN 1520-6106 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : guanidinium * neutron scattering * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.377, year: 2013

  4. Phenotypic and molecular assessment of seven patients with 6p25 deletion syndrome: Relevance to ocular dysgenesis and hearing impairment

    Directory of Open Access Journals (Sweden)

    Ritch Robert

    2004-06-01

    Full Text Available Abstract Background Thirty-nine patients have been described with deletions involving chromosome 6p25. However, relatively few of these deletions have had molecular characterization. Common phenotypes of 6p25 deletion syndrome patients include hydrocephalus, hearing loss, and ocular, craniofacial, skeletal, cardiac, and renal malformations. Molecular characterization of deletions can identify genes that are responsible for these phenotypes. Methods We report the clinical phenotype of seven patients with terminal deletions of chromosome 6p25 and compare them to previously reported patients. Molecular characterization of the deletions was performed using polymorphic marker analysis to determine the extents of the deletions in these seven 6p25 deletion syndrome patients. Results Our results, and previous data, show that ocular dysgenesis and hearing impairment are the two most highly penetrant phenotypes of the 6p25 deletion syndrome. While deletion of the forkhead box C1 gene (FOXC1 probably underlies the ocular dysgenesis, no gene in this region is known to be involved in hearing impairment. Conclusions Ocular dysgenesis and hearing impairment are the two most common phenotypes of 6p25 deletion syndrome. We conclude that a locus for dominant hearing loss is present at 6p25 and that this locus is restricted to a region distal to D6S1617. Molecular characterization of more 6p25 deletion patients will aid in refinement of this locus and the identification of a gene involved in dominant hearing loss.

  5. Investigation of droplet nucleation in CCS relevant systems – design and testing of the expansion chamber

    Directory of Open Access Journals (Sweden)

    Čenský Miroslav

    2018-01-01

    Full Text Available A unique in-house designed experimental apparatus for investigation of nucleation of droplets in CCS relevant systems is being developed by the present team. The apparatus allows simulating various processes relevant to CCS technologies. Gaseous mixtures with CO2 are prepared in a Mixture Preparation Device (MPD based on accurate adjustment of flow rates of individual components [EPJ Web of Conferences 143, 02140 (2017]. The mixture then flows into an expansion chamber, where it undergoes a rapid adiabatic expansion. As a consequence of adiabatic cooling, the mixture becomes supersaturated and nucleation and simultaneous growth of droplets occurs. In this study, we describe the design and testing of the expansion part of the experimental setup. The rapid expansion was realized using two valve systems, one for low pressures (up to 0.7 MPa and the other for high pressures (up to 10 MPa. A challenge for a proper design of the expansion system is avoiding acoustic oscillations. These can occur either in the mode of Helmholtz resonator, where the compressible gas in the chamber acts as a spring and the rapidly moving gas in the valve system as a mass, or in the “flute” mode, where acoustic waves are generated in a long outlet tubing.

  6. Investigation of droplet nucleation in CCS relevant systems - design and testing of the expansion chamber

    Science.gov (United States)

    Čenský, Miroslav; Hrubý, Jan; Vinš, Václav; Hykl, Jiří; Šmíd, Bohuslav

    2018-06-01

    A unique in-house designed experimental apparatus for investigation of nucleation of droplets in CCS relevant systems is being developed by the present team. The apparatus allows simulating various processes relevant to CCS technologies. Gaseous mixtures with CO2 are prepared in a Mixture Preparation Device (MPD) based on accurate adjustment of flow rates of individual components [EPJ Web of Conferences 143, 02140 (2017)]. The mixture then flows into an expansion chamber, where it undergoes a rapid adiabatic expansion. As a consequence of adiabatic cooling, the mixture becomes supersaturated and nucleation and simultaneous growth of droplets occurs. In this study, we describe the design and testing of the expansion part of the experimental setup. The rapid expansion was realized using two valve systems, one for low pressures (up to 0.7 MPa) and the other for high pressures (up to 10 MPa). A challenge for a proper design of the expansion system is avoiding acoustic oscillations. These can occur either in the mode of Helmholtz resonator, where the compressible gas in the chamber acts as a spring and the rapidly moving gas in the valve system as a mass, or in the "flute" mode, where acoustic waves are generated in a long outlet tubing.

  7. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  8. Laboratory Studies of Ethane Ice Relevant to Outer Solar System Surfaces

    Science.gov (United States)

    Moore, Marla H.; Hudson, Reggie; Raines, Lily

    2009-01-01

    Oort Cloud comets, as well as TNOs Makemake (2045 FYg), Quaoar, and Pluto, are known to contain ethane. However, even though this molecule is found on several outer Solar System objects relatively little information is available about its amorphous and crystalline phases. In new experiments, we have prepared ethane ices at temperatures applicable to the outer Solar System, and have heated and ion-irradiated these ices to study phase changes and ethane's radiation chemistry using mid-IR spectroscopy (2.2 - 16.6 microns). Included in our work is the meta-stable phase that exists at 35 - 55 K. These results, including newly obtained optical constants, are relevant to ground-based observational campaigns, the New Horizons mission, and supporting laboratory work. An improved understanding of solid-phase ethane may contribute to future searches for this and other hydrocarbons in the outer Solar System.

  9. Exponential growth for self-reproduction in a catalytic reaction network: relevance of a minority molecular species and crowdedness

    Science.gov (United States)

    Kamimura, Atsushi; Kaneko, Kunihiko

    2018-03-01

    Explanation of exponential growth in self-reproduction is an important step toward elucidation of the origins of life because optimization of the growth potential across rounds of selection is necessary for Darwinian evolution. To produce another copy with approximately the same composition, the exponential growth rates for all components have to be equal. How such balanced growth is achieved, however, is not a trivial question, because this kind of growth requires orchestrated replication of the components in stochastic and nonlinear catalytic reactions. By considering a mutually catalyzing reaction in two- and three-dimensional lattices, as represented by a cellular automaton model, we show that self-reproduction with exponential growth is possible only when the replication and degradation of one molecular species is much slower than those of the others, i.e., when there is a minority molecule. Here, the synergetic effect of molecular discreteness and crowding is necessary to produce the exponential growth. Otherwise, the growth curves show superexponential growth because of nonlinearity of the catalytic reactions or subexponential growth due to replication inhibition by overcrowding of molecules. Our study emphasizes that the minority molecular species in a catalytic reaction network is necessary for exponential growth at the primitive stage of life.

  10. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    International Nuclear Information System (INIS)

    De Yoreo, J.J.; Bartelt, M.C.; Orme, C.A.; Villacampa, A.; Weeks, B.L.; Miller, A.E.

    2002-01-01

    Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

  11. The Systemic Theory of Living Systems and Relevance to CAM: the Theory (Part III

    Directory of Open Access Journals (Sweden)

    José A. Olalde Rangel

    2005-01-01

    Full Text Available Western medical science lacks a solid philosophical and theoretical approach to disease cognition and therapeutics. My first two articles provided a framework for a humane medicine based on Modern Biophysics. Its precepts encompass modern therapeutics and CAM. Modern Biophysics and its concepts are presently missing in medicine, whether orthodox or CAM, albeit they probably provide the long sought explanation that bridges the abyss between East and West. Key points that differentiate Systemic from other systems' approaches are ‘Intelligence’, ‘Energy’ and the objective ‘to survive’. The General System Theory (GST took a forward step by proposing a departure from the mechanistic biological concept—of analyzing parts and processes in isolation—and brought us towards an organismic model. GST examines the system's components and results of their interaction. However, GST still does not go far enough. GST assumes ‘Self-Organization’ as a spontaneous phenomenon, ignoring a causative entity or central controller to all systems: Intelligence. It also neglects ‘Survive’ as the directional motivation common to any living system, and scarcely assigns ‘Energy’ its true inherent value. These three parameters, Intelligence, Energy and Survive, are vital variables to be considered, in our human quest, if we are to achieve a unified theory of life.

  12. The Collection of Event Data and its Relevance to the Optimisation of Decay Heat Rejection Systems

    International Nuclear Information System (INIS)

    Roughley, R.; Jones, N.

    1975-01-01

    The precision with which the reliability of DHR (Decay Heat Rejection) systems for nuclear reactors can be predicted depends not only upon model representation but also on the accuracy of the data used. In the preliminary design stages when models are being used to arrive at major engineering decisions in relation to plant configuration, the best the designer can do is use the data available at the time. With the present state of the art it is acknowledged that some degree of judgement will have to be exercised particularly for plant involving sodium technology where a large amount of operational experience has not yet been generated. This paper reviews the current efforts being deployed in the acquisition of field data relevant to DHR systems so that improvements in reliability predictions may be realised

  13. Assessing Hospital Physicians' Acceptance of Clinical Information Systems: A Review of the Relevant Literature

    Directory of Open Access Journals (Sweden)

    Bram Pynoo

    2013-06-01

    Full Text Available In view of the tremendous potential benefits of clinical information systems (CIS for the quality of patient care; it is hard to understand why not every CIS is embraced by its targeted users, the physicians. The aim of this study is to propose a framework for assessing hospital physicians' CIS-acceptance that can serve as a guidance for future research into this area. Hereto, a review of the relevant literature was performed in the ISI Web-of-Science database. Eleven studies were withheld from an initial dataset of 797 articles. Results show that just as in business settings, there are four core groups of variables that influence physicians' acceptance of a CIS: its usefulness and ease of use, social norms, and factors in the working environment that facilitate use of the CIS (such as providing computers/workstations, compatibility between the new and existing system.... We also identified some additional variables as predictors of CIS-acceptance.

  14. Bleomycin Induces Molecular Changes Directly Relevant to Idiopathic Pulmonary Fibrosis: A Model for “Active” Disease

    Science.gov (United States)

    Tyagi, Gaurav; Phillips, Jonathan E.; Garrido, Rosario; Harris, Paul; Burns, Lisa; Renteria, Lorena; Woods, John; Chen, Leena; Allard, John; Ravindran, Palanikumar; Bitter, Hans; Liang, Zhenmin; Hogaboam, Cory M.; Kitson, Chris; Budd, David C.; Fine, Jay S.; Bauer, Carla MT.; Stevenson, Christopher S.

    2013-01-01

    The preclinical model of bleomycin-induced lung fibrosis, used to investigate mechanisms related to idiopathic pulmonary fibrosis (IPF), has incorrectly predicted efficacy for several candidate compounds suggesting that it may be of limited value. As an attempt to improve the predictive nature of this model, integrative bioinformatic approaches were used to compare molecular alterations in the lungs of bleomycin-treated mice and patients with IPF. Using gene set enrichment analysis we show for the first time that genes differentially expressed during the fibrotic phase of the single challenge bleomycin model were significantly enriched in the expression profiles of IPF patients. The genes that contributed most to the enrichment were largely involved in mitosis, growth factor, and matrix signaling. Interestingly, these same mitotic processes were increased in the expression profiles of fibroblasts isolated from rapidly progressing, but not slowly progressing, IPF patients relative to control subjects. The data also indicated that TGFβ was not the sole mediator responsible for the changes observed in this model since the ALK-5 inhibitor SB525334 effectively attenuated some but not all of the fibrosis associated with this model. Although some would suggest that repetitive bleomycin injuries may more effectively model IPF-like changes, our data do not support this conclusion. Together, these data highlight that a single bleomycin instillation effectively replicates several of the specific pathogenic molecular changes associated with IPF, and may be best used as a model for patients with active disease. PMID:23565148

  15. Identification of clinically relevant Corynebacterium strains by Api Coryne, MALDI-TOF-mass spectrometry and molecular approaches.

    Science.gov (United States)

    Alibi, S; Ferjani, A; Gaillot, O; Marzouk, M; Courcol, R; Boukadida, J

    2015-09-01

    We evaluated the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for the identification of 97 Corynebacterium clinical in comparison to identification strains by Api Coryne and MALDI-TOF-MS using 16S rRNA gene and hypervariable region of rpoB genes sequencing as a reference method. C. striatum was the predominant species isolated followed by C. amycolatum. There was an agreement between Api Coryne strips and MALDI-TOF-MS identification in 88.65% of cases. MALDI-TOF-MS was unable to differentiate C. aurimucosum from C. minutissimum and C. minutissimum from C. singulare but reliably identify 92 of 97 (94.84%) strains. Two strains remained incompletely identified to the species level by MALDI-TOF-MS and molecular approaches. They belonged to Cellulomonas and Pseudoclavibacter genus. In conclusion, MALDI-TOF-MS is a rapid and reliable method for the identification of Corynebacterium species. However, some limits have been noted and have to be resolved by the application of molecular methods. Copyright © 2015. Published by Elsevier SAS.

  16. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  17. Sustainable transportation according to certification systems: A viability analysis based on neighborhood size and context relevance

    International Nuclear Information System (INIS)

    Gouda, Amr Ah.; Masoumi, Houshmand E.

    2017-01-01

    Urban sustainability certification (USC) systems comprehensively assess and benchmark the sustainability of neighborhoods, communities, etc. However, it is important to understand what USCs mean by neighborhoods and communities in terms of definition and their certified developments' size. This study focuses on sustainable transportation and its measures in USCs in order to discern: how relevant are these measures to the varied local conditions, especially in developing countries? And whether they can generate palpable benefits vis-à-vis the certified developments' site areas. Taking descriptive analysis methods, this study focuses on four prominent USCs, namely, LEED for Neighborhood Development, BREEAM Communities, CASBEE for Urban Development, and The Pearl Community Rating System. The four USCs prescribed multiple measures for sustainable transportation, particularly in favor of active transportation and public transportation. However, the relatively small size of their citified developments and the varying transportation conditions among different contexts attenuate the viability and relevance of the advocated measures for both modes. In order to yield more benefits, USCs should underscore the integrative nature of neighborhoods and communities, and transportation within their prescribed criteria and measures. Moreover, sustainable transportation as a theme should be tailored to the local conditions rather than being adopted or adapted from global USCs. - Highlights: • Transportation measures in four prominent certification systems were investigated. • Most certified neighborhoods, communities and developments have small site areas. • Certifications are insensitive to realities of transport in developing countries. • Benefits from advocating active transport only within certified areas are minimal. • Certifications devalue the integrative nature of neighborhoods and transportation.

  18. Sustainable transportation according to certification systems: A viability analysis based on neighborhood size and context relevance

    Energy Technology Data Exchange (ETDEWEB)

    Gouda, Amr Ah., E-mail: amr.gouda@eng.asu.edu.eg [Center for Technology and Society, Technische Universität Berlin, Hardenbergstr, 16-18, Berlin 10623 (Germany); Architecture Department, Faculty of Engineering, Ain Shams University, 1 Sarayat St., Abassia, Cairo (Egypt); Masoumi, Houshmand E. [Center for Technology and Society, Technische Universität Berlin, Hardenbergstr, 16-18, Berlin 10623 (Germany)

    2017-03-15

    Urban sustainability certification (USC) systems comprehensively assess and benchmark the sustainability of neighborhoods, communities, etc. However, it is important to understand what USCs mean by neighborhoods and communities in terms of definition and their certified developments' size. This study focuses on sustainable transportation and its measures in USCs in order to discern: how relevant are these measures to the varied local conditions, especially in developing countries? And whether they can generate palpable benefits vis-à-vis the certified developments' site areas. Taking descriptive analysis methods, this study focuses on four prominent USCs, namely, LEED for Neighborhood Development, BREEAM Communities, CASBEE for Urban Development, and The Pearl Community Rating System. The four USCs prescribed multiple measures for sustainable transportation, particularly in favor of active transportation and public transportation. However, the relatively small size of their citified developments and the varying transportation conditions among different contexts attenuate the viability and relevance of the advocated measures for both modes. In order to yield more benefits, USCs should underscore the integrative nature of neighborhoods and communities, and transportation within their prescribed criteria and measures. Moreover, sustainable transportation as a theme should be tailored to the local conditions rather than being adopted or adapted from global USCs. - Highlights: • Transportation measures in four prominent certification systems were investigated. • Most certified neighborhoods, communities and developments have small site areas. • Certifications are insensitive to realities of transport in developing countries. • Benefits from advocating active transport only within certified areas are minimal. • Certifications devalue the integrative nature of neighborhoods and transportation.

  19. Degradation of TBC Systems in Environments Relevant to Advanced Gas Turbines for IGCC Systems

    Energy Technology Data Exchange (ETDEWEB)

    Gleeson, Brian [Univ. of Pittsburgh, PA (United States)

    2014-09-30

    Air plasma sprayed (APS) thermal barrier coatings (TBCs) are used to provide thermal insulation for the hottest components in gas turbines. Zirconia stabilized with 7wt% yttria (7YSZ) is the most common ceramic top coat used for turbine blades. The 7YSZ coating can be degraded from the buildup of fly-ash deposits created in the power-generation process. Fly ash from an integrated gasification combined cycle (IGCC) system can result from coal-based syngas. TBCs are also exposed to harsh gas environments containing CO2, SO2, and steam. Degradation from the combined effects of fly ash and harsh gas atmospheres has the potential to severely limit TBC lifetimes. The main objective of this study was to use lab-scale testing to systematically elucidate the interplay between prototypical deposit chemistries (i.e., ash and its constituents, K2SO4, and FeS) and environmental oxidants (i.e., O2, H2O and CO2) on the degradation behavior of advanced TBC systems. Several mechanisms of early TBC failure were identified, as were the specific fly-ash constituents responsible for degradation. The reactivity of MCrAlY bondcoats used in TBC systems was also investigated. The specific roles of oxide and sulfate components were assessed, together with the complex interplay between gas composition, deposit chemistry and alloy reactivity. Bondcoat composition design strategies to mitigate corrosion were established, particularly with regard to controlling phase constitution and the amount of reactive elements the bondcoat contains in order to achieve optimal corrosion resistance.

  20. Integration of Transport-relevant Data within Image Record of the Surveillance System

    Directory of Open Access Journals (Sweden)

    Adam Stančić

    2016-10-01

    Full Text Available Integration of the collected information on the road within the image recorded by the surveillance system forms a unified source of transport-relevant data about the supervised situation. The basic assumption is that the procedure of integration changes the image to the extent that is invisible to the human eye, and the integrated data keep identical content. This assumption has been proven by studying the statistical properties of the image and integrated data using mathematical model modelled in the programming language Python using the combinations of the functions of additional libraries (OpenCV, NumPy, SciPy and Matplotlib. The model has been used to compare the input methods of meta-data and methods of steganographic integration by correcting the coefficients of Discrete Cosine Transform JPEG compressed image. For the procedures of steganographic data processing the steganographic algorithm F5 was used. The review paper analyses the advantages and drawbacks of the integration methods and present the examples of situations in traffic in which the formed unified sources of transport-relevant information could be used.

  1. Bridging the gap: linking molecular simulations and systemic descriptions of cellular compartments.

    Directory of Open Access Journals (Sweden)

    Tihamér Geyer

    Full Text Available Metabolic processes in biological cells are commonly either characterized at the level of individual enzymes and metabolites or at the network level. Often these two paradigms are considered as mutually exclusive because concepts from neither side are suited to describe the complete range of scales. Additionally, when modeling metabolic or regulatory cellular systems, often a large fraction of the required kinetic parameters are unknown. This even applies to such simple and extensively studied systems like the photosynthetic apparatus of purple bacteria. Using the chromatophore vesicles of Rhodobacter sphaeroides as a model system, we show that a consistent kinetic model emerges when fitting the dynamics of a molecular stochastic simulation to a set of time dependent experiments even though about two thirds of the kinetic parameters in this system are not known from experiment. Those kinetic parameters that were previously known all came out in the expected range. The simulation model was built from independent protein units composed of elementary reactions processing single metabolites. This pools-and-proteins approach naturally compiles the wealth of available molecular biological data into a systemic model and can easily be extended to describe other systems by adding new protein or nucleic acid types. The automated parameter optimization, performed with an evolutionary algorithm, reveals the sensitivity of the model to the value of each parameter and the relative importances of the experiments used. Such an analysis identifies the crucial system parameters and guides the setup of new experiments that would add most knowledge for a systemic understanding of cellular compartments. The successful combination of the molecular model and the systemic parametrization presented here on the example of the simple machinery for bacterial photosynthesis shows that it is actually possible to combine molecular and systemic modeling. This framework can now

  2. Review of relevant studies of isolated systems[Integration of wind energy

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, L.H.; Lundsager, P.

    2000-12-01

    The report presents the results of a review of studies relating to integration of wind energy in isolated power supply systems, based on a systematic literature survey. The purpose of the study is to develop a methodology consisting of a set of guidelines for wind energy projects in isolated energy systems and a set of tools and models that are operational on an engineering level. The review is based on a literature search in the ETDE Energy Database with a main search covering the period 7/88 to 6/97 and supplemented by partial update periods. A few newer references have been included in the review, most notably the IEC/PAS 62111 specification. The amount of wind energy literature related to the subject is excessively large, and a complete review in which every relevant abstract is identified and examined is not feasible within the framework of this (or probably any other) study. The review results have been organised according to the following keywords: methods & guides, economics, concept of application, system solutions, case studies, financial programmes, dedicated software tools. None of the found references presents methods or tools that contradict the philosophy of Risoe's methodology as it is described in the report. It is therefore concluded that Risoe's methodology makes a good platform for further development. (au)

  3. Studying the molecular mechanisms of radiation damage : low-energy electron interactions with biomolecules and medically relevant molecules

    International Nuclear Information System (INIS)

    Tanzer, K.

    2015-01-01

    were developed to enhance the radiation damage in these tumor sites, however, the molecular mechanism at which radiosensitizers operate is still unknown to this date. Investigating radiosensitizers with low-energy electrons might enlighten the mystery of their working mechanism. We performed an extensive DEA study to the proposed radiosensitizer 4-nitroimidazole (4NI) and two methylated nitroimidazoles, and found quite unexpected results. While 4NI is very sensitive towards electrons, which trigger a rich chemistry in the molecule, leading to the formation of a variety of reactive radical species at very low energies below 2 eV, these reactions are completely blocked in the methylated compounds. This means, that only small changes in the structure of this molecule can have immense effects on its radiosensitizing properties, which is an important aspect to take into consideration when searching for new radiosensitizers. Chemotherapy is also among the most efficient treatment methods for cancer and it has been shown, that the concomitant administration of chemo- and radiotherapy can have a superadditive benefit. However, also in this case the exact molecular processes responsible for this effect are not known, making further investigations necessary. In this thesis I present the study of platinum(II) bromide as a model molecule for platinum-based chemotherapeutic drugs and metal halides, that have shown good radiosensitizing abilities. It was found that the most effective reaction upon low-electron interaction is the formation of the fragment anion Br– , that is most probably coupled with ion pair formation. (author) [de

  4. Degradation of TBC Systems in Environments Relevant to Advanced Gas Turbines for IGCC Systems

    Science.gov (United States)

    Bohna, Nathaniel Allan

    Plasma sprayed (PS) thermal barrier coatings (TBCs) are used to provide thermal insulation for the hottest components in gas turbines. Zirconia stabilized with 7wt% yttria (7YSZ) is the most common ceramic top coat used for turbine blades. The 7YSZ coating can be degraded by the buildup of fly-ash deposits which can arise from the fuel source (coal/biomass) used in the combustion process in gas turbines. Fly-ash from the integrated gasification combined cycle (IGCC) process can result from coal-based syngas and also from ambient air which passes through the system. TBCs are also exposed to harsh gas environments containing CO2, SO2, and steam. As presented in this thesis, degradation from the combined effects of fly-ash and harsh gas atmosphere can severely limit TBC lifetimes. It is well established that degradation at very high temperatures (≥1250°C) from deposits consisting of the oxides CaO-MgO-Al2O3-SiO 2 results from extensive liquid silicate infiltration into the porous top coat of the YSZ. This infiltration causes early failure resulting from chemical and/or mechanical damage to the ceramic layer. Damage resulting from liquid infiltration, however, is not typically considered at relatively lower temperatures around 1100°C because liquid silicates would not be expected to form from the oxides in the deposit. A key focus of this study is to assess the mode and extent of TBC degradation at 1100°C in cases when some amount of liquid forms owing to the presence of K2SO4 as a minor ash constituent. Two types of liquid infiltrations are observed depending on the principal oxide (i.e., CaO or SiO2) in the deposit. The degradation is primarily the result of mechanical damage, which results from infiltration caused by the interaction of liquid K2SO4 with either the CaO or SiO2. The TBCs used in this work are representative of commonly used coatings used in the hottest sections of land-based gas turbines. The specimens consist of 7YSZ top coats deposited on

  5. Clinical relevance of the ROC and free-response paradigms for comparing imaging system efficacies

    International Nuclear Information System (INIS)

    Chakraborty, D. P.

    2010-01-01

    Observer performance studies are widely used to assess medical imaging systems. Unlike technical/engineering measurements observer performance include the entire imaging chain and the radiologist. However, the widely used receiver operating characteristic (ROC) method ignores lesion localisation information. The free-response ROC (FROC) method uses the location information to appropriately reward or penalise correct or incorrect localizations, respectively. This paper describes a method for improving the clinical relevance of FROC studies. The method consists of assigning appropriate risk values to the different lesions that may be present on a single image. A high-risk lesion is one that is critical to detect and act upon, and is assigned a higher risk value than a low-risk lesion, one that is relatively innocuous. Instead of simply counting the number of lesions that are detected, as is done in conventional FROC analysis, a risk-weighted count is used. This has the advantage of rewarding detections of high-risk lesions commensurately more than detections of lower risk lesions. Simulations were used to demonstrate that the new method, termed case-based analysis, results in a higher figure of merit for an expert who detects more high-risk lesions than a naive observer who detects more low-risk lesions, even though both detect the same total number of lesions. Conventional free-response analysis is unable to distinguish between the two types of observers. This paper also comments on the issue of clinical relevance of ROC analysis vs. FROC for tasks that involve lesion localisation. (authors)

  6. Phase diagram, thermodynamic investigations, and modelling of systems relevant to lithium-ion batteries

    International Nuclear Information System (INIS)

    Fuertauer, Siegfried; Beutl, Alexander; Flanorfer, Hans; Henriques, David; Giel, Hans; Markus, Thorsten

    2017-01-01

    This article reports on two consecutive joint projects titled ''Experimental Thermodynamics and Phase Relations of New Electrode Materials for Lithium-Ion Batteries'', which were performed in the framework of the WenDeLIB 1473 priority program ''Materials with new Design for Lithium Ion Batteries''. Hundreds of samples were synthesized using experimental techniques specifically developed to deal with highly reactive lithium and lithium-containing compounds to generate electrochemical, phase diagram and crystal structure data in the Cu-Li, Li-Sn, Li-Sb, Cu-Li-Sn, Cu-Li-Sb and selected oxide systems. The thermochemical and phase diagram data were subsequently used to develop self-consistent thermodynamic descriptions of several binary systems. In the present contribution, the experimental techniques, working procedures, results and their relevance to the development of new electrode materials for lithium ion batteries are discussed and summarized. The collaboration between the three groups has resulted in more than fifteen (15) published articles during the six-year funding period.

  7. Rotational patient setup errors in IGRT with XVI system in Elekta Synergy and their clinical relevance

    International Nuclear Information System (INIS)

    Madhusudhana Sresty, N.V.N.; Muralidhar, K.R.; Raju, A.K.; Sha, R.L.; Ramanjappa

    2008-01-01

    The goal of Image Guided Radiotherapy (IGRT) is to improve the accuracy of treatment delivery. In this technique, it is possible to get volumetric images of patient anatomy before delivery of treatment.XVI( release 3.5) system in Elekta Synergy linear accelerator (Elekta,Crawley,UK) has the potential to ensure that, the relative positions of the target volume is same as in the treatment plan. It involves acquiring planar images produced by a kilo Voltage cone beam rotating about the patient in the treatment position. After 3 dimensional match between reference and localization images, the system gives rotational errors also along with translational shifts. One can easily perform translational shifts with treatment couch. But rotational shifts cannot be performed. Most of the studies dealt with translational shifts only. Few studies reported regarding rotational errors. It is found that in the treatment of elongated targets, even small rotational errors can show difference in results. The main objectives of this study is 1) To verify the magnitude of rotational errors in different clinical sites observed and to compare with the other reports. 2) To find its clinical relevance 3) To find difference in rotational shift results with improper selection of kV collimator

  8. 6,7-dimethoxy-coumarin as a probe of hydration dynamics in biologically relevant systems

    Science.gov (United States)

    Ghose, Avisek; Amaro, Mariana; Kovaricek, Petr; Hof, Martin; Sykora, Jan

    2018-04-01

    Coumarin derivatives are well known fluorescence reporters for investigating biological systems due to their strong micro-environment sensitivity. Despite having wide range of environment sensitive fluorescence probes, the potential of 6,7-dimethoxy-coumarin has not been studied extensively so far. With a perspective of its use in protein studies, namely using the unnatural amino acid technology or as a substrate for hydrolase enzymes, we study acetyloxymethyl-6,7-dimethoxycoumarin (Ac-DMC). We investigate the photophysics and hydration dynamics of this dye in aerosol-OT (AOT) reverse micelles at various water contents using the time dependent fluorescence shift (TDFS) method. The TDFS response in AOT reverse micelles from water/surfactant ratio of 0 to 20 confirms its sensitivity towards the hydration and mobility of its microenvironment. Moreover, we show that the fluorophore can be efficiently quenched by halide ions. Hence, we conclude that the 6,7-dimethoxy-methylcoumarin fluorophore is useful for studying hydration parameters in biologically relevant systems.

  9. Phase diagram, thermodynamic investigations, and modelling of systems relevant to lithium-ion batteries

    Energy Technology Data Exchange (ETDEWEB)

    Fuertauer, Siegfried; Beutl, Alexander; Flanorfer, Hans [Vienna Univ. (Austria). Dept. of Inorganic Chemistry - Functional Materials; Li, Dajian; Cupid, Damian [Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen (Germany). Inst. for Applied Materials - Applied Materials Physics (IAM-AWP); Henriques, David; Giel, Hans; Markus, Thorsten [Mannheim Univ. of Applied Sciences (Germany). Inst. for Thermo- and Fluiddynamics

    2017-11-15

    This article reports on two consecutive joint projects titled ''Experimental Thermodynamics and Phase Relations of New Electrode Materials for Lithium-Ion Batteries'', which were performed in the framework of the WenDeLIB 1473 priority program ''Materials with new Design for Lithium Ion Batteries''. Hundreds of samples were synthesized using experimental techniques specifically developed to deal with highly reactive lithium and lithium-containing compounds to generate electrochemical, phase diagram and crystal structure data in the Cu-Li, Li-Sn, Li-Sb, Cu-Li-Sn, Cu-Li-Sb and selected oxide systems. The thermochemical and phase diagram data were subsequently used to develop self-consistent thermodynamic descriptions of several binary systems. In the present contribution, the experimental techniques, working procedures, results and their relevance to the development of new electrode materials for lithium ion batteries are discussed and summarized. The collaboration between the three groups has resulted in more than fifteen (15) published articles during the six-year funding period.

  10. Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

    Science.gov (United States)

    Li, Jianwei; Nowak, Piotr; Otto, Sijbren

    2013-06-26

    Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

  11. Elucidation of molecular kinetic schemes from macroscopic traces using system identification.

    Directory of Open Access Journals (Sweden)

    Miguel Fribourg

    2017-02-01

    Full Text Available Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic processes from the overall (macroscopic response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE. SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology

  12. Molecular biophysics: detection and characterization of damage in molecular, cellular, and physiological systems

    International Nuclear Information System (INIS)

    Danyluk, S.S.

    1979-01-01

    This section contains summaries of research on the detection and characterization of damage in molecular, cellular, and physiological systems. Projects under investigation in this section include: chemical synthesis of nucleic acid derivatives; structural and conformational properties of biological molecules in solution; crystallographic and chemical studies of immunoglobulin structure; instrument design and development for x-ray and neutron scattering studies of biological molecules; and chromobiology and circadian regulation

  13. Perceiving active listening activates the reward system and improves the impression of relevant experiences.

    Science.gov (United States)

    Kawamichi, Hiroaki; Yoshihara, Kazufumi; Sasaki, Akihiro T; Sugawara, Sho K; Tanabe, Hiroki C; Shinohara, Ryoji; Sugisawa, Yuka; Tokutake, Kentaro; Mochizuki, Yukiko; Anme, Tokie; Sadato, Norihiro

    2015-01-01

    Although active listening is an influential behavior, which can affect the social responses of others, the neural correlates underlying its perception have remained unclear. Sensing active listening in social interactions is accompanied by an improvement in the recollected impressions of relevant experiences and is thought to arouse positive feelings. We therefore hypothesized that the recognition of active listening activates the reward system, and that the emotional appraisal of experiences that had been subject to active listening would be improved. To test these hypotheses, we conducted functional magnetic resonance imaging (fMRI) on participants viewing assessments of their own personal experiences made by evaluators with or without active listening attitude. Subjects rated evaluators who showed active listening more positively. Furthermore, they rated episodes more positively when they were evaluated by individuals showing active listening. Neural activation in the ventral striatum was enhanced by perceiving active listening, suggesting that this was processed as rewarding. It also activated the right anterior insula, representing positive emotional reappraisal processes. Furthermore, the mentalizing network was activated when participants were being evaluated, irrespective of active listening behavior. Therefore, perceiving active listening appeared to result in positive emotional appraisal and to invoke mental state attribution to the active listener.

  14. Medically relevant assays with a simple smartphone and tablet based fluorescence detection system.

    Science.gov (United States)

    Wargocki, Piotr; Deng, Wei; Anwer, Ayad G; Goldys, Ewa M

    2015-05-20

    Cell phones and smart phones can be reconfigured as biomedical sensor devices but this requires specialized add-ons. In this paper we present a simple cell phone-based portable bioassay platform, which can be used with fluorescent assays in solution. The system consists of a tablet, a polarizer, a smart phone (camera) and a box that provides dark readout conditions. The assay in a well plate is placed on the tablet screen acting as an excitation source. A polarizer on top of the well plate separates excitation light from assay fluorescence emission enabling assay readout with a smartphone camera. The assay result is obtained by analysing the intensity of image pixels in an appropriate colour channel. With this device we carried out two assays, for collagenase and trypsin using fluorescein as the detected fluorophore. The results of collagenase assay with the lowest measured concentration of 3.75 µg/mL and 0.938 µg in total in the sample were comparable to those obtained by a microplate reader. The lowest measured amount of trypsin was 930 pg, which is comparable to the low detection limit of 400 pg for this assay obtained in a microplate reader. The device is sensitive enough to be used in point-of-care medical diagnostics of clinically relevant conditions, including arthritis, cystic fibrosis and acute pancreatitis.

  15. Medically Relevant Assays with a Simple Smartphone and Tablet Based Fluorescence Detection System

    Directory of Open Access Journals (Sweden)

    Piotr Wargocki

    2015-05-01

    Full Text Available Cell phones and smart phones can be reconfigured as biomedical sensor devices but this requires specialized add-ons. In this paper we present a simple cell phone-based portable bioassay platform, which can be used with fluorescent assays in solution. The system consists of a tablet, a polarizer, a smart phone (camera and a box that provides dark readout conditions. The assay in a well plate is placed on the tablet screen acting as an excitation source. A polarizer on top of the well plate separates excitation light from assay fluorescence emission enabling assay readout with a smartphone camera. The assay result is obtained by analysing the intensity of image pixels in an appropriate colour channel. With this device we carried out two assays, for collagenase and trypsin using fluorescein as the detected fluorophore. The results of collagenase assay with the lowest measured concentration of 3.75 µg/mL and 0.938 µg in total in the sample were comparable to those obtained by a microplate reader. The lowest measured amount of trypsin was 930 pg, which is comparable to the low detection limit of 400 pg for this assay obtained in a microplate reader. The device is sensitive enough to be used in point-of-care medical diagnostics of clinically relevant conditions, including arthritis, cystic fibrosis and acute pancreatitis.

  16. Atomic and Molecular Systems in Intense Ultrashort Laser Pulses

    Science.gov (United States)

    Saenz, A.

    2008-07-01

    The full quantum mechanical treatment of atomic and molecular systems exposed to intense laser pulses is a so far unsolved challenge, even for systems as small as molecular hydrogen. Therefore, a number of simplified qualitative and quantitative models have been introduced in order to provide at least some interpretational tools for experimental data. The assessment of these models describing the molecular response is complicated, since a comparison to experiment requires often a number of averages to be performed. This includes in many cases averaging of different orientations of the molecule with respect to the laser field, focal volume effects, etc. Furthermore, the pulse shape and even the peak intensity is experimentally not known with very high precision; considering, e.g., the exponential intensity dependence of the ionization signal. Finally, experiments usually provide only relative yields. As a consequence of all these averagings and uncertainties, it is possible that different models may successfully explain some experimental results or features, although these models disagree substantially, if their predictions are compared before averaging. Therefore, fully quantum-mechanical approaches at least for small atomic and molecular systems are highly desirable and have been developed in our group. This includes efficient codes for solving the time-dependent Schrodinger equation of atomic hydrogen, helium or other effective one- or two-electron atoms as well as for the electronic motion in linear (effective) one-and two-electron diatomic molecules like H_2.Very recently, a code for larger molecular systems that adopts the so-called single-active electron approximation was also successfully implemented and applied. In the first part of this talk popular models describing intense laser-field ionization of atoms and their extensions to molecules are described. Then their validity is discussed on the basis of quantum-mechanical calculations. Finally, some

  17. Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems.

    Science.gov (United States)

    Dresselhaus, Thomas; Yang, Jack; Kumbhar, Sadhana; Waller, Mark P

    2013-04-09

    Accurate modeling of molecular systems requires a good knowledge of the structure; therefore, conformation searching/optimization is a routine necessity in computational chemistry. Here we present a hybrid metaheuristic optimization (HMO) algorithm, which combines ant colony optimization (ACO) and particle swarm optimization (PSO) for the optimization of molecular systems. The HMO implementation meta-optimizes the parameters of the ACO algorithm on-the-fly by the coupled PSO algorithm. The ACO parameters were optimized on a set of small difluorinated polyenes where the parameters exhibited small variance as the size of the molecule increased. The HMO algorithm was validated by searching for the closed form of around 100 molecular balances. Compared to the gradient-based optimized molecular balance structures, the HMO algorithm was able to find low-energy conformations with a 87% success rate. Finally, the computational effort for generating low-energy conformation(s) for the phenylalanyl-glycyl-glycine tripeptide was approximately 60 CPU hours with the ACO algorithm, in comparison to 4 CPU years required for an exhaustive brute-force calculation.

  18. Molecular mechanisms of aging and immune system regulation in Drosophila.

    Science.gov (United States)

    Eleftherianos, Ioannis; Castillo, Julio Cesar

    2012-01-01

    Aging is a complex process that involves the accumulation of deleterious changes resulting in overall decline in several vital functions, leading to the progressive deterioration in physiological condition of the organism and eventually causing disease and death. The immune system is the most important host-defense mechanism in humans and is also highly conserved in insects. Extensive research in vertebrates has concluded that aging of the immune function results in increased susceptibility to infectious disease and chronic inflammation. Over the years, interest has grown in studying the molecular interaction between aging and the immune response to pathogenic infections. The fruit fly Drosophila melanogaster is an excellent model system for dissecting the genetic and genomic basis of important biological processes, such as aging and the innate immune system, and deciphering parallel mechanisms in vertebrate animals. Here, we review the recent advances in the identification of key players modulating the relationship between molecular aging networks and immune signal transduction pathways in the fly. Understanding the details of the molecular events involved in aging and immune system regulation will potentially lead to the development of strategies for decreasing the impact of age-related diseases, thus improving human health and life span.

  19. Selective excitation, relaxation, and energy channeling in molecular systems

    International Nuclear Information System (INIS)

    Rhodes, W.C.

    1993-08-01

    Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems

  20. Time-dependent theoretical treatments of the dynamics of electrons and nuclei in molecular systems

    International Nuclear Information System (INIS)

    Deumens, E.; Diz, A.; Longo, R.; Oehrn, Y.

    1994-01-01

    An overview is presented of methods for time-dependent treatments of molecules as systems of electrons and nuclei. The theoretical details of these methods are reviewed and contrasted in the light of a recently developed time-dependent method called electron-nuclear dynamics. Electron-nuclear dynamics (END) is a formulation of the complete dynamics of electrons and nuclei of a molecular system that eliminates the necessity of constructing potential-energy surfaces. Because of its general formulation, it encompasses many aspects found in other formulations and can serve as a didactic device for clarifying many of the principles and approximations relevant in time-dependent treatments of molecular systems. The END equations are derived from the time-dependent variational principle applied to a chosen family of efficiently parametrized approximate state vectors. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. The approach leads to a simple formulation of the fully nonlinear time-dependent Hartree-Fock theory including nuclear dynamics. The nonlinear END equations with the ab initio Coulomb Hamiltonian have been implemented at this level of theory in a computer program, ENDyne, and have been shown feasible for the study of small molecular systems. Implementation of the Austin Model 1 semiempirical Hamiltonian is discussed as a route to large molecular systems. The linearized END equations at this level of theory are shown to lead to the random-phase approximation for the coupled system of electrons and nuclei. The qualitative features of the general nonlinear solution are analyzed using the results of the linearized equations as a first approximation. Some specific applications of END are presented, and the comparison with experiment and other theoretical approaches is discussed

  1. Developing decision-relevant data and information systems for California water through listening and collaboration

    Science.gov (United States)

    Bales, R. C.; Bernacchi, L.; Conklin, M. H.; Viers, J. H.; Fogg, G. E.; Fisher, A. T.; Kiparsky, M.

    2017-12-01

    California's historic drought of 2011-2015 provided excellent conditions for researchers to listen to water-management challenges from decision makers, particularly with regard to data and information needs for improved decision making. Through the UC Water Security and Sustainability Research Initiative (http://ucwater.org/) we began a multi-year dialog with water-resources decision makers and state agencies that provide data and technical support for water management. Near-term products of that collaboration will be both a vision for a 21st-century water data and information system, and near-term steps to meet immediate legislative deadlines in a way that is consistent with the longer-term vision. While many university-based water researchers engage with state and local agencies on both science and policy challenges, UC Water's focus was on: i) integrated system management, from headwaters through groundwater and agriculture, and on ii) improved decision making through better water information systems. This focus aligned with the recognition by water leaders that fundamental changes in the way the state manages water were overdue. UC Water is focused on three "I"s: improved water information, empowering Institutions to use and to create new information, and enabling decision makers to make smart investments in both green and grey Infrastructure. Effective communication with water decision makers has led to engagement on high-priority programs where large knowledge gaps remain, including more-widespread groundwater recharge of storm flows, restoration of mountain forests in important source-water areas, governance structures for groundwater sustainability, and filling information gaps by bringing new technology to bear on measurement and data programs. Continuing engagement of UC Water researchers in public dialog around water resources, through opinion pieces, feature articles, blogs, white papers, social media, video clips and a feature documentary film have

  2. Assembly, destruction and manipulation of atomic, molecular and complex systems

    International Nuclear Information System (INIS)

    Le Padellec, Arnaud Pierre Frederic

    2003-04-01

    In this report for Accreditation to Supervise Researches (HDR), the author first indicates his professional curriculum (diplomas, teaching activities, responsibilities in the field of education and research, publications), and then proposes a presentation of his scientific works and researches. He notably proposes an overview of the different experimental techniques he implemented: CRYRING storage ring, confluent beams, flow post-discharge with mass spectrometry and Langmuir probe, crossed beams, and so on. He reports works dealing with the manipulation and destruction of atomic, molecular and complex systems: detachment of atomic anions by electronic impact, detachment and dissociation of small carbon aggregates by electronic impact, dissociative recombination, dissociative ionisation and excitation, creation of pairs of ions, manipulation of sodium fluoride aggregates. He finally presents research projects regarding the assembly of molecular and complex systems

  3. Interactive display of molecular models using a microcomputer system

    Science.gov (United States)

    Egan, J. T.; Macelroy, R. D.

    1980-01-01

    A simple, microcomputer-based, interactive graphics display system has been developed for the presentation of perspective views of wire frame molecular models. The display system is based on a TERAK 8510a graphics computer system with a display unit consisting of microprocessor, television display and keyboard subsystems. The operating system includes a screen editor, file manager, PASCAL and BASIC compilers and command options for linking and executing programs. The graphics program, written in USCD PASCAL, involves the centering of the coordinate system, the transformation of centered model coordinates into homogeneous coordinates, the construction of a viewing transformation matrix to operate on the coordinates, clipping invisible points, perspective transformation and scaling to screen coordinates; commands available include ZOOM, ROTATE, RESET, and CHANGEVIEW. Data file structure was chosen to minimize the amount of disk storage space. Despite the inherent slowness of the system, its low cost and flexibility suggests general applicability.

  4. Catecholaminergic systems in stress: structural and molecular genetic approaches.

    Science.gov (United States)

    Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

    2009-04-01

    Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

  5. Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering

    International Nuclear Information System (INIS)

    Cavillon, F.

    2004-10-01

    This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N 14 /N 15 . The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules

  6. SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance.

    Science.gov (United States)

    Chowbina, Sudhir; Hammamieh, Rasha; Kumar, Raina; Chakraborty, Nabarun; Yang, Ruoting; Mudunuri, Uma; Jett, Marti; Palma, Joseph M; Stephens, Robert

    2013-01-01

    SysBioCube is an integrated data warehouse and analysis platform for experimental data relating to diseases of military relevance developed for the US Army Medical Research and Materiel Command Systems Biology Enterprise (SBE). It brings together, under a single database environment, pathophysio-, psychological, molecular and biochemical data from mouse models of post-traumatic stress disorder and (pre-) clinical data from human PTSD patients.. SysBioCube will organize, centralize and normalize this data and provide an access portal for subsequent analysis to the SBE. It provides new or expanded browsing, querying and visualization to provide better understanding of the systems biology of PTSD, all brought about through the integrated environment. We employ Oracle database technology to store the data using an integrated hierarchical database schema design. The web interface provides researchers with systematic information and option to interrogate the profiles of pan-omics component across different data types, experimental designs and other covariates.

  7. Review and application of group theory to molecular systems biology.

    Science.gov (United States)

    Rietman, Edward A; Karp, Robert L; Tuszynski, Jack A

    2011-06-22

    In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer.

  8. Olfactory memory formation in Drosophila: from molecular to systems neuroscience.

    Science.gov (United States)

    Davis, Ronald L

    2005-01-01

    The olfactory nervous system of insects and mammals exhibits many similarities, which suggests that the mechanisms for olfactory learning may be shared. Molecular genetic investigations of Drosophila learning have uncovered numerous genes whose gene products are essential for olfactory memory formation. Recent studies of the products of these genes have continued to expand the range of molecular processes known to underlie memory formation. Recent research has also broadened the neuroanatomical areas thought to mediate olfactory learning to include the antennal lobes in addition to a previously accepted and central role for the mushroom bodies. The roles for neurons extrinsic to the mushroom body neurons are becoming better defined. Finally, the genes identified to participate in Drosophila olfactory learning have conserved roles in mammalian organisms, highlighting the value of Drosophila for gene discovery.

  9. Nucleocytoplasmic Transport: A Paradigm for Molecular Logistics in Artificial Systems.

    Science.gov (United States)

    Vujica, Suncica; Zelmer, Christina; Panatala, Radhakrishnan; Lim, Roderick Y H

    2016-01-01

    Artificial organelles, molecular factories and nanoreactors are membrane-bound systems envisaged to exhibit cell-like functionality. These constitute liposomes, polymersomes or hybrid lipo-polymersomes that display different membrane-spanning channels and/or enclose molecular modules. To achieve more complex functionality, an artificial organelle should ideally sustain a continuous influx of essential macromolecular modules (i.e. cargoes) and metabolites against an outflow of reaction products. This would benefit from the incorporation of selective nanopores as well as specific trafficking factors that facilitate cargo selectivity, translocation efficiency, and directionality. Towards this goal, we describe how proteinaceous cargoes are transported between the nucleus and cytoplasm by nuclear pore complexes and the biological trafficking machinery in living cells (i.e. nucleocytoplasmic transport). On this basis, we discuss how biomimetic control may be implemented to selectively import, compartmentalize and accumulate diverse macromolecular modules against concentration gradients in artificial organelles.

  10. Inelastic molecular collisions: application of theoretical methods to problems relevant to laser operation. Progress report, February 1, 1976--November 1, 1976. [Summary of research activities at Princeton Univ

    Energy Technology Data Exchange (ETDEWEB)

    Rabitz, H

    1976-01-01

    The main goals of this research are to develop and implement various techniques for describing molecular collision phenomena. The aim is to achieve sufficient understanding of these processes such that collision rates of interest (e.g., for gas lasers) may be reliably estimated. Several areas of research are being explored to achieve this goal. The specific molecular systems of H/sub 2/-H/sub 2/, HF-He, HF-Ar and HCl-Ar are being studied as examples of inelastic molecular collisions. In addition, during the past year further theoretical development was conducted in the area of decomposition techniques and effective Hamiltonian theory. Considerable progress was made in these various areas during the past year. This research represents a collaboration under this contract and with Professor R. Conn, University of Wisconsin, under contract AT(11-1)-2555. Much of the material in this report has been published or is presently in press (items indicated by * in the references).

  11. A Parallel Relational Database Management System Approach to Relevance Feedback in Information Retrieval.

    Science.gov (United States)

    Lundquist, Carol; Frieder, Ophir; Holmes, David O.; Grossman, David

    1999-01-01

    Describes a scalable, parallel, relational database-drive information retrieval engine. To support portability across a wide range of execution environments, all algorithms adhere to the SQL-92 standard. By incorporating relevance feedback algorithms, accuracy is enhanced over prior database-driven information retrieval efforts. Presents…

  12. Term Relevance Feedback and Mediated Database Searching: Implications for Information Retrieval Practice and Systems Design.

    Science.gov (United States)

    Spink, Amanda

    1995-01-01

    This study uses the human approach to examine the sources and effectiveness of search terms selected during 40 mediated interactive database searches and focuses on determining the retrieval effectiveness of search terms identified by users and intermediaries from retrieved items during term relevance feedback. (Author/JKP)

  13. Genomics and systems biology - How relevant are the developments to veterinary pharmacology, toxicology and therapeutics?

    NARCIS (Netherlands)

    Witkamp, R.F.

    2005-01-01

    This review discusses some of the recent developments in genomics and its current and future relevance for veterinary pharmacology and toxicology. With the rapid progress made in this field several new approaches in pharmacological and toxicological research have developed and drug discovery and

  14. A new parallel molecular dynamics algorithm for organic systems

    International Nuclear Information System (INIS)

    Plimpton, S.; Hendrickson, B.; Heffelfinger, G.

    1993-01-01

    A new parallel algorithm for simulating bonded molecular systems such as polymers and proteins by molecular dynamics (MD) is presented. In contrast to methods that extract parallelism by breaking the spatial domain into sub-pieces, the new method does not require regular geometries or uniform particle densities to achieve high parallel efficiency. For very large, regular systems spatial methods are often the best choice, but in practice the new method is faster for systems with tens-of-thousands of atoms simulated on large numbers of processors. It is also several times faster than the techniques commonly used for parallelizing bonded MD that assign a subset of atoms to each processor and require all-to-all communication. Implementation of the algorithm in a CHARMm-like MD model with many body forces and constraint dynamics is discussed and timings on the Intel Delta and Paragon machines are given. Example calculations using the algorithm in simulations of polymers and liquid-crystal molecules will also be briefly discussed

  15. Towards Intelligible Query Processing in Relevance Feedback-Based Image Retrieval Systems

    OpenAIRE

    Mohammed, Belkhatir

    2008-01-01

    We have specified within the scope of this paper a framework combining semantics and relational (spatial) characterizations within a coupled architecture in order to address the semantic gap. This framework is instantiated by an operational model based on a sound logic-based formalism, allowing to define a representation for image documents and a matching function to compare index and query structures. We have specified a query framework coupling keyword-based querying with a relevance feedba...

  16. DNA barcode-based molecular identification system for fish species.

    Science.gov (United States)

    Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

    2010-12-01

    In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp .

  17. The Relevance of the Renin-Angiotensin System in the Development of Drugs to Combat Preeclampsia

    OpenAIRE

    Ueki, Norikazu; Takeda, Satoru; Koya, Daisuke; Kanasaki, Keizo

    2015-01-01

    Preeclampsia is a hypertensive disorder that occurs during pregnancy. It has an unknown etiology and affects approximately 5?8% of pregnancies worldwide. The pathophysiology of preeclampsia is not yet known, and preeclampsia has been called ?a disease of theories.? The central symptom of preeclampsia is hypertension. However, the etiology of the hypertension is unknown. In this review, we analyze the molecular mechanisms of preeclampsia with a particular focus on the pathogenesis of the hyper...

  18. DCMS: A data analytics and management system for molecular simulation.

    Science.gov (United States)

    Kumar, Anand; Grupcev, Vladimir; Berrada, Meryem; Fogarty, Joseph C; Tu, Yi-Cheng; Zhu, Xingquan; Pandit, Sagar A; Xia, Yuni

    Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface ( i.e. , SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression.

  19. Assessment of efficiency of functioning the infocommunication systems a special purpose in the conditions of violation quality of relevance information

    Science.gov (United States)

    Parinov, A. V.; Korotkikh, L. P.; Desyatov, D. B.; Stepanov, L. V.

    2018-03-01

    The uniqueness of information processing mechanisms in special-purpose infocommunication systems and the increased interest of intruders lead to an increase in the relevance of the problems associated with their protection. The paper considers the issues of building risk-models for the violation of the relevance and value of information in infocommunication systems for special purposes. Also, special attention is paid to the connection between the qualities of relevance and the value of information obtained as a result of the operation of infocommunication systems for special purposes. Analytical expressions for the risk and damage function in the time range in special-purpose infocommunication systems are obtained, which can serve as a mathematical basis for risk assessment. Further, an analytical expression is obtained to assess the chance of obtaining up-to-date information in the operation of infocommunication systems up to the time the information quality is violated. An analytical expression for estimating the chance can be used to calculate the effectiveness of a special-purpose infocommunication system.

  20. A Method for The Assessing of Reliability Characteristics Relevant to an Assumed Position-Fixing Accuracy in Navigational Positioning Systems

    Directory of Open Access Journals (Sweden)

    Specht Cezary

    2016-09-01

    Full Text Available This paper presents a method which makes it possible to determine reliability characteristics of navigational positioning systems, relevant to an assumed value of permissible error in position fixing. The method allows to calculate: availability , reliability as well as operation continuity of position fixing system for an assumed, determined on the basis of formal requirements - both worldwide and national, position-fixing accuracy. The proposed mathematical model allows to satisfy, by any navigational positioning system, not only requirements as to position-fixing accuracy of a given navigational application (for air , sea or land traffic but also the remaining characteristics associated with technical serviceability of a system.

  1. Why relevance theory is relevant for lexicography

    DEFF Research Database (Denmark)

    Bothma, Theo; Tarp, Sven

    2014-01-01

    This article starts by providing a brief summary of relevance theory in information science in relation to the function theory of lexicography, explaining the different types of relevance, viz. objective system relevance and the subjective types of relevance, i.e. topical, cognitive, situational...... that is very important for lexicography as well as for information science, viz. functional relevance. Since all lexicographic work is ultimately aimed at satisfying users’ information needs, the article then discusses why the lexicographer should take note of all these types of relevance when planning a new...... dictionary project, identifying new tasks and responsibilities of the modern lexicographer. The article furthermore discusses how relevance theory impacts on teaching dictionary culture and reference skills. By integrating insights from lexicography and information science, the article contributes to new...

  2. To bail out or not to bail out systemically relevant financial institutions: The incentives of policy makers

    Directory of Open Access Journals (Sweden)

    Lucas Marc Fuhrer

    2012-11-01

    Full Text Available The recent financial crisis has shown that many financial institutions may be systemically relevant. Their bankruptcy would cause significant costs for the overall economy. However, a clear definition of systemic risks still does not exist. Thus, the decision, whether an institution is, or is not systemically relevant is in the end made by policy makers. This paper takes a closer look at the incentives available to policy makers and their influence on the bailout decision. In the model presented here it is possible to show, that too many financial institutions get bailed out, when assuming that policy makers tend to be more risk-averse than socially optimal. The costs due to this misallocation of resources can be significant.

  3. International Conference on Intelligent Systems for Molecular Biology (ISMB)

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao

    2009-12-29

    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  4. Diffusion-controlled interface kinetics-inclusive system-theoretic propagation models for molecular communication systems

    Science.gov (United States)

    Chude-Okonkwo, Uche A. K.; Malekian, Reza; Maharaj, B. T.

    2015-12-01

    Inspired by biological systems, molecular communication has been proposed as a new communication paradigm that uses biochemical signals to transfer information from one nano device to another over a short distance. The biochemical nature of the information transfer process implies that for molecular communication purposes, the development of molecular channel models should take into consideration diffusion phenomenon as well as the physical/biochemical kinetic possibilities of the process. The physical and biochemical kinetics arise at the interfaces between the diffusion channel and the transmitter/receiver units. These interfaces are herein termed molecular antennas. In this paper, we present the deterministic propagation model of the molecular communication between an immobilized nanotransmitter and nanoreceiver, where the emission and reception kinetics are taken into consideration. Specifically, we derived closed-form system-theoretic models and expressions for configurations that represent different communication systems based on the type of molecular antennas used. The antennas considered are the nanopores at the transmitter and the surface receptor proteins/enzymes at the receiver. The developed models are simulated to show the influence of parameters such as the receiver radius, surface receptor protein/enzyme concentration, and various reaction rate constants. Results show that the effective receiver surface area and the rate constants are important to the system's output performance. Assuming high rate of catalysis, the analysis of the frequency behavior of the developed propagation channels in the form of transfer functions shows significant difference introduce by the inclusion of the molecular antennas into the diffusion-only model. It is also shown that for t > > 0 and with the information molecules' concentration greater than the Michaelis-Menten kinetic constant of the systems, the inclusion of surface receptors proteins and enzymes in the models

  5. Electronic structure, transport, and collective effects in molecular layered systems

    Directory of Open Access Journals (Sweden)

    Torsten Hahn

    2017-10-01

    Full Text Available The great potential of organic heterostructures for organic device applications is exemplified by the targeted engineering of the electronic properties of phthalocyanine-based systems. The transport properties of two different phthalocyanine systems, a pure copper phthalocyanine (CoPc and a flourinated copper phthalocyanine–manganese phthalocyanine (F16CoPc/MnPc heterostructure, are investigated by means of density functional theory (DFT and the non-equilibrium Green’s function (NEGF approach. Furthermore, a master-equation-based approach is used to include electronic correlations beyond the mean-field-type approximation of DFT. We describe the essential theoretical tools to obtain the parameters needed for the master equation from DFT results. Finally, an interacting molecular monolayer is considered within a master-equation approach.

  6. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

  7. Intermolecular thermoelectric-like effects in molecular nano electronic systems

    International Nuclear Information System (INIS)

    Sabzyan, H.; Safari, R.

    2012-01-01

    Intramolecular thermoelectric-like coefficients are introduced and computed of a single molecule nano electronic system. Values of the electronic Intramolecular thermoelectric-like coefficients are calculated based on the density and energy transfers between different parts of the molecule using quantum theory of atoms in molecule. Since, Joule and Peltier heating are even (symmetrical) and odd (antisymmetric) functions of the external bias, it is possible to divide Intramolecular thermoelectric-like coefficients into two components, symmetrical and antisymmetrical Intramolecular thermoelectric-like coefficients, which describe the intramolecular Joule-like and Peltier-like effects, respectively. In addition, a semiclassical temperature model is presented to describe intramolecular temperature mapping (intramolecular energy distributions) in molecular nano electronic systems.

  8. Encounters of The Solar System With Molecular Clouds

    International Nuclear Information System (INIS)

    Wickramasinghe, J. T.

    2008-01-01

    The solar system has penetrated about 5 -- 10 giant molecular clouds over its history, and passes within 5 parsecs of a star-forming nebula every 100 million years or so. Numerical simulations of the effect of such encounters in perturbing the Oort cloud of comets are carried out using standard n-body computational techniques. It is found that the ingress of comets into the inner planetary system during such encounters amounts to factors of ∼100 over the average. During an encounter the impact rate of comets onto Earth increases by a comparable factor. The of ages of impact craters on the Earth is shown to be consistent with predictions from the model

  9. Application of the finite-field coupled-cluster method to calculate molecular properties relevant to electron electric-dipole-moment searches

    Science.gov (United States)

    Abe, M.; Prasannaa, V. S.; Das, B. P.

    2018-03-01

    Heavy polar diatomic molecules are currently among the most promising probes of fundamental physics. Constraining the electric dipole moment of the electron (e EDM ), in order to explore physics beyond the standard model, requires a synergy of molecular experiment and theory. Recent advances in experiment in this field have motivated us to implement a finite-field coupled-cluster (FFCC) approach. This work has distinct advantages over the theoretical methods that we had used earlier in the analysis of e EDM searches. We used relativistic FFCC to calculate molecular properties of interest to e EDM experiments, that is, the effective electric field (Eeff) and the permanent electric dipole moment (PDM). We theoretically determine these quantities for the alkaline-earth monofluorides (AEMs), the mercury monohalides (Hg X ), and PbF. The latter two systems, as well as BaF from the AEMs, are of interest to e EDM searches. We also report the calculation of the properties using a relativistic finite-field coupled-cluster approach with single, double, and partial triples' excitations, which is considered to be the gold standard of electronic structure calculations. We also present a detailed error estimate, including errors that stem from our choice of basis sets, and higher-order correlation effects.

  10. Rhenium(V) oxo complexes relevant to technetium renal imaging agents derived from mercaptoacetylglycylglycylaminobenzoic acid isomers. Structural and molecular mechanics studies

    International Nuclear Information System (INIS)

    Hansen, L.; Taylor, A. Jr; Marzilli, L.G.; Cini, R.

    1992-01-01

    The synthesis and characterization of three rhenium(V) oxo complexes derived from isomers of mercaptoacetylglycylglycylaminobenzoic acid (MAG 2 -ABAH 5 ) are reported. The isomers were synthesized from o-, m- and p-aminobenzoic acid and differed in the position of the terminal carboxyl group. The anions of 8-10, [ReO(MAG 2 -*ABAH)] - (* = para (8), meta (9), ortho (10)), contained the tetraanionic form of the ligands with the carboxyl group protonated. Compounds 8,9, and 10 were synthesized by exchange reactions of ReOCl 3 (Me 2 SO)(Ph 3 P) under moderate conditions and were isolated as [Ph 4 P] + , [Bu 4 N] + , and [Ph 4 P] + salts, respectively. The structures of 8 and 10 were determined by X-ray diffraction methods; except for the location of the carboxyl group, the structures are similar. The coordination geometry is pseudo square pyramidal, with nitrogen and sulfur donor atoms forming a square base and the oxo ligand at the apex. The orientation of the carboxyl group in 10 is anti to the Re double-bond O group. Since the carboxyl groups are protonated in 8 and 10 and in other relevant structures from this class of radiopharmaceuticals including [Ph 4 As][TcO(MAG 3 H)] (MAG 3 H = tetraanionic form of mercaptoacetyltriglycine), the authors developed molecular mechanics parameters that allowed them to calculate the structures of 8, 10, and [TcO(MAG 3 H)] - . They then extended the calculations to all three isomeric complexes in their deprotonated forms and to [TcO(MAG 3 )] 2- in order to approximate their solution phase structures. They conclude that the [TcO(MAG 3 )] 2- species is conformationally flexible, and they have made an initial assessment of structures vs renal clearance

  11. Radio-controlled automatic gas meter-reading system; Releve automatique de compteur par radio

    Energy Technology Data Exchange (ETDEWEB)

    Yasui, M. [Osaka Gas Co., Ltd (Japan); Ishikawa, K.; Fujiwara, J. [Tokyo Gas Co., Ltd. (Japan); Ichihashi, T. [Toho Gas Co., Ltd. (Japan)

    2000-07-01

    In Japan, an automatic gas meter-reading system is in operation, also incorporating the functions of monitoring for abnormalities in gas use and remote-controlled emergency gas supply shutoff. This system has been realized by linking microcomputer-controlled gas meters(It's called 'Intelligent gas mater') equipped with automatic shutoff mechanism to the gas utility company operation center via communication lines. While the present system uses cable communication lines, we of Tokyo Gas Co., Ltd., Osaka Gas Co., Ltd. and Toho Gas Co., Ltd., have jointly developed a new system based on radio communication. This paper introduces this new system. While radio-controlled meter-reading systems are used in many countries around the world solely for automatic meter reading, our recently developed system is also capable of monitoring for abnormalities in gas use and remote-controlled emergency gas supply shutoff, thanks to its almost real-time two-way communication function. The new system can serve for a period of ten years without recharging. It is also characterized by its applicability as different systems according to purposes: 1) conventional automatic meter-reading system (terminal network control unit or T-NCU), 2) large-scale radio-controlled meter-reading system, and 3) portable terminal-type radio-controlled meter-reading system. (authors)

  12. Phase equilibria and molecular interaction studies on (naphthols + vanillin) systems

    International Nuclear Information System (INIS)

    Gupta, Preeti; Agrawal, Tanvi; Das, Shiva Saran; Singh, Nakshatra Bahadur

    2012-01-01

    Highlights: ► Phase equilibria of (naphthol + vanillin) systems have been studied for the first time. ► Eutectic type phase diagrams are obtained. ► Eutectic mixtures show nonideal behaviour. ► There is a weak molecular interaction between the components in the eutectic mixtures. ► α-Naphthol–vanillin eutectic is more stable as compared to β-naphthol–vanillin. - Abstract: Phase equilibria between (α-naphthol + vanillin) and (β-naphthol + vanillin) systems have been studied by thaw-melt method and the results show the formation of simple eutectic mixtures. Crystallization velocities of components and eutectic mixtures were determined at different stages under cooling. With the help of differential scanning calorimeter (DSC), the enthalpy of fusion of components and eutectic mixtures was determined and from the values excess thermodynamic functions viz., excess Gibbs free energy (G E ), excess entropy (S E ), excess enthalpy (H E ) of hypo-, hyper- and eutectic mixtures were calculated. Flexural strength measurements were made in order to understand the non-ideal nature of eutectics. FT-IR spectral studies indicate the formation of hydrogen bond in the eutectic mixture. Anisotropic and isotropic microstructural studies of components, hypo-, hyper- and eutectic mixtures were made. Jackson’s roughness parameter was calculated and found to be greater than 2 suggesting the faceted morphology with irregular structures. The overall results have shown that there is a weak molecular interaction between the components in the eutectic mixtures and the (α-naphthol + vanillin) eutectic is more stable as compared to the (β-naphthol + vanillin) eutectic system.

  13. Costs Systems: Relevance, Feasibility And Usefulness According To Public Officials In The State Of Paraná (Brazil

    Directory of Open Access Journals (Sweden)

    Luciane Maria Gonçalves Franco

    2013-06-01

    Full Text Available The aim in this study is to get to know the level of understanding and adoption of cost systems in cities in the State of Paraná. A descriptive study with a qualitative approach was undertaken. Data were collected through the application of a questionnaire in 67 cities in the State of Paraná. Descriptive analysis was used and Spearman’s correlation coefficient was applied to achieve the research objective. Among the study results, the following stand out: the incipient nature of knowledge about the relevance, feasibility and usefulness of a cost system; resulting from public officials’ limited knowledge, mainly about topics related to the budgetary and financial feasibility of adopting cost systems; an environment for the cost system, implemented costs systems and operating systems; although the answers obtained to proposals about cost information and control were significantly coherent.

  14. Microbial quality and molecular identification of cultivable microorganisms isolated from an urban drinking water distribution system (Limassol, Cyprus).

    Science.gov (United States)

    Botsaris, George; Kanetis, Loukas; Slaný, Michal; Parpouna, Christiana; Makris, Konstantinos C

    2015-12-01

    Microorganisms can survive and multiply in aged urban drinking water distribution systems, leading to potential health risks. The objective of this work was to investigate the microbial quality of tap water and molecularly identify its predominant cultivable microorganisms. Tap water samples collected from 24 different households scattered in the urban area of Limassol, Cyprus, were microbiologically tested following standard protocols for coliforms, E. coli, Pseudomonas spp., Enterococcus spp., and total viable count at 22 and 37 °C. Molecular identification was performed on isolated predominant single colonies using 16SrRNA sequencing. Approximately 85% of the household water samples were contaminated with one or more microorganisms belonging to the genera of Pseudomonas, Corynebacterium, Agrobacterium, Staphylococcus, Bacillus, Delftia, Acinetobacter, Enterococcus, Enterobacter, and Aeromonas. However, all samples tested were free from E. coli. This is the first report in Cyprus molecularly confirming specific genera of relevant microbial communities in tap water.

  15. Charge migration and charge transfer in molecular systems

    Directory of Open Access Journals (Sweden)

    Hans Jakob Wörner

    2017-11-01

    Full Text Available The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of research. An important recent impetus comes from the ability to resolve ever faster temporal events, down to the attosecond time scale. Such a high temporal resolution now offers the possibility to unravel the most elementary quantum dynamics of both electrons and nuclei that participate in the complex process of charge transfer. This review covers recent research that addresses the following questions. Can we reconstruct the migration of charge across a molecule on the atomic length and electronic time scales? Can we use strong laser fields to control charge migration? Can we temporally resolve and understand intramolecular charge transfer in dissociative ionization of small molecules, in transition-metal complexes and in conjugated polymers? Can we tailor molecular systems towards specific charge-transfer processes? What are the time scales of the elementary steps of charge transfer in liquids and nanoparticles? Important new insights into each of these topics, obtained from state-of-the-art ultrafast spectroscopy and/or theoretical methods, are summarized in this review.

  16. Evidence for systems-level molecular mechanisms of tumorigenesis

    Directory of Open Access Journals (Sweden)

    Capellá Gabriel

    2007-06-01

    Full Text Available Abstract Background Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth. Results Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs" defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree and global (betweenness and closeness measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis. Conclusion Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins.

  17. Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems

    Science.gov (United States)

    Stanton, L. G.; Glosli, J. N.; Murillo, M. S.

    2018-04-01

    Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.

  18. The global stock of research evidence relevant to health systems policymaking

    OpenAIRE

    Wilson, Michael G; Moat, Kaelan A; Lavis, John N

    2013-01-01

    Background: Policymakers and stakeholders need immediate access to many types of research evidence to make informed decisions about the full range of questions that may arise regarding health systems. Methods: We examined all types of research evidence about governance, financial and delivery arrangements, and implementation strategies within health systems contained in Health Systems Evidence (HSE) (http://www.healthsystemsevidence.org). The research evidence types include evidence briefs fo...

  19. Relevance of deterministic chaos theory to studies in functioning of dynamical systems

    Science.gov (United States)

    Glagolev, S. N.; Bukhonova, S. M.; Chikina, E. D.

    2018-03-01

    The paper considers chaotic behavior of dynamical systems typical for social and economic processes. Approaches to analysis and evaluation of system development processes are studies from the point of view of controllability and determinateness. Explanations are given for necessity to apply non-standard mathematical tools to explain states of dynamical social and economic systems on the basis of fractal theory. Features of fractal structures, such as non-regularity, self-similarity, dimensionality and fractionality are considered.

  20. Artificial liver support with the molecular adsorbent recirculating system: activation of coagulation and bleeding complications.

    Science.gov (United States)

    Bachli, Esther B; Schuepbach, Reto A; Maggiorini, Marco; Stocker, Reto; Müllhaupt, Beat; Renner, Eberhard L

    2007-05-01

    Numerous, mostly uncontrolled, observations suggest that artificial liver support with the Molecular Adsorbent Recirculating System (MARS) improves pathophysiologic sequelae and outcome of acute and acute-on-chronic liver failure. MARS is felt to be safe, but extracorporeal circuits may activate coagulation. To assess the frequency of and risk factors for activation of coagulation during MARS treatment. Retrospective analysis of coagulopathy/bleeding complications observed during 83 consecutive MARS sessions in 21 patients (11 men; median age 46 years; median three sessions per patient; median duration of session 8 h). Nine clinically relevant episodes of coagulopathy/bleeding were observed in eight patients, forced to premature cessation of MARS in seven and ended lethal in four. Four complications occurred during the first, five during later (third to seventh) MARS sessions and two bleeders tolerated further sessions without complications. Coagulation parameters worsened significantly also during MARS sessions not associated with bleeding (PMARS therapy, potentially leading to bleeding complications and mortality.

  1. Stability of Naturally Relevant Ternary Phases in the Cu–Sn–S system in Contact with an Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Andrea Giaccherini

    2016-07-01

    Full Text Available A relevant research effort is devoted to the synthesis and characterization of phases belonging to the ternary system Cu–Sn–S, mainly for their possible applications in semiconductor technology. Among all ternary phases, kuramite, Cu3SnS4, mohite, Cu2SnS3, and Cu4Sn7S16 have attracted the highest interest. Numerous studies were carried out claiming for the description of new phases in the ternary compositional field. In this study, we revise the existing literature on this ternary system, with a special focus on the phases stable in a temperature range at 25 °C. The only two ternary phases observed in nature are mohite and kuramite. Their occurrence is described as very rare. A numerical modelling of the stable solid phases in contact with a water solution was underwent to define stability relationships of the relevant phases of the system. The numerical modelling of the Eh-pH diagrams was carried out through the phreeqc software with the lnll.dat thermodynamic database. Owing to the complexity of this task, the subsystems Cu–O–H, Sn–O–H, Cu–S–O–H and Sn–S–O–H were firstly considered. The first Pourbaix diagram for the two naturally relevant ternary phases is then proposed.

  2. Greenhouse gas emission mitigation relevant to changes in municipal solid waste management system.

    Science.gov (United States)

    Pikoń, Krzysztof; Gaska, Krzysztof

    2010-07-01

    Standard methods for assessing the environmental impact of waste management systems are needed to underpin the development and implementation of sustainable waste management practice. Life cycle assessment (LCA) is a tool for comprehensively ensuring such assessment and covers all impacts associated with waste management. LCA is often called "from cradle to grave" analysis. This paper integrates information on the greenhouse gas (GHG) implications of various management options for some of the most common materials in municipal solid waste (MSW). Different waste treatment options for MSW were studied in a system analysis. Different combinations of recycling (cardboard, plastics, glass, metals), biological treatment (composting), and incineration as well as land-filling were studied. The index of environmental burden in the global warming impact category was calculated. The calculations are based on LCA methodology. All emissions taking place in the whole life cycle system were taken into account. The analysis included "own emissions," or emissions from the system at all stages of the life cycle, and "linked emissions," or emissions from other sources linked with the system in an indirect way. Avoided emissions caused by recycling and energy recovery were included in the analysis. Displaced emissions of GHGs originate from the substitution of energy or materials derived from waste for alternative sources. The complex analysis of the environmental impact of municipal waste management systems before and after application of changes in MSW systems according to European Union regulations is presented in this paper. The evaluation is made for MSW systems in Poland.

  3. Cutting the gordian knot-development and biological relevance of hepatitis C virus cell culture systems

    DEFF Research Database (Denmark)

    Gottwein, Judith Margarete; Bukh, Jens

    2008-01-01

    described. Research on the viral life cycle, efficient therapeutics, and a vaccine has been hampered by the absence of suitable cell culture systems. The first system permitting studies of the full viral life cycle was intrahepatic transfection of RNA transcripts of HCV consensus complementary DNA (c...... studies of the function of viral proteins, their interaction with each other and host proteins, new antivirals, and neutralizing antibodies in the context of the full viral life cycle. However, several challenges remain, including development of cell culture systems for all major HCV genotypes...... isolate JFH1, which for unknown reasons showed an exceptional replication capability and resulted in formation of infectious viral particles in the human hepatoma cell line Huh7, led in 2005 to the development of the first full viral life cycle in vitro systems. JFH1-based systems now enable in vitro...

  4. Molecular dynamic simulations of the sputtering of multilayer organic systems

    CERN Document Server

    Postawa, Z; Piaskowy, J; Krantzman, K; Winograd, N; Garrison, B J

    2003-01-01

    Sputtering of organic overlayers has been modeled using molecular dynamics computer simulations. The investigated systems are composed of benzene molecules condensed into one, two and three layers on an Ag left brace 1 1 1 right brace surface. The formed organic overlayers were bombarded with 4 keV Ar projectiles at normal incidence. The development of the collision cascade in the organic overlayer was investigated. The sputtering yield, mass, internal and kinetic energy distributions of ejected particles have been analyzed as a function of the thickness of the organic layer. The results show that all emission characteristics are sensitive to the variation of layer thickness. Although most of the ejected intact benzene molecules originate from the topmost layer, the emission of particles located initially in second and third layers is significant. The analysis indicates that the metallic substrate plays a dominant role in the ejection of intact organic molecules.

  5. Pancreatic Cancer Gene Therapy: From Molecular Targets to Delivery Systems

    Energy Technology Data Exchange (ETDEWEB)

    Fillat, Cristina, E-mail: cristina.fillat@crg.es; Jose, Anabel; Ros, Xavier Bofill-De; Mato-Berciano, Ana; Maliandi, Maria Victoria; Sobrevals, Luciano [Programa Gens i Malaltia, Centre de Regulació Genòmica-CRG, UPF, Parc de Recerca Biomedica de Barcelona-PRBB and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona (Spain)

    2011-01-18

    The continuous identification of molecular changes deregulating critical pathways in pancreatic tumor cells provides us with a large number of novel candidates to engineer gene-targeted approaches for pancreatic cancer treatment. Targets—both protein coding and non-coding—are being exploited in gene therapy to influence the deregulated pathways to facilitate cytotoxicity, enhance the immune response or sensitize to current treatments. Delivery vehicles based on viral or non-viral systems as well as cellular vectors with tumor homing characteristics are a critical part of the design of gene therapy strategies. The different behavior of tumoral versus non-tumoral cells inspires vector engineering with the generation of tumor selective products that can prevent potential toxic-associated effects. In the current review, a detailed analysis of the different targets, the delivery vectors, the preclinical approaches and a descriptive update on the conducted clinical trials are presented. Moreover, future possibilities in pancreatic cancer treatment by gene therapy strategies are discussed.

  6. Isolating strong-field dynamics in molecular systems

    Science.gov (United States)

    Orenstein, Gal; Pedatzur, Oren; Uzan, Ayelet J.; Bruner, Barry D.; Mairesse, Yann; Dudovich, Nirit

    2017-05-01

    Strong-field ionization followed by recollision provides a unique pump-probe measurement which reveals a range of electronic processes, combining sub-Angstrom spatial and attosecond temporal resolution. A major limitation of this approach is imposed by the coupling between the spatial and temporal degrees of freedom. In this paper we focus on the study of high harmonic generation and demonstrate the ability to isolate the internal dynamics—decoupling the temporal information from the spatial one. By applying an in situ approach we reveal the universality of the intrinsic pump-probe measurement and establish its validity in molecular systems. When several orbitals are involved we identify the fingerprint of the transition from the single-channel case into the multiple-channel dynamics, where complex multielectron phenomena are expected to be observed.

  7. Cocaine and MDMA Induce Cellular and Molecular Changes in Adult Neurogenic Systems: Functional Implications

    Directory of Open Access Journals (Sweden)

    Vivian Capilla-Gonzalez

    2011-06-01

    Full Text Available The capacity of the brain to generate new adult neurons is a recent discovery that challenges the old theory of an immutable adult brain. A new and fascinating field of research now focuses on this regenerative process. The two brain systems that constantly produce new adult neurons, known as the adult neurogenic systems, are the dentate gyrus (DG of the hippocampus and the lateral ventricules/olfactory bulb system. Both systems are involved in memory and learning processes. Different drugs of abuse, such as cocaine and MDMA, have been shown to produce cellular and molecular changes that affect adult neurogenesis. This review summarizes the effects that these drugs have on the adult neurogenic systems. The functional relevance of adult neurogenesis is obscured by the functions of the systems that integrate adult neurons. Therefore, we explore the effects that cocaine and MDMA produce not only on adult neurogenesis, but also on the DG and olfactory bulbs. Finally, we discuss the possible role of new adult neurons in cocaine- and MDMA-induced impairments. We conclude that, although harmful drug effects are produced at multiple physiological and anatomical levels, the specific consequences of reduced hippocampus neurogenesis are unclear and require further exploration.

  8. Earth applications of closed ecological systems: relevance to the development of sustainability in our global biosphere.

    Science.gov (United States)

    Nelson, M; Allen, J; Alling, A; Dempster, W F; Silverstone, S

    2003-01-01

    The parallels between the challenges facing bioregenerative life support in artificial closed ecological systems and those in our global biosphere are striking. At the scale of the current global technosphere and expanding human population, it is increasingly obvious that the biosphere can no longer safely buffer and absorb technogenic and anthropogenic pollutants. The loss of biodiversity, reliance on non-renewable natural resources, and conversion of once wild ecosystems for human use with attendant desertification/soil erosion, has led to a shift of consciousness and the widespread call for sustainability of human activities. For researchers working on bioregenerative life support in closed systems, the small volumes and faster cycling times than in the Earth's biosphere make it starkly clear that systems must be designed to ensure renewal of water and atmosphere, nutrient recycling, production of healthy food, and safe environmental methods of maintaining technical systems. The development of technical systems that can be fully integrated and supportive of living systems is a harbinger of new perspectives as well as technologies in the global environment. In addition, closed system bioregenerative life support offers opportunities for public education and consciousness changing of how to live with our global biosphere. c2003 COSPAR. Published by Elsevier Science Ltd. All rights reserved.

  9. The Neuromodulation of the Intestinal Immune System and Its Relevance in Inflammatory Bowel Disease.

    Science.gov (United States)

    Di Giovangiulio, Martina; Verheijden, Simon; Bosmans, Goele; Stakenborg, Nathalie; Boeckxstaens, Guy E; Matteoli, Gianluca

    2015-01-01

    One of the main tasks of the immune system is to discriminate and appropriately react to "danger" or "non-danger" signals. This is crucial in the gastrointestinal tract, where the immune system is confronted with a myriad of food antigens and symbiotic microflora that are in constant contact with the mucosa, in addition to any potential pathogens. This large number of antigens and commensal microflora, which are essential for providing vital nutrients, must be tolerated by the intestinal immune system to prevent aberrant inflammation. Hence, the balance between immune activation versus tolerance should be tightly regulated to maintain intestinal homeostasis and to prevent immune activation indiscriminately against all luminal antigens. Loss of this delicate equilibrium can lead to chronic activation of the intestinal immune response resulting in intestinal disorders, such as inflammatory bowel diseases (IBD). In order to maintain homeostasis, the immune system has evolved diverse regulatory strategies including additional non-immunological actors able to control the immune response. Accumulating evidence strongly indicates a bidirectional link between the two systems in which the brain modulates the immune response via the detection of circulating cytokines and via direct afferent input from sensory fibers and from enteric neurons. In the current review, we will highlight the most recent findings regarding the cross-talk between the nervous system and the mucosal immune system and will discuss the potential use of these neuronal circuits and neuromediators as novel therapeutic tools to reestablish immune tolerance and treat intestinal chronic inflammation.

  10. Biomass-fuelled PEMFC systems: Evaluation of two conversion paths relevant for different raw materials

    International Nuclear Information System (INIS)

    Guan, Tingting; Chutichai, Bhawasut; Alvfors, Per; Arpornwichanop, Amornchai

    2015-01-01

    Highlights: • Anaerobic digestion and gasification are viable biomass conversion technologies. • GF-PEMFC system yields a 20% electric efficiency and 57% thermal efficiency. • AD-PEMFC system has a 9% electric efficiency and 13% thermal efficiency. • AD-PEMFC system has an efficient land-use. • GF-PEMFC system has a high CO_2 emissions offset factor. - Abstract: Biomass-fuelled polymer electrolyte membrane fuel cells (PEMFCs) offer a solution for replacing fossil fuel with hydrogen production. This paper uses simulation methods for investigating biomass-fuelled PEMFCs for different raw materials and conversion paths. For liquid and solid biomass, anaerobic digestion (AD) and gasification (GF), respectively, are relatively viable and developed conversion technologies. Therefore, the AD-PEMFC system and the GF-PEMFC system are simulated for residential applications in order to evaluate the performance of the biomass-fuelled PEMFC systems. The results of the evaluation show that renewable hydrogen-rich gas from manure or forest residues is usable for the PEMFCs and makes the fuel cell stack work in a stable manner. For 100 kWe generation, the GF-PEMFC system yields an excellent technical performance with a 20% electric efficiency and 57% thermal efficiency, whereas the AD-PEMFC system only has an 9% electric efficiency and 13% thermal efficiency due to the low efficiency of the anaerobic digester (AD) and the high internal heat consumption of the AD and the steam reformer (SR). Additionally, in this study, the environmental performances of the AD-PEMFC and the GF-PEMFC in terms of CO_2 emission offset and land-use efficiency are discussed.

  11. Radar-based alert system to operate a sewerage network: relevance and operational effectiveness after several years of use.

    Science.gov (United States)

    Faure, D; Payrastre, O; Auchet, P

    2005-01-01

    Since January 2000, the sewerage network of a very urbanised catchment area in the Greater Nancy Urban Community has been operated according to the alarms generated in real time by a storm alert system using weather radar data. This alert system is based on an automatic identification of intense rain cells in the radar images. This paper presents the characteristics of this alert system and synthesises the main results of two complementary studies realised in 2002 in order to estimate the relevance and the operational effectiveness of the alert system. The first study consisted in an off-line analysis of almost 50,000 intense rain cells detected in four years of historical radar data. The second study was an analysis of the experience feedback after two years of operational use of this alert system. The results of these studies are discussed in function of the initial operational objectives.

  12. Absolute cross sections measurement for the 12C + 12C system at astrophysically relevant energies

    International Nuclear Information System (INIS)

    Barron-Palos, L.; Aguilera, E.F.; Aspiazu, J.; Huerta, A.; Martinez-Quiroz, E.; Monroy, R.; Moreno, E.; Murillo, G.; Ortiz, M.E.; Policroniades, R.; Varela, A.; Chavez, E.

    2006-01-01

    The 12 C + 12 C fusion reaction has been studied in the center-of-mass energy range of 2.25 to 6.01 MeV. Through the detection of gamma rays from the first excited states of the residual nuclei 20 Ne, 23 Na and 23 Mg, absolute cross sections for the 12 C( 12 C,-bar α), 12 C( 12 C,-bar p) and 12 C( 12 C,-bar n) reactions have been obtained. In this new measurement, the energy dependence of the S-factor is found to increase as the energy decreases below 3 MeV in the center of mass. This tendency was observed in previous measurements by Mazarakis et al., and has since then become a subject of controversy. In this work, where the cross sections are measured at even lower energies, we confirm the rise in the S-factor toward the energy region relevant for star evolution and nucleosynthesis calculations (E c.m. =1-3 MeV)

  13. Genetic traits of relevance to sustainability of smallholder sheep farming systems in South Africa

    NARCIS (Netherlands)

    Molotsi, Annelin; Dube, Bekezela; Oosting, Simon; Marandure, Tawanda; Mapiye, Cletos; Cloete, Schalk; Dzama, Kennedy

    2017-01-01

    Sustainable livestock production is important to ensure continuous availability of resources for future generations. Most smallholder livestock farming systems in developing countries have been perceived to be environmentally, socially and economically unsustainable. Farming with livestock that is

  14. Thermodynamics and phase equilibria of ternary systems relevant to contact materials for compound semiconductors

    International Nuclear Information System (INIS)

    Ipser, H.; Richter, K.; Micke, K.

    1997-01-01

    In order to investigate the stability of ohmic contacts to compound semiconductors, it is necessary to know the phase equilibria in the corresponding multi-component systems. We are currently studying the phase equilibria and thermophysical properties of several ternary systems which are of interest in view of the use of nickel, palladium and platinum as contact materials for GaSb and InSb compound semiconductors: Ga-Ni-Sb, In-Ni-Sb, Ga-Pd-Sb and Ga-Pt-Sb. Phase equilibria are investigated by thermal analyses, X-ray powder diffraction methods as well as electron microprobe analysis. Thermodynamic properties are derived from vapour pressure measurements using an isopiestic method. It is planned to combine all information on phase equilibria and thermochemistry for the ternary and the limiting binary systems to perform an optimization of the ternary systems by computer calculations using standard software. (author)

  15. Calculation of the reliability of large complex systems by the relevant path method

    International Nuclear Information System (INIS)

    Richter, G.

    1975-03-01

    In this paper, analytical methods are presented and tested with which the probabilistic reliability data of technical systems can be determined for given fault trees and block diagrams and known reliability data of the components. (orig./AK) [de

  16. Relevance of the formal red meat classification system to the South ...

    African Journals Online (AJOL)

    zimmy

    2015-08-01

    Aug 1, 2015 ... Keywords: Communal farmers, marketing system, meat industry .... Goat production. There are about 6.6 million goats in South Africa (De Villiers et al., 2009). Sixty-three ...... North West Province, South Africa. MSc thesis ...

  17. Earth Applications of Closed Ecological Systems: Relevance to the Development of Sustainability in our Global Biosphere

    Science.gov (United States)

    Dempster, W.; van Thillo, M.; Alling, A.; Allen, J.; Silverstone, S.; Nelson, M.

    The parallels between the challenges facing bioregenerative life support and closed ecological systems and those in our global biosphere are striking. At the scale of the current global technosphere and human population, it is increasingly obvious that the biosphere can no longer be counted on to be vast enough to safely buffer and absorb technogenic and anthropogenic pollutants. With an increasing percentage of the world's natural resources and primary productivity being dictated by, and directed to, humans, our species is starting to appreciate its survival and quality of life depends on regulating its activities, and insuring that crucial biogeochemical cycles continue to function. This shift of consciousness has led to the widespread call for moving towards the sustainability of human activities. For researchers working on bioreenerative life support, the small volumes and faster cycling times have made it obvious that systems must be created in to ensure renewal of water and atmosphere, nutrient recycling, and where all technical systems can be safely integrated with the maintenance of safe environmental conditions. The development of technical systems that can be fully integrated with the living systems that they support should be a harbinger of new perspectives in the global environment. The paper will review some of these environmental technologies which are emerging from bioregenerative life support system research such as high-yield intensive agricultural methods, waste treatment and nutrient recycling, air purification, modeling, sensor and control systems and their potential applications in the global biosphere. In addition, a review of the human experience in closed ecological systems shows that these can offer opportunities for public education and consciousness-changing of how humans regard our global biosphere.

  18. Which Management Control System principles and aspects are relevant when deploying a learning machine?

    OpenAIRE

    Martin, Johansson; Mikael, Göthager

    2017-01-01

    How shall a business adapt its management control systems when learning machines enter the arena? Will the control system continue to focus on humans aspects and continue to consider a learning machine to be an automation tool as any other historically programmed computer? Learning machines introduces productivity capabilities that achieve very high levels of efficiency and quality. A learning machine can sort through large amounts of data and make conclusions difficult by a human mind. Howev...

  19. Applying the System Component and Operationally Relevant Evaluation (SCORE) Framework to Evaluate Advanced Military Technologies

    Science.gov (United States)

    2010-03-01

    and charac- terize the actions taken by the soldier (e.g., running, walking, climbing stairs ). Real-time image capture and exchange N The ability of...multimedia information sharing among soldiers in the field, two-way speech translation systems, and autonomous robotic platforms. Key words: Emerging...soldiers in the field, two-way speech translation systems, and autonomous robotic platforms. It has been the foundation for 10 technology evaluations

  20. Infectious Disease Surveillance in the Big Data Era: Towards Faster and Locally Relevant Systems

    Science.gov (United States)

    Simonsen, Lone; Gog, Julia R.; Olson, Don; Viboud, Cécile

    2016-01-01

    While big data have proven immensely useful in fields such as marketing and earth sciences, public health is still relying on more traditional surveillance systems and awaiting the fruits of a big data revolution. A new generation of big data surveillance systems is needed to achieve rapid, flexible, and local tracking of infectious diseases, especially for emerging pathogens. In this opinion piece, we reflect on the long and distinguished history of disease surveillance and discuss recent developments related to use of big data. We start with a brief review of traditional systems relying on clinical and laboratory reports. We then examine how large-volume medical claims data can, with great spatiotemporal resolution, help elucidate local disease patterns. Finally, we review efforts to develop surveillance systems based on digital and social data streams, including the recent rise and fall of Google Flu Trends. We conclude by advocating for increased use of hybrid systems combining information from traditional surveillance and big data sources, which seems the most promising option moving forward. Throughout the article, we use influenza as an exemplar of an emerging and reemerging infection which has traditionally been considered a model system for surveillance and modeling. PMID:28830112

  1. Infectious Disease Surveillance in the Big Data Era: Towards Faster and Locally Relevant Systems.

    Science.gov (United States)

    Simonsen, Lone; Gog, Julia R; Olson, Don; Viboud, Cécile

    2016-12-01

    While big data have proven immensely useful in fields such as marketing and earth sciences, public health is still relying on more traditional surveillance systems and awaiting the fruits of a big data revolution. A new generation of big data surveillance systems is needed to achieve rapid, flexible, and local tracking of infectious diseases, especially for emerging pathogens. In this opinion piece, we reflect on the long and distinguished history of disease surveillance and discuss recent developments related to use of big data. We start with a brief review of traditional systems relying on clinical and laboratory reports. We then examine how large-volume medical claims data can, with great spatiotemporal resolution, help elucidate local disease patterns. Finally, we review efforts to develop surveillance systems based on digital and social data streams, including the recent rise and fall of Google Flu Trends. We conclude by advocating for increased use of hybrid systems combining information from traditional surveillance and big data sources, which seems the most promising option moving forward. Throughout the article, we use influenza as an exemplar of an emerging and reemerging infection which has traditionally been considered a model system for surveillance and modeling. Published by Oxford University Press for the Infectious Diseases Society of America 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  2. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  3. Bicanonical ab Initio Molecular Dynamics for Open Systems.

    Science.gov (United States)

    Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

    2017-08-08

    Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

  4. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, Evangelia; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plechá č, P.; Harmandaris, V.

    2016-01-01

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  5. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, Evangelia

    2016-10-18

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  6. Neural representation of calling songs and their behavioral relevance in the grasshopper auditory system

    Directory of Open Access Journals (Sweden)

    Gundula eMeckenhäuser

    2014-12-01

    Full Text Available Acoustic communication plays a key role for mate attraction in grasshoppers. Males use songs to advertise themselves to females. Females evaluate the song pattern, a repetitive structure of sound syllables separated by short pauses, to recognize a conspecific male and as proxy to its fitness. In their natural habitat females often receive songs with degraded temporal structure. Perturbations may, for example, result from the overlap with other songs. We studied the response behavior of females to songs that show different signal degradations. A perturbation of an otherwise attractive song at later positions in the syllable diminished the behavioral response, whereas the same perturbation at the onset of a syllable did not affect song attractiveness. We applied naïve Bayes classifiers to the spike trains of identified neurons in the auditory pathway to explore how sensory evidence about the acoustic stimulus and its attractiveness is represented in the neuronal responses. We find that populations of three or more neurons were sufficient to reliably decode the acoustic stimulus and to predict its behavioral relevance from the single-trial integrated firing rate. A simple model of decision making simulates the female response behavior. It computes for each syllable the likelihood for the presence of an attractive song pattern as evidenced by the population firing rate. Integration across syllables allows the likelihood to reach a decision threshold and to elicit the behavioral response. The close match between model performance and animal behavior shows that a spike rate code is sufficient to enable song pattern recognition.

  7. Analysis of ancestral and functionally relevant CD5 variants in systemic lupus erythematosus patients.

    Directory of Open Access Journals (Sweden)

    Maria Carmen Cenit

    Full Text Available CD5 plays a crucial role in autoimmunity and is a well-established genetic risk factor of developing RA. Recently, evidence of positive selection has been provided for the CD5 Pro224-Val471 haplotype in East Asian populations. The aim of the present work was to further analyze the functional relevance of non-synonymous CD5 polymorphisms conforming the ancestral and the newly derived haplotypes (Pro224-Ala471 and Pro224-Val471, respectively as well as to investigate the potential role of CD5 on the development of SLE and/or SLE nephritis.The CD5 SNPs rs2241002 (C/T; Pro224Leu and rs2229177 (C/T; Ala471Val were genotyped using TaqMan allelic discrimination assays in a total of 1,324 controls and 681 SLE patients of Spanish origin. In vitro analysis of CD3-mediated T cell proliferative and cytokine response profiles of healthy volunteers homozygous for the above mentioned CD5 haplotypes were also analyzed.T-cell proliferation and cytokine release were significantly increased showing a bias towards to a Th2 profile after CD3 cross-linking of peripheral mononuclear cells from healthy individuals homozygous for the ancestral Pro224-Ala471 (CC haplotype, compared to the more recently derived Pro224-Val471 (CT. The same allelic combination was statistically associated with Lupus nephritis.The ancestral Ala471 CD5 allele confers lymphocyte hyper-responsiveness to TCR/CD3 cross-linking and is associated with nephritis in SLE patients.

  8. RELEVANT OBJECTIVES OF ASSURANCE OF RELIABILITY OF FACADE SYSTEMS SERVING THERMAL INSULATION AND FINISHING PURPOSES

    Directory of Open Access Journals (Sweden)

    Yavorskiy Andrey Andreevich

    2012-12-01

    Full Text Available The authors consider up-to-date methods of implementation of requirements stipulated by Federal Law no. 261-FZ that encompasses reduction of heat losses through installation of progressive heat-insulation systems, cement plaster system (CPS, and ventilated facades (VF. Unresolved problems of their efficient application caused by the absence of the all-Russian regulatory documents capable of controlling the processes of their installation and maintenance, as well as the projection of their behaviour, are also considered in the article. The authors argue that professional skills of designers and construction workers responsible for the design and installation of façade systems influence the quality and reliability of design and construction works. Unavailability of unified solutions or regulations serves as the objective reason for the unavailability of the respective database; therefore, there is an urgent need to perform a set of researches to have the unified database compiled. The authors use the example of thermal insulation cement plaster systems designated for facades as results of researches into the quantitative analysis of safety systems. Collected and systematized data that cover defects that have proven to be reasons for failures, as well as potential methods of their prevention are also studied. Data on pilot studies of major factors of influence onto reliability of glutinous adhesion of CPS to the base of a wall are provided.

  9. Materials degradation in fission reactors: Lessons learned of relevance to fusion reactor systems

    International Nuclear Information System (INIS)

    Was, Gary S.

    2007-01-01

    The management of materials in power reactor systems has become a critically important activity in assuring the safe, reliable and economical operation of these facilities. Over the years, the commercial nuclear power reactor industry has faced numerous 'surprises' and unexpected occurrences in materials. Mitigation strategies have sometimes solved one problem at the expense of creating another. Other problems have been solved successfully and have motivated the development of techniques to foresee problems before they occur. This paper focuses on three aspects of fission reactor experience that may benefit future fusion systems. The first is identification of parameters and processes that have had a large impact on the behavior of materials in fission systems such as temperature, dose rate, surface condition, gradients, metallurgical variability and effects of the environment. The second is the development of materials performance and failure models to provide a basis for assuring component integrity. Last is the development of proactive materials management programs that identify and pre-empt degradation processes before they can become problems. These aspects of LWR experience along with the growing experience with materials in the more demanding advanced fission reactor systems form the basis for a set of 'lessons learned' to aid in the successful management of materials in fusion reactor systems

  10. Molecular tailoring of interfaces for thin film on substrate systems

    Science.gov (United States)

    Grady, Martha Elizabeth

    Thin film on substrate systems appear most prevalently within the microelectronics industry, which demands that devices operate in smaller and smaller packages with greater reliability. The reliability of these multilayer film systems is strongly influenced by the adhesion of each of the bimaterial interfaces. During use, microelectronic components undergo thermo-mechanical cycling, which induces interfacial delaminations leading to failure of the overall device. The ability to tailor interfacial properties at the molecular level provides a mechanism to improve thin film adhesion, reliability and performance. This dissertation presents the investigation of molecular level control of interface properties in three thin film-substrate systems: photodefinable polyimide films on passivated silicon substrates, self-assembled monolayers at the interface of Au films and dielectric substrates, and mechanochemically active materials on rigid substrates. For all three materials systems, the effect of interfacial modifications on adhesion is assessed using a laser-spallation technique. Laser-induced stress waves are chosen because they dynamically load the thin film interface in a precise, noncontacting manner at high strain rates and are suitable for both weak and strong interfaces. Photodefinable polyimide films are used as dielectrics in flip chip integrated circuit packages to reduce the stress between silicon passivation layers and mold compound. The influence of processing parameters on adhesion is examined for photodefinable polyimide films on silicon (Si) substrates with three different passivation layers: silicon nitride (SiNx), silicon oxynitride (SiOxNy), and the native silicon oxide (SiO2). Interfacial strength increases when films are processed with an exposure step as well as a longer cure cycle. Additionally, the interfacial fracture energy is assessed using a dynamic delamination protocol. The high toughness of this interface (ca. 100 J/m2) makes it difficult

  11. System for steam-reactivity measurements on fusion-relevant materials

    International Nuclear Information System (INIS)

    Anderl, R.A.; Pawelko, R.J.; Oates, M.A.; Smolik, G.R.; McCarthy, K.A.

    1996-01-01

    This paper describes an experimental system developed to investigate steam-metal reactions important to fusion technology. The system is configured specifically to measure hydrogen generation rates and tritium mobilization rates for irradiated beryllium specimens that are heated and exposed to steam. Results are presented for extensive performance and scoping tests of the system to validate the experimental technique, to determine hydrogen-generation rate detection sensitivity, and to establish appropriate calibration methods. These results include measurements of the hydrogen generation rates for steam interactions with austenitic steel, tungsten and beryllium metal specimens. The results of these scoping tests compare favorably with previous work, and they indicate a significant improvement in hydrogen detection sensitivity over previous approaches. 6 refs., 9 figs., 1 tab

  12. Inorganic concepts relevant to metal binding, activity, and toxicity in a biological system

    Energy Technology Data Exchange (ETDEWEB)

    Hoeschele, J.D. (Warner-Lambert Co., Ann Arbor, MI (USA). Parke-Davis Pharmaceutical Research Div.); Turner, J.E.; England, M.W. (Oak Ridge National Lab., TN (USA))

    1990-01-01

    The purpose of this paper is to review selected physical and inorganic concepts and factors which might be important in assessing and/or understanding the fact and disposition of a metal system in a biological environment. Hopefully, such inquiries will ultimately permit us to understand, rationalize, and predict differences and trends in biological effects as a function of the basic nature of a metal system and, in optimal cases, serve as input to a system of guidelines for the notion of Chemical Dosimetry.'' The plan of this paper is to first review, in general terms, the basic principles of the Crystal Field Theory (CFT), a unifying theory of bonding in metal complexes. This will provide the necessary theoretical background for the subsequent discussion of selected concepts and factors. 21 refs., 7 figs., 6 tabs.

  13. Maintenance systems and procedures used in a nuclear power station and their relevance to other industries

    International Nuclear Information System (INIS)

    Kirk, R.R.

    1985-01-01

    The maintenance systems and procedures used at the Forsmark Nuclear Power Plant in Sweden can be viewed as a model which maintenance managers in other non-nuclear industries may adapt for their purposes. With the aid of a computerized information system covering the functions of work orders, preventative maintenance, documentation and others, plus a more conventional personnel structure, the result is an efficient, confident and well informed maintenance group. By following the basic design principles of the computerized information system used at the Forsmark Nuclear Power Station plus similar personnel structures, the performance of maintenance teams in non-nuclear manufacturing, processing and other industries could be improved to the standards of those observed

  14. An ITER-relevant evacuated waveguide transmission system for the JET-EP ECRH project

    International Nuclear Information System (INIS)

    Henderson, M.A.; Alberti, S.; Bird, J.

    2003-01-01

    An over-moded evacuated waveguide line was chosen for use in the transmission system for the proposed JET-enhanced performance project (JET-EP) electron cyclotron resonance heating (ECRH) system. A comparison between the quasi-optical, atmospheric waveguide and evacuated waveguide systems was performed for the project with a strong emphasis placed on the technical and financial aspects. The evacuated waveguide line was chosen as the optimal system in light of the above criteria. The system includes six lines of 63.5mm wave guide for transmitting 6.0 MW(10 s) at 113.3 GHz from the gyrotrons to the launching antenna. The designed lines are on average 72m in length and consist of nine mitre bends, for an estimated transmission efficiency of ∼90%. Each line is designed to include an evacuated switch leading to a calorimetric load, two dc breaks, two gate valves, one pump out tee, a power monitor mitre bend and a double-disc CVD window near the torus. The location of waveguide support is positioned to minimize the power converted to higher-order modes from waveguide sagging and misalignment. The two gate valves and CVD window are designed to be used as tritium barriers at the torus and between the J1T and J1D buildings. The last leg of the waveguide leading to the torus has to be designed to accommodate the torus movement during disruptions and thermal cycles. All lines are also designed to be compatible with the ITER ECRH system operating at 170 GHz. (author)

  15. Socio-technical systems and interaction design - 21st century relevance.

    Science.gov (United States)

    Maguire, Martin

    2014-03-01

    This paper focuses on the relationship between the socio-technical system and the user-technology interface. It looks at specific aspects of the organisational context such as multiple user roles, job change, work processes and workflows, technical infrastructure, and the challenges they present for the interaction designer. The implications of trends such as more mobile and flexible working, the use of social media, and the growth of the virtual organisation, are also considered. The paper also reviews rapidly evolving technologies such as pervasive systems and artificial intelligence, and the skills that workers will need to engage with them. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  16. Contact dose rates and relevant radioactive inventory in ITER TBM systems

    International Nuclear Information System (INIS)

    Zucchetti, M.; Guerrini, L.; Poitevin, Y.; Ricapito, I.; Zmitko, M.

    2011-01-01

    The determination of the radioactive inventory and of the contact dose rates in the different ITER Test Blanket Modules systems is carried out, both for Helium-Cooled Lithium-Lead (HCLL) concept and the Helium-Cooled Pebble-Bed (HCPB) concept. The evaluations have been carried out by means of the MICROSHIELD code, starting from the data on the neutron-induced radioactivity in the blanket materials, already available for both the blanket modules. The possible sources of radioactive material in all the systems have been individuated and their contributes estimated.

  17. Contact dose rates and relevant radioactive inventory in ITER TBM systems

    Energy Technology Data Exchange (ETDEWEB)

    Zucchetti, M., E-mail: massimo.zucchetti@polito.it [EURATOM/ENEA Fusion Association Politecnico di Torino, Torino (Italy); Guerrini, L., E-mail: Laurent.Guerrini@f4e.europa.eu [Fusion for Energy, ITER Department, Test Blanket Modules Group, Barcelona (Spain); Poitevin, Y.; Ricapito, I.; Zmitko, M. [Fusion for Energy, ITER Department, Test Blanket Modules Group, Barcelona (Spain)

    2011-10-15

    The determination of the radioactive inventory and of the contact dose rates in the different ITER Test Blanket Modules systems is carried out, both for Helium-Cooled Lithium-Lead (HCLL) concept and the Helium-Cooled Pebble-Bed (HCPB) concept. The evaluations have been carried out by means of the MICROSHIELD code, starting from the data on the neutron-induced radioactivity in the blanket materials, already available for both the blanket modules. The possible sources of radioactive material in all the systems have been individuated and their contributes estimated.

  18. The GEKKO XII-HIPER (High Intensity Plasma Experimental Research) system relevant to ignition targets

    International Nuclear Information System (INIS)

    Miyanaga, N.; Nakatsuka, M.; Azechi, H.

    2001-01-01

    To test high gain targets surrogated in the planar geometry, we have constructed a new experimental system (HIPER) which provides the high ablation pressure with a uniform irradiance profile. These performances were achieved by bundling twelve beams of the existing GEKKO XII into a F/3 focus cone. The partially coherent light is introduced for the beam smoothing of a green foot pulse consisting of three beams, and the three-directional smoothing by spectral dispersion is utilized for residual nine beams delivering a blue main drive pulse. The detail of design concept and results of initial activation of this system are reported. (author)

  19. Policy-Relevant Systematic Reviews to Strengthen Health Systems: Models and Mechanisms to Support Their Production

    Science.gov (United States)

    Oliver, Sandra; Dickson, Kelly

    2016-01-01

    Support for producing systematic reviews about health systems is less well developed than for those about clinical practice. From interviewing policy makers and systematic reviewers we identified institutional mechanisms which bring systematic reviews and policy priorities closer by harnessing organisational and individual motivations, emphasising…

  20. Modernization of the accident localisation system and relevant dose exposure on unit four of KNPP

    International Nuclear Information System (INIS)

    Valtchev, G.; Neshkova, M.; Nikilov, A.

    2005-01-01

    In 2001 a modernization of the accident localisation system (ALS) on Unit 4 was accomplished. The outage duration was longer then usually and special dose budget was elaborated. All ALS work was performed by external organisation. An ALARA implementation was recognised priority. The really accumulated collective doses were analysed and conclusions drawn. A short film on CD was prepared. (authors)

  1. DNS with detailed and tabulated chemistry of engine relevant igniting systems

    NARCIS (Netherlands)

    Bekdemir, C.; Somers, L.M.T.; Goey, de L.P.H.

    2014-01-01

    Developments in modern engine technology are moving towards a regime with fuel injection uncoupled from combustion. Auto-ignition is an essential characteristic in these systems. The accurate prediction of this chemical process is of paramount importance. Tabulation techniques can provide a detailed

  2. Energy band theory of heterometal superposed film and relevant comments on superconductivity in heterometal systems

    International Nuclear Information System (INIS)

    Zhang, L.; Yin, D.

    1981-08-01

    A method for calculating the electronic structure of a heterogeneous metal-metal interface is discussed. It combines a series of well-defined interface plane-wave orbitals and the muffin-tin orbitals. The problem of high-Tsub(c) superconductivity in systems containing metal-metal interfaces and the related problem in compounds is addressed

  3. Role of the endocannabinoid system in human brain functions relevant for psychiatric disorders

    NARCIS (Netherlands)

    Bossong, M.G.

    2012-01-01

    Impaired cognitive function is a fundamental characteristic of many psychiatric and neurological disorders such as schizophrenia or Alzheimer’s disease. The endocannabinoid (eCB) system, consisting of cannabinoid receptors and accompanying ligands, has been implicated in these disorders. In

  4. The National Ecosystem Services Classification System: A Framework for Identifying and Reducing Relevant Uncertainties

    Science.gov (United States)

    Rhodes, C. R.; Sinha, P.; Amanda, N.

    2013-12-01

    In recent years the gap between what scientists know and what policymakers should appreciate in environmental decision making has received more attention, as the costs of the disconnect have become more apparent to both groups. Particularly for water-related policies, the EPA's Office of Water has struggled with benefit estimates held low by the inability to quantify ecological and economic effects that theory, modeling, and anecdotal or isolated case evidence suggest may prove to be larger. Better coordination with ecologists and hydrologists is being explored as a solution. The ecosystem services (ES) concept now nearly two decades old links ecosystem functions and processes to the human value system. But there remains no clear mapping of which ecosystem goods and services affect which individual or economic values. The National Ecosystem Services Classification System (NESCS, 'nexus') project brings together ecologists, hydrologists, and social scientists to do this mapping for aquatic and other ecosystem service-generating systems. The objective is to greatly reduce the uncertainty in water-related policy making by mapping and ultimately quantifying the various functions and products of aquatic systems, as well as how changes to aquatic systems impact the human economy and individual levels of non-monetary appreciation for those functions and products. Primary challenges to fostering interaction between scientists, social scientists, and policymakers are lack of a common vocabulary, and the need for a cohesive comprehensive framework that organizes concepts across disciplines and accommodates scientific data from a range of sources. NESCS builds the vocabulary and the framework so both may inform a scalable transdisciplinary policy-making application. This talk presents for discussion the process and progress in developing both this vocabulary and a classifying framework capable of bridging the gap between a newer but existing ecosystem services classification

  5. INDUSTRIAL CONTROL SYSTEM CYBER SECURITY: QUESTIONS AND ANSWERS RELEVANT TO NUCLEAR FACILITIES, SAFEGUARDS AND SECURITY

    Energy Technology Data Exchange (ETDEWEB)

    Robert S. Anderson; Mark Schanfein; Trond Bjornard; Paul Moskowitz

    2011-07-01

    Typical questions surrounding industrial control system (ICS) cyber security always lead back to: What could a cyber attack do to my system(s) and; how much should I worry about it? These two leading questions represent only a fraction of questions asked when discussing cyber security as it applies to any program, company, business, or organization. The intent of this paper is to open a dialog of important pertinent questions and answers that managers of nuclear facilities engaged in nuclear facility security and safeguards should examine, i.e., what questions should be asked; and how do the answers affect an organization's ability to effectively safeguard and secure nuclear material. When a cyber intrusion is reported, what does that mean? Can an intrusion be detected or go un-noticed? Are nuclear security or safeguards systems potentially vulnerable? What about the digital systems employed in process monitoring, and international safeguards? Organizations expend considerable efforts to ensure that their facilities can maintain continuity of operations against physical threats. However, cyber threats particularly on ICSs may not be well known or understood, and often do not receive adequate attention. With the disclosure of the Stuxnet virus that has recently attacked nuclear infrastructure, many organizations have recognized the need for an urgent interest in cyber attacks and defenses against them. Several questions arise including discussions about the insider threat, adequate cyber protections, program readiness, encryption, and many more. These questions, among others, are discussed so as to raise the awareness and shed light on ways to protect nuclear facilities and materials against such attacks.

  6. Supporting Instruction By Defining Conceptual Relevance Of Materials: Alignment Of Resources To An Earth Systems Framework

    Science.gov (United States)

    Menicucci, A. J.; Bean, J. R.

    2017-12-01

    Environmental, geological, and climatological sciences are important facets of physical science education. However, it is often difficult for educators to acquire the necessary resources to facilitate content explanations, and demonstration of the conceptual links between individual lessons. The Understanding Global Change (UGC) Project at the University of California Museum of Paleontology (UCMP) at UC Berkeley is aligning new and existing Earth systems educational resources that are high-quality, interactive and inquiry based. Learning resources are organized by the UGC framework topics (Causes of Change, How the Earth System Works, and Measurable Changes), and focus on exploring topic relationships. Resources are currently aligned with both the UGC framework and the Next Generation Science Standards (NGSS), facilitating broad utility among K-16 educators. The overarching goal of the UGC Project is to provide the necessary resources that guide the construction of coherent, interdisciplinary instructional units. These units can be reinforced through system models, providing visual learning scaffolds for assessments of student content knowledge. Utilizing the central framework of UGC alleviates the long-standing problem of creating coherent instructional units from multiple learning resources, each organized and categorized independently across multiple platforms that may not provide explicit connections among Earth science subjects UGC topic cross listing of learning modules establishes conceptual links. Each resource is linked across several Earth system components, facilitating exploration of relationships and feedbacks between processes. Cross listed topics are therefore useful for development of broad picture learning goals via targeted instructional units. We also anticipate cultivating summaries of the explicit conceptual links explored in each resource from both current teachers and content specialists. Insructional units currated and aligned under the UGC

  7. Industrial Control System Cyber Security: Questions And Answers Relevant To Nuclear Facilities, Safeguards And Security

    International Nuclear Information System (INIS)

    Anderson, Robert S.; Schanfein, Mark; Bjornard, Trond; Moskowitz, Paul

    2011-01-01

    Typical questions surrounding industrial control system (ICS) cyber security always lead back to: What could a cyber attack do to my system(s) and; how much should I worry about it? These two leading questions represent only a fraction of questions asked when discussing cyber security as it applies to any program, company, business, or organization. The intent of this paper is to open a dialog of important pertinent questions and answers that managers of nuclear facilities engaged in nuclear facility security and safeguards should examine, i.e., what questions should be asked; and how do the answers affect an organization's ability to effectively safeguard and secure nuclear material. When a cyber intrusion is reported, what does that mean? Can an intrusion be detected or go un-noticed? Are nuclear security or safeguards systems potentially vulnerable? What about the digital systems employed in process monitoring, and international safeguards? Organizations expend considerable efforts to ensure that their facilities can maintain continuity of operations against physical threats. However, cyber threats particularly on ICSs may not be well known or understood, and often do not receive adequate attention. With the disclosure of the Stuxnet virus that has recently attacked nuclear infrastructure, many organizations have recognized the need for an urgent interest in cyber attacks and defenses against them. Several questions arise including discussions about the insider threat, adequate cyber protections, program readiness, encryption, and many more. These questions, among others, are discussed so as to raise the awareness and shed light on ways to protect nuclear facilities and materials against such attacks.

  8. Molecular Physiology of Root System Architecture in Model Grasses

    Science.gov (United States)

    Hixson, K.; Ahkami, A. H.; Anderton, C.; Veličković, D.; Myers, G. L.; Chrisler, W.; Lindenmaier, R.; Fang, Y.; Yabusaki, S.; Rosnow, J. J.; Farris, Y.; Khan, N. E.; Bernstein, H. C.; Jansson, C.

    2017-12-01

    Unraveling the molecular and physiological mechanisms involved in responses of Root System Architecture (RSA) to abiotic stresses and shifts in microbiome structure is critical to understand and engineer plant-microbe-soil interactions in the rhizosphere. In this study, accessions of Brachypodium distachyon Bd21 (C3 model grass) and Setaria viridis A10.1 (C4 model grass) were grown in phytotron chambers under current and elevated CO2 levels. Detailed growth stage-based phenotypic analysis revealed different above- and below-ground morphological and physiological responses in C3 and C4 grasses to enhanced CO2 levels. Based on our preliminary results and by screening values of total biomass, water use efficiency, root to shoot ratio, RSA parameters and net assimilation rates, we postulated a three-phase physiological mechanism, i.e. RootPlus, BiomassPlus and YieldPlus phases, for grass growth under elevated CO2 conditions. Moreover, this comprehensive set of morphological and process-based observations are currently in use to develop, test, and calibrate biophysical whole-plant models and in particular to simulate leaf-level photosynthesis at various developmental stages of C3 and C4 using the model BioCro. To further link the observed phenotypic traits at the organismal level to tissue and molecular levels, and to spatially resolve the origin and fate of key metabolites involved in primary carbohydrate metabolism in different root sections, we complement root phenotypic observations with spatial metabolomics data using mass spectrometry imaging (MSI) methods. Focusing on plant-microbe interactions in the rhizosphere, six bacterial strains with plant growth promoting features are currently in use in both gel-based and soil systems to screen root growth and development in Brachypodium. Using confocal microscopy, GFP-tagged bacterial systems are utilized to study the initiation of different root types of RSA, including primary root (PR), coleoptile node axile root (CNR

  9. Creating European guidelines for Chiropractic Incident Reporting and Learning Systems (CIRLS: relevance and structure

    Directory of Open Access Journals (Sweden)

    Wangler Martin

    2011-04-01

    Full Text Available Abstract Background In 2009, the heads of the Executive Council of the European Chiropractors' Union (ECU and the European Academy of Chiropractic (EAC involved in the European Committee for Standardization (CEN process for the chiropractic profession, set out to establish European guidelines for the reporting of adverse reactions to chiropractic treatment. There were a number of reasons for this: first, to improve the overall quality of patient care by aiming to reduce the application of potentially harmful interventions and to facilitate the treatment of patients within the context of achieving maximum benefit with a minimum risk of harm; second, to inform the training objectives for the Graduate Education and Continuing Professional Development programmes of all 19 ECU member nations, regarding knowledge and skills to be acquired for maximising patient safety; and third, to develop a guideline on patient safety incident reporting as it is likely to be part of future CEN standards for ECU member nations. Objective To introduce patient safety incident reporting within the context of chiropractic practice in Europe and to help individual countries and their national professional associations to develop or improve reporting and learning systems. Discussion Providing health care of any kind, including the provision of chiropractic treatment, can be a complex and, at times, a risky activity. Safety in healthcare cannot be guaranteed, it can only be improved. One of the most important aspects of any learning and reporting system lies in the appropriate use of the data and information it gathers. Reporting should not just be seen as a vehicle for obtaining information on patient safety issues, but also be utilised as a tool to facilitate learning, advance quality improvement and to ultimately minimise the rate of the occurrence of errors linked to patient care. Conclusions Before a reporting and learning system can be established it has to be clear

  10. Putting solar home system programmes into perspective: What lessons are relevant?

    International Nuclear Information System (INIS)

    Vleuten, F. van der; Stam, N.; Plas, R. van der

    2007-01-01

    Solar Home Systems (SHSs) have gradually become a household name in Africa. Pioneering efforts to make a new technology available to rural households have over the years developed into a few mass markets for the 'base of the pyramid'. This paper focuses on the lessons that can be learned from these experiences. Have policy makers and donors supported SHSs in an efficient way? Are they a luxury item or an essential element in the development process? Can they trigger or facilitate rural electrification? The answer to these questions is that photovoltaic (PV) systems can play a useful role for rural development and rural electrification purposes, but the desire to deploy them on a more massive scale to rural Africans demands a new type of energy policy support, creating new partnerships with local SMEs

  11. Cost-Efficient Methods and Processes for Safety Relevant Embedded Systems (CESAR) - An Objective Overview

    Science.gov (United States)

    Jolliffe, Graham

    For developing embedded safety critical systems, industrial companies have to face increasing complexity and variety coupled with increasing regulatory constraints, while costs, performances and time to market are constantly challenged. This has led to a profusion of enablers (new processes, methods and tools), which are neither integrated nor interoperable because they have been developed more or less independently (addressing only a part of the complexity: e.g. Safety) in the absence of internationally recognized open standards. CESAR has been established under ARTEMIS, the European Union's Joint Technology Initiative for research in embedded systems, with the aim to improve this situation and this pa-per will explain what CESAR's objectives are, how they are expected to be achieved and, in particular, how current best practice can ensure that safety engineering requirements can be met.

  12. Relevance of Peptide Uptake Systems to the Physiology and Virulence of Streptococcus agalactiae

    OpenAIRE

    Samen, Ulrike; Gottschalk, Birgit; Eikmanns, Bernhard J.; Reinscheid, Dieter J.

    2004-01-01

    Streptococcus agalactiae is a major cause of invasive infections in human newborns. To satisfy its growth requirements, S. agalactiae takes up 9 of the 20 proteinogenic amino acids from the environment. Defined S. agalactiae mutants in one or several of four putative peptide permease systems were constructed and tested for peptide uptake, growth in various media, and expression of virulence traits. Oligopeptide uptake by S. agalactiae was shown to be mediated by the ABC transporter OppA1-F, w...

  13. Proposed high voltage power supply for the ITER relevant lower hybrid current drive system

    International Nuclear Information System (INIS)

    Sharma, P.K.; Kazarian, F.; Garibaldi, P.; Gassman, T.; Artaud, J.F.; Bae, Y.S.; Belo, J.; Berger-By, G.; Bernard, J.M.; Cara, Ph.; Cardinali, A.; Castaldo, C.; Ceccuzzi, S.; Cesario, R.; Decker, J.; Delpech, L.; Ekedahl, A.; Garcia, J.; Goniche, M.; Guilhem, D.

    2011-01-01

    In the framework of the EFDA task HCD-08-03-01, the ITER lower hybrid current drive (LHCD) system design has been reviewed. The system aims to generate 24 MW of RF power at 5 GHz, of which 20 MW would be coupled to the plasmas. The present state of the art does not allow envisaging a unitary output of the klystrons exceeding 500 kW, so the project is based on 48 klystron units, leaving some margin when the transmission lines losses are taken into account. A high voltage power supply (HVPS), required to operate the klystrons, is proposed. A single HVPS would be used to feed and operate four klystrons in parallel configuration. Based on the above considerations, it is proposed to design and develop twelve HVPS, based on pulse step modulator (PSM) technology, each rated for 90 kV/90 A. This paper describes in details, the typical electrical requirements and the conceptual design of the proposed HVPS for the ITER LHCD system.

  14. The Relevance of the Doctrine on Restorative Justice in the Indonesian Sentencing System

    Directory of Open Access Journals (Sweden)

    Bambang Waluyo

    2015-08-01

    Full Text Available Referring on the development of criminal law recently, it is inevitable to reform the criminal law through changes on the Indonesian Criminal Code (KUHP. Being derived from the foreign law (relic of the colonial era, the Criminal Code has been obsolete, injustice, outmoded and unrealistic irrelevant for the present reality. The type of research employed in this paper is normative research, reviewing the restorative justice principle from the perspective of the criminal law system, with the aim of constructing a restorative justice concept which is ideal to be applied in the Indonesian criminal law system. The concept of restorative justice is an approach of problem solving that emphasizes the recovery of victims and to restore the relationship between the perpetrator and the victim and to their respective communities. By using such approach, the parties are expected to reach a mutual agreement related to the settlement of disputes which expected to harmonize the relationship of the parties prior the occurrence of the crime. On the practical level, the principles on restorative justice for the settlement of criminal case may need to be implemented imminently as part of the criminal system in Indonesia.

  15. The cobas® 6800/8800 System: a new era of automation in molecular diagnostics.

    Science.gov (United States)

    Cobb, Bryan; Simon, Christian O; Stramer, Susan L; Body, Barbara; Mitchell, P Shawn; Reisch, Natasa; Stevens, Wendy; Carmona, Sergio; Katz, Louis; Will, Stephen; Liesenfeld, Oliver

    2017-02-01

    Molecular diagnostics is a key component of laboratory medicine. Here, the authors review key triggers of ever-increasing automation in nucleic acid amplification testing (NAAT) with a focus on specific automated Polymerase Chain Reaction (PCR) testing and platforms such as the recently launched cobas® 6800 and cobas® 8800 Systems. The benefits of such automation for different stakeholders including patients, clinicians, laboratory personnel, hospital administrators, payers, and manufacturers are described. Areas Covered: The authors describe how molecular diagnostics has achieved total laboratory automation over time, rivaling clinical chemistry to significantly improve testing efficiency. Finally, the authors discuss how advances in automation decrease the development time for new tests enabling clinicians to more readily provide test results. Expert Commentary: The advancements described enable complete diagnostic solutions whereby specific test results can be combined with relevant patient data sets to allow healthcare providers to deliver comprehensive clinical recommendations in multiple fields ranging from infectious disease to outbreak management and blood safety solutions.

  16. Thermal hydraulic studies for passive heat transport systems relevant to advanced reactors

    International Nuclear Information System (INIS)

    Vijayan, P.K.; Sharma, M.; Borgohain, A.; Srivastava, A.K.; Pilkhwal, D.S.; Maheshwari, N.K.

    2014-01-01

    Nuclear is the only non-green house gas generating power source that can replace fossil fuels and can be commercially deployed in large scale. However, the enormous developmental efforts and safety upgrades during the past six decades have somewhat eroded the economic competitiveness of water-cooled reactors which form the mainstay of the current nuclear power programme. Further, the introduction of the supercritical Rankine cycle and the gas turbine based advanced fuel cycles have enhanced the efficiency of fossil fired power plants (FPP) thereby reducing its greenhouse gas emissions. The ongoing development of ultra-supercritical and advanced ultra-supercritical turbines aims to further reduce the greenhouse gas emissions and economic competitiveness of FPPs. In the backdrop of these developments, the nuclear industry also initiated development of advanced nuclear power plants (NPP) with improved efficiency, sustainability and enhanced safety as the main goals. A review of the advanced reactor concepts being investigated currently reveals that excepting the SCWR, all other concepts use coolants other than water. The coolants used are lead, lead bismuth eutectic, liquid sodium, molten salts, helium and supercritical water. Besides, some of these are employing passive systems to transport heat from the core under normal operating conditions. In view of this, a study is in progress at BARC to examine the performance of simple passive systems using SC CO 2 , SCW, LBE and molten salts as the coolant. This paper deals with some of the recent results of these studies. The study focuses on the steady state, transient and stability behaviour of the passive systems with these coolants. (author)

  17. Modernization of the accident localization system and relevant dose exposure on Unit 4 of KNPP

    Energy Technology Data Exchange (ETDEWEB)

    Valtchev, G.; Neshkova, A.; Nikolov, M. [Nuclear Power Plant Kozloduy, 3321 Kozloduy (Bulgaria)

    2004-07-01

    In 2001 a modernization of the Accident Localization System (ALS) on unit 4 was accomplished. The outage duration was longer then usually and special dose budget was elaborated. All ALS work was performed by external organization. An ALARA implementation was recognized priority. The really accumulated collective doses were analyzed and conclusions drawn. A short film on CD was prepared. Two conclusions are drawn: 1. Good work management and a first attempt of effective empowerment of the workers gave satisfactory results; 2. Although the work was not typical, and performed for a first time, the ALARA implementation reduced the projected collective dose with 19%.

  18. The Human Terrain System: Operationally Relevant Social Science Research in Iraq and Afghanistan

    Science.gov (United States)

    2015-12-01

    nations of the world.”32 It was Camelot’s work in Chile which broke the project to the media; in June 1965, Chilean newspaper El Siglo ran the headline...regionalism, religion , politics, and an inherent mistrust of ‘out- side’ influence and authority.”70 The term resurfaced 4 decades later in 2000 when...organization or the ideas that people have in their heads,” unhelpful in explaining tribal systems, kinship organizations, religion , and the fact that “not

  19. Medically Relevant Assays with a Simple Smartphone and Tablet Based Fluorescence Detection System

    OpenAIRE

    Wargocki, Piotr; Deng, Wei; Anwer, Ayad G.; Goldys, Ewa M.

    2015-01-01

    Cell phones and smart phones can be reconfigured as biomedical sensor devices but this requires specialized add-ons. In this paper we present a simple cell phone-based portable bioassay platform, which can be used with fluorescent assays in solution. The system consists of a tablet, a polarizer, a smart phone (camera) and a box that provides dark readout conditions. The assay in a well plate is placed on the tablet screen acting as an excitation source. A polarizer on top of the well plate s...

  20. Mobile health systems for bipolar disorder: the relevance of non-functional requirements in MONARCA project

    DEFF Research Database (Denmark)

    Mayora, Oscar; Frost, Mads; Arnrich, Bert

    2016-01-01

    This paper presents a series of challenges for developing mobile health solutions for mental health as a result of MONARCA project three-year activities. The lessons learnt on the design, development and evaluation of a mobile health system for supporting the treatment of bipolar disorder....... The findings presented here are the result of over 3 years of activity within the MONARCA EU project. The challenges listed and detailed in this paper may be used in future research as a starting point for identifying important non-functional requirements involved in mobile health provisioning...

  1. Japanese Quality Assurance System Regarding the Provision of Material Accounting Reports and the Safeguards Relevant Information to the IAEA

    International Nuclear Information System (INIS)

    Goto, Y.; Namekawa, M.; Kumekawa, H.; Usui, A.; Sano, K.

    2015-01-01

    The provision of the safeguards relevant reports and information in accordance with the comprehensive safeguards agreement (CSA) and the additional protocol (AP) is the basis for the IAEA safeguards. The government of Japan (Japan Safeguards Office, JSGO) has believed that the correct reports contribute to effective and efficient safeguards therefore the domestic quality assurance system for the reporting to the IAEA was already established at the time of the accession of the CSA in 1977. It consists of Code 10 interpretation (including the seminars for operators in Japan), SSAC's checks for syntax error, code and internal consistency (computer based consistency check between facilities) and the discussion with the IAEA on the facilities' measurement system for bulk-handling facilities, which contributes to the more accurate reports from operators. This spirit has been maintained for the entry into force of the AP. For example, questions and amplification from the IAEA will be taken into account the review of the AP declaration before sending to the IAEA and the open source information such as news article and scientific literature in Japanese is collected and translated into English, and the translated information is provided to the IAEA as the supplementary information, which may contribute to broadening the IAEA information source and to their comprehensive evaluation. The other safeguards relevant information, such as the mail-box information for SNRI at LEU fuel fabrication plants, is also checked by the JSGO's QC software before posting. The software was developed by JSGO and it checks data format, batch IDs, birth/death date, shipper/receiver information and material description code. This paper explains the history of the development of the Japanese quality assurance system regarding the reports and the safeguards relevant information to the IAEA. (author)

  2. Autonomous urban reconnaissance ingress system (AURIS): providing a tactically relevant autonomous door-opening kit for unmanned ground vehicles

    Science.gov (United States)

    Shane, David J.; Rufo, Michael A.; Berkemeier, Matthew D.; Alberts, Joel A.

    2012-06-01

    The Autonomous Urban Reconnaissance Ingress System (AURIS™) addresses a significant limitation of current military and first responder robotics technology: the inability of reconnaissance robots to open doors. Leveraging user testing as a baseline, the program has derived specifications necessary for military personnel to open doors with fielded UGVs (Unmanned Ground Vehicles), and evaluates the technology's impact on operational mission areas: duration, timing, and user patience in developing a tactically relevant, safe, and effective system. Funding is provided through the US ARMY Tank Automotive Research, Development and Engineering Center (TARDEC) and the project represents a leap forward in perception, autonomy, robotic implements, and coordinated payload operation in UGVs. This paper describes high level details of specification generation, status of the last phase of development, an advanced view of the system autonomy capability, and a short look ahead towards the ongoing work on this compelling and important technology.

  3. Database Quality and Access Issues Relevant to Research Using Anesthesia Information Management System Data.

    Science.gov (United States)

    Epstein, Richard H; Dexter, Franklin

    2018-07-01

    For this special article, we reviewed the computer code, used to extract the data, and the text of all 47 studies published between January 2006 and August 2017 using anesthesia information management system (AIMS) data from Thomas Jefferson University Hospital (TJUH). Data from this institution were used in the largest number (P = .0007) of papers describing the use of AIMS published in this time frame. The AIMS was replaced in April 2017, making this finite sample finite. The objective of the current article was to identify factors that made TJUH successful in publishing anesthesia informatics studies. We examined the structured query language used for each study to examine the extent to which databases outside of the AIMS were used. We examined data quality from the perspectives of completeness, correctness, concordance, plausibility, and currency. Our results were that most could not have been completed without external database sources (36/47, 76.6%; P = .0003 compared with 50%). The operating room management system was linked to the AIMS and was used significantly more frequently (26/36, 72%) than other external sources. Access to these external data sources was provided, allowing exploration of data quality. The TJUH AIMS used high-resolution timestamps (to the nearest 3 milliseconds) and created audit tables to track changes to clinical documentation. Automatic data were recorded at 1-minute intervals and were not editable; data cleaning occurred during analysis. Few paired events with an expected order were out of sequence. Although most data elements were of high quality, there were notable exceptions, such as frequent missing values for estimated blood loss, height, and weight. Some values were duplicated with different units, and others were stored in varying locations. Our conclusions are that linking the TJUH AIMS to the operating room management system was a critical step in enabling publication of multiple studies using AIMS data. Access to this and

  4. Enhanced chlorine dioxide decay in the presence of metal oxides: Relevance to drinking water distribution systems

    KAUST Repository

    Liu, Chao; von Gunten, Urs; Croue, Jean-Philippe

    2013-01-01

    Chlorine dioxide (ClO2) decay in the presence of typical metal oxides occurring in distribution systems was investigated. Metal oxides generally enhanced ClO2 decay in a second-order process via three pathways: (1) catalytic disproportionation with equimolar formation of chlorite and chlorate, (2) reaction to chlorite and oxygen, and (3) oxidation of a metal in a reduced form (e.g., cuprous oxide) to a higher oxidation state. Cupric oxide (CuO) and nickel oxide (NiO) showed significantly stronger abilities than goethite (α-FeOOH) to catalyze the ClO2 disproportionation (pathway 1), which predominated at higher initial ClO2 concentrations (56-81 μM). At lower initial ClO2 concentrations (13-31 μM), pathway 2 also contributed. The CuO-enhanced ClO2 decay is a base-assisted reaction with a third-order rate constant of 1.5 × 10 6 M-2 s-1 in the presence of 0.1 g L -1 CuO at 21 ± 1 C, which is 4-5 orders of magnitude higher than in the absence of CuO. The presence of natural organic matter (NOM) significantly enhanced the formation of chlorite and decreased the ClO 2 disproportionation in the CuO-ClO2 system, probably because of a higher reactivity of CuO-activated ClO2 with NOM. Furthermore, a kinetic model was developed to simulate CuO-enhanced ClO 2 decay at various pH values. Model simulations that agree well with the experimental data include a pre-equilibrium step with the rapid formation of a complex, namely, CuO-activated Cl2O4. The reaction of this complex with OH- is the rate-limiting and pH-dependent step for the overall reaction, producing chlorite and an intermediate that further forms chlorate and oxygen in parallel. These novel findings suggest that the possible ClO2 loss and the formation of chlorite/chlorate should be carefully considered in drinking water distribution systems containing copper pipes. © 2013 American Chemical Society.

  5. Enhanced chlorine dioxide decay in the presence of metal oxides: Relevance to drinking water distribution systems

    KAUST Repository

    Liu, Chao

    2013-07-19

    Chlorine dioxide (ClO2) decay in the presence of typical metal oxides occurring in distribution systems was investigated. Metal oxides generally enhanced ClO2 decay in a second-order process via three pathways: (1) catalytic disproportionation with equimolar formation of chlorite and chlorate, (2) reaction to chlorite and oxygen, and (3) oxidation of a metal in a reduced form (e.g., cuprous oxide) to a higher oxidation state. Cupric oxide (CuO) and nickel oxide (NiO) showed significantly stronger abilities than goethite (α-FeOOH) to catalyze the ClO2 disproportionation (pathway 1), which predominated at higher initial ClO2 concentrations (56-81 μM). At lower initial ClO2 concentrations (13-31 μM), pathway 2 also contributed. The CuO-enhanced ClO2 decay is a base-assisted reaction with a third-order rate constant of 1.5 × 10 6 M-2 s-1 in the presence of 0.1 g L -1 CuO at 21 ± 1 C, which is 4-5 orders of magnitude higher than in the absence of CuO. The presence of natural organic matter (NOM) significantly enhanced the formation of chlorite and decreased the ClO 2 disproportionation in the CuO-ClO2 system, probably because of a higher reactivity of CuO-activated ClO2 with NOM. Furthermore, a kinetic model was developed to simulate CuO-enhanced ClO 2 decay at various pH values. Model simulations that agree well with the experimental data include a pre-equilibrium step with the rapid formation of a complex, namely, CuO-activated Cl2O4. The reaction of this complex with OH- is the rate-limiting and pH-dependent step for the overall reaction, producing chlorite and an intermediate that further forms chlorate and oxygen in parallel. These novel findings suggest that the possible ClO2 loss and the formation of chlorite/chlorate should be carefully considered in drinking water distribution systems containing copper pipes. © 2013 American Chemical Society.

  6. Glutamate system, amyloid β peptides and tau protein: functional interrelationships and relevance to Alzheimer disease pathology

    Science.gov (United States)

    Revett, Timothy J.; Baker, Glen B.; Jhamandas, Jack; Kar, Satyabrata

    2013-01-01

    Alzheimer disease is the most prevalent form of dementia globally and is characterized premortem by a gradual memory loss and deterioration of higher cognitive functions and postmortem by neuritic plaques containing amyloid β peptide and neurofibrillary tangles containing phospho-tau protein. Glutamate is the most abundant neurotransmitter in the brain and is essential to memory formation through processes such as long-term potentiation and so might be pivotal to Alzheimer disease progression. This review discusses how the glutamatergic system is impaired in Alzheimer disease and how interactions of amyloid β and glutamate influence synaptic function, tau phosphorylation and neurodegeneration. Interestingly, glutamate not only influences amyloid β production, but also amyloid β can alter the levels of glutamate at the synapse, indicating that small changes in the concentrations of both molecules could influence Alzheimer disease progression. Finally, we describe how the glutamate receptor antagonist, memantine, has been used in the treatment of individuals with Alzheimer disease and discuss its effectiveness. PMID:22894822

  7. Flexible manufacturing systems and their relevance in nuclear fuel fabrication in India

    International Nuclear Information System (INIS)

    Ramakumar, M.S.

    1989-01-01

    Fabrication of nuclear reactor fuel bundle involves several materials and a number of complicated technologies and the process of manufacture has to conform to stringent standards. The Indian Nuclear Programme relies heavily on indigeneous capability of manufacture of nuclear fuels as well as automation of the related facilities. Automation of the existing nuclear facilities is a challenge in view of the characteristic plant environments and process demands as well as the various mechanical and metallurgical steps involved. This paper discusses their requirements and the measures initiated for achieving a high order of automation in Indian nuclear facilities. As a first step, specific automation steps are being incorporated in the existing plants. Such interface automation will enhance productivity and avoid the need for building new totally automated palnts. Flexible manufacturing system as applied here, has a different connotation vis-a-vis conventional manufacturing industry. Robotic devices, even for stacking jobs, have not been used on a large scale the world over. (author). 6 figs

  8. Fast electronic structure methods for strongly correlated molecular systems

    International Nuclear Information System (INIS)

    Head-Gordon, Martin; Beran, Gregory J O; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given

  9. The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions.

    Science.gov (United States)

    Vandervalk, Ben; McCarthy, E Luke; Cruz-Toledo, José; Klein, Artjom; Baker, Christopher J O; Dumontier, Michel; Wilkinson, Mark D

    2013-04-05

    The Web provides widespread access to vast quantities of health-related information that can improve quality-of-life through better understanding of personal symptoms, medical conditions, and available treatments. Unfortunately, identifying a credible and personally relevant subset of information can be a time-consuming and challenging task for users without a medical background. The objective of the Personal Health Lens system is to aid users when reading health-related webpages by providing warnings about personally relevant drug interactions. More broadly, we wish to present a prototype for a novel, generalizable approach to facilitating interactions between a patient, their practitioner(s), and the Web. We utilized a distributed, Semantic Web-based architecture for recognizing personally dangerous drugs consisting of: (1) a private, local triple store of personal health information, (2) Semantic Web services, following the Semantic Automated Discovery and Integration (SADI) design pattern, for text mining and identifying substance interactions, (3) a bookmarklet to trigger analysis of a webpage and annotate it with personalized warnings, and (4) a semantic query that acts as an abstract template of the analytical workflow to be enacted by the system. A prototype implementation of the system is provided in the form of a Java standalone executable JAR file. The JAR file bundles all components of the system: the personal health database, locally-running versions of the SADI services, and a javascript bookmarklet that triggers analysis of a webpage. In addition, the demonstration includes a hypothetical personal health profile, allowing the system to be used immediately without configuration. Usage instructions are provided. The main strength of the Personal Health Lens system is its ability to organize medical information and to present it to the user in a personalized and contextually relevant manner. While this prototype was limited to a single knowledge domain

  10. The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions

    Science.gov (United States)

    Vandervalk, Ben; McCarthy, E Luke; Cruz-Toledo, José; Klein, Artjom; Baker, Christopher J O; Dumontier, Michel

    2013-01-01

    Background The Web provides widespread access to vast quantities of health-related information that can improve quality-of-life through better understanding of personal symptoms, medical conditions, and available treatments. Unfortunately, identifying a credible and personally relevant subset of information can be a time-consuming and challenging task for users without a medical background. Objective The objective of the Personal Health Lens system is to aid users when reading health-related webpages by providing warnings about personally relevant drug interactions. More broadly, we wish to present a prototype for a novel, generalizable approach to facilitating interactions between a patient, their practitioner(s), and the Web. Methods We utilized a distributed, Semantic Web-based architecture for recognizing personally dangerous drugs consisting of: (1) a private, local triple store of personal health information, (2) Semantic Web services, following the Semantic Automated Discovery and Integration (SADI) design pattern, for text mining and identifying substance interactions, (3) a bookmarklet to trigger analysis of a webpage and annotate it with personalized warnings, and (4) a semantic query that acts as an abstract template of the analytical workflow to be enacted by the system. Results A prototype implementation of the system is provided in the form of a Java standalone executable JAR file. The JAR file bundles all components of the system: the personal health database, locally-running versions of the SADI services, and a javascript bookmarklet that triggers analysis of a webpage. In addition, the demonstration includes a hypothetical personal health profile, allowing the system to be used immediately without configuration. Usage instructions are provided. Conclusions The main strength of the Personal Health Lens system is its ability to organize medical information and to present it to the user in a personalized and contextually relevant manner. While this

  11. A Patchwork of Marriages: The Legal Relevance of Marriage in a Plural Legal System

    Directory of Open Access Journals (Sweden)

    Elsje Bonthuys

    2016-12-01

    Full Text Available Like many former colonies, South Africa has a plural system of family law which has historically recognized the polygynous marriages practiced by the indigenous African inhabitants of the country. However, recognition of these marriages by way of legal pluralism does not afford them equal status with the monogamous Judaeo-Christian marriage imported by European colonisers, nor does it ensure gender equality within families. Instead, the interaction between the colonial and apartheid socio-economic oppression of black people on the one hand, and legal pluralism on the other hand, produces a highly complex family law system, accurately described as ‘a patchwork of patriarchies.’ This paper argues that a far more radical transformation of family law, and one which is more likely to enhance gender equality, would be to move away from conjugality, or a sexual bond, as the basis of marriage and family law. The aim of this shift would be legal rules which recognize those relationships of kinship which have been central to African family practices and which have assisted many families to weather the multiple forms of colonial and white domination. A move away from conjugality as the primary basis of family law would also acknowledge the ever decreasing incidence of marriage and nuclear families, which characterizes contemporary South African society and would place the focus of legal regulation on the protection of socially valuable relationships, rather than the protection of marriage as an institution. Al igual que otras antiguas colonias, Sudáfrica tiene un sistema de derecho de familia plural, que ha reconocido históricamente los matrimonios en poliginia practicados por personas indígenas africanas. Sin embargo, el reconocimiento de estos matrimonios mediante pluralismo jurídico no les garantiza el mismo estatus que el matrimonio monogámico judeocristiano, ni garantiza la igualdad de género dentro de las familias. Al contrario, la

  12. Bacterial-based systems for expression and purification of recombinant Lassa virus proteins of immunological relevance

    Directory of Open Access Journals (Sweden)

    Cashman Kathleen A

    2008-06-01

    Full Text Available Abstract Background There is a significant requirement for the development and acquisition of reagents that will facilitate effective diagnosis, treatment, and prevention of Lassa fever. In this regard, recombinant Lassa virus (LASV proteins may serve as valuable tools in diverse antiviral applications. Bacterial-based systems were engineered for expression and purification of recombinant LASV nucleoprotein (NP, glycoprotein 1 (GP1, and glycoprotein 2 (GP2. Results Full-length NP and the ectodomains of GP1 and GP2 were generated as maltose-binding protein (MBP fusions in the Rosetta strains of Escherichia coli (E. coli using pMAL-c2x vectors. Average fusion protein yields per liter of culture for MBP-NP, MBP-GP1, and MBP-GP2 were 10 mg, 9 mg, and 9 mg, respectively. Each protein was captured from cell lysates using amylose resin, cleaved with Factor Xa, and purified using size-exclusion chromatography (SEC. Fermentation cultures resulted in average yields per liter of 1.6 mg, 1.5 mg, and 0.7 mg of purified NP, GP1 and GP2, respectively. LASV-specific antibodies in human convalescent sera specifically detected each of the purified recombinant LASV proteins, highlighting their utility in diagnostic applications. In addition, mouse hyperimmune ascitic fluids (MHAF against a panel of Old and New World arenaviruses demonstrated selective cross reactivity with LASV proteins in Western blot and enzyme-linked immunosorbent assay (ELISA. Conclusion These results demonstrate the potential for developing broadly reactive immunological assays that employ all three arenaviral proteins individually and in combination.

  13. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    Energy Technology Data Exchange (ETDEWEB)

    Kashiwagi, H [Institute for Molecular Science, Okazaki, Aichi (Japan)

    1982-06-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience.

  14. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    International Nuclear Information System (INIS)

    Kashiwagi, H.

    1982-01-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience. (orig.)

  15. Application range affected by software failures in safety relevant instrumentation and control systems of nuclear power plants

    International Nuclear Information System (INIS)

    Jopen, Manuela; Mbonjo, Herve; Sommer, Dagmar; Ulrich, Birte

    2017-03-01

    This report presents results that have been developed within a BMUB-funded research project (Promotion Code 3614R01304). The overall objective of this project was to broaden the knowledge base of GRS regarding software failures and their impact in software-based instrumentation and control (I and C) systems. To this end, relevant definitions and terms in standards and publications (DIN, IEEE standards, IAEA standards, NUREG publications) as well as in the German safety requirements for nuclear power plants were analyzed first. In particular, it was found that the term ''software fault'' is defined differently and partly contradictory in the considered literature sources. For this reason, a definition of software fault was developed on the basis of the software life cycle of software-based I and C systems within the framework of this project, which takes into account the various aspects relevant to software faults and their related effects. It turns out that software failures result from latent faults in a software-based control system, which can lead to a non-compliant behavior of a software-based I and C system. Hereby a distinction should be made between programming faults and specification faults. In a further step, operational experience with software failures in software-based I and C systems in nuclear facilities and in nonnuclear sector was investigated. The identified events were analyzed with regard to their cause and impacts and the analysis results were summarized. Based on the developed definition of software failure and on the COMPSIS-classification scheme for events related to software based I and C systems, the COCS-classification scheme was developed to classify events from operating experience with software failures, in which the events are classified according to the criteria ''cause'', ''affected system'', ''impact'' and ''CCF potential''. This classification scheme was applied to evaluate the events identified in the framework of this project

  16. Performance of multi-aperture grid extraction systems for an ITER-relevant RF-driven negative hydrogen ion source

    Science.gov (United States)

    Franzen, P.; Gutser, R.; Fantz, U.; Kraus, W.; Falter, H.; Fröschle, M.; Heinemann, B.; McNeely, P.; Nocentini, R.; Riedl, R.; Stäbler, A.; Wünderlich, D.

    2011-07-01

    The ITER neutral beam system requires a negative hydrogen ion beam of 48 A with an energy of 0.87 MeV, and a negative deuterium beam of 40 A with an energy of 1 MeV. The beam is extracted from a large ion source of dimension 1.9 × 0.9 m2 by an acceleration system consisting of seven grids with 1280 apertures each. Currently, apertures with a diameter of 14 mm in the first grid are foreseen. In 2007, the IPP RF source was chosen as the ITER reference source due to its reduced maintenance compared with arc-driven sources and the successful development at the BATMAN test facility of being equipped with the small IPP prototype RF source ( {\\sim}\\frac{1}{8} of the area of the ITER NBI source). These results, however, were obtained with an extraction system with 8 mm diameter apertures. This paper reports on the comparison of the source performance at BATMAN of an ITER-relevant extraction system equipped with chamfered apertures with a 14 mm diameter and 8 mm diameter aperture extraction system. The most important result is that there is almost no difference in the achieved current density—being consistent with ion trajectory calculations—and the amount of co-extracted electrons. Furthermore, some aspects of the beam optics of both extraction systems are discussed.

  17. Performance of multi-aperture grid extraction systems for an ITER-relevant RF-driven negative hydrogen ion source

    International Nuclear Information System (INIS)

    Franzen, P.; Gutser, R.; Fantz, U.; Kraus, W.; Falter, H.; Froeschle, M.; Heinemann, B.; McNeely, P.; Nocentini, R.; Riedl, R.; Staebler, A.; Wuenderlich, D.

    2011-01-01

    The ITER neutral beam system requires a negative hydrogen ion beam of 48 A with an energy of 0.87 MeV, and a negative deuterium beam of 40 A with an energy of 1 MeV. The beam is extracted from a large ion source of dimension 1.9 x 0.9 m 2 by an acceleration system consisting of seven grids with 1280 apertures each. Currently, apertures with a diameter of 14 mm in the first grid are foreseen. In 2007, the IPP RF source was chosen as the ITER reference source due to its reduced maintenance compared with arc-driven sources and the successful development at the BATMAN test facility of being equipped with the small IPP prototype RF source ( ∼ 1/8 of the area of the ITER NBI source). These results, however, were obtained with an extraction system with 8 mm diameter apertures. This paper reports on the comparison of the source performance at BATMAN of an ITER-relevant extraction system equipped with chamfered apertures with a 14 mm diameter and 8 mm diameter aperture extraction system. The most important result is that there is almost no difference in the achieved current density-being consistent with ion trajectory calculations-and the amount of co-extracted electrons. Furthermore, some aspects of the beam optics of both extraction systems are discussed.

  18. Current systematic carbon-cycle observations and the need for implementing a policy-relevant carbon observing system

    International Nuclear Information System (INIS)

    Ciais, P.; Peregon, A.; Chevallier, F.; Bopp, L.; Breon, F.M.; Broquet, G.; Luyssaert, S.; Moulin, C.; Paris, J.D.; Poulter, B.; Rivier, L.; Wang, R.

    2014-01-01

    A globally integrated carbon observation and analysis system is needed to improve the fundamental understanding of the global carbon cycle, to improve our ability to project future changes, and to verify the effectiveness of policies aiming to reduce greenhouse gas emissions and increase carbon sequestration. Building an integrated carbon observation system requires transformational advances from the existing sparse, exploratory framework towards a dense, robust, and sustained system in all components: anthropogenic emissions, the atmosphere, the ocean, and the terrestrial biosphere. The paper is addressed to scientists, policy makers, and funding agencies who need to have a global picture of the current state of the (diverse) carbon observations. We identify the current state of carbon observations, and the needs and notional requirements for a global integrated carbon observation system that can be built in the next decade. A key conclusion is the substantial expansion of the ground-based observation networks required to reach the high spatial resolution for CO 2 and CH 4 fluxes, and for carbon stocks for addressing policy-relevant objectives, and attributing flux changes to underlying processes in each region. In order to establish flux and stock diagnostics over areas such as the southern oceans, tropical forests, and the Arctic, in situ observations will have to be complemented with remote-sensing measurements. Remote sensing offers the advantage of dense spatial coverage and frequent revisit. A key challenge is to bring remote-sensing measurements to a level of long-term consistency and accuracy so that they can be efficiently combined in models to reduce uncertainties, in synergy with ground based data. Bringing tight observational constraints on fossil fuel and land use change emissions will be the biggest challenge for deployment of a policy-relevant integrated carbon observation system. This will require in situ and remotely sensed data at much higher

  19. Thermodynamic limits set relevant constraints to the soil-plant-atmosphere system and to optimality in terrestrial vegetation

    Science.gov (United States)

    Kleidon, Axel; Renner, Maik

    2016-04-01

    The soil-plant-atmosphere system is a complex system that is strongly shaped by interactions between the physical environment and vegetation. This complexity appears to demand equally as complex models to fully capture the dynamics of the coupled system. What we describe here is an alternative approach that is based on thermodynamics and which allows for comparatively simple formulations free of empirical parameters by assuming that the system is so complex that its emergent dynamics are only constrained by the thermodynamics of the system. This approach specifically makes use of the second law of thermodynamics, a fundamental physical law that is typically not being considered in Earth system science. Its relevance to land surface processes is that it fundamentally sets a direction as well as limits to energy conversions and associated rates of mass exchange, but it requires us to formulate land surface processes as thermodynamic processes that are driven by energy conversions. We describe an application of this approach to the surface energy balance partitioning at the diurnal scale. In this application the turbulent heat fluxes of sensible and latent heat are described as the result of a convective heat engine that is driven by solar radiative heating of the surface and that operates at its thermodynamic limit. The predicted fluxes from this approach compare very well to observations at several sites. This suggests that the turbulent exchange fluxes between the surface and the atmosphere operate at their thermodynamic limit, so that thermodynamics imposes a relevant constraint to the land surface-atmosphere system. Yet, thermodynamic limits do not entirely determine the soil-plant-atmosphere system because vegetation affects these limits, for instance by affecting the magnitude of surface heating by absorption of solar radiation in the canopy layer. These effects are likely to make the conditions at the land surface more favorable for photosynthetic activity

  20. Molecular photoionization studies of nucleobases and correlated systems

    Energy Technology Data Exchange (ETDEWEB)

    Poliakoff, Erwin D. [Louisiana State Univ., Baton Rouge, LA (United States)

    2015-03-11

    We proposed molecular photoionization studies in order to probe correlated events in fundamental scattering phenomena. In particular, we suggested that joint theoretical-experimental studies would provide a window into the microscopic aspects that are of central importance in AMO and chemical physics generally, and would generate useful data for wide array of important DOE topics, such as ultrafast dynamics, high harmonic generation, and probes of nonadiabatic processes. The unifying theme is that correlations between electron scattering dynamics and molecular geometry highlight inherently molecular aspects of the photoelectron behavior.

  1. Diffracted X-ray tracking: new system for single molecular detection with X-rays

    CERN Document Server

    Sasaki, Y C; Adachi, S; Suzuki, Y; Yagi, N

    2001-01-01

    We propose a new X-ray methodology for direct observations of the behaviors of single molecular units in real time and real space. This new system, which we call Diffracted X-ray Tracking (DXT), monitors the Brownian motions of a single molecular unit by observations of X-ray diffracted spots from a nanocrystal, tightly bound to the individual single molecular unit in bio-systems. DXT does not determine any translational movements, but only orientational movements.

  2. Diffracted X-ray tracking: new system for single molecular detection with X-rays

    International Nuclear Information System (INIS)

    Sasaki, Y.C.; Okumura, Y.; Adachi, S.; Suzuki, Y.; Yagi, N.

    2001-01-01

    We propose a new X-ray methodology for direct observations of the behaviors of single molecular units in real time and real space. This new system, which we call Diffracted X-ray Tracking (DXT), monitors the Brownian motions of a single molecular unit by observations of X-ray diffracted spots from a nanocrystal, tightly bound to the individual single molecular unit in bio-systems. DXT does not determine any translational movements, but only orientational movements

  3. Molecular Genetic and Gene Therapy Studies of the Musculoskeletal System

    National Research Council Canada - National Science Library

    Baylink, David

    2004-01-01

    The primary goal of the proposed work is to apply several state of the art molecular genetic and gene therapy technologies to address fundamental questions in bone biology with a particular emphasis on attempting: l...

  4. Building New Bridges between In Vitro and In Vivo in Early Drug Discovery: Where Molecular Modeling Meets Systems Biology.

    Science.gov (United States)

    Pearlstein, Robert A; McKay, Daniel J J; Hornak, Viktor; Dickson, Callum; Golosov, Andrei; Harrison, Tyler; Velez-Vega, Camilo; Duca, José

    2017-01-01

    Cellular drug targets exist within networked function-generating systems whose constituent molecular species undergo dynamic interdependent non-equilibrium state transitions in response to specific perturbations (i.e.. inputs). Cellular phenotypic behaviors are manifested through the integrated behaviors of such networks. However, in vitro data are frequently measured and/or interpreted with empirical equilibrium or steady state models (e.g. Hill, Michaelis-Menten, Briggs-Haldane) relevant to isolated target populations. We propose that cells act as analog computers, "solving" sets of coupled "molecular differential equations" (i.e. represented by populations of interacting species)via "integration" of the dynamic state probability distributions among those populations. Disconnects between biochemical and functional/phenotypic assays (cellular/in vivo) may arise with targetcontaining systems that operate far from equilibrium, and/or when coupled contributions (including target-cognate partner binding and drug pharmacokinetics) are neglected in the analysis of biochemical results. The transformation of drug discovery from a trial-and-error endeavor to one based on reliable design criteria depends on improved understanding of the dynamic mechanisms powering cellular function/dysfunction at the systems level. Here, we address the general mechanisms of molecular and cellular function and pharmacological modulation thereof. We outline a first principles theory on the mechanisms by which free energy is stored and transduced into biological function, and by which biological function is modulated by drug-target binding. We propose that cellular function depends on dynamic counter-balanced molecular systems necessitated by the exponential behavior of molecular state transitions under non-equilibrium conditions, including positive versus negative mass action kinetics and solute-induced perturbations to the hydrogen bonds of solvating water versus kT. Copyright© Bentham

  5. Simple Rules for an Efficient Use of Geographic Information Systems in Molecular Ecology

    Directory of Open Access Journals (Sweden)

    Kevin Leempoel

    2017-04-01

    Full Text Available Geographic Information Systems (GIS are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such, allow us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA. This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS that are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages.

  6. The Relevance of External Quality Assessment for Molecular Testing for ALK Positive Non-Small Cell Lung Cancer : Results from Two Pilot Rounds Show Room for Optimization

    NARCIS (Netherlands)

    Tembuyser, Lien; Tack, Veronique; Zwaenepoel, Karen; Pauwels, Patrick; Miller, Keith; Bubendorf, Lukas; Kerr, Keith; Schuuring, Ed; Thunnissen, Erik; Dequeker, Elisabeth M. C.

    2014-01-01

    Background and Purpose: Molecular profiling should be performed on all advanced non-small cell lung cancer with non-squamous histology to allow treatment selection. Currently, this should include EGFR mutation testing and testing for ALK rearrangements. ROS1 is another emerging target. ALK

  7. Bacteriophage lambda: early pioneer and still relevant

    Science.gov (United States)

    Casjens, Sherwood R.; Hendrix, Roger W.

    2015-01-01

    Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid 1950's to mid 1980's was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives have continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle. PMID:25742714

  8. Ion-molecular equilibria and activity determination in the RbF-ZrF4 system

    International Nuclear Information System (INIS)

    Skokan, E.V.; Nikitin, M.I.; Sorokin, I.D.; Korenev, Yu.M.; Sidorov, L.N.

    1983-01-01

    Activity of zirconium tetrofluoride in 100-33.3 mol % ZrF 4 concentration range was determined during isothermal evaporation of samples of different initial composition of RbF-ZrF 4 system, using ion-molecular equilibrium method. It became possible, using the exchange ion-molecular reactions to determine ZrF 4 activity approximately 10 -10 in the region of state diagram of RbF-ZrF 4 system, adjoining to rubidium fluoride. The comparative analysis of results, obtained by the methods of isothermal evaporation, ion-molecular equilibria is given; the advantages and restrictions of ion-molecular equilibrium method are presented

  9. Spatial resolution measurements of the advanced radiographic capability x-ray imaging system at energies relevant to Compton radiography

    Energy Technology Data Exchange (ETDEWEB)

    Hall, G. N., E-mail: hall98@llnl.gov; Izumi, N.; Landen, O. L.; Tommasini, R.; Holder, J. P.; Hargrove, D.; Bradley, D. K.; Lumbard, A.; Cruz, J. G.; Piston, K.; Bell, P. M.; Carpenter, A. C.; Palmer, N. E.; Felker, B.; Rekow, V.; Allen, F. V. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550 (United States); Lee, J. J.; Romano, E. [National Security Technologies LLC, 161 S Vasco Rd., Livermore, California 94551 (United States)

    2016-11-15

    Compton radiography provides a means to measure the integrity, ρR and symmetry of the DT fuel in an inertial confinement fusion implosion near peak compression. Upcoming experiments at the National Ignition Facility will use the ARC (Advanced Radiography Capability) laser to drive backlighter sources for Compton radiography experiments and will use the newly commissioned AXIS (ARC X-ray Imaging System) instrument as the detector. AXIS uses a dual-MCP (micro-channel plate) to provide gating and high DQE at the 40–200 keV x-ray range required for Compton radiography, but introduces many effects that contribute to the spatial resolution. Experiments were performed at energies relevant to Compton radiography to begin characterization of the spatial resolution of the AXIS diagnostic.

  10. Optimization of fuel ethanol recovery systems using molecular sieves

    International Nuclear Information System (INIS)

    Scheller, W.A.

    1989-01-01

    The use of molecular sieves for the dehydration of rectified fuel ethanol requires only about 58% of the energy required by azeotropic distillation, the usual commercial process. Recently molecular sieve prices have become low enough that their use can be economically competitive with azeotropic distillation. This paper contains results of mass and energy balances to determine the water content of the rectified ethanol (6.15 weight percent) that will result in the minimum energy requirement for producing anhydrous ethanol with the molecular sieve process and byproduct distillers soluble syrup from fermented corn mash containing 7.23 weight percent ethanol. In this paper results of economic evaluations to determine the water content of the rectified ethanol (7.58 weight percent) which results in a minimum investment and operating cost are presented

  11. Subtle Monte Carlo Updates in Dense Molecular Systems

    DEFF Research Database (Denmark)

    Bottaro, Sandro; Boomsma, Wouter; Johansson, Kristoffer E.

    2012-01-01

    Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce...... as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results...... suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions....

  12. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  13. FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

    KAUST Repository

    Harmandaris, Vagelis

    2017-10-03

    The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

  14. Environmental Molecular Sciences Laboratory Operations System: Version 4.0 - system requirements specification

    Energy Technology Data Exchange (ETDEWEB)

    Kashporenko, D.

    1996-07-01

    This document is intended to provide an operations standard for the Environmental Molecular Sciences Laboratory OPerations System (EMSL OPS). It is directed toward three primary audiences: (1) Environmental Molecular Sciences Laboratory (EMSL) facility and operations personnel; (2) laboratory line managers and staff; and (3) researchers, equipment operators, and laboratory users. It is also a statement of system requirements for software developers of EMSL OPS. The need for a finely tuned, superior research environment as provided by the US Department of Energy`s (DOE) Environmental Molecular Sciences Laboratory has never been greater. The abrupt end of the Cold War and the realignment of national priorities caused major US and competing overseas laboratories to reposition themselves in a highly competitive research marketplace. For a new laboratory such as the EMSL, this means coming into existence in a rapidly changing external environment. For any major laboratory, these changes create funding uncertainties and increasing global competition along with concomitant demands for higher standards of research product quality and innovation. While more laboratories are chasing fewer funding dollars, research ideas and proposals, especially for molecular-level research in the materials and biological sciences, are burgeoning. In such an economically constrained atmosphere, reduced costs, improved productivity, and strategic research project portfolio building become essential to establish and maintain any distinct competitive advantage. For EMSL, this environment and these demands require clear operational objectives, specific goals, and a well-crafted strategy. Specific goals will evolve and change with the evolution of the nature and definition of DOE`s environmental research needs. Hence, EMSL OPS is designed to facilitate migration of these changes with ease into every pertinent job function, creating a facile {open_quotes}learning organization.{close_quotes}

  15. Hierarchthis: An Interactive Interface for Identifying Mission-Relevant Components of the Advanced Multi-Mission Operations System

    Science.gov (United States)

    Litomisky, Krystof

    2012-01-01

    Even though NASA's space missions are many and varied, there are some tasks that are common to all of them. For example, all spacecraft need to communicate with other entities, and all spacecraft need to know where they are. These tasks use tools and services that can be inherited and reused between missions, reducing systems engineering effort and therefore reducing cost.The Advanced Multi-Mission Operations System, or AMMOS, is a collection of multimission tools and services, whose development and maintenance are funded by NASA. I created HierarchThis, a plugin designed to provide an interactive interface to help customers identify mission-relevant tools and services. HierarchThis automatically creates diagrams of the AMMOS database, and then allows users to show/hide specific details through a graphical interface. Once customers identify tools and services they want for a specific mission, HierarchThis can automatically generate a contract between the Multimission Ground Systems and Services Office, which manages AMMOS, and the customer. The document contains the selected AMMOS components, along with their capabilities and satisfied requirements. HierarchThis reduces the time needed for the process from service selections to having a mission-specific contract from the order of days to the order of minutes.

  16. Molecular materials and devices: developing new functional systems based on the coordination chemistry approach

    Directory of Open Access Journals (Sweden)

    Toma Henrique E.

    2003-01-01

    Full Text Available At the onset of the nanotechnology age, molecular designing of materials and single molecule studies are opening wide possibilities of using molecular systems in electronic and photonic devices, as well as in technological applications based on molecular switching or molecular recognition. In this sense, inorganic chemists are privileged by the possibility of using the basic strategies of coordination chemistry to build up functional supramolecular materials, conveying the remarkable chemical properties of the metal centers and the characteristics of the ancillary ligands. Coordination chemistry also provides effective self-assembly strategies based on specific metal-ligand affinity and stereochemistry. Several molecular based materials, derived from inorganic and metal-organic compounds are focused on this article, with emphasis on new supramolecular porphyrins and porphyrazines, metal-clusters and metal-polyimine complexes. Such systems are also discussed in terms of their applications in catalysis, sensors and molecular devices.

  17. Electrochemistry of single molecules and biomolecules, molecular scale nanostructures, and low-dimensional systems

    DEFF Research Database (Denmark)

    Nazmutdinov, Renat R.; Zinkicheva, Tamara T.; Zinkicheva, Tamara T.

    2018-01-01

    Electrochemistry at ultra-small scales, where even the single molecule or biomolecule can be characterized and manipulated, is on the way to a consolidated status. At the same time molecular electrochemistry is expanding into other areas of sophisticated nano- and molecular scale systems includin...... molecular scale metal and semiconductor nanoparticles (NPs) and other nanostructures, e.g. nanotubes, “nanoflowers” etc.. The new structures offer both new electronic properties and highly confined novel charge transfer environments....

  18. The Physics of Coupled Atomic-Molecular Condensate System

    Science.gov (United States)

    2010-10-09

    electric dipoles represents a novel state of matter with long-range and anisotropic dipole-dipole interactions, that are highly amenable to the...free-bound FC factor. Simultaneously, a series of laser �elds of (molecular) Rabi frequency i (i 2) are applied to move the molecules from the

  19. Integrative pathway knowledge bases as a tool for systems molecular medicine.

    Science.gov (United States)

    Liang, Mingyu

    2007-08-20

    There exists a sense of urgency to begin to generate a cohesive assembly of biomedical knowledge as the pace of knowledge accumulation accelerates. The urgency is in part driven by the emergence of systems molecular medicine that emphasizes the combination of systems analysis and molecular dissection in the future of medical practice and research. A potentially powerful approach is to build integrative pathway knowledge bases that link organ systems function with molecules.

  20. Effect and relevance of the artificial drainage system when assessing the hydrologic impact of the imperviousness distribution within the watershed

    Science.gov (United States)

    Thenoux, M.; Gironas, J. A.; Mejia, A.

    2013-12-01

    Cities and urban growth have relevant environmental and social impacts, which could eventually be enhanced or reduced during the urban planning process. From the point of view of hydrology, impermeability and natural soil compaction are one of the main problems that urbanization brings to watershed. Previous studies demonstrate and quantify the impacts of the distribution of imperviousness in a watershed, both on runoff volumes and flow, and the quality and integrity of streams and receiving bodies. Moreover, some studies have investigated the optimal distribution of imperviousness, based on simulating different scenarios of land use change and its effects on runoff, mostly at the outlet of the watershed. However, these studies typically do not address the impact of artificial drainage system associated with the imperviousness scenarios, despite it is known that storm sewer coverage affects the flow accumulation and generation of flow hydrographs. This study seeks to quantify the effects and relevance of the artificial system when it comes to assess the hydrological impacts of the spatial distribution of imperviousness and to determine the characteristics of this influence. For this purpose, an existing model to generate imperviousness distribution scenarios is coupled with a model developed to automatically generate artificial drainage networks. These models are applied to a natural watershed to generate a variety of imperviousness and storm sewer layout scenarios, which are evaluate with a morphoclimatic instantaneous unit hydrograph model. We first tested the ability of this approach to represent the joint effects of imperviousness (i.e. level and distribution) and storm sewer coverage. We then quantified the effects of these variables on the hydrological response, considering also different return period in order to take into account the variability of the precipitation regime. Overall, we show that the layout and spatial coverage of the storm sewer system

  1. Simultaneous-Fault Diagnosis of Automotive Engine Ignition Systems Using Prior Domain Knowledge and Relevance Vector Machine

    Directory of Open Access Journals (Sweden)

    Chi-Man Vong

    2013-01-01

    Full Text Available Engine ignition patterns can be analyzed to identify the engine fault according to both the specific prior domain knowledge and the shape features of the patterns. One of the challenges in ignition system diagnosis is that more than one fault may appear at a time. This kind of problem refers to simultaneous-fault diagnosis. Another challenge is the acquisition of a large amount of costly simultaneous-fault ignition patterns for constructing the diagnostic system because the number of the training patterns depends on the combination of different single faults. The above problems could be resolved by the proposed framework combining feature extraction, probabilistic classification, and decision threshold optimization. With the proposed framework, the features of the single faults in a simultaneous-fault pattern are extracted and then detected using a new probabilistic classifier, namely, pairwise coupling relevance vector machine, which is trained with single-fault patterns only. Therefore, the training dataset of simultaneous-fault patterns is not necessary. Experimental results show that the proposed framework performs well for both single-fault and simultaneous-fault diagnoses and is superior to the existing approach.

  2. From Heavy-Ion Collisions to Compact Stars: Equation of State and Relevance of the System Size

    Directory of Open Access Journals (Sweden)

    Sylvain Mogliacci

    2018-01-01

    Full Text Available In this article, we start by presenting state-of-the-art methods allowing us to compute moments related to the globally conserved baryon number, by means of first principle resummed perturbative frameworks. We focus on such quantities for they convey important properties of the finite temperature and density equation of state, being particularly sensitive to changes in the degrees of freedom across the quark-hadron phase transition. We thus present various number susceptibilities along with the corresponding results as obtained by lattice quantum chromodynamics collaborations, and comment on their comparison. Next, omitting the importance of coupling corrections and considering a zero-density toy model for the sake of argument, we focus on corrections due to the small size of heavy-ion collision systems, by means of spatial compactifications. Briefly motivating the relevance of finite size effects in heavy-ion physics, in opposition to the compact star physics, we present a few preliminary thermodynamic results together with the speed of sound for certain finite size relativistic quantum systems at very high temperature.

  3. A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

    Science.gov (United States)

    Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.

    2011-01-01

    Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

  4. Exploring coherent transport through π-stacked systems for molecular electronic devices

    DEFF Research Database (Denmark)

    Li, Qian; Solomon, Gemma

    2014-01-01

    Understanding electron transport across π-stacked systems can help to elucidate the role of intermolecular tunneling in molecular junctions and potentially with the design of high-efficiency molecular devices. Here we show how conjugation length and substituent groups influence the electron trans...

  5. Identification and molecular profiling of DC-SIGN-like from big belly seahorse (Hippocampus abdominalis) inferring its potential relevancy in host immunity.

    Science.gov (United States)

    Jo, Eunyoung; Elvitigala, Don Anushka Sandaruwan; Wan, Qiang; Oh, Minyoung; Oh, Chulhong; Lee, Jehee

    2017-12-01

    Dendritic-cell-specific ICAM-3-grabbing non-integrin (DC-SIGN) is a C-type lectin that functions as a pattern recognition receptor by recognizing pathogen-associated molecular patterns (PAMPs). It is also involved in various events of the dendritic cell (DC) life cycle, such as DC migration, antigen capture and presentation, and T cell priming. In this study, a DC-SIGN-like gene from the big belly seahorse Hippocampus abdominalis (designated as ShDCS-like) was identified and molecularly characterized. The putative, complete ORF was found to be 1368 bp in length, encoding a protein of 462 amino acids with a molecular mass of 52.6 kDa and a theoretical isoelectric point of 8.26. The deduced amino acid sequence contains a single carbohydrate recognition domain (CRD), in which six conserved cysteine residues and two Ca 2+ -binding site motifs (QPN, WND) were identified. Based on pairwise sequence analysis, ShDCS-like exhibits the highest amino acid identity (94.6%) and similarity (97.4%) with DC-SIGN-like counterpart from tiger tail seahorse Hippocampus comes. Quantitative real-time PCR revealed that ShDCS-like mRNA is transcribed universally in all tissues examined, but with abundance in kidney and gill tissues. The basal mRNA expression of ShDCS-like was modulated in blood cell, kidney, gill and liver tissues in response to the stimulation of healthy fish with lipopolysaccharides (LPS), Edwardsiella tarda, or Streptococcus iniae. Moreover, recombinant ShDCS-like-CRD domain exhibited detectable agglutination activity against different bacteria. Collectively, these results suggest that ShDCS-like may potentially involve in immune function in big belly seahorses. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Molecular Dynamics Simulations of displacement cascades in metallic systems

    International Nuclear Information System (INIS)

    Doan, N.V.; Tietze, H.

    1995-01-01

    We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)

  7. Molecular and supramolecular speciation of monoamide extractant systems

    International Nuclear Information System (INIS)

    Ferru, G.

    2012-01-01

    DEHiBA (N,N-di-(ethyl-2-hexyl)isobutyramide, a monoamide, was chosen as selective extractant for the recovery of uranium in the first cycle of the GANEX process, which aims to realize the grouped extraction of actinides in the second step of the process. The aim of this work is an improved description of monoamide organic solutions in alkane diluent after solutes extraction: water, nitric acid and uranyl nitrate. A parametric study was undertaken to characterize species at molecular scale (by IR spectroscopy, UV-visible spectroscopy, time-resolved laser-induced fluorescence spectroscopy, and electro-spray ionisation mass spectrometry) and at supramolecular scale (by vapor pressure osmometry and small angle X-ray scattering coupled to molecular dynamic simulations). Extraction isotherms were modelled taking into account the molecular and supramolecular speciation. These works showed that the organization of the organic solution depends on the amide concentration, the nature and the concentration of the extracted solute. Three regimes can be distinguished. 1/For extractant concentration less than 0.5 mol/L, monomers are predominate species. 2/ For extractant concentrations between 0.5 and 1 mol/L, small aggregates are formed containing 2 to 4 molecules of monoamide. 3/ For more concentrated solutions (greater than 1 mol/L), slightly larger species can be formed after water or nitric acid extraction. Concerning uranyl nitrate extraction, an important and strong organization of the organic phase is observed, which no longer allows the formation of well spherical defined aggregates. At molecular scale, complexes are not sensitive to the organization of the solution: the same species are observed, regardless of the solute and extractant concentrations in organic phase. (author) [fr

  8. Molecular environment of stable iodine and radioiodine (129I) in natural organic matter: Evidence inferred from NMR and binding experiments at environmentally relevant concentrations

    Science.gov (United States)

    Xu, Chen; Zhong, Junyan; Hatcher, Patrick G.; Zhang, Saijin; Li, Hsiu-Ping; Ho, Yi-Fang; Schwehr, Kathleen A.; Kaplan, Daniel I.; Roberts, Kimberly A.; Brinkmeyer, Robin; Yeager, Chris M.; Santschi, Peter H.

    2012-11-01

    129I is a major by-product of nuclear fission and had become one of the major radiation risk drivers at Department of Energy (DOE) sites. 129I is present at elevated levels in the surface soils of the Savannah River Site (SRS) F-Area and was found to be bound predominantly to soil organic matter (SOM). Naturally bound 127I and 129I to sequentially extracted humic acids (HAs), fulvic acids (FAs) and a water extractable colloid (WEC) were measured in a 129I-contaminated wetland surface soil located on the SRS. WEC is a predominantly colloidal organic fraction obtained from soil re-suspension experiments to mimic the fraction that may be released during groundwater exfiltration, storm water or surface runoff events. For the first time, NMR techniques were applied to infer the molecular environment of naturally occurring stable iodine and radioiodine binding to SOM. Iodine uptake partitioning coefficients (Kd) by these SOM samples at ambient iodine concentrations were also measured and related to quantitative structural analyses by 13C DPMAS NMR and solution state 1H NMR on the eight humic acid fractions. By assessing the molecular environment of iodine, it was found that it was closely associated with the aromatic regions containing esterified products of phenolic and formic acids or other aliphatic carboxylic acids, amide functionalities, quinone-like structures activated by electron-donating groups (e.g., NH2), or a hemicellulose-lignin-like complex with phenyl-glycosidic linkages. However, FAs and WEC contained much greater concentrations of 127I or 129I than HAs. The contrasting radioiodine contents among the three different types of SOM (HAs, FAs and WEC) suggest that the iodine binding environment cannot be explained solely by the difference in the amount of their reactive binding sites. Instead, indirect evidence indicates that the macro-molecular conformation, such as the hydrophobic aliphatic periphery hindering the active aromatic cores and the hydrophilic

  9. Molecular-beam epitaxial growth and ion-beam analysis systems for functional materials research

    International Nuclear Information System (INIS)

    Takeshita, H.; Aoki, Y.; Yamamoto, S.; Naramoto, H.

    1992-01-01

    Experimental systems for molecular beam epitaxial growth and ion beam analysis have been designed and constructed for the research of inorganic functional materials such as thin films and superlattices. (author)

  10. Materials learning from life: concepts for active, adaptive and autonomous molecular systems.

    Science.gov (United States)

    Merindol, Rémi; Walther, Andreas

    2017-09-18

    Bioinspired out-of-equilibrium systems will set the scene for the next generation of molecular materials with active, adaptive, autonomous, emergent and intelligent behavior. Indeed life provides the best demonstrations of complex and functional out-of-equilibrium systems: cells keep track of time, communicate, move, adapt, evolve and replicate continuously. Stirred by the understanding of biological principles, artificial out-of-equilibrium systems are emerging in many fields of soft matter science. Here we put in perspective the molecular mechanisms driving biological functions with the ones driving synthetic molecular systems. Focusing on principles that enable new levels of functionalities (temporal control, autonomous structures, motion and work generation, information processing) rather than on specific material classes, we outline key cross-disciplinary concepts that emerge in this challenging field. Ultimately, the goal is to inspire and support new generations of autonomous and adaptive molecular devices fueled by self-regulating chemistry.

  11. Pulse radiolysis studies of fast reactions in molecular systems. Progress report, November 1976--October 1977

    International Nuclear Information System (INIS)

    Dorfman, L.M.

    1977-01-01

    Results from research in the following two areas are given: formation, properties, and reactivity of molecular ionic species in irradiated liquid systems; and pulse radiolysis of elementary reactions in protein function

  12. Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology (Final Report)

    Science.gov (United States)

    EPA announced the release of the final report, Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology. This report describes new approaches that are faster, less resource intensive, and more robust that can help ...

  13. FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

    KAUST Repository

    Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plechac, Petr

    2017-01-01

    The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from

  14. A note on the relevance of human population genetic variation and molecular epidemiology to assessing radiation health risk for space travellers

    International Nuclear Information System (INIS)

    Brackley, M.E.; Curry, J.; Glickman, B.W.

    1999-01-01

    We discuss the relevance to space medicine of studies concerning human genetic variation and consequent variable disease susceptibility or sensitivity between individuals. The size of astronaut and cosmonaut populations is both presently and cumulatively small, and despite the launch of the International Space Station, unlikely to increase by orders of magnitude within the foreseeable future. In addition, astronauts-cosmonauts constitute unrepresentative samples of their national populations. While the context of exposure for the astronaut-cosmonaut group is one unlikely to be replicated elsewhere than in space, aspects of specific exposures may be simulated by events such as occupational radiation exposure or radiation therapy. Hence, population-based studies of genetic susceptibility or sensitivity to disease, especially where it is precipitated by events that may simulate consequences of the space environment, likely will prove of value in assessing long-term health risks

  15. Neural network modelling and dynamical system theory: are they relevant to study the governing dynamics of association football players?

    Science.gov (United States)

    Dutt-Mazumder, Aviroop; Button, Chris; Robins, Anthony; Bartlett, Roger

    2011-12-01

    Recent studies have explored the organization of player movements in team sports using a range of statistical tools. However, the factors that best explain the performance of association football teams remain elusive. Arguably, this is due to the high-dimensional behavioural outputs that illustrate the complex, evolving configurations typical of team games. According to dynamical system analysts, movement patterns in team sports exhibit nonlinear self-organizing features. Nonlinear processing tools (i.e. Artificial Neural Networks; ANNs) are becoming increasingly popular to investigate the coordination of participants in sports competitions. ANNs are well suited to describing high-dimensional data sets with nonlinear attributes, however, limited information concerning the processes required to apply ANNs exists. This review investigates the relative value of various ANN learning approaches used in sports performance analysis of team sports focusing on potential applications for association football. Sixty-two research sources were summarized and reviewed from electronic literature search engines such as SPORTDiscus, Google Scholar, IEEE Xplore, Scirus, ScienceDirect and Elsevier. Typical ANN learning algorithms can be adapted to perform pattern recognition and pattern classification. Particularly, dimensionality reduction by a Kohonen feature map (KFM) can compress chaotic high-dimensional datasets into low-dimensional relevant information. Such information would be useful for developing effective training drills that should enhance self-organizing coordination among players. We conclude that ANN-based qualitative analysis is a promising approach to understand the dynamical attributes of association football players.

  16. The Effect of the Human Peptide GHK on Gene Expression Relevant to Nervous System Function and Cognitive Decline

    Directory of Open Access Journals (Sweden)

    Loren Pickart

    2017-02-01

    Full Text Available Neurodegeneration, the progressive death of neurons, loss of brain function, and cognitive decline is an increasing problem for senior populations. Its causes are poorly understood and therapies are largely ineffective. Neurons, with high energy and oxygen requirements, are especially vulnerable to detrimental factors, including age-related dysregulation of biochemical pathways caused by altered expression of multiple genes. GHK (glycyl-l-histidyl-l-lysine is a human copper-binding peptide with biological actions that appear to counter aging-associated diseases and conditions. GHK, which declines with age, has health promoting effects on many tissues such as chondrocytes, liver cells and human fibroblasts, improves wound healing and tissue regeneration (skin, hair follicles, stomach and intestinal linings, boney tissue, increases collagen, decorin, angiogenesis, and nerve outgrowth, possesses anti-oxidant, anti-inflammatory, anti-pain and anti-anxiety effects, increases cellular stemness and the secretion of trophic factors by mesenchymal stem cells. Studies using the Broad Institute Connectivity Map show that GHK peptide modulates expression of multiple genes, resetting pathological gene expression patterns back to health. GHK has been recommended as a treatment for metastatic cancer, Chronic Obstructive Lung Disease, inflammation, acute lung injury, activating stem cells, pain, and anxiety. Here, we present GHK’s effects on gene expression relevant to the nervous system health and function.

  17. Molecular quenching and relaxation in a plasmonic tunable system

    Science.gov (United States)

    Baffou, Guillaume; Girard, Christian; Dujardin, Erik; Colas Des Francs, Gérard; Martin, Olivier J. F.

    2008-03-01

    Molecular fluorescence decay is significantly modified when the emitting molecule is located near a plasmonic structure. When the lateral sizes of such structures are reduced to nanometer-scale cross sections, they can be used to accurately control and amplify the emission rate. In this Rapid Communication, we extend Green’s dyadic method to quantitatively investigate both radiative and nonradiative decay channels experienced by a single fluorescent molecule confined in an adjustable dielectric-metal nanogap. The technique produces data in excellent agreement with current experimental work.

  18. Mixed 2D molecular systems: Mechanic, thermodynamic and dielectric properties

    Energy Technology Data Exchange (ETDEWEB)

    Beno, Juraj [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Weis, Martin [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)], E-mail: Martin.Weis@stuba.sk; Dobrocka, Edmund [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Institute of Electrical Engineering, Slovak Academy of Sciences, Dubravska cesta 9, 841 04-SK Bratislava (Slovakia); Hasko, Daniel [International Laser Centre, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)

    2008-08-15

    Study of Langmuir monolayers consisting of stearic acid (SA) and dipalmitoylphosphatidylcholine (DPPC) molecules was done by surface pressure-area isotherms ({pi}-A), the Maxwell displacement current (MDC) measurement, X-ray reflectivity (XRR) and atomic force microscopy (AFM) to investigate the selected mechanic, thermodynamic and dielectric properties based on orientational structure of monolayers. On the base of {pi}-A isotherms analysis we explain the creation of stable structures and found optimal monolayer composition. The dielectric properties represented by MDC generated monolayers were analyzed in terms of excess dipole moment, proposing the effect of dipole-dipole interaction. XRR and AFM results illustrate deposited film structure and molecular ordering.

  19. Chemical reactions in the nitrogen-acetone ice induced by cosmic ray analogues: relevance for the Solar system

    Science.gov (United States)

    de Barros, A. L. F.; Andrade, D. P. P.; da Silveira, E. F.; Alcantara, K. F.; Boduch, P.; Rothard, H.

    2018-02-01

    The radiolysis of 10:1 nitrogen:acetone mixture, condensed at 11 K, by 40 MeV 58Ni11 + ions is studied. These results are representative of studies concerning Solar system objects, such as transneptunian objects, exposed to cosmic rays. Bombardment by cosmic rays triggers chemical reactions leading to synthesis of larger molecules. In this work, destruction cross-sections of acetone and nitrogen molecules in solid phase are determined and compared with those for pure acetone. The N2 column density decreases very fast indicating that, under irradiation, nitrogen leaves quickly a porous sample. The most abundant molecular species formed in the radiolysis are C3H6, C2H6, N3, CO, CH4 and CO2. Some N-bearing species are also formed, but with low production yield. Dissolving acetone in nitrogen decreases the formation cross-sections of CH4, CO2 and H2CO, while increases those for CO and C2H6 species. This fact may explain the presence of C2H6 in Pluto's surface where CH4 is not pure, but diluted in an N2 matrix. The formation of more complex molecules, such as HNCO and, possibly, glycine is observed, suggesting the formation of small prebiotic species in objects beyond Neptune from acetone diluted in a N2 matrix irradiated by cosmic rays.

  20. Characterization of the radiation resistance of ITER-relevant and innovative fiber composites for the ITER magnet system

    International Nuclear Information System (INIS)

    Bittner-Rohrhofer, K.

    2003-06-01

    The application of glass-fiber reinforced composites for the insulation of the superconducting magnet coils of the ITER (International Thermonuclear Experimental Reactor ) fusion device requires high material performance. The mechanical integrity of the insulation is influenced by the neutron- and g-environment and by the high mechanical stresses of the magnet system over the entire plant lifetime of 20 years. Materials suggested as insulation have to be investigated in extensive test programs with respect to the present ITER design criteria. In particular, the ultimate tensile strength as well as the interlaminar shear behavior will change under static and dynamic load (tension-tension fatigue) at 77 K after irradiation to the ITER design fluence level of 1x1022 m-2 (E620.1 MeV). Therefore, a frequency of 10 Hz and a ratio of 0.1 were chosen, in order to simulate the pulsed TOKAMAK-operation as closely as possible. Furthermore, the fatigue behavior of the material is investigated over more than 3x104 cycles, which is the ITER- relevant design fatigue limit. Basically, these insulation systems are based on combined glass-fiber/Kapton tapes, which are impregnated with di-functional DGEBA epoxy resins. Several mechanical investigations showed that the radiation resistance of these organic resins is dramatically affected by radiation at a neutron fluence of 1x1022 m-2 (E620.1 MeV). Moreover, the material strength after irradiation is strongly influenced by these factors: the winding direction of the tapes, the quality of fabrication and the drastic delamination process of the whole compound. Furthermore, the radiation induced damage of adhesives applied for supporting the interfacial bonding between the glass-fiber tape and Kapton has an adverse effect on the material performance. In addition, the poor interlaminar shear behavior does not fulfil the requirements of ITER. These test-results motivated for the development of innovative resin systems with higher stability

  1. Raman spectroscopy on simple molecular systems at very high density

    International Nuclear Information System (INIS)

    Schiferl, D.; LeSar, R.S.; Moore, D.S.

    1988-01-01

    We present an overview of how Raman spectroscopy is done on simple molecular substances at high pressures. Raman spectroscopy is one of the most powerful tools for studying these substances. It is often the quickest means to explore changes in crystal and molecular structures, changes in bond strength, and the formation of new chemical species. Raman measurements have been made at pressures up to 200 GPa (2 Mbar). Even more astonishing is the range of temperatures (4-5200/degree/K) achieved in various static and dynamic (shock-wave) pressure experiments. One point we particularly wish to emphasize is the need for a good theoretical understanding to properly interpret and use experimental results. This is particularly true at ultra-high pressures, where strong crystal field effects can be misinterpreted as incipient insulator-metal transitions. We have tried to point out apparatus, techniques, and results that we feel are particularly noteworthy. We have also included some of the /open quotes/oral tradition/close quotes/ of high pressure Raman spectroscopy -- useful little things that rarely or never appear in print. Because this field is rapidly expanding, we discuss a number of exciting new techniques that have been informally communicated to us, especially those that seem to open new possibilities. 58 refs., 18 figs

  2. Biologically relevant conformational features of linear and cyclic proteolipid protein (PLP) peptide analogues obtained by high-resolution nuclear magnetic resonance and molecular dynamics

    Science.gov (United States)

    Kordopati, Golfo G.; Tzoupis, Haralambos; Troganis, Anastassios N.; Tsivgoulis, Gerasimos M.; Golic Grdadolnik, Simona; Simal, Carmen; Tselios, Theodore V.

    2017-09-01

    Proteolipid protein (PLP) is one of the main proteins of myelin sheath that are destroyed during the progress of multiple sclerosis (MS). The immunodominant PLP139-151 epitope is known to induce experimental autoimmune encephalomyelitis (EAE, animal model of MS), wherein residues 144 and 147 are recognized by T cell receptor (TCR) during the formation of trimolecular complex with peptide-antigen and major histocompability complex. The conformational behavior of linear and cyclic peptide analogues of PLP, namely PLP139-151 and cyclic (139-151) (L144, R147) PLP139-151, have been studied in solution by means of nuclear magnetic resonance (NMR) methods in combination with unrestrained molecular dynamics simulations. The results indicate that the side chains of mutated amino acids in the cyclic analogue have different spatial orientation compared with the corresponding side chains of the linear analogue, which can lead to reduced affinity to TCR. NMR experiments combined with theoretical calculations pave the way for the design and synthesis of potent restricted peptides of immunodominant PLP139-151 epitope as well as non peptide mimetics that rises as an ultimate goal.

  3. Systems biology for molecular life sciences and its impact in biomedicine.

    Science.gov (United States)

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  4. Water activity in liquid food systems: A molecular scale interpretation.

    Science.gov (United States)

    Maneffa, Andrew J; Stenner, Richard; Matharu, Avtar S; Clark, James H; Matubayasi, Nobuyuki; Shimizu, Seishi

    2017-12-15

    Water activity has historically been and continues to be recognised as a key concept in the area of food science. Despite its ubiquitous utilisation, it still appears as though there is confusion concerning its molecular basis, even within simple, single component solutions. Here, by close examination of the well-known Norrish equation and subsequent application of a rigorous statistical theory, we are able to shed light on such an origin. Our findings highlight the importance of solute-solute interactions thus questioning traditional, empirically based "free water" and "water structure" hypotheses. Conversely, they support the theory of "solute hydration and clustering" which advocates the interplay of solute-solute and solute-water interactions but crucially, they do so in a manner which is free of any estimations and approximations. Copyright © 2017. Published by Elsevier Ltd.

  5. Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

    Science.gov (United States)

    Rahman, Mahabubur; Watabe, Hiroshi

    2018-05-01

    Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid

  6. Protection of safety-relevant information in distributed energy information systems; Schutz sicherheitsrelevanter Informationen in verteilten Energieinformationssystemen

    Energy Technology Data Exchange (ETDEWEB)

    Beenken, Petra

    2010-07-01

    encryption systems and a corresponding separated and decentralized key management. The ENERTRUST security model allows people to identify their security relevant data and the need of protection of this data by reasoning. Moreover it allows people to make a definition of a suitable - that means a conflict free - protection measurement as an encryption system. Furthermore the security model mentions authentification operations for a secure key exchange and the model gives an opportunity to find out which subjects need an access to which energy data.

  7. Self-assembled structures and pKa value of oleic acid in systems of biological relevance.

    Science.gov (United States)

    Salentinig, Stefan; Sagalowicz, Laurent; Glatter, Otto

    2010-07-20

    In the human digestion process, triglycerides are hydrolyzed by lipases to monoglycerides and the corresponding fatty acids. Here we report the self-assembly of structures in biologically relevant, emulsified oleic acid-monoolein mixtures at various pH values and oleic acid concentrations. Small-angle X-ray scattering, cryogenic transmission electron microscopy, and dynamic light scattering were used to investigate the structures formed, and to follow their transitions while these factors were varied. The addition of oleic acid to monoolein-based cubosomes was found to increase the critical packing parameter in the system. Structural transitions from bicontinuous cubosomes through hexosomes and micellar cubosomes (Fd3m symmetry) to emulsified microemulsions occur with increasing oleic acid concentration. At sufficiently high oleic acid concentration, the internal particle structure was also found to strongly depend on the pH of the aqueous phase: transformations from emulsified microemulsion through micellar cubosomes, hexosomes, and bicontinuous cubosomes to vesicles can be observed as a function of increasing pH. The reversible transition from liquid crystals to vesicles occurs at intestinal pH values (between pH 7 and 8). The hydrodynamic radius of the particles decreases from around 120 nm for internally structured particles to around 60 nm for vesicles. All transitions with pH are reversible. Finally, the apparent pK(a) for oleic acid in monoolein could be determined from the change of structure with pH. This value is within the physiological pH range of the intestine and depends somewhat on composition.

  8. Time-resolved and steady-state studies of biologically and chemically relevant systems using laser, absorption, and fluorescence spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Barnes, Charles Ashley [Iowa State Univ., Ames, IA (United States)

    2014-12-20

    In Chapter 2 several experimental and data analysis methods used in this thesis are described. In Chapter 3 steady-state fluorescence spectroscopy was used to determine the concentration of the efflux pump inhibitors (EPIs), pheophorbide a and pyropheophorbide a, in the feces of animals and it was found that their levels far exceed those reported to be inhibitory to efflux pumps. In Chapter 4 the solvation dynamics of 6-Propionyl-2-(N,Ndimethyl) aminonaphthalene (PRODAN) was studied in reverse micelles. The two fluorescent states of PRODAN solvate on different time scales and as such care must be exercised in solvation dynamic studies involving it and its analogs. In Chapter 5 we studied the experimental and theoretical solvation dynamics of coumarin 153 (C153) in wild-type (WT) and modified myoglobins. Based on the nuclear magnetic resonance (NMR) spectroscopy and time-resolved fluorescence studies, we have concluded that it is important to thoroughly characterize the structure of a protein and probe system before comparing the theoretical and experimental results. In Chapter 6 the photophysical and spectral properties of a derivative of the medically relevant compound curcumin called cyclocurcumin was studied. Based on NMR, fluorescence, and absorption studies, the ground- and excited-states of cyclocurcumin are complicated by the existence of multiple structural isomers. In Chapter 7 the hydrolysis of cellulose by a pure form of cellulase in an ionic liquid, HEMA, and its aqueous mixtures at various temperatures were studied with the goal of increasing the cellulose to glucose conversion for biofuel production. It was found that HEMA imparts an additional stability to cellulase and can allow for faster conversion of cellulose to glucose using a pre-treatment step in comparison to only buffer.

  9. Clinical relevance of nine transcriptional molecular markers for the diagnosis of head and neck squamous cell carcinoma in tissue and saliva rinse

    International Nuclear Information System (INIS)

    Lallemant, Benjamin; Hollande, Frédéric; Lallemant, Jean-Gabriel; Lumbroso, Serge; Brouillet, Jean-Paul; Evrard, Alexandre; Combescure, Christophe; Chapuis, Heliette; Chambon, Guillaume; Raynal, Caroline; Reynaud, Christophe; Sabra, Omar; Joubert, Dominique

    2009-01-01

    Analysis of 23 published transcriptome studies allowed us to identify nine genes displaying frequent alterations in HNSCC (FN1, MMP1, PLAU, SPARC, IL1RN, KRT4, KRT13, MAL, and TGM3). We aimed to independently confirm these dysregulations and to identify potential relationships with clinical data for diagnostic, staging and prognostic purposes either at the tissue level or in saliva rinse. For a period of two years, we systematically collected tumor tissue, normal matched mucosa and saliva of patients diagnosed with primary untreated HNSCC. Expression levels of the nine genes of interest were measured by RT-qPCR in tumor and healthy matched mucosa from 46 patients. MMP1 expression level was measured by RT-qPCR in the salivary rinse of 51 HNSCC patients and 18 control cases. Dysregulation of the nine genes was confirmed by the Wilcoxon test. IL1RN, MAL and MMP1 were the most efficient diagnostic markers of HNSCC, with ROC AUC > 0.95 and both sensitivity and specificity above 91%. No clinically relevant correlation was found between gene expression level in tumor and T stage, N stage, tumor grade, global survival or disease-free survival. Our preliminary results suggests that with 100% specificity, MMP1 detection in saliva rinse is potentially useful for non invasive diagnosis of HNSCC of the oral cavity or oropharynx, but technical improvement is needed since sensitivity was only 20%. IL1RN, MAL and MMP1 are prospective tumor diagnostic markers for HNSCC. MMP1 overexpression is the most promising marker, and its detection could help identify tumor cells in tissue or saliva

  10. Overexpression of c-erbB-2 and loss of p16 have molecular diagnostic relevance but no prognostic value in lung cancer.

    Science.gov (United States)

    Feng, Xiao-li; Li, Ling; Gao, Yan-ning; Zhang, Jian-jun; Xiao, Ting; Ying, Jian-ming; Gao, Ji-dong; Sun, Yun-tian; Cheng, Shu-jun

    2011-03-01

    This study was designed to evaluate the expression of C-erbB-2 and p16 in lung cancers using tissue microarray technology and to determine their clinical and pathological significance. Immunohistochemical C-erbB-2 and p16 expressions and their associations with clinical and pathological features were analyzed in two tissue microarrays. The membranous and cytoplasmic expression rates of C-erbB-2 were 40.5 and 66.5% in non-small cell lung cancers (NSCLCs), and 0 and 9.5% in small cell lung cancers (SCLCs), respectively. The nuclear and cytoplasmic expression rates of p16 were 11.5 and 32.2% in NSCLs, and 45 and 80% in SCLCs, respectively. The cytoplasmic expression of both C-erbB-2 and p16 was more frequent than the membranous expression of C-erbB-2 and the nuclear expression of p16. The rates of overexpression of C-erbB-2 and loss of p16 expression were significantly higher in NSCLCs than in SCLCs (P < 0.05). Neither C-erbB-2 nor p16 expression was significantly associated with age, tumor grade or stage, presence of lymph node metastasis or survival duration. The abnormal expressions of p16 and C-erbB-2 may play a role in the progression of lung cancers. The variations in the expression patterns of C-erbB-2 and p16 between NSCLCs and SCLCs may aid the molecular classification of lung cancer. The abnormal expression of p16 may be involved in the development of NSCLCs, and the overexpression of C-erbB-2 in NSCLCs indicates that it can be a candidate target for gene therapy.

  11. A grass molecular identification system for forensic botany: a critical evaluation of the strengths and limitations.

    Science.gov (United States)

    Ward, Jodie; Gilmore, Simon R; Robertson, James; Peakall, Rod

    2009-11-01

    Plant material is frequently encountered in criminal investigations but often overlooked as potential evidence. We designed a DNA-based molecular identification system for 100 Australian grasses that consisted of a series of polymerase chain reaction assays that enabled the progressive identification of grasses to different taxonomic levels. The identification system was based on DNA sequence variation at four chloroplast and two mitochondrial loci. Seventeen informative indels and 68 single-nucleotide polymorphisms were utilized as molecular markers for subfamily to species-level identification. To identify an unknown sample to subfamily level required a minimum of four markers or nine markers for species identification. The accuracy of the system was confirmed by blind tests. We have demonstrated "proof of concept" of a molecular identification system for trace botanical samples. Our evaluation suggests that the adoption of a system that combines this approach with DNA sequencing could assist the morphological identification of grasses found as forensic evidence.

  12. The rise of a novel classification system for endometrial carcinoma; integration of molecular subclasses.

    Science.gov (United States)

    McAlpine, Jessica; Leon-Castillo, Alicia; Bosse, Tjalling

    2018-04-01

    Endometrial cancer is a clinically heterogeneous disease and it is becoming increasingly clear that this heterogeneity may be a function of the diversity of the underlying molecular alterations. Recent large-scale genomic studies have revealed that endometrial cancer can be divided into at least four distinct molecular subtypes, with well-described underlying genomic aberrations. These subtypes can be reliably delineated and carry significant prognostic as well as predictive information; embracing and incorporating them into clinical practice is thus attractive. The road towards the integration of molecular features into current classification systems is not without obstacles. Collaborative studies engaging research teams from across the world are working to define pragmatic assays, improve risk stratification systems by combining molecular features and traditional clinicopathological parameters, and determine how molecular classification can be optimally utilized to direct patient care. Pathologists and clinicians caring for women with endometrial cancer need to engage with and understand the possibilities and limitations of this new approach, because integration of molecular classification of endometrial cancers is anticipated to become an essential part of gynaecological pathology practice. This review will describe the challenges in current systems of endometrial carcinoma classification, the evolution of new molecular technologies that define prognostically distinct molecular subtypes, and potential applications of molecular classification as a step towards precision medicine and refining care for individuals with the most common gynaecological cancer in the developed world. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  13. Calculation on uranium carbon oxygen system molecular structure by DFT

    International Nuclear Information System (INIS)

    Zhang Guangfeng; Wang Xiaolin; Zou Lexi; Sun Ying; Xue Weidong; Zhu Zhenghe; Wang Hongyan

    2001-01-01

    The authors study on the possible molecular structures U-C-O, U-O-C, C-U-O (angular structure C a nd linear structure C ∞υ ) of carbon monoxide interacting on uranium metal surface by Density functional theory (DFT). The uranium atom is used RECP (Relativistic Effective Core Potential) and contracted valence basis sets (6s5p2d4f)/[3s3p2d2f], and for carbon and oxygen atoms all are 6-311G basis sets. The author presents the results of energy optimum which shows that triple and quintuple state are more stable. The authors get the electronic state, geometry structure, energy, harmonic frequency, mechanical property, etc. of these twelve triple and quintuple state relative stable structures. The normal vibrational analytical figure of angular structure (C s ) and linear structure (C ∞υ ) is given at the same time. It is indicated that angular structure has lower energy than linear structure, moreover the angular structure of U-C-O( 3 A ) has the lowest energy. The bond strength between uranium atom and carbon monoxide is weak and between uranium atom and oxygen atom is slightly stronger than between uranium atom and carbon atom which the authors can know by superposition population and bond energy analysis among atoms

  14. Molecular characterization of the thioredoxin system from Methanosarcina acetivorans

    OpenAIRE

    McCarver, Addison C.; Lessner, Daniel J.

    2014-01-01

    The thioredoxin system, composed of thioredoxin reductase (TrxR) and thioredoxin (Trx), is widely distributed in nature, where it serves key roles in electron transfer and in defense against oxidative stress. Although recent evidence reveals Trx homologues are almost universally present among the methane-producing archaea (methanogens), a complete thioredoxin system has not been characterized from any methanogen. We examined the phylogeny of Trx homologues among methanogens and characterized ...

  15. Molecular spectral imaging system for quantitative immunohistochemical analysis of early diabetic retinopathy.

    Science.gov (United States)

    Li, Qingli; Zhang, Jingfa; Wang, Yiting; Xu, Guoteng

    2009-12-01

    A molecular spectral imaging system has been developed based on microscopy and spectral imaging technology. The system is capable of acquiring molecular spectral images from 400 nm to 800 nm with 2 nm wavelength increments. The basic principles, instrumental systems, and system calibration method as well as its applications for the calculation of the stain-uptake by tissues are introduced. As a case study, the system is used for determining the pathogenesis of diabetic retinopathy and evaluating the therapeutic effects of erythropoietin. Some molecular spectral images of retinal sections of normal, diabetic, and treated rats were collected and analyzed. The typical transmittance curves of positive spots stained for albumin and advanced glycation end products are retrieved from molecular spectral data with the spectral response calibration algorithm. To explore and evaluate the protective effect of erythropoietin (EPO) on retinal albumin leakage of streptozotocin-induced diabetic rats, an algorithm based on Beer-Lambert's law is presented. The algorithm can assess the uptake by histologic retinal sections of stains used in quantitative pathology to label albumin leakage and advanced glycation end products formation. Experimental results show that the system is helpful for the ophthalmologist to reveal the pathogenesis of diabetic retinopathy and explore the protective effect of erythropoietin on retinal cells of diabetic rats. It also highlights the potential of molecular spectral imaging technology to provide more effective and reliable diagnostic criteria in pathology.

  16. Systems theoretic analysis of the central dogma of molecular biology: some recent results.

    Science.gov (United States)

    Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin

    2010-03-01

    This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

  17. Cleavage and formation of molecular dinitrogen in a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine.

    Science.gov (United States)

    Miyazaki, Takamasa; Tanaka, Hiromasa; Tanabe, Yoshiaki; Yuki, Masahiro; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki

    2014-10-20

    The N≡N bond of molecular dinitrogen bridging two molybdenum atoms in the pentamethylcyclopentadienyl molybdenum complexes that bear ferrocenyldiphosphine as an auxiliary ligand is homolytically cleaved under visible light irradiation at room temperature to afford two molar molybdenum nitride complexes. Conversely, the bridging molecular dinitrogen is reformed by the oxidation of the molybdenum nitride complex at room temperature. This result provides a successful example of the cleavage and formation of molecular dinitrogen induced by a pair of two different external stimuli using a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine under ambient conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    International Nuclear Information System (INIS)

    Li, King C.P.

    2009-01-01

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  19. All-organic microelectromechanical systems integrating specific molecular recognition--a new generation of chemical sensors.

    Science.gov (United States)

    Ayela, Cédric; Dubourg, Georges; Pellet, Claude; Haupt, Karsten

    2014-09-03

    Cantilever-type all-organic microelectromechanical systems based on molecularly imprinted polymers for specific analyte recognition are used as chemical sensors. They are produced by a simple spray-coating-shadow-masking process. Analyte binding to the cantilever generates a measurable change in its resonance frequency. This allows label-free detection by direct mass sensing of low-molecular-weight analytes at nanomolar concentrations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Systems biological approach of molecular descriptors connectivity: optimal descriptors for oral bioavailability prediction.

    Science.gov (United States)

    Ahmed, Shiek S S J; Ramakrishnan, V

    2012-01-01

    Poor oral bioavailability is an important parameter accounting for the failure of the drug candidates. Approximately, 50% of developing drugs fail because of unfavorable oral bioavailability. In silico prediction of oral bioavailability (%F) based on physiochemical properties are highly needed. Although many computational models have been developed to predict oral bioavailability, their accuracy remains low with a significant number of false positives. In this study, we present an oral bioavailability model based on systems biological approach, using a machine learning algorithm coupled with an optimal discriminative set of physiochemical properties. The models were developed based on computationally derived 247 physicochemical descriptors from 2279 molecules, among which 969, 605 and 705 molecules were corresponds to oral bioavailability, intestinal absorption (HIA) and caco-2 permeability data set, respectively. The partial least squares discriminate analysis showed 49 descriptors of HIA and 50 descriptors of caco-2 are the major contributing descriptors in classifying into groups. Of these descriptors, 47 descriptors were commonly associated to HIA and caco-2, which suggests to play a vital role in classifying oral bioavailability. To determine the best machine learning algorithm, 21 classifiers were compared using a bioavailability data set of 969 molecules with 47 descriptors. Each molecule in the data set was represented by a set of 47 physiochemical properties with the functional relevance labeled as (+bioavailability/-bioavailability) to indicate good-bioavailability/poor-bioavailability molecules. The best-performing algorithm was the logistic algorithm. The correlation based feature selection (CFS) algorithm was implemented, which confirms that these 47 descriptors are the fundamental descriptors for oral bioavailability prediction. The logistic algorithm with 47 selected descriptors correctly predicted the oral bioavailability, with a predictive accuracy

  1. Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

    Science.gov (United States)

    Nistor, Razvan A.

    The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high

  2. Reaction-diffusion systems in intracellular molecular transport and control.

    Science.gov (United States)

    Soh, Siowling; Byrska, Marta; Kandere-Grzybowska, Kristiana; Grzybowski, Bartosz A

    2010-06-07

    Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.

  3. Simulation of Molecular Transport in Systems Containing Mobile Obstacles.

    Science.gov (United States)

    Polanowski, Piotr; Sikorski, Andrzej

    2016-08-04

    In this paper, we investigate the movement of molecules in crowded environments with obstacles undergoing Brownian motion by means of extensive Monte Carlo simulations. Our investigations were performed using the dynamic lattice liquid model, which was based on the cooperative movement concept and allowed to mimic systems at high densities where the motion of all elements (obstacles as well as moving particles) were highly correlated. The crowded environments are modeled on a two-dimensional triangular lattice containing obstacles (particles whose mobility was significantly reduced) moving by a Brownian motion. The subdiffusive motion of both elements in the system was analyzed. It was shown that the percolation transition does not exist in such systems in spite of the cooperative character of the particles' motion. The reduction of the obstacle mobility leads to the longer caging of liquid particles by mobile obstacles.

  4. Perioperative Temperature Measurement Considerations Relevant to Reporting Requirements for National Quality Programs Using Data From Anesthesia Information Management Systems.

    Science.gov (United States)

    Epstein, Richard H; Dexter, Franklin; Hofer, Ira S; Rodriguez, Luis I; Schwenk, Eric S; Maga, Joni M; Hindman, Bradley J

    2018-02-01

    Perioperative hypothermia may increase the incidences of wound infection, blood loss, transfusion, and cardiac morbidity. US national quality programs for perioperative normothermia specify the presence of at least 1 "body temperature" ≥35.5°C during the interval from 30 minutes before to 15 minutes after the anesthesia end time. Using data from 4 academic hospitals, we evaluated timing and measurement considerations relevant to the current requirements to guide hospitals wishing to report perioperative temperature measures using electronic data sources. Anesthesia information management system databases from 4 hospitals were queried to obtain intraoperative temperatures and intervals to the anesthesia end time from discontinuation of temperature monitoring, end of surgery, and extubation. Inclusion criteria included age >16 years, use of a tracheal tube or supraglottic airway, and case duration ≥60 minutes. The end-of-case temperature was determined as the maximum intraoperative temperature recorded within 30 minutes before the anesthesia end time (ie, the temperature that would be used for reporting purposes). The fractions of cases with intervals >30 minutes between the last intraoperative temperature and the anesthesia end time were determined. Among the hospitals, averages (binned by quarters) of 34.5% to 59.5% of cases had intraoperative temperature monitoring discontinued >30 minutes before the anesthesia end time. Even if temperature measurement had been continued until extubation, averages of 5.9% to 20.8% of cases would have exceeded the allowed 30-minute window. Averages of 8.9% to 21.3% of cases had end-of-case intraoperative temperatures <35.5°C (ie, a quality measure failure). Because of timing considerations, a substantial fraction of cases would have been ineligible to use the end-of-case intraoperative temperature for national quality program reporting. Thus, retrieval of postanesthesia care unit temperatures would have been necessary. A

  5. A Novel Relevance Feedback Approach Based on Similarity Measure Modification in an X-Ray Image Retrieval System Based on Fuzzy Representation Using Fuzzy Attributed Relational Graph

    Directory of Open Access Journals (Sweden)

    Hossien Pourghassem

    2011-04-01

    Full Text Available Relevance feedback approaches is used to improve the performance of content-based image retrieval systems. In this paper, a novel relevance feedback approach based on similarity measure modification in an X-ray image retrieval system based on fuzzy representation using fuzzy attributed relational graph (FARG is presented. In this approach, optimum weight of each feature in feature vector is calculated using similarity rate between query image and relevant and irrelevant images in user feedback. The calculated weight is used to tune fuzzy graph matching algorithm as a modifier parameter in similarity measure. The standard deviation of the retrieved image features is applied to calculate the optimum weight. The proposed image retrieval system uses a FARG for representation of images, a fuzzy matching graph algorithm as similarity measure and a semantic classifier based on merging scheme for determination of the search space in image database. To evaluate relevance feedback approach in the proposed system, a standard X-ray image database consisting of 10000 images in 57 classes is used. The improvement of the evaluation parameters shows proficiency and efficiency of the proposed system.

  6. A Strategy to Suppress Phonon Transport in Molecular Junctions Using pi-Stacked Systems

    DEFF Research Database (Denmark)

    Li, Qian; Strange, Mikkel; Duchemin, Ivan

    2017-01-01

    to suppress phonon transport in graphene-based molecular junctions preserving high electronic power factor, using nonbonded pi-stackal systems. Using first-principles calculations, we find that the thermal conductance of pi-stacked systems can be reduced by about 95%, compared with that of a covalently bonded...

  7. Fulminant hepatic failure following marijuana drug abuse: Molecular adsorbent recirculation system therapy

    Directory of Open Access Journals (Sweden)

    G Swarnalatha

    2013-01-01

    Full Text Available Marijuana is used for psychoactive and recreational purpose. We report a case of fulminant hepatic failure following marijuana drug abuse who recovered following artificial support systems for acute liver failure. There is no published literature of management of marijuana intoxication with molecular adsorbent recirculation system (MARS. MARS is effective and safe in patients with fulminant hepatic failure following marijuana intoxication.

  8. Relativistic Green function for atomic and molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Gruzdev, P.F.; Sherstyuk, A.I.

    1981-12-01

    The problem on Green function construction of Dirac equation is solved for a wide class of single electron potentials in the atom and molecule theory. The solution is obtained in the form of a spectrum analysis according to the total system of eigenfuctions of the generalized Dirac problem for eigenvalues. The problem possesses a purely discrete spectrum.

  9. The chloroplast thylakoid membrane system is a molecular conveyor belt.

    Science.gov (United States)

    Critchley, C

    1988-10-01

    Light drives photosynthesis, but paradoxically light is also the most variable environmental factor influencing photosynthesis both qualitatively and quantitatively. The photosynthetic apparatus of higher plants is adaptable in the extreme, as exemplified by its capacity for acclimation to very bright sunny or deeply shaded conditions. It can also respond to rapid changes in light such as sunflecks. In this paper I offer a model that i) explains the thylakoid membrane organisation into grana stacks and stroma lamellae, ii) proposes a role for rapid D1 protein turnover and LHCII phosphorylation, and iii) suggests a mechanism for photoinhibition. I argue that the photosynthetic membrane system is dynamic in three dimensions, so much so that, in the light, it is in constant motion and operates in a manner somewhat analogous to a conveyor belt. D1 protein degradation is proposed to be the motor that drives this system. Photoinhibition is suggested to be due to the arrest of D1 protein turnover.

  10. epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens

    Directory of Open Access Journals (Sweden)

    González-Candelas Fernando

    2007-04-01

    Full Text Available Abstract Background Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support. Results From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data. Conclusion epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the

  11. Molecular pathology of systemic lupus erythematosus in Asians

    OpenAIRE

    Chai, Hwa Chia

    2017-01-01

    Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease affecting various parts of the body. Polymorphisms in genes involved in toll-like receptor (TLR)/interferon (IFN) signalling pathways have been reported previously to be associated with SLE in many populations. This study aimed to investigate the role of seven single nucleotide polymorphisms (SNPs) within TNFAIP3 (rs2230936 and rs3757173), STAT4 (rs7574865, rs10168266, and rs7601754), and IRF5 (rs4728142 and rs729302), that...

  12. Bound states and molecular structure of systems with hyperons

    International Nuclear Information System (INIS)

    Akaishi, Y.

    1992-01-01

    Microscopic calculations are done for Σ-hypernuclear few-body systems by a method named ATMS. Among two- to five-body systems, only the Σ 4 He(0 + ) and Σ 4 H(0 + ) hypernuclei are expected to be bound: The binding energy and the width of the former are calculated to be 3.7 ∼ 4.6 MeV and 4.5 ∼ 7.9 MeV, respectively. The observation of Σ 4 He at KEK is in good agreement with the above prediction. The nucleus-Σ potential has a strong Lane term and a repulsive bump at short distance. The Lane term makes the system bound and the bump suppresses the ΣN → ΛN conversion. X-ray measurement of level shifts in the 4 He-Σ - , 3 He-Σ - and 3 H-Σ - atoms can provide another information on the Lane term. In 208 Pb, there may exist a peculiar state, Coulomb-assisted (atomnucleus) hybrid state, where Σ - is trapped in the surface region by the strong interaction with the aid of the inner centrifugal repulsion and the outer Coulomb attraction. An analysis is given for new data of Ξ -.12 C atomic or nuclear systems from the emulsion-counter experiment at KEK. The double-Λ hypernucleus formation rate is calculated for a stopped Ξ - on 4 He. A high branching ratio of 37% is obtained for the ΛΛ 4 H formation from a Ξ -.4 He atom. The detection of about 2.3 MeV neutron is proposed to search for lightest double-Λ hypernucleus ΛΛ 4 H. (author)

  13. Biomedical wellness monitoring system based upon molecular markers

    Science.gov (United States)

    Ingram, Whitney

    2012-06-01

    We wish to assist caretakers with a sensor monitoring systems for tracking the physiological changes of homealone patients. One goal is seeking biomarkers and modern imaging sensors like stochastic optical reconstruction microscopy (STORM), which has achieved visible imaging at the nano-scale range. Imaging techniques like STORM can be combined with a fluorescent functional marker in a system to capture the early transformation signs from wellness to illness. By exploiting both microscopic knowledge of genetic pre-disposition and the macroscopic influence of epigenetic factors we hope to target these changes remotely. We adopt dual spectral infrared imaging for blind source separation (BSS) to detect angiogenesis changes and use laser speckle imaging for hypertension blood flow monitoring. Our design hypothesis for the monitoring system is guided by the user-friendly, veteran-preferred "4-Non" principles (noninvasive, non-contact, non-tethered, non-stop-to-measure) and by the NIH's "4Ps" initiatives (predictive, personalized, preemptive, and participatory). We augment the potential storage system with the recent know-how of video Compressive Sampling (CSp) from surveillance cameras. In CSp only major changes are saved, which reduces the manpower cost of caretakers and medical analysts. This CSp algorithm is based on smart associative memory (AM) matrix storage: change features and detailed scenes are written by the outer-product and read by the inner product without the usual Harsh index for image searching. From this approach, we attempt to design an effective household monitoring approach to save healthcare costs and maintain the quality of life of seniors.

  14. Supra-molecular Association and Polymorphic Behaviour In Systems Containing Bile Acid Salts

    Directory of Open Access Journals (Sweden)

    Camillo La Mesa

    2007-08-01

    Full Text Available A wide number of supra-molecular association modes are observed in mixtures containing water and bile salts, BS, (with, eventually, other components. Molecular or micellar solutions transform into hydrated solids, fibres, lyotropic liquid crystals and/or gels by raising the concentration, the temperature, adding electrolytes, surfactants, lipids and proteins. Amorphous or ordered phases may be formed accordingly. The forces responsible for this very rich polymorphism presumably arise from the unusual combination of electrostatic, hydrophobic and hydrogen-bond contributions to the system stability, with subsequent control of the supra-molecular organisation modes. The stabilising effect due to hydrogen bonds does not occur in almost all surfactants or lipids and is peculiar to bile acids and salts. Some supra-molecular organisation modes, supposed to be related to malfunctions and dis-metabolic diseases in vivo, are briefly reported and discussed.

  15. Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

    Science.gov (United States)

    Muto, Yutaka; Yokoyama, Shigeyuki

    2012-01-01

    'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. Copyright © 2012 John Wiley & Sons, Ltd.

  16. Molecular alteration of a muscarinic acetylcholine receptor system during synaptogenesis

    International Nuclear Information System (INIS)

    Large, T.H.; Cho, N.J.; De Mello, F.G.; Klein, W.L.

    1985-01-01

    Biochemical properties of the muscarinic acetylcholine receptor system of the avian retina were found to change during the period when synapses form in ovo. Comparison of ligand binding to membranes obtained before and after synaptogenesis showed a significant increase in the affinity, but not proportion, of the high affinity agonist-binding state. There was no change in receptor sensitivity to antagonists during this period. Pirenzepine binding, which can discriminate muscarinic receptor subtypes, showed the presence of a single population of low affinity sites (M2) before and after synaptogenesis. The change in agonist binding was not due to the late development of receptor function. However, detergent-solubilization of membranes eliminated differences in agonist binding between receptors from embryos and hatched chicks, suggesting a developmental change in interactions of the receptor with functionally related membrane components. A possible basis for altered interactions was obtained from isoelectric point data showing that the muscarinic receptor population underwent a transition from a predominantly low pI form (4.25) in 13 day embryos to a predominantly high pI form (4.50) in newly hatched chicks. The possibility that biochemical changes in the muscarinic receptor play a role in differentiation of the system by controlling receptor position on the surface of nerve cells is discussed

  17. Chapter 5: Quantum Dynamics in Dissipative Molecular Systems

    Science.gov (United States)

    Zhang, Hou-Dao; Xu, J.; Xu, Rui-Xue; Yan, Y. J.

    2014-04-01

    The following sections are included: * Introduction * HEOM versus Path Integral Formalism: Background * Generic form and terminology of HEOM * Statistical mechanics description of bath influence * Feynman-Vernon influence functional formalism * General comments * Memory-Frequency Decomposition of Bath Correlation Functions * PSD of Bose function * Brownian oscillators decomposition of bath spectral density function * Optimized HEOM Theory With Accuracy Control * Construction of HEOM via path integral formalism * Accuracy control on white-noise residue ansatz * Efficient HEOM propagator: Numerical filtering and indexing algorithm * HEOM in Quantum Mechanics for Open Systems * The HEOM space and the Schrödinger picture * HEOM in the Heisenberg picture * Mixed Heisenberg-Schrödinger block-matrix dynamics in nonlinear optical response functions * Two-Dimensional Spectroscopy: Model Calculations * Concluding Remarks * Acknowledgments * References

  18. Intracellular Chemistry: Integrating Molecular Inorganic Catalysts with Living Systems.

    Science.gov (United States)

    Ngo, Anh H; Bose, Sohini; Do, Loi H

    2018-03-23

    This concept article focuses on the rapid growth of intracellular chemistry dedicated to the integration of small-molecule metal catalysts with living cells and organisms. Although biological systems contain a plethora of biomolecules that can deactivate inorganic species, researchers have shown that small-molecule metal catalysts could be engineered to operate in heterogeneous aqueous environments. Synthetic intracellular reactions have recently been reported for olefin hydrogenation, hydrolysis/oxidative cleavage, azide-alkyne cycloaddition, allylcarbamate cleavage, C-C bond cross coupling, and transfer hydrogenation. Other promising targets for new biocompatible reaction discovery will also be discussed, with a special emphasis on how such innovations could lead to the development of novel technologies and chemical tools. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Molecular dynamics coupled with a virtual system for effective conformational sampling.

    Science.gov (United States)

    Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

    2018-07-15

    An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  20. Phases of polymer systems in solution studied via molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Joshua Allen [Iowa State Univ., Ames, IA (United States)

    2009-05-01

    Polymers are amazingly versatile molecules with a tremendous range of applications. Our lives would be very different without them. There would be no multitudes of plastic encased electronic gizmos, no latex paint on the walls and no rubber tires, just to name a few of the many commonplace polymer materials. In fact, life as we know it wouldn’t exist without polymers as two of the most essential types of molecules central to cellular life, Proteins and DNA, are both polymers! [1] With their wide range of application to a variety of uses, polymers are still a very active field in basic research. Of particular current interest is the idea of combining polymers with inorganic particles to form novel composite materials. [2] As computers are becoming faster, they are becoming all the more powerful tools for modeling and simulating real systems. With recent advances in computing on graphics processing units (GPUs) [3–7], questions can now be answered via simulation that could not even be asked before. This thesis focuses on the use of computer simulations to model novel polymerinorganic composite systems in order to predict what possible phases can form and under what conditions. The goal is to provide some direction for future experiments and to gain a deeper understanding of the fundamental physics involved. Along the way, there are some interesting and essential side-tracks in the areas of equilibrating complicated phases and accelerating the available computer power with GPU computing, both of which are necessary steps to enable the study of polymer nanocomposites.

  1. Modulated molecular beam mass spectrometry: A generalized expression for the ''reaction product vector'' for linear systems

    International Nuclear Information System (INIS)

    Chang, H.; Weinberg, W.H.

    1977-01-01

    A generalized expression is developed that relates the ''reaction product vector'', epsilon exp(-iphi), to the kinetic parameters of a linear system. The formalism is appropriate for the analysis of modulated molecular beam mass spectrometry data and facilitates the correlation of experimental results to (proposed) linear models. A study of stability criteria appropriate for modulated molecular beam mass spectrometry experiments is also presented. This investigation has led to interesting inherent limitations which have not heretofore been emphasized, as well as a delineation of the conditions under which stable chemical oscillations may occur in the reacting system

  2. Potentiometric investigations of molecular heteroconjugation equilibria of substituted phenol+n-butylamine systems in dimethyl sulfoxide

    International Nuclear Information System (INIS)

    Czaja, MaIgorzata; Baginska, Katarzyna; Kozak, Anna; Makowski, Mariusz; Chmurzynski, Lech

    2005-01-01

    Molecular heteroconjugation constants, K BHA DMSO and K AHB DMSO , expressed as their logarithms, have been determined by potentiometric titration for eleven substituted phenol+n-butylamine systems in a polar protophilic aprotic solvent, dimethyl sulfoxide (DMSO). An increasing tendency towards molecular heteroconjugation in these systems without proton transfer has been found with increasing pK a DMSO (HA), i.e., with decreasing phenol acidity. Moreover, a linear correlation has been established between the determined lgK BHA DMSO values and pK a DMSO (HA). Furthermore, overall stability constants, lgK o DMSO , could be correlated linearly with pK a DMSO (HA) values

  3. Low molecular mass chitosan as carrier for hydrodynamically balanced system for sustained delivery of ciprofloxacin hydrochloride

    OpenAIRE

    VERMA, ANURAG; BANSAL, ASHOK K.; GHOSH, AMITAVA; PANDIT, JAYANTA K.

    2012-01-01

    Chitosan has become a focus of major interest in recent years due to its excellent biocompatibility, biodegradability and non-toxicity. Although this material has already been extensively investigated in the design of different types of drug delivery systems, it is still little explored for stomach specific drug delivery systems. The objective of the present investigation was to explore the potential of low molecular mass chitosan (LMCH) as carrier for a hydrodynamically balanced system (HBS)...

  4. Molecular evolution of peptidergic signaling systems in bilaterians

    Science.gov (United States)

    Mirabeau, Olivier; Joly, Jean-Stéphane

    2013-01-01

    Peptide hormones and their receptors are widespread in metazoans, but the knowledge we have of their evolutionary relationships remains unclear. Recently, accumulating genome sequences from many different species have offered the opportunity to reassess the relationships between protostomian and deuterostomian peptidergic systems (PSs). Here we used sequences of all human rhodopsin and secretin-type G protein-coupled receptors as bait to retrieve potential homologs in the genomes of 15 bilaterian species, including nonchordate deuterostomian and lophotrochozoan species. Our phylogenetic analysis of these receptors revealed 29 well-supported subtrees containing mixed sets of protostomian and deuterostomian sequences. This indicated that many vertebrate and arthropod PSs that were previously thought to be phyla specific are in fact of bilaterian origin. By screening sequence databases for potential peptides, we then reconstructed entire bilaterian peptide families and showed that protostomian and deuterostomian peptides that are ligands of orthologous receptors displayed some similarity at the level of their primary sequence, suggesting an ancient coevolution between peptide and receptor genes. In addition to shedding light on the function of human G protein-coupled receptor PSs, this work presents orthology markers to study ancestral neuron types that were probably present in the last common bilaterian ancestor. PMID:23671109

  5. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics †

    Science.gov (United States)

    Chen, Wei; Shen, Jana K.

    2014-01-01

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

  6. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

    Science.gov (United States)

    Chen, Wei; Shen, Jana K

    2014-10-15

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma. Copyright © 2014 Wiley Periodicals, Inc.

  7. Coherent Rabi oscillations in a molecular system and sub-diffraction-limited pattern generation

    International Nuclear Information System (INIS)

    Liao, Zeyang; Al-Amri, M; Zubairy, M Suhail

    2015-01-01

    The resolution of a photolithography and optical imaging system is restricted by the diffraction limit. Coherent Rabi oscillations have been shown to be able to overcome the diffraction limit in a simple two-level atomic system (Z Liao, M Al-amri, and M S Zubairy 2010 Phys. Rev. Lett. 105 183601). In this paper, we numerically calculate the wave packet dynamics of a molecular system interacting with an ultrashort laser pulse and show that coherent Rabi oscillations in a molecular system are also possible. Moreover, a sub-diffraction-limited pattern can be generated in this system by introducing spatially modulated Rabi oscillations. We also discuss several techniques to improve the visibility of the sub-diffraction-limited pattern. Our result may have important applications in super-resolution optical lithography and optical imaging. (paper)

  8. A neural network approach to the study of dynamics and structure of molecular systems

    International Nuclear Information System (INIS)

    Getino, C.; Sumpter, B.G.; Noid, D.W.

    1994-01-01

    Neural networks are used to study intramolecular energy flow in molecular systems (tetratomics to macromolecules), developing new techniques for efficient analysis of data obtained from molecular-dynamics and quantum mechanics calculations. Neural networks can map phase space points to intramolecular vibrational energies along a classical trajectory (example of complicated coordinate transformation), producing reasonably accurate values for any region of the multidimensional phase space of a tetratomic molecule. Neural network energy flow predictions are found to significantly enhance the molecular-dynamics method to longer time-scales and extensive averaging of trajectories for macromolecular systems. Pattern recognition abilities of neural networks can be used to discern phase space features. Neural networks can also expand model calculations by interpolation of costly quantum mechanical ab initio data, used to develop semiempirical potential energy functions

  9. Comparative analysis of three drug-drug interaction screening systems against probable clinically relevant drug-drug interactions: a prospective cohort study.

    Science.gov (United States)

    Muhič, Neža; Mrhar, Ales; Brvar, Miran

    2017-07-01

    Drug-drug interaction (DDI) screening systems report potential DDIs. This study aimed to find the prevalence of probable DDI-related adverse drug reactions (ADRs) and compare the clinical usefulness of different DDI screening systems to prevent or warn against these ADRs. A prospective cohort study was conducted in patients urgently admitted to medical departments. Potential DDIs were checked using Complete Drug Interaction®, Lexicomp® Online™, and Drug Interaction Checker®. The study team identified the patients with probable clinically relevant DDI-related ADRs on admission, the causality of which was assessed using the Drug Interaction Probability Scale (DIPS). Sensitivity, specificity, and positive and negative predictive values of screening systems to prevent or warn against probable DDI-related ADRs were evaluated. Overall, 50 probable clinically relevant DDI-related ADRs were found in 37 out of 795 included patients taking at least two drugs, most common of them were bleeding, hyperkalemia, digitalis toxicity, and hypotension. Complete Drug Interaction showed the best sensitivity (0.76) for actual DDI-related ADRs, followed by Lexicomp Online (0.50), and Drug Interaction Checker (0.40). Complete Drug Interaction and Drug Interaction Checker had positive predictive values of 0.07; Lexicomp Online had 0.04. We found no difference in specificity and negative predictive values among these systems. DDI screening systems differ significantly in their ability to detect probable clinically relevant DDI-related ADRs in terms of sensitivity and positive predictive value.

  10. Large-scale molecular dynamics simulations of self-assembling systems.

    Science.gov (United States)

    Klein, Michael L; Shinoda, Wataru

    2008-08-08

    Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.

  11. Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

    Science.gov (United States)

    Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

    2010-01-01

    The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

  12. Molecular subtypes of systemic sclerosis in association with anti-centromere antibodies and digital ulcers

    NARCIS (Netherlands)

    Bos, C. L.; van Baarsen, L. G. M.; Timmer, T. C. G.; Overbeek, M. J.; Basoski, N. M.; Rustenburg, F.; Baggen, J. M. C.; Thiesen, H. J.; Dijkmans, B. A. C.; van der Pouw Kraan, T. C. T. M.; Voskuyl, A. E.; Verweij, C. L.

    2009-01-01

    The objective of this study was to identify molecular profiles that may distinguish clinical subtypes in systemic sclerosis (SSc). Large-scale gene expression profiling was performed on peripheral blood (PB) from 12 SSc patients and 6 healthy individuals. Significance analysis of microarrays,

  13. On the effects of transforming the vibrational spectra of molecular systems under microwave radiation

    International Nuclear Information System (INIS)

    Serikov, A.A.

    1993-01-01

    This problem is analyzed within the quantum-classical theory of molecular spectra. It is shown that the above-mentioned spectrum transformation could be, in principle, realized in macromolecular systems with strong interaction, and attention is drawn to the resonance character of the effect. (author). 19 refs., 1 fig

  14. Advances of Molecular Imaging for Monitoring the Anatomical and Functional Architecture of the Olfactory System.

    Science.gov (United States)

    Zhang, Xintong; Bi, Anyao; Gao, Quansheng; Zhang, Shuai; Huang, Kunzhu; Liu, Zhiguo; Gao, Tang; Zeng, Wenbin

    2016-01-20

    The olfactory system of organisms serves as a genetically and anatomically model for studying how sensory input can be translated into behavior output. Some neurologic diseases are considered to be related to olfactory disturbance, especially Alzheimer's disease, Parkinson's disease, multiple sclerosis, and so forth. However, it is still unclear how the olfactory system affects disease generation processes and olfaction delivery processes. Molecular imaging, a modern multidisciplinary technology, can provide valid tools for the early detection and characterization of diseases, evaluation of treatment, and study of biological processes in living subjects, since molecular imaging applies specific molecular probes as a novel approach to produce special data to study biological processes in cellular and subcellular levels. Recently, molecular imaging plays a key role in studying the activation of olfactory system, thus it could help to prevent or delay some diseases. Herein, we present a comprehensive review on the research progress of the imaging probes for visualizing olfactory system, which is classified on different imaging modalities, including PET, MRI, and optical imaging. Additionally, the probes' design, sensing mechanism, and biological application are discussed. Finally, we provide an outlook for future studies in this field.

  15. Structure and properties of simple molecular systems at very high density

    International Nuclear Information System (INIS)

    LeSar, R.

    1989-01-01

    The use of computer simulations in the study of molecular systems at very high density is reviewed. Applications to the thermodynamics of dense fluid nitrogen and phase transitions in solid oxygen are presented. The effects of changes in the atomic electronic structure on the equation of state of very dense helium are discussed. 19 refs., 2 figs

  16. Development of Optical Molecular Imaging System for the Acquisition of Bioluminescence Signals from Small Animals

    International Nuclear Information System (INIS)

    Lee, Byeong Il; Kim, Hyeon Sik; Jeong, Hye Jin; Lee, Hyung Jae; Moon, Seung Min; Kwon, Seung Young; Jeong, Shin Young; Bom, Hee Seung; Min, Jung Joon; Choi, Eun Seo

    2009-01-01

    Optical imaging is providing great advance and improvement in genetic and molecular imaging of animals and humans. Optical imaging system consists of optical imaging devices, which carry out major function for monitoring, tracing, and imaging in most of molecular in-vivo researches. In bio-luminescent imaging, small animals containing luciferase gene locally irradiate light, and emitted photons transmitted through skin of the small animals are imaged by using a high sensitive charged coupled device (CCD) camera. In this paper, we introduced optical imaging system for the image acquisition of bio-luminescent signals emitted from small animals. In the system, Nikon lens and four LED light sources were mounted at the inside of a dark box. A cooled CCD camera equipped with a control module was used. We tested the performance of the optical imaging system using effendorf tube and light emitting bacteria which injected intravenously into CT26 tumor bearing nude mouse. The performance of implemented optical imaging system for bio-luminescence imaging was demonstrated and the feasibility of the system in small animal imaging application was proved. We anticipate this system could be a useful tool for the molecular imaging of small animals adaptable for various experimental conditions in future

  17. Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

    Science.gov (United States)

    Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

    2018-01-01

    Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

  18. Studies of isotopic effects in the excited electronic states of molecular systems

    International Nuclear Information System (INIS)

    1982-01-01

    Rare gas halogen (RGH) lasers serve as convenient tools for a range of photophysical processes which exhibit isotope effects. This document summarizes progress in the production of molecular systems in their electronic excited states with the aid of RGH lasers, and the various isotopic effects one can study under these conditions. We conclude that the basic physical mechanisms involved in the isotopically sensitive characteristics of excited molecular electronic states are sufficiently selective to be useful in both the detection and separation of many atomic materials

  19. Advanced in study of cellular and molecular mechanisms of radiation effects on central nervous system

    International Nuclear Information System (INIS)

    Zhang Wei; Tu Yu; Wang Lili

    2008-01-01

    Along with radiation treatment extensively applied, radiation injury also is valued gradually. The effect of radiation to the cellular and molecular of central nervous system (CNS) is a complicated and moderately advanced process and the mechanism is remains incompletely clear yet. Inquiring into the possible mechanism of the CNS including the injury and the restoration of neuron, neuroglia cells, endotheliocyte cell and blood-brain barrier and the molecular level of change induced by radiation, so as to provide beneficial thought for preventing and curing radiation injury clinically. Some neuroprotective strategies are also addressed in the review. (authors)

  20. Stability of therapeutic albumin solutions used for molecular adsorbent recirculating system-based liver dialysis.

    Science.gov (United States)

    De Bruyn, Tom; Meijers, Björn; Evenepoel, Pieter; Laub, Ruth; Willems, Ludo; Augustijns, Patrick; Annaert, Pieter

    2012-01-01

    Mounting evidence suggests beneficial effects of albumin dialysis-based liver support in patients suffering from acute-on-chronic liver failure. Molecular adsorbent recirculating system (MARS) is a nonbiological liver support device, based on the exchange of albumin-bound toxins between the patient's blood and a 20% human serum albumin solution in a secondary circuit. Bound toxins are continuously removed from the circulating albumin by exposure to activated charcoal and an ion-exchange resin. The aim of the present in vitro study was to determine the impact of exposure to charcoal and resin on the ligand binding properties of albumins, containing various levels of stabilizers and obtained from different suppliers (Baxter, CAF-DCF [Red Cross], and Sigma-Aldrich). Albumin binding properties were assessed by measuring equilibrium binding properties of warfarin, diazepam, and salicylate before and after incubation (for up to 7 h) with adsorbing materials; albumin-associated esterase-like activities were also determined. Notable changes in albumin binding upon incubation with adsorbing materials were only observed when using warfarin as a ligand. Affinity of warfarin for the Baxter and Sigma albumins showed a pronounced decrease (higher K(d) ) after the 1-7-h exposure to charcoal or resin. In the absence of adsorbing materials, similar effects were found, indicating that incubation time per se affects albumin binding properties. Following exposure to resin, Baxter albumin binding capacity (B(max)) increased about twofold. For albumin obtained from CAF-DCF, binding affinity and capacity for warfarin were constant under all conditions tested. Esterase-like activities associated with these albumins were either maintained or enhanced (up to 2.5-fold in case of Sigma albumin) following 7-h incubations with adsorbing materials. Our data suggest limited direct influence of the presence of stabilizers in therapeutic albumin solutions on baseline binding properties of human

  1. Relevance of equilibrium in multifragmentation

    International Nuclear Information System (INIS)

    Furuta, Takuya; Ono, Akira

    2009-01-01

    The relevance of equilibrium in a multifragmentation reaction of very central 40 Ca + 40 Ca collisions at 35 MeV/nucleon is investigated by using simulations of antisymmetrized molecular dynamics (AMD). Two types of ensembles are compared. One is the reaction ensemble of the states at each reaction time t in collision events simulated by AMD, and the other is the equilibrium ensemble prepared by solving the AMD equation of motion for a many-nucleon system confined in a container for a long time. The comparison of the ensembles is performed for the fragment charge distribution and the excitation energies. Our calculations show that there exists an equilibrium ensemble that well reproduces the reaction ensemble at each reaction time t for the investigated period 80≤t≤300 fm/c. However, there are some other observables that show discrepancies between the reaction and equilibrium ensembles. These may be interpreted as dynamical effects in the reaction. The usual static equilibrium at each instant is not realized since any equilibrium ensemble with the same volume as that of the reaction system cannot reproduce the fragment observables

  2. Energy transformation in molecular electronic systems: Comprehensive progress report, 1986--1989

    International Nuclear Information System (INIS)

    Kasha, M.

    1989-01-01

    Our research focuses on discovering the fundamental issues in proton-transfer and charge-transfer excitations in model systems, with an eye on which molecular systems will serve as the best guide to biological systems. This report addresses an intramolecular proton transfer classification system, proton-transfer potentials, proton-transfer spectroscopy of benzanilides, proton-transfer in aminosalicylates, proton-transfer in lumichrome, development of proton-transfer lasers, and triplet excitation enhancement via proton-transfer tunneling. 6 refs., 2 figs

  3. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    Energy Technology Data Exchange (ETDEWEB)

    Li, King C.P. [Department of Radiology, Methodist Hospital, Weill Cornell Medical College, 6565 Fannin Street, D280 Houston, TX 77030 (United States)], E-mail: kli@tmhs.org

    2009-05-15

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  4. Dynamic analysis of electron density in the course of the internal motion of molecular system

    International Nuclear Information System (INIS)

    Tachibana, A.; Hori, K.; Asai, Y.; Yamabe, T.

    1984-01-01

    The general dynamic aspect of electron density of a molecular system is studied on the basis of the general equation of the electron orbital which is formulated for the dynamic study of electronic motion. The newly defined electron orbital incorporates the dynamics of molecular vibration into the electronic structures. In this scheme, the change of electron distribution caused by excitation of vibrational state is defined as the ''dynamic electron transfer.'' The dynamic electron density is found to have the remarkable ''additive'' property. The time-dependent aspect of the dynamic electron redistribution is also analyzed on the basis of the ''coherent state.'' The new method relates the classical vibrational amplitude to the quantum number of the vibrational state. As a preliminary application of the present treatment, the dynamic electron densities of H 2 , HD, HT, HF, and HCl molecules are calculated by use of ab initio molecular orbital method

  5. Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes.

    Science.gov (United States)

    Kulasiri, Don

    2011-01-01

    We discuss the quantification of molecular fluctuations in the biochemical reaction systems within the context of intracellular processes associated with gene expression. We take the molecular reactions pertaining to circadian rhythms to develop models of molecular fluctuations in this chapter. There are a significant number of studies on stochastic fluctuations in intracellular genetic regulatory networks based on single cell-level experiments. In order to understand the fluctuations associated with the gene expression in circadian rhythm networks, it is important to model the interactions of transcriptional factors with the E-boxes in the promoter regions of some of the genes. The pertinent aspects of a near-equilibrium theory that would integrate the thermodynamical and particle dynamic characteristics of intracellular molecular fluctuations would be discussed, and the theory is extended by using the theory of stochastic differential equations. We then model the fluctuations associated with the promoter regions using general mathematical settings. We implemented ubiquitous Gillespie's algorithms, which are used to simulate stochasticity in biochemical networks, for each of the motifs. Both the theory and the Gillespie's algorithms gave the same results in terms of the time evolution of means and variances of molecular numbers. As biochemical reactions occur far away from equilibrium-hence the use of the Gillespie algorithm-these results suggest that the near-equilibrium theory should be a good approximation for some of the biochemical reactions. © 2011 Elsevier Inc. All rights reserved.

  6. Current systematic carbon-cycle observations and the need for implementing a policy-relevant carbon observing system

    Science.gov (United States)

    P. Ciais; A. J. Dolman; A. Bombelli; R. Duren; A. Peregon; P. J. Rayner; C. Miller; N. Gobron; G. Kinderman; G. Marland; N. Gruber; F. Chevallier; R. J. Andres; G. Balsamo; L. Bopp; F.-M. Bréon; G. Broquet; R. Dargaville; T. J. Battin; A. Borges; H. Bovensmann; M. Buchwitz; J. Butler; J. G. Canadell; R. B. Cook; R. DeFries; R. Engelen; K. R. Gurney; C. Heinze; M. Heimann; A. Held; M. Henry; B. Law; S. Luyssaert; J. Miller; T. Moriyama; C. Moulin; R. B. Myneni; C. Nussli; M. Obersteiner; D. Ojima; Y. Pan; J.-D. Paris; S. L. Piao; B. Poulter; S. Plummer; S. Quegan; P. Raymond; M. Reichstein; L. Rivier; C. Sabine; D. Schimel; O. Tarasova; R. Valentini; R. Wang; G. van der Werf; D. Wickland; M. Williams; C. Zehner

    2014-01-01

    A globally integrated carbon observation and analysis system is needed to improve the fundamental understanding of the global carbon cycle, to improve our ability to project future changes, and to verify the effectiveness of policies aiming to reduce greenhouse gas emissions and increase carbon sequestration. Building an integrated carbon observation system requires...

  7. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

    Science.gov (United States)

    Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

    2014-06-14

    Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

  8. An analytic approach to 2D electronic PE spectra of molecular systems

    International Nuclear Information System (INIS)

    Szoecs, V.

    2011-01-01

    Graphical abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems using direct calculation from electronic Hamiltonians allows peak classification from 3P-PE spectra dynamics. Display Omitted Highlights: → RWA approach to electronic photon echo. → A straightforward calculation of 2D electronic spectrograms in finite molecular systems. → Importance of population time dynamics in relation to inter-site coherent coupling. - Abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems and simplified line broadening models is presented. The Fourier picture of a heterodyne detected three-pulse rephasing PE signal in the δ-pulse limit of the external field is derived in analytic form. The method includes contributions of one and two-excitonic states and allows direct calculation of Fourier PE spectrogram from corresponding Hamiltonian. As an illustration, the proposed treatment is applied to simple systems, e.g. 2-site two-level system (TLS) and n-site TLS model of photosynthetic unit. The importance of relation between Fourier picture of 3P-PE dynamics (corresponding to nonzero population time, T) and coherent inter-state coupling is emphasized.

  9. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

    Directory of Open Access Journals (Sweden)

    Sophie S Abby

    Full Text Available Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose.Macromolecular System Finder (MacSyFinder provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate "Cas-finder" using publicly available protein profiles.MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher. It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The "Cas-finder" (models and HMM profiles is distributed as a compressed tarball archive as Supporting Information.

  10. Review and assessment of research relevant to design aspects of nuclear power plant piping systems. Final report

    International Nuclear Information System (INIS)

    Rodabaugh, E.C.; Maxey, W.A.; Eiber, R.J.

    1977-06-01

    Significant research on piping systems is evaluated, and the correlation of that research with design practices is presented. The objective is to quantify the research/design practices in terms of the reliability of piping used in nuclear power plants

  11. Golden mean relevance for chaos inhibition in a system of two coupled modified van der Pol oscillators

    International Nuclear Information System (INIS)

    Stan, Cristina; Cristescu, C.P.; Agop, M.

    2007-01-01

    In this work, we present a novel evidence of the importance of the golden mean criticality of a system of oscillators in agreement with El Naschie's E-infinity theory. We focus on chaos inhibition in a system of two coupled modified van der Pol oscillators. Depending on the coupling between the two oscillators, the system shows chaotic behavior for different ranges of the coupling parameter. Chaos suppression, as a transition from irregular behavior to a periodical one, is induced by perturbing the system with a harmonic signal with amplitude considerably lower than the value which causes entrainment. The frequency of the perturbation is related to the main frequencies in the spectrum of the freely running system (without perturbation) by the golden mean. We demonstrate that this effect is also obtained for a perturbation with frequency such that the ratio of half the frequency of the first main component in the freely running chaotic spectrum over the frequency of the perturbation is very close (five digits coincidence) to the golden mean. This result is shown to hold for arbitrary values of the coupling parameter in the various ranges of chaotic dynamics of the free running system

  12. Molecular Force Spectroscopy on Cells

    Science.gov (United States)

    Liu, Baoyu; Chen, Wei; Zhu, Cheng

    2015-04-01

    Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

  13. [Motivation and Emotional States: Structural Systemic, Neurochemical, Molecular and Cellular Mechanisms].

    Science.gov (United States)

    Bazyan, A S

    2016-01-01

    The structural, systemic, neurochemical, molecular and cellular mechanisms of organization and coding motivation and emotional states are describe. The GABA and glutamatergic synaptic systems of basal ganglia form a neural network and participate in the implementation of voluntary behavior. Neuropeptides, neurohormones and paracrine neuromodulators involved in the organization of motivation and emotional states, integrated with synaptic systems, controlled by neural networks and organizing goal-directed behavior. Structural centers for united and integrated of information in voluntary and goal-directed behavior are globus pallidus. Substantia nigra pars reticulata switches the information from corticobasal networks to thalamocortical networks, induces global dopaminergic (DA) signal and organize interaction of mesolimbic and nigostriatnoy DA systems controlled by prefrontal and motor cortex. Together with the motor cortex, substantia nigra displays information in the brainstem and spinal cord to implementation of behavior. Motivation states are formed in the interaction of neurohormonal and neuropeptide systems by monoaminergic systems of brain. Emotional states are formed by monoaminergic systems of the mid-brain, where the leading role belongs to the mesolimbic DA system. The emotional and motivation state of the encoded specific epigenetic molecular and chemical pattern of neuron.

  14. A molecular beam/quadrupole mass spectrometer system with synchronized beam modulation and digital waveform analysis

    Science.gov (United States)

    Pellett, G. L.; Adams, B. R.

    1983-01-01

    A performance evaluation is conducted for a molecular beam/mass spectrometer (MB/MS) system, as applied to a 1-30 torr microwave-discharge flow reactor (MWFR) used in the formation of the methylperoxy radical and a study of its subsequent destruction in the presence or absence of NO(x). The modulated MB/MS system is four-staged and differentially pumped. The results obtained by the MWFR study is illustrative of overall system performance, including digital waveform analysis; significant improvements over previous designs are noted in attainable S/N ratio, detection limit, and accuracy.

  15. The main but not the accessory olfactory system is involved in the processing of socially relevant chemosignals in ungulates.

    Directory of Open Access Journals (Sweden)

    Matthieu eKELLER

    2012-09-01

    Full Text Available Ungulates like sheep and goats have, like many other mammalian species, two complementary olfactory systems. The relative role played by these two systems has long been of interest regarding the sensory control of social behavior. The study of ungulate social behavior could represent a complimentary alternative to rodent studies because they live in a more natural environment and their social behaviors depend heavily on olfaction. In addition, the relative size of the main olfactory bulb (in comparison to the accessory olfactory bulb is more developped than in many other lissencephalic species like rodents. In this review, we present data showing a clear involvement of the main olfactory system in two well-characterized social situations under olfactory control in ungulates, namely maternal behavior and offspring recognition at birth and the reactivation of the gonadotropic axis of females exposed to males during the anestrous season. In conclusion, we discuss the apparent discrepancy between the absence of evidence for a role of the vomeronasal system in ungulate social behavior and the existence of a developed accessory olfactory system in these species.

  16. A Clinical Decision Support System for Chronic Pain Management in Primary Care: Usability testing and its relevance.

    Science.gov (United States)

    Nair, Kalpana Maria; Malaeekeh, Raheleh; Schabort, Inge; Taenzer, Paul; Radhakrishnan, Arun; Guenter, Dale

    2015-08-13

    Clinical decision support systems (CDSSs) that are integrated into electronic medical records may be useful for encouraging practice change compliant with clinical practice guidelines. To engage end users to inform early phase CDSS development through a process of usability testing. A sequential exploratory mixed method approach was used. Interprofessional clinician participants (seven in iteration 1 and six in iteration 2) were asked to 'think aloud' while performing various tasks on the CDSS and then complete the System Usability Scale (SUS). Changes were made to the CDSS after each iteration.Results Barriers and facilitators were identified: systemic; user interface (most numerous barriers); content (most numerous facilitators) and technical. The mean SUS score was 81.1 (SD = 12.02) in iteration 1 and 70.40 (SD = 6.78) in iteration 2 (p > 0.05). Qualitative data from usability testing were valuable in the CDSS development process. SUS scores were of limited value at this development stage.

  17. Radiopharmaceuticals: nanoparticles like multi-functional systems for the obtaining in vivo of molecular images

    International Nuclear Information System (INIS)

    Ferro F, G.; Ramirez de la Cruz, F. M.; Ocampo G, B. E.; Morales A, E.; Santos C, C. L.; Mendoza S, A. N.

    2010-01-01

    The techniques of obtaining direct or indirect molecular images detect and register the space-temporary distribution of molecular or cellular processes for biochemical, biological, diagnostic and therapeutic applications. The advanced techniques of image like the nuclear magnetic resonance, the single photon emission computed tomography, the positron emission tomography and the images of optic fluorescence have been used successfully to detect these processes. On the other hand, the utility of the nanoparticles for any application is dependent of the physicochemical properties that present, being possible to modify their surface when making them react with different biomolecules what allows the formation of conjugates with specific molecular recognition. The joint of various protein molecules, peptides or oligonucleotides to the surface of a nanoparticle produce a multi-functional system able to increase the multivalent joints from the nanoparticles-biomolecules to their receivers for the obtaining of molecular images in vivo. The peptides stimulate, regulate or inhibit numerous functions of the life, acting mainly as information transmitters and activity coordinators of several tissues in the organism. The receivers of regulator peptides are over represented in numerous types of cancer cells and they are protein structures. These receivers have been used as white molecular of marked peptides, to locate primary malignant tumors and their metastasis, using the diagnostic techniques of molecular image mentioned above, which consist basically on the radio peptides use and conjugated peptides to fluoro chromes, to metallic nanoparticles and nano crystals. A summary of the work is presented carried out by the personnel of the Radio-active Materials and Chemistry Departments of the Instituto Nacional de Investigaciones Nucleares in this field. (Author)

  18. Chemical and biological relationships relevant to the effect of acid rainfall on the soil-plant system

    Science.gov (United States)

    Marvin Nyborg

    1976-01-01

    This paper deals with problems of measuring acidity in rainfall and the interpretation of these measurements in terms of effects on the soil-plant system. Theoretical relationships of the carbon-dioxide-bicarbonate equalibria and its effect on rainfall acidity measurements are given. The relationship of a cation-anion balance model of acidity in rainfall to plant...

  19. Early passage bone marrow stromal cells express genes involved in nervous system development supporting their relevance for neural repair

    NARCIS (Netherlands)

    Nandoe Tewarie, R.D.S.; Bossers, K.; Ritfeld, G.J.; Blits, B.; Grotenhuis, J.A.; Verhaagen, J.; Oudega, M.

    2011-01-01

    PURPOSE: The assessment of the capacity of bone marrow stromal cells (BMSC) to repair the nervous system using gene expression profiling. The evaluation of effects of long-term culturing on the gene expression profile of BMSC. METHODS: Fourty four k whole genome rat microarrays were used to study

  20. Anti-double stranded DNA antibodies in systemic lupus erythematosus : Detection and clinical relevance of IgM-class antibodies

    NARCIS (Netherlands)

    Bootsma, H; Spronk, PE; Hummel, EJ; deBoer, G; terBorg, EJ; Limburg, PC; Kallenberg, CGM

    1996-01-01

    We determined the discriminative value of the Farr assay in comparison to ELISA and Crithidia luciliae immunofluorescence assay (IFT) for detecting anti-dsDNA antibodies as a diagnostic tool for systemic lupus erythematosus (SLE). Special attention was paid to the diagnostic significance of

  1. Potentiometric investigations of molecular heteroconjugation equilibria of substituted phenol+n-butylamine systems in dimethyl sulfoxide

    Energy Technology Data Exchange (ETDEWEB)

    Czaja, MaIgorzata [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Baginska, Katarzyna [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Kozak, Anna [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Makowski, Mariusz [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Chmurzynski, Lech [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland)]. E-mail: lech@chem.univ.gda.pl

    2005-08-15

    Molecular heteroconjugation constants, K{sub BHA}{sup DMSO} and K{sub AHB}{sup DMSO}, expressed as their logarithms, have been determined by potentiometric titration for eleven substituted phenol+n-butylamine systems in a polar protophilic aprotic solvent, dimethyl sulfoxide (DMSO). An increasing tendency towards molecular heteroconjugation in these systems without proton transfer has been found with increasing pK{sub a}{sup DMSO} (HA), i.e., with decreasing phenol acidity. Moreover, a linear correlation has been established between the determined lgK{sub BHA}{sup DMSO} values and pK{sub a}{sup DMSO} (HA). Furthermore, overall stability constants, lgK{sub o}{sup DMSO}, could be correlated linearly with pK{sub a}{sup DMSO} (HA) values.

  2. Hybrid artificial photosynthetic systems comprising semiconductors as light harvesters and biomimetic complexes as molecular cocatalysts.

    Science.gov (United States)

    Wen, Fuyu; Li, Can

    2013-11-19

    Solar fuel production through artificial photosynthesis may be a key to generating abundant and clean energy, thus addressing the high energy needs of the world's expanding population. As the crucial components of photosynthesis, the artificial photosynthetic system should be composed of a light harvester (e.g., semiconductor or molecular dye), a reduction cocatalyst (e.g., hydrogenase mimic, noble metal), and an oxidation cocatalyst (e.g., photosystem II mimic for oxygen evolution from water oxidation). Solar fuel production catalyzed by an artificial photosynthetic system starts from the absorption of sunlight by the light harvester, where charge separation takes place, followed by a charge transfer to the reduction and oxidation cocatalysts, where redox reaction processes occur. One of the most challenging problems is to develop an artificial photosynthetic solar fuel production system that is both highly efficient and stable. The assembly of cocatalysts on the semiconductor (light harvester) not only can facilitate the charge separation, but also can lower the activation energy or overpotential for the reactions. An efficient light harvester loaded with suitable reduction and oxidation cocatalysts is the key for high efficiency of artificial photosynthetic systems. In this Account, we describe our strategy of hybrid photocatalysts using semiconductors as light harvesters with biomimetic complexes as molecular cocatalysts to construct efficient and stable artificial photosynthetic systems. We chose semiconductor nanoparticles as light harvesters because of their broad spectral absorption and relatively robust properties compared with a natural photosynthesis system. Using biomimetic complexes as cocatalysts can significantly facilitate charge separation via fast charge transfer from the semiconductor to the molecular cocatalysts and also catalyze the chemical reactions of solar fuel production. The hybrid photocatalysts supply us with a platform to study the

  3. Quantitative computational models of molecular self-assembly in systems biology.

    Science.gov (United States)

    Thomas, Marcus; Schwartz, Russell

    2017-05-23

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  4. A Pilot-Scale System for Carbon Molecular Sieve Hollow Fiber Membrane Manufacturing

    KAUST Repository

    Karvan, O.

    2012-12-21

    Carbon molecular sieve (CMS) membranes offer advantages over traditional polymeric membrane materials, but scale-up of manufacturing systems has not received much attention. In the recent decade, there has been a dramatic increase in fundamental research on these materials with a variety of applications being studied. The results from a pilot-scale CMS production system are presented. This system was designed based on extensive laboratory research, and hollow fiber membranes produced in this system show similar performance compared to membranes produced using a smaller bench-scale system. After optimizing the system design, a 93% recovery of the precursor fibers for use in membrane module preparation were obtained. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Synthesis of Heteroaromatic Compounds by Oxidative Aromatization Using an Activated Carbon/Molecular Oxygen System

    Directory of Open Access Journals (Sweden)

    Masahiko Hayashi

    2009-08-01

    Full Text Available A variety of heteroaromatic compounds, such as substituted pyridines, pyrazoles, indoles, 2-substituted imidazoles, 2-substituted imidazoles, 2-arylbenzazoles and pyrimidin-2(1H-ones are synthesized by oxidative aromatization using the activated carbon and molecular oxygen system. Mechanistic study focused on the role of activated carbon in the synthesis of 2-arylbenzazoles is also discussed. In the final section, we will disclose the efficient synthesis of substituted 9,10-anthracenes via oxidative aromatization.

  6. AUTOMR: An automatic processing program system for the molecular replacement method

    International Nuclear Information System (INIS)

    Matsuura, Yoshiki

    1991-01-01

    An automatic processing program system of the molecular replacement method AUTMR is presented. The program solves the initial model of the target crystal structure using a homologous molecule as the search model. It processes the structure-factor calculation of the model molecule, the rotation function, the translation function and the rigid-group refinement successively in one computer job. Test calculations were performed for six protein crystals and the structures were solved in all of these cases. (orig.)

  7. Gene expression-based molecular diagnostic system for malignant gliomas is superior to histological diagnosis.

    Science.gov (United States)

    Shirahata, Mitsuaki; Iwao-Koizumi, Kyoko; Saito, Sakae; Ueno, Noriko; Oda, Masashi; Hashimoto, Nobuo; Takahashi, Jun A; Kato, Kikuya

    2007-12-15

    Current morphology-based glioma classification methods do not adequately reflect the complex biology of gliomas, thus limiting their prognostic ability. In this study, we focused on anaplastic oligodendroglioma and glioblastoma, which typically follow distinct clinical courses. Our goal was to construct a clinically useful molecular diagnostic system based on gene expression profiling. The expression of 3,456 genes in 32 patients, 12 and 20 of whom had prognostically distinct anaplastic oligodendroglioma and glioblastoma, respectively, was measured by PCR array. Next to unsupervised methods, we did supervised analysis using a weighted voting algorithm to construct a diagnostic system discriminating anaplastic oligodendroglioma from glioblastoma. The diagnostic accuracy of this system was evaluated by leave-one-out cross-validation. The clinical utility was tested on a microarray-based data set of 50 malignant gliomas from a previous study. Unsupervised analysis showed divergent global gene expression patterns between the two tumor classes. A supervised binary classification model showed 100% (95% confidence interval, 89.4-100%) diagnostic accuracy by leave-one-out cross-validation using 168 diagnostic genes. Applied to a gene expression data set from a previous study, our model correlated better with outcome than histologic diagnosis, and also displayed 96.6% (28 of 29) consistency with the molecular classification scheme used for these histologically controversial gliomas in the original article. Furthermore, we observed that histologically diagnosed glioblastoma samples that shared anaplastic oligodendroglioma molecular characteristics tended to be associated with longer survival. Our molecular diagnostic system showed reproducible clinical utility and prognostic ability superior to traditional histopathologic diagnosis for malignant glioma.

  8. Systems Biology Methods for Alzheimer's Disease Research Toward Molecular Signatures, Subtypes, and Stages and Precision Medicine: Application in Cohort Studies and Trials.

    Science.gov (United States)

    Castrillo, Juan I; Lista, Simone; Hampel, Harald; Ritchie, Craig W

    2018-01-01

    Alzheimer's disease (AD) is a complex multifactorial disease, involving a combination of genomic, interactome, and environmental factors, with essential participation of (a) intrinsic genomic susceptibility and (b) a constant dynamic interplay between impaired pathways and central homeostatic networks of nerve cells. The proper investigation of the complexity of AD requires new holistic systems-level approaches, at both the experimental and computational level. Systems biology methods offer the potential to unveil new fundamental insights, basic mechanisms, and networks and their interplay. These may lead to the characterization of mechanism-based molecular signatures, and AD hallmarks at the earliest molecular and cellular levels (and beyond), for characterization of AD subtypes and stages, toward targeted interventions according to the evolving precision medicine paradigm. In this work, an update on advanced systems biology methods and strategies for holistic studies of multifactorial diseases-particularly AD-is presented. This includes next-generation genomics, neuroimaging and multi-omics methods, experimental and computational approaches, relevant disease models, and latest genome editing and single-cell technologies. Their progressive incorporation into basic research, cohort studies, and trials is beginning to provide novel insights into AD essential mechanisms, molecular signatures, and markers toward mechanism-based classification and staging, and tailored interventions. Selected methods which can be applied in cohort studies and trials, with the European Prevention of Alzheimer's Dementia (EPAD) project as a reference example, are presented and discussed.

  9. Assessment of a combined gas chromatography mass spectrometer sensor (GC-MSS) system for detecting biologically relevant volatile compounds (VCs).

    Science.gov (United States)

    Gould, Oliver; Wieczorek, Tomas; de Lacy Costello, Ben P J; Persad, Raj; Ratcliffe, Norman

    2017-09-26

    There have been a number of studies in which metal oxide sensors (MOS) have replaced conventional analytical detectors in gas chromatography systems. However, despite the use of these instruments in a range of applications including breath research the sensor responses (i.e. resistance changes w.r.t. concentration of VCs) remain largely unreported. This paper addresses that issue by comparing the response of a metal oxide sensor directly with a mass spectrometer (MS), whereby both detectors are interfaced to the same GC column using an s-swafer. It was demonstrated that the sensitivity of an in-house fabricated ZnO/ SnO2 thick film MOS was superior to a modern MS for the detection of a wide range of volatile compounds (VCs) of different functionalities and masses. Better techniques for detection and quantification of these VCs is valuable, as many of these compounds are commonly reported throughout the scientific literature. This is also the first published report of a combined GC-MS sensor system. These 2 different detector technologies when combined, should enhance discriminatory abilities to aid disease diagnoses using volatiles from e.g. breath, and bodily fluids. 29 chemical standards have been tested using solid phase micro-extraction; 25 of these compounds are found on human breath. In all but 2 instances the sensor exhibited the same or superior limit of detection compared to the MS. 12 stool samples from healthy participants were analysed, the sensor detected, on average 1.6 peaks more per sample than the MS. Similarly analysing the headspace of E. coli broth cultures the sensor detected 6.9 more peaks per sample versus the MS. This greater sensitivity is primarily a function of the superior limits of detection of the metal oxide sensor. This shows that systems based on the combination of chromatography systems with solid state sensors shows promise for a range of applications. © 2017 IOP Publishing Ltd.

  10. Rapid assessment of infrastructure of primary health care facilities - a relevant instrument for health care systems management.

    Science.gov (United States)

    Scholz, Stefan; Ngoli, Baltazar; Flessa, Steffen

    2015-05-01

    Health care infrastructure constitutes a major component of the structural quality of a health system. Infrastructural deficiencies of health services are reported in literature and research. A number of instruments exist for the assessment of infrastructure. However, no easy-to-use instruments to assess health facility infrastructure in developing countries are available. Present tools are not applicable for a rapid assessment by health facility staff. Therefore, health information systems lack data on facility infrastructure. A rapid assessment tool for the infrastructure of primary health care facilities was developed by the authors and pilot-tested in Tanzania. The tool measures the quality of all infrastructural components comprehensively and with high standardization. Ratings use a 2-1-0 scheme which is frequently used in Tanzanian health care services. Infrastructural indicators and indices are obtained from the assessment and serve for reporting and tracing of interventions. The tool was pilot-tested in Tanga Region (Tanzania). The pilot test covered seven primary care facilities in the range between dispensary and district hospital. The assessment encompassed the facilities as entities as well as 42 facility buildings and 80 pieces of technical medical equipment. A full assessment of facility infrastructure was undertaken by health care professionals while the rapid assessment was performed by facility staff. Serious infrastructural deficiencies were revealed. The rapid assessment tool proved a reliable instrument of routine data collection by health facility staff. The authors recommend integrating the rapid assessment tool in the health information systems of developing countries. Health authorities in a decentralized health system are thus enabled to detect infrastructural deficiencies and trace the effects of interventions. The tool can lay the data foundation for district facility infrastructure management.

  11. A field-deployable mobile molecular diagnostic system for malaria at the point of need.

    Science.gov (United States)

    Choi, Gihoon; Song, Daniel; Shrestha, Sony; Miao, Jun; Cui, Liwang; Guan, Weihua

    2016-11-01

    In response to the urgent need of a field-deployable and highly sensitive malaria diagnosis, we developed a standalone, "sample-in-answer-out" molecular diagnostic system (AnyMDx) to enable quantitative molecular analysis of blood-borne malaria in low resource areas. The system consists of a durable battery-powered analyzer and a disposable microfluidic compact disc loaded with reagents ready for use. A low power thermal module and a novel fluorescence-sensing module are integrated into the analyzer for real-time monitoring of loop-mediated isothermal nucleic acid amplification (LAMP) of target parasite DNA. With 10 μL of raw blood sample, the AnyMDx system automates the nucleic acid sample preparation and subsequent LAMP and real-time detection. Under laboratory conditions with whole-blood samples spiked with cultured Plasmodium falciparum, we achieved a detection limit of ∼0.6 parasite per μL, much lower than those for the conventional microscopy and rapid diagnostic tests (∼50-100 parasites per μL). The turnaround time from sample to answer is less than 40 minutes. The AnyMDx is user-friendly requiring minimal technological training. The analyzer and the disposable reagent compact discs are cost-effective, making AnyMDx a potential tool for malaria molecular diagnosis under field settings for malaria elimination.

  12. Resolution of identity approximation for the Coulomb term in molecular and periodic systems

    Science.gov (United States)

    Burow, Asbjörn M.; Sierka, Marek; Mohamed, Fawzi

    2009-12-01

    A new formulation of resolution of identity approximation for the Coulomb term is presented, which uses atom-centered basis and auxiliary basis functions and treats molecular and periodic systems of any dimensionality on an equal footing. It relies on the decomposition of an auxiliary charge density into charged and chargeless components. Applying the Coulomb metric under periodic boundary conditions constrains the explicit form of the charged part. The chargeless component is determined variationally and converged Coulomb lattice sums needed for its determination are obtained using chargeless linear combinations of auxiliary basis functions. The lattice sums are partitioned in near- and far-field portions which are treated through an analytical integration scheme employing two- and three-center electron repulsion integrals and multipole expansions, respectively, operating exclusively in real space. Our preliminary implementation within the TURBOMOLE program package demonstrates consistent accuracy of the method across molecular and periodic systems. Using common auxiliary basis sets the errors of the approximation are small, in average about 20 μhartree per atom, for both molecular and periodic systems.

  13. High Molecular Weight Isoforms of Growth Hormone In Cells of the Immune System

    Science.gov (United States)

    Weigent, Douglas A.

    2013-01-01

    A substantial body of research exists to support the idea that cells of the immune system produce growth hormone (GH). However, the structure and mechanism of action of lymphocyte-derived GH continues to remain largely unknown. Here we present the results of Western analysis of whole cell extracts showing that different molecular weight isoforms of GH of approximately 100 kDa, 65 kDa, and 48 kDa can be detected in primary mouse cells of the immune system and in the mouse EL4 cell line. The identity of the 65 kDa and 48 kDa isoforms of GH were confirmed by mass spectrometry. The various isoforms were detected in both enriched T and B spleen cell populations. The large molecular weight isoform appears to reside primarily in the cytoplasm whereas the lower molecular weight 65 kDa and 48 kDa isoforms were detected primarily in the nucleus. These results also suggest that GH isoforms are induced by oxidative stress. In EL4 cells overexpressing GH, the expression of luciferase controlled by a promoter containing the antioxidant response element is increased almost three-fold above control. The data suggest that the induction of isoforms of the GH molecule in cells of the immune system may be an important mechanism of adaptation and/or protection of lymphoid cells under conditions of oxidative stress. PMID:21741628

  14. Photonic Integrated Circuit (PIC) Device Structures: Background, Fabrication Ecosystem, Relevance to Space Systems Applications, and Discussion of Related Radiation Effects

    Science.gov (United States)

    Alt, Shannon

    2016-01-01

    Electronic integrated circuits are considered one of the most significant technological advances of the 20th century, with demonstrated impact in their ability to incorporate successively higher numbers transistors and construct electronic devices onto a single CMOS chip. Photonic integrated circuits (PICs) exist as the optical analog to integrated circuits; however, in place of transistors, PICs consist of numerous scaled optical components, including such "building-block" structures as waveguides, MMIs, lasers, and optical ring resonators. The ability to construct electronic and photonic components on a single microsystems platform offers transformative potential for the development of technologies in fields including communications, biomedical device development, autonomous navigation, and chemical and atmospheric sensing. Developing on-chip systems that provide new avenues for integration and replacement of bulk optical and electro-optic components also reduces size, weight, power and cost (SWaP-C) limitations, which are important in the selection of instrumentation for specific flight projects. The number of applications currently emerging for complex photonics systems-particularly in data communications-warrants additional investigations when considering reliability for space systems development. This Body of Knowledge document seeks to provide an overview of existing integrated photonics architectures; the current state of design, development, and fabrication ecosystems in the United States and Europe; and potential space applications, with emphasis given to associated radiation effects and reliability.

  15. A new extranodal scoring system based on the prognostically relevant extranodal sites in diffuse large B-cell lymphoma, not otherwise specified treated with chemoimmunotherapy.

    Science.gov (United States)

    Hwang, Hee Sang; Yoon, Dok Hyun; Suh, Cheolwon; Huh, Jooryung

    2016-08-01

    Extranodal involvement is a well-known prognostic factor in patients with diffuse large B-cell lymphomas (DLBCL). Nevertheless, the prognostic impact of the extranodal scoring system included in the conventional international prognostic index (IPI) has been questioned in an era where rituximab treatment has become widespread. We investigated the prognostic impacts of individual sites of extranodal involvement in 761 patients with DLBCL who received rituximab-based chemoimmunotherapy. Subsequently, we established a new extranodal scoring system based on extranodal sites, showing significant prognostic correlation, and compared this system with conventional scoring systems, such as the IPI and the National Comprehensive Cancer Network-IPI (NCCN-IPI). An internal validation procedure, using bootstrapped samples, was also performed for both univariate and multivariate models. Using multivariate analysis with a backward variable selection, we found nine extranodal sites (the liver, lung, spleen, central nervous system, bone marrow, kidney, skin, adrenal glands, and peritoneum) that remained significant for use in the final model. Our newly established extranodal scoring system, based on these sites, was better correlated with patient survival than standard scoring systems, such as the IPI and the NCCN-IPI. Internal validation by bootstrapping demonstrated an improvement in model performance of our modified extranodal scoring system. Our new extranodal scoring system, based on the prognostically relevant sites, may improve the performance of conventional prognostic models of DLBCL in the rituximab era and warrants further external validation using large study populations.

  16. Deep learning relevance

    DEFF Research Database (Denmark)

    Lioma, Christina; Larsen, Birger; Petersen, Casper

    2016-01-01

    train a Recurrent Neural Network (RNN) on existing relevant information to that query. We then use the RNN to "deep learn" a single, synthetic, and we assume, relevant document for that query. We design a crowdsourcing experiment to assess how relevant the "deep learned" document is, compared...... to existing relevant documents. Users are shown a query and four wordclouds (of three existing relevant documents and our deep learned synthetic document). The synthetic document is ranked on average most relevant of all....

  17. Diagnostic imaging capabilities of the Ocelot -Optical Coherence Tomography System, ex-vivo evaluation and clinical relevance

    International Nuclear Information System (INIS)

    Dohad, Suhail; Shao, John; Cawich, Ian; Kankaria, Manish; Desai, Arjun

    2015-01-01

    Optical coherence tomography (OCT) is a high-resolution sub-surface imaging modality using near-infrared light to provide accurate and high contrast intra-vascular images. This enables accurate assessment of diseased arteries before and after intravascular intervention. This study was designed to corroborate diagnostic imaging equivalence between the Ocelot and the Dragonfly OCT systems with regards to the intravascular features that are most important in clinical management of patients with atherosclerotic vascular disease. These intravascular features were then corroborated in vivo during treatment of peripheral arterial disease (PAD) pathology using the Ocelot catheter. In order to compare the diagnostic information obtained by Ocelot (Avinger Inc., Redwood City, CA) and Dragonfly (St. Jude Medical, Minneapolis, MN) OCT systems, we utilized ex-vivo preparations of arterial segments. Ocelot and Dragonfly catheters were inserted into identical cadaveric femoral peripheral arteries for image acquisition and interpretation. Three independent physician interpreters assessed the images to establish accuracy and sensitivity of the diagnostic information. Histologic evaluation of the corresponding arterial segments provided the gold standard for image interpretation. In vivo clinical images were obtained during therapeutic interventions that included crossing of peripheral chronic total occlusions (CTOs) using the Ocelot catheter. Strong concordance was demonstrated when matching image characteristics between both OCT systems and histology. The Dragonfly and Ocelot system’s vessel features were interpreted with high sensitivity (91.1–100 %) and specificity (86.7–100 %). Inter-observer concordance was documented with excellent correlation across all vessel features. The clinical benefit that the Ocelot OCT system provided was demonstrated by comparable procedural images acquired at the point of therapy. The study demonstrates equivalence of image acquisition and

  18. Molecular machines in living cells. Seibutsu no bunshi kikai to sono system

    Energy Technology Data Exchange (ETDEWEB)

    Osawa, F. (Aichi Inst. of Tech., Nagoya (Japan))

    1992-12-20

    At first, flagellar motors of bacteria are reviewed as a typical example of molecular machines in living cells. A rotational motor is embedded in the cell membrane at the root of the flagellum. The driving power of the rotation is the flow of hydrogen ion from the inside to the outside of the cell. In a normal state of a bacterium, potential difference of about 0.2 V is produced by the ion pump existing in the cell membrane. A molecular motor of sliding motion of muscle attracts the attention on the relation of the input and output of the molecular motor. The mechanism of the smooth motion without fluctuation in the fluctuated environment and the fluctuated input is unknown. Next, the motion of Paramecium is discussed as an example of a system composed of a number of molecular machines. Paramecium moves to a place of a suitable temperature when placed in a water tank with temperature gradient, however, it does not stop the motion at the place of the suitable temperature and increases a probability to change the direction when leaving, that is it takes a method of indirect probabilistic control. 12 refs., 8 figs.

  19. On the theory of frequency-shifted secondary emission of light-harvesting molecular systems

    International Nuclear Information System (INIS)

    Morozov, V.A.

    2001-01-01

    The expressions are obtained for the intensity of the frequency-shifted secondary emission of a chromophore playing the role of a reaction center in the simplest model three-chromophore molecular 'light-harvesting' antenna, which is constructed and oriented in space so that the incident photons coherently excite two of its chromophore pigments. The quantum-field formalism was used, which takes into account the generalized (quantum-electrodynamic) dipole-dipole, as well as radiative and nonradiative dissipative interactions between pigments and the reaction center of the antenna. The special features of the excitation spectrum of the Raman scattering line and the frequency-shifted fluorescence spectrum of the reaction center of the molecular antenna under study are discussed. A comparison of the expressions obtained for the excitation and fluorescence spectra and with the corresponding expressions obtained for a bichromophore molecular system, which differs from a three-chromophore antenna by the absence of one of the pigments, revealed the properties of the mechanism of action of light-harvesting molecular antennas that have not been found earlier. In particular, it is shown that 'the light-harvesting' caused by the collective dissipative interactions of pigments with the reaction center of the antenna can substantially exceed a sum of contributions from separate pigments

  20. An approach towards understanding the structure of complex molecular systems: the case of lower aliphatic alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Vrhovsek, Aleksander; Gereben, Orsolya; Pothoczki, Szilvia; Pusztai, Laszlo [Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, H-1525 Budapest, PO Box 49 (Hungary); Tomsic, Matija; Jamnik, Andrej [Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, SI-1001 Ljubljana (Slovenia); Kohara, Shinji, E-mail: aleksander.vrhovsek@gmail.co [Research and Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI, SPring-8), 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2010-10-13

    An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applying reverse Monte Carlo modelling as a method of interpretation of diffraction data, is presented. The emphasis is on the evaluation of several computational strategies in view of their suitability to obtain high quality molecular models via the reverse Monte Carlo procedure. A consistent set of distances of closest approach and fixed neighbour constraints applicable to all three investigated systems was developed. An all-atom description is compared with a united-atom approach. The potentialities of employment of neutron diffraction data of completely deuterated and isotopically substituted samples, x-ray diffraction data, and results of either molecular dynamics or Monte Carlo calculations were investigated. Results show that parallel application of x-ray and neutron diffraction data, the latter being from completely deuterated samples, within an all-atom reverse Monte Carlo procedure is the most successful strategy towards attaining reliable, detailed, and well-structured molecular models, especially if the models are subsequently refined with the results of molecular dynamics simulations.

  1. Net emission coefficient for CO–H2 thermal plasmas with the consideration of molecular systems

    International Nuclear Information System (INIS)

    Billoux, T.; Cressault, Y.; Gleizes, A.

    2015-01-01

    This paper deals with the calculation of net emission coefficients (NECs) for CO–H 2 thermal plasmas. This task required the elaboration of a complete spectroscopic database including atoms and molecules formed by carbon, oxygen and hydrogen elements. We have used a systematic line by line method to calculate all the main radiative contributions which are the atomic and molecular continua, the atomic lines and the molecular (diatomic and polyatomic) lines. The main diatomic electronic systems for CO–H 2 plasmas and the triatomic molecular bands were considered. We present some variations of the net emission coefficient versus temperature, for various pressures and for two relative proportions of the components. The role of the diatomic molecules is important at temperatures lower than 5000 K whereas the net emission coefficient presents an unusual peak at temperature around 1000 K, due to the presence of the CO 2 molecule presenting a strong infrared radiation. Finally, the results show that the NEC slightly depends on the relative proportion of CO and H 2 . - highlights: • We calculate radiative losses from CO–H 2 thermal plasmas. • We use the up-to-date atomic and molecular databases. • The influence of CO 2 molecule is very important at low temperature. • The relative maximum of the net emission coefficient at low temperature is unusual

  2. From Molecular Classification to Targeted Therapeutics: The Changing Face of Systemic Therapy in Metastatic Gastroesophageal Cancer

    Directory of Open Access Journals (Sweden)

    Adrian Murphy

    2015-01-01

    Full Text Available Histological classification of adenocarcinoma or squamous cell carcinoma for esophageal cancer or using the Lauren classification for intestinal and diffuse type gastric cancer has limited clinical utility in the management of advanced disease. Germline mutations in E-cadherin (CDH1 or mismatch repair genes (Lynch syndrome were identified many years ago but given their rarity, the identification of these molecular alterations does not substantially impact treatment in the advanced setting. Recent molecular profiling studies of upper GI tumors have added to our knowledge of the underlying biology but have not led to an alternative classification system which can guide clinician’s therapeutic decisions. Recently the Cancer Genome Atlas Research Network has proposed four subtypes of gastric cancer dividing tumors into those positive for Epstein-Barr virus, microsatellite unstable tumors, genomically stable tumors, and tumors with chromosomal instability. Unfortunately to date, many phase III clinical trials involving molecularly targeted agents have failed to meet their survival endpoints due to their use in unselected populations. Future clinical trials should utilize molecular profiling of individual tumors in order to determine the optimal use of targeted therapies in preselected patients.

  3. Intelligent Techniques Using Molecular Data Analysis in Leukaemia: An Opportunity for Personalized Medicine Support System.

    Science.gov (United States)

    Banjar, Haneen; Adelson, David; Brown, Fred; Chaudhri, Naeem

    2017-01-01

    The use of intelligent techniques in medicine has brought a ray of hope in terms of treating leukaemia patients. Personalized treatment uses patient's genetic profile to select a mode of treatment. This process makes use of molecular technology and machine learning, to determine the most suitable approach to treating a leukaemia patient. Until now, no reviews have been published from a computational perspective concerning the development of personalized medicine intelligent techniques for leukaemia patients using molecular data analysis. This review studies the published empirical research on personalized medicine in leukaemia and synthesizes findings across studies related to intelligence techniques in leukaemia, with specific attention to particular categories of these studies to help identify opportunities for further research into personalized medicine support systems in chronic myeloid leukaemia. A systematic search was carried out to identify studies using intelligence techniques in leukaemia and to categorize these studies based on leukaemia type and also the task, data source, and purpose of the studies. Most studies used molecular data analysis for personalized medicine, but future advancement for leukaemia patients requires molecular models that use advanced machine-learning methods to automate decision-making in treatment management to deliver supportive medical information to the patient in clinical practice.

  4. Molecular stratification and precision medicine in systemic sclerosis from genomic and proteomic data.

    Science.gov (United States)

    Martyanov, Viktor; Whitfield, Michael L

    2016-01-01

    The goal of this review is to summarize recent advances into the pathogenesis and treatment of systemic sclerosis (SSc) from genomic and proteomic studies. Intrinsic gene expression-driven molecular subtypes of SSc are reproducible across three independent datasets. These subsets are a consistent feature of SSc and are found in multiple end-target tissues, such as skin and esophagus. Intrinsic subsets as well as baseline levels of molecular target pathways are potentially predictive of clinical response to specific therapeutics, based on three recent clinical trials. A gene expression-based biomarker of modified Rodnan skin score, a measure of SSc skin severity, can be used as a surrogate outcome metric and has been validated in a recent trial. Proteome analyses have identified novel biomarkers of SSc that correlate with SSc clinical phenotypes. Integrating intrinsic gene expression subset data, baseline molecular pathway information, and serum biomarkers along with surrogate measures of modified Rodnan skin score provides molecular context in SSc clinical trials. With validation, these approaches could be used to match patients with the therapies from which they are most likely to benefit and thus increase the likelihood of clinical improvement.

  5. Joint project. Retention of radionuclides relevant for final disposal in natural clay rock and saline systems. Subproject 2. Geochemical behavior and transport of radionuclides in saline systems in the presence of repository-relevant organics. Final report

    International Nuclear Information System (INIS)

    Schmeide, Katja; Fritsch, Katharina; Lippold, Holger

    2016-01-01

    The objective of this project was to study the influence of increased salinities on interaction processes in the system radionuclide - organics - clay - aquifer. For this purpose, complexation, redox, sorption, and diffusion studies were performed under variation of the ionic strength (up to 4 mol kg -1 ) and the background electrolyte. The U(VI) complexation by propionate was studied in dependence on ionic strength (up to 4 mol kg -1 NaClO 4 ) by TRLFS, ATR FT-IR spectroscopy, and DFT calculations. An influence of ionic strength on stability constants was detected, depending on the charge of the respective complexes. The conditional stability constants, determined for 1:1, 1:2, and 1:3 complexes at specific ionic strengths, were extrapolated to zero ionic strength. The interaction of the bacteria Sporomusa sp. MT-2.99 and Paenibacillus sp. MT-2.2 cells, isolated from Opalinus Clay, with Pu was studied. The experiments can be divided into such without an electron donor where biosorption is favored and such with addition of Na-pyruvate as an electron donor stimulating also bioreduction processes. Moreover, experiments were performed to study the interactions of the halophilic archaeon Halobacterium noricense DSM-15987 with U(VI), Eu(III), and Cm(III) in 3 M NaCl solutions. Research for improving process understanding with respect to the mobility of multivalent metals in systems containing humic matter was focused on the reversibility of elementary processes and on their interaction. Kinetic stabilization processes in the dynamics of humate complexation equilibria were quantified in isotope exchange studies. The influence of high salinity on the mobilizing potential of humic-like clay organics was systematically investigated and was described by modeling. The sorption of Tc(VII)/Tc(IV) onto the iron(II)-containing minerals magnetite and siderite was studied by means of batch sorption experiments, ATR FT-IR and X-ray absorption spectroscopy. The strong Tc retention at

  6. Joint project. Retention of radionuclides relevant for final disposal in natural clay rock and saline systems. Subproject 2. Geochemical behavior and transport of radionuclides in saline systems in the presence of repository-relevant organics. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Schmeide, Katja; Fritsch, Katharina; Lippold, Holger [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Inst. of Ressource Ecology; and others

    2016-08-01

    The objective of this project was to study the influence of increased salinities on interaction processes in the system radionuclide - organics - clay - aquifer. For this purpose, complexation, redox, sorption, and diffusion studies were performed under variation of the ionic strength (up to 4 mol kg{sup -1}) and the background electrolyte. The U(VI) complexation by propionate was studied in dependence on ionic strength (up to 4 mol kg{sup -1} NaClO{sub 4}) by TRLFS, ATR FT-IR spectroscopy, and DFT calculations. An influence of ionic strength on stability constants was detected, depending on the charge of the respective complexes. The conditional stability constants, determined for 1:1, 1:2, and 1:3 complexes at specific ionic strengths, were extrapolated to zero ionic strength. The interaction of the bacteria Sporomusa sp. MT-2.99 and Paenibacillus sp. MT-2.2 cells, isolated from Opalinus Clay, with Pu was studied. The experiments can be divided into such without an electron donor where biosorption is favored and such with addition of Na-pyruvate as an electron donor stimulating also bioreduction processes. Moreover, experiments were performed to study the interactions of the halophilic archaeon Halobacterium noricense DSM-15987 with U(VI), Eu(III), and Cm(III) in 3 M NaCl solutions. Research for improving process understanding with respect to the mobility of multivalent metals in systems containing humic matter was focused on the reversibility of elementary processes and on their interaction. Kinetic stabilization processes in the dynamics of humate complexation equilibria were quantified in isotope exchange studies. The influence of high salinity on the mobilizing potential of humic-like clay organics was systematically investigated and was described by modeling. The sorption of Tc(VII)/Tc(IV) onto the iron(II)-containing minerals magnetite and siderite was studied by means of batch sorption experiments, ATR FT-IR and X-ray absorption spectroscopy. The strong Tc

  7. Estimating chlorophyll with thermal and broadband multispectral high resolution imagery from an unmanned aerial system using relevance vector machines for precision agriculture

    Science.gov (United States)

    Elarab, Manal; Ticlavilca, Andres M.; Torres-Rua, Alfonso F.; Maslova, Inga; McKee, Mac

    2015-12-01

    Precision agriculture requires high-resolution information to enable greater precision in the management of inputs to production. Actionable information about crop and field status must be acquired at high spatial resolution and at a temporal frequency appropriate for timely responses. In this study, high spatial resolution imagery was obtained through the use of a small, unmanned aerial system called AggieAirTM. Simultaneously with the AggieAir flights, intensive ground sampling for plant chlorophyll was conducted at precisely determined locations. This study reports the application of a relevance vector machine coupled with cross validation and backward elimination to a dataset composed of reflectance from high-resolution multi-spectral imagery (VIS-NIR), thermal infrared imagery, and vegetative indices, in conjunction with in situ SPAD measurements from which chlorophyll concentrations were derived, to estimate chlorophyll concentration from remotely sensed data at 15-cm resolution. The results indicate that a relevance vector machine with a thin plate spline kernel type and kernel width of 5.4, having LAI, NDVI, thermal and red bands as the selected set of inputs, can be used to spatially estimate chlorophyll concentration with a root-mean-squared-error of 5.31 μg cm-2, efficiency of 0.76, and 9 relevance vectors.

  8. The effects of ecstasy on neurotransmitter systems: a review on the findings of molecular imaging studies.

    Science.gov (United States)

    Vegting, Yosta; Reneman, Liesbeth; Booij, Jan

    2016-10-01

    Ecstasy is a commonly used psychoactive drug with 3,4-methylenedioxymethamphetamine (MDMA) as the main content. Importantly, it has been suggested that use of MDMA may be neurotoxic particularly for serotonergic (5-hydroxytryptamine (5-HT)) neurons. In the past decades, several molecular imaging studies examined directly in vivo the effects of ecstasy/MDMA on neurotransmitter systems. The objective of the present study is to review the effects of ecstasy/MDMA on neurotransmitter systems as assessed by molecular imaging studies in small animals, non-human primates and humans. A search in PubMed was performed. Eighty-eight articles were found on which inclusion and exclusion criteria were applied. Thirty-three studies met the inclusion criteria; all were focused on the 5-HT or dopamine (DA) system. Importantly, 9 out of 11 of the animal studies that examined the effects of MDMA on 5-HT transporter (SERT) availability showed a significant loss of binding potential. In human studies, this was the case for 14 out of 16 studies, particularly in heavy users. In abstinent users, significant recovery of SERT binding was found over time. Most imaging studies in humans that focused on the DA system did not find any significant effect of ecstasy/MDMA use. Preclinical and clinical molecular imaging studies on the effects of ecstasy/MDMA use/administration on neurotransmitter systems show quite consistent alterations of the 5-HT system. Particularly, in human studies, loss of SERT binding was observed in heavy ecstasy users, which might reflect 5-HT neurotoxicity, although alternative explanations (e.g. down-regulation of the SERT) cannot be excluded.

  9. Design strategies for organic semiconductors beyond the molecular formula.

    Science.gov (United States)

    Henson, Zachary B; Müllen, Klaus; Bazan, Guillermo C

    2012-09-01

    Organic semiconducting materials based on polymers and molecular systems containing an electronically delocalized structure are the basis of emerging optoelectronic technologies such as plastic solar cells and flexible transistors. For isolated molecules, guidelines exist that rely on the molecular formula to tailor the frontier (highest occupied or lowest unoccupied) molecular orbital energy levels and optical absorption profiles. Much less control can be achieved over relevant properties, however, as one makes the transition to the ensemble behaviour characteristic of the solid state. Polymeric materials are also challenging owing to the statistical description of the average number of repeat units. Here we draw attention to the limitations of molecular formulae as predictive tools for achieving properties relevant to device performances. Illustrative examples highlight the relevance of organization across multiple length scales, and how device performances--although relevant for practical applications--poorly reflect the success of molecular design.

  10. Reclamation of a molecular beam epitaxy system and conversion for oxide epitaxy

    International Nuclear Information System (INIS)

    Carver, Alexander G.; Henderson, Walter; Doolittle, W. Alan

    2008-01-01

    An early 1980s vintage molecular beam epitaxy system, a Varian Gen II system, originally used for HgCdTe epitaxy, was converted into a system capable of growing thin-film complex metal oxides. The nature of some of the alternative oxides requires a thorough cleaning and, in some cases, complete replacement of system components. Details are provided regarding the chemistry of the etchants used, safety requirements for properly handling, and disposal of large quantities of etchants and etch by-products, and components that can be reused versus components that require replacement are given. Following the given procedures, an ultimate base pressure of 2x10 -10 Torr was obtained. Films grown in the system after reclamation contained no evidence of previously present materials down to the detection limit of secondary ion mass spectrometry

  11. A clinical decision support system algorithm for intravenous to oral antibiotic switch therapy: validity, clinical relevance and usefulness in a three-step evaluation study.

    Science.gov (United States)

    Akhloufi, H; Hulscher, M; van der Hoeven, C P; Prins, J M; van der Sijs, H; Melles, D C; Verbon, A

    2018-04-26

    To evaluate a clinical decision support system (CDSS) based on consensus-based intravenous to oral switch criteria, which identifies intravenous to oral switch candidates. A three-step evaluation study of a stand-alone CDSS with electronic health record interoperability was performed at the Erasmus University Medical Centre in the Netherlands. During the first step, we performed a technical validation. During the second step, we determined the sensitivity, specificity, negative predictive value and positive predictive value in a retrospective cohort of all hospitalized adult patients starting at least one therapeutic antibacterial drug between 1 and 16 May 2013. ICU, paediatric and psychiatric wards were excluded. During the last step the clinical relevance and usefulness was prospectively assessed by reports to infectious disease specialists. An alert was considered clinically relevant if antibiotics could be discontinued or switched to oral therapy at the time of the alert. During the first step, one technical error was found. The second step yielded a positive predictive value of 76.6% and a negative predictive value of 99.1%. The third step showed that alerts were clinically relevant in 53.5% of patients. For 43.4% it had already been decided to discontinue or switch the intravenous antibiotics by the treating physician. In 10.1%, the alert resulted in advice to change antibiotic policy and was considered useful. This prospective cohort study shows that the alerts were clinically relevant in >50% (n = 449) and useful in 10% (n = 85). The CDSS needs to be evaluated in hospitals with varying activity of infectious disease consultancy services as this probably influences usefulness.

  12. Mathematical models of non-linear phenomena, processes and systems: from molecular scale to planetary atmosphere

    CERN Document Server

    2013-01-01

    This book consists of twenty seven chapters, which can be divided into three large categories: articles with the focus on the mathematical treatment of non-linear problems, including the methodologies, algorithms and properties of analytical and numerical solutions to particular non-linear problems; theoretical and computational studies dedicated to the physics and chemistry of non-linear micro-and nano-scale systems, including molecular clusters, nano-particles and nano-composites; and, papers focused on non-linear processes in medico-biological systems, including mathematical models of ferments, amino acids, blood fluids and polynucleic chains.

  13. Unraveling the effect of the hydration level on the molecular mobility of nanolayered polymeric systems.

    Science.gov (United States)

    Borges, João; Caridade, Sofia G; Silva, Joana M; Mano, João F

    2015-02-01

    This work investigates the influence of the hydration level on the molecular mobility and glass transition dynamics of freestanding chitosan/alginate (CHT/ALG) nanolayered systems. Nonconventional dynamic mechanical analysis identifies two relaxation processes assigned to the α-relaxation of the two biopolymers, respectively, CHT and ALG, when immersed in water/ethanol mixtures. This phenomenon explains the shape memory properties of the multilayered systems induced by hydration, thus constituting promising smart materials that would be of paramount importance in a plethora of research fields, including in the biomedical and biotechnological fields. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Optical activity of oriented molecular systems in terms of the magnetoelectric tensor of gyrotropy

    International Nuclear Information System (INIS)

    Arteaga, Oriol

    2014-01-01

    The optical activity of oriented molecular systems is investigated using bianisotropic material constitutives for Maxwell's equations. It is shown that the circular birefringence and circular dichroism for an oriented system can be conveniently expressed in terms of the two components of the symmetric magnetoelectric tensor of gyrotropy that are perpendicular to this direction of light propagation. This description establishes a direct link between the optical activity measured at a certain direction and the tensors that describe the oscillating electric and magnetic dipole and electric quadrupole moments induced by the optical wave. (paper)

  15. Insight into the Local Solvent Environment of Biologically Relevant Iron-nitroysl Systems through Two-Dimensional Infrared Spectroscopy

    Science.gov (United States)

    Brookes, Jennifer Faith

    Iron-nitrosyl systems, particularly in the form of heme proteins, with their iron metal active sites play an important role in biological systems. Heme proteins act as storage, transporters, and receptors for nitric oxide (NO), a signaling molecule that is important in immune, nervous, and cardiovascular systems of mammals. By better understanding the local environment of the active site of NO binding heme proteins we can gain insight into disease in which the NO pathways have been implicated. This is an important step to being able to develop pharmaceuticals targeting NO pathways in humans. Sodium nitroprusside ((SNP, Na2[Fe(CN)5is NO]·2H 2O) investigated as a model system for the active site of nitric oxide binding heme proteins. Using two-dimensional infrared spectroscopy (2D IR) to obtain dephasing dynamics of the nitrosyl stretch (nuNO) in a series of solvents we are able to better understand the local environment of the more complicated metalloproteins. Rigorous line shape analysis is performed by using nonlinear response theory to simulate 2D IR spectra which are then fit to experimental data in an iterative process to extract frequency-frequency correlation functions (FFCFs). The time scales obtained are then correlated to empirical solvent polarity parameters. The analysis of the 2D IR lineshapes reveal that the spectral diffusion timescale of the nuNO in SNP varies from 0.8 -- 4 ps and is negatively correlated with the empirical solvent polarity scales. We continue to investigate NO binding of metalloproteins through 2D IR experiments on nitrophorin 4 (NP4). NP4 is a pH-sensitive NO transporter protein present in the salivary gland of the blood sucking insect Rhodius prolixus which undergoes a pH sensitive structural change between a closed and open conformation allowing for the storage and delivery of NO. The two structures are observed spectroscopically as two distinct pH-dependent nu NO frequencies at ~1904 and ~1917 cm-1. We obtain FFCFs by globally

  16. Role of Transporters in Central Nervous System Drug Delivery and Blood-Brain Barrier Protection: Relevance to Treatment of Stroke

    Directory of Open Access Journals (Sweden)

    Hrvoje Brzica

    2017-03-01

    Full Text Available Ischemic stroke is a leading cause of morbidity and mortality in the United States. The only approved pharmacologic treatment for ischemic stroke is thrombolysis via recombinant tissue plasminogen activator (r-tPA. A short therapeutic window and serious adverse events (ie, hemorrhage, excitotoxicity greatly limit r-tPA therapy, which indicates an essential need to develop novel stroke treatment paradigms. Transporters expressed at the blood-brain barrier (BBB provide a significant opportunity to advance stroke therapy via central nervous system delivery of drugs that have neuroprotective properties. Examples of such transporters include organic anion–transporting polypeptides (Oatps and organic cation transporters (Octs. In addition, multidrug resistance proteins (Mrps are transporter targets in brain microvascular endothelial cells that can be exploited to preserve BBB integrity in the setting of stroke. Here, we review current knowledge on stroke pharmacotherapy and demonstrate how endogenous BBB transporters can be targeted for improvement of ischemic stroke treatment.

  17. Preliminary Design of Molecular Sieve for Removing Organic Iodide in Containment Filtered Venting System

    Energy Technology Data Exchange (ETDEWEB)

    Park, Tong Kyu; Shin, So Eun; Lee, Byung Chul [Heungdeok IT Valley Bldg., Yongin (Korea, Republic of); Kim, Hong Hyun; Lee, Kyung Jun [Gemvax and KAEL Inc., Daejeon (Korea, Republic of)

    2014-05-15

    In this paper, to increase the DF for gaseous iodine species, especially organic iodide, molecular sieve filled by silver exchanged zeolites is proposed and designed preliminarily. Its aerodynamic analysis is also performed and presented. In order to increase the DF for gaseous organic iodide, deep-bed type molecular sieve was proposed and designed preliminarily. Total 1,620kg of silver exchanged zeolites were filled evenly in 10 beds of the molecular sieve. The safety factor in the case of 20m{sup 3}/s will be smaller than the counterpart of the standard case (6m{sup 3}/s). However, if the adsorption capacity of the zeolites is larger than 3.09mg/g when the residence time is 0.09 second, the designed molecular sieve can be used at 20m3/s of volumetric flow rate. The removal efficiency for organic iodide should be considered as well as economical aspects in the design of molecular sieve. In the event of nuclear power plant (NPP) severe accident, the nuclear reactor containment might suffer damage resulting from overpressure caused by decay heat. In order to prevent this containment damage, containment venting has been considered as one of effective methods. However, since vented gases contain radioactive fission products, they should be filtered to be released to environment. Generally, containment filtered venting system (CFVS) is installed on NPP to achieve this aim. Even though great amount of efforts have been devoted to developing the CFVS using various filtering methods, the decontaminant factor (DF) for radioactive gaseous iodide is still unsatisfactory while DFs for radioactive aerosols and elemental iodine are very high.

  18. Molecular depth profiling of multi-layer systems with cluster ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Juan [Department of Chemistry, Penn State University, University Park, PA 16802 (United States); Winograd, Nicholas [Department of Chemistry, Penn State University, University Park, PA 16802 (United States)]. E-mail: nxw@psu.edu

    2006-07-30

    Cluster bombardment of molecular films has created new opportunities for SIMS research. To more quantitatively examine the interaction of cluster beams with organic materials, we have developed a reproducible platform consisting of a well-defined sugar film (trehalose) doped with peptides. Molecular depth profiles have been acquired with these systems using C{sub 60} {sup +} bombardment. In this study, we utilize this platform to determine the feasibility of examining buried interfaces for multi-layer systems. Using C{sub 60} {sup +} at 20 keV, several systems have been tested including Al/trehalose/Si, Al/trehalose/Al/Si, Ag/trehalose/Si and ice/trehalose/Si. The results show that there can be interactions between the layers during the bombardment process that prevent a simple interpretation of the depth profile. We find so far that the best results are obtained when the mass of the overlayer atoms is less than or nearly equal to the mass of the atoms in buried molecules. In general, these observations suggest that C{sub 60} {sup +} bombardment can be successfully applied to interface characterization of multi-layer systems if the systems are carefully chosen.

  19. Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis.

    Science.gov (United States)

    Hudson, Marie; Bernatsky, Sasha; Colmegna, Ines; Lora, Maximilien; Pastinen, Tomi; Klein Oros, Kathleen; Greenwood, Celia M T

    2017-06-03

    We undertook this study to identify DNA methylation signatures of three systemic autoimmune rheumatic diseases (SARDs), namely rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis, compared to healthy controls. Using a careful design to minimize confounding, we restricted our study to subjects with incident disease and performed our analyses on purified CD4 + T cells, key effector cells in SARD. We identified differentially methylated (using the Illumina Infinium HumanMethylation450 BeadChip array) and expressed (using the Illumina TruSeq stranded RNA-seq protocol) sites between cases and controls, and investigated the biological significance of this SARD signature using gene annotation databases. We recruited 13 seropositive rheumatoid arthritis, 19 systemic sclerosis, 12 systemic lupus erythematosus subjects, and 8 healthy controls. We identified 33 genes that were both differentially methylated and expressed (26 over- and 7 under-expressed) in SARD cases versus controls. The most highly overexpressed gene was CD1C (log fold change in expression = 1.85, adjusted P value = 0.009). In functional analysis (Ingenuity Pathway Analysis), the top network identified was lipid metabolism, molecular transport, small molecule biochemistry. The top canonical pathways included the mitochondrial L-carnitine shuttle pathway (P = 5E-03) and PTEN signaling (P = 8E-03). The top upstream regulator was HNF4A (P = 3E-05). This novel SARD signature contributes to ongoing work to further our understanding of the molecular mechanisms underlying SARD and provides novel targets of interest.

  20. System geometry optimization for molecular breast tomosynthesis with focusing multi-pinhole collimators

    Science.gov (United States)

    van Roosmalen, Jarno; Beekman, Freek J.; Goorden, Marlies C.

    2018-01-01

    Imaging of 99mTc-labelled tracers is gaining popularity for detecting breast tumours. Recently, we proposed a novel design for molecular breast tomosynthesis (MBT) based on two sliding focusing multi-pinhole collimators that scan a modestly compressed breast. Simulation studies indicate that MBT has the potential to improve the tumour-to-background contrast-to-noise ratio significantly over state-of-the-art planar molecular breast imaging. The aim of the present paper is to optimize the collimator-detector geometry of MBT. Using analytical models, we first optimized sensitivity at different fixed system resolutions (ranging from 5 to 12 mm) by tuning the pinhole diameters and the distance between breast and detector for a whole series of automatically generated multi-pinhole designs. We evaluated both MBT with a conventional continuous crystal detector with 3.2 mm intrinsic resolution and with a pixelated detector with 1.6 mm pixels. Subsequently, full system simulations of a breast phantom containing several lesions were performed for the optimized geometry at each system resolution for both types of detector. From these simulations, we found that tumour-to-background contrast-to-noise ratio was highest for systems in the 7 mm-10 mm system resolution range over which it hardly varied. No significant differences between the two detector types were found.

  1. Positron annihilation lifetime spectroscopy (PALS): a probe for molecular organisation in self-assembled biomimetic systems.

    Science.gov (United States)

    Fong, Celesta; Dong, Aurelia W; Hill, Anita J; Boyd, Ben J; Drummond, Calum J

    2015-07-21

    Positron annihilation lifetime spectroscopy (PALS) has been shown to be highly sensitive to conformational, structural and microenvironmental transformations arising from subtle geometric changes in molecular geometry in self-assembling biomimetic systems. The ortho-positronium (oPs) may be considered an active probe that can provide information on intrinsic packing and mobility within low molecular weight solids, viscous liquids, and soft matter systems. In this perspective we provide a critical overview of the literature in this field, including the evolution of analysis software and experimental protocols with commentary upon the practical utility of PALS. In particular, we discuss how PALS can provide unique insight into the macroscopic transport properties of several porous biomembrane-like nanostructures and suggest how this insight may provide information on the release of drugs from these matrices to aid in developing therapeutic interventions. We discuss the potentially exciting and fruitful application of this technique to membrane dynamics, diffusion and permeability. We propose that PALS can provide novel molecular level information that is complementary to conventional characterisation techniques.

  2. A neural network approach to the study of internal energy flow in molecular systems

    International Nuclear Information System (INIS)

    Sumpter, B.G.; Getino, C.; Noid, D.W.

    1992-01-01

    Neural networks are used to develop a new technique for efficient analysis of data obtained from molecular-dynamics calculations and is applied to the study of mode energy flow in molecular systems. The methodology is based on teaching an appropriate neural network the relationship between phase-space points along a classical trajectory and mode energies for stretch, bend, and torsion vibrations. Results are discussed for reactive and nonreactive classical trajectories of hydrogen peroxide (H 2 O 2 ) on a semiempirical potential-energy surface. The neural-network approach is shown to produce reasonably accurate values for the mode energies, with average errors between 1% and 12%, and is applicable to any region within the 24-dimensional phase space of H 2 O 2 . In addition, the generic knowledge learned by the neural network allows calculations to be made for other molecular systems. Results are discussed for a series of tetratomic molecules: H 2 X 2 , X=C, N, O, Si, S, or Se, and preliminary results are given for energy flow predictions in macromolecules

  3. Theoretical study on the molecular tautomerism of the 3-hydroxy-pyridin-4-one system

    Science.gov (United States)

    Zborowski, Krzysztof K.; Mohammadpour, Mehrdad; Sadeghi, Amir; Proniewicz, Leonard M.

    2013-04-01

    3-hydroxy-pyridin-4-one is a parent molecule for the family of hydroxypyridinones that are known in coordination chemistry as efficient metal ions chelators. In this work, relative stabilities of some possible tautomers were investigated using several quantum chemical methods: CBS (complete basis set methods), Gn, DFT (density functional theory), Hartree-Fock and MP2. Performed calculations show that the system under consideration exists as a mixture of two tautomers with comparable energies. Among them, the hydroxypyridinone structure of the studied molecular system seems to be a bit more stable than the o-dihydroxypyridine one, by a few kJ/mol only. Aromaticity and intra-molecular hydrogen bonding are the main effects influencing the stability of the studied tautomeric structures. Consequently, aromatic effects were calculated using several indices of aromaticity: HOMA (harmonic oscillator model of aromaticity), NICS (nucleus independent chemical shift), H, PDI (para delocalisation index), MCI (multi-centre index) and ASE (aromatic stabilisation energy). The strength of possible intra-molecular hydrogen bonds (H-bonds) was determined by means of the AIM (atoms-in-molecules) method and by calculating enthalpies for theoretical reactions that do or do not involve H-bonds. The AIM method was employed to understand how variations in atomic energies influence the stability of different tautomeric structures.

  4. A Protoplast Transient Expression System to Enable Molecular, Cellular, and Functional Studies in Phalaenopsis orchids

    Directory of Open Access Journals (Sweden)

    Hsiang-Yin Lin

    2018-06-01

    Full Text Available The enigmatic nature of the specialized developmental programs of orchids has fascinated plant biologists for centuries. The recent releases of orchid genomes indicate that orchids possess new gene families and family expansions and contractions to regulate a diverse suite of developmental processes. However, the extremely long orchid life cycle and lack of molecular toolkit have hampered the advancement of orchid biology research. To overcome the technical difficulties and establish a platform for rapid gene regulation studies, in this study, we developed an efficient protoplast isolation and transient expression system for Phalaenopsis aphrodite. This protocol was successfully applied to protein subcellular localization and protein–protein interaction studies. Moreover, it was confirmed to be useful in delineating the PaE2F/PaDP-dependent cell cycle pathway and studying auxin response. In summary, the established orchid protoplast transient expression system provides a means to functionally characterize orchid genes at the molecular level allowing assessment of transcriptome responses to transgene expression and widening the scope of molecular studies in orchids.

  5. Predicting crash-relevant violations at stop sign-controlled intersections for the development of an intersection driver assistance system.

    Science.gov (United States)

    Scanlon, John M; Sherony, Rini; Gabler, Hampton C

    2016-09-01

    Intersection crashes resulted in over 5,000 fatalities in the United States in 2014. Intersection Advanced Driver Assistance Systems (I-ADAS) are active safety systems that seek to help drivers safely traverse intersections. I-ADAS uses onboard sensors to detect oncoming vehicles and, in the event of an imminent crash, can either alert the driver or take autonomous evasive action. The objective of this study was to develop and evaluate a predictive model for detecting whether a stop sign violation was imminent. Passenger vehicle intersection approaches were extracted from a data set of typical driver behavior (100-Car Naturalistic Driving Study) and violations (event data recorders downloaded from real-world crashes) and were assigned weighting factors based on real-world frequency. A k-fold cross-validation procedure was then used to develop and evaluate 3 hypothetical stop sign warning algorithms (i.e., early, intermediate, and delayed) for detecting an impending violation during the intersection approach. Violation detection models were developed using logistic regression models that evaluate likelihood of a violation at various locations along the intersection approach. Two potential indicators of driver intent to stop-that is, required deceleration parameter (RDP) and brake application-were used to develop the predictive models. The earliest violation detection opportunity was then evaluated for each detection algorithm in order to (1) evaluate the violation detection accuracy and (2) compare braking demand versus maximum braking capabilities. A total of 38 violating and 658 nonviolating approaches were used in the analysis. All 3 algorithms were able to detect a violation at some point during the intersection approach. The early detection algorithm, as designed, was able to detect violations earlier than all other algorithms during the intersection approach but gave false alarms for 22.3% of approaches. In contrast, the delayed detection algorithm sacrificed

  6. Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo

    DEFF Research Database (Denmark)

    Jovanovic, Goran; Sheng, Xia; Ale, Angelique

    2015-01-01

    the functional relevance of the dimerization of a non-orthodox or hybrid histidine kinase along which the phosphorelay takes place has been a subject of debate. We use a combination of molecular and genetic approaches, coupled to mathematical and statistical modelling, to demonstrate that the different possible...... intra- and inter-molecular mechanisms of phosphotransfer are formally non-identifiable in Escherichia coli expressing the ArcB non-orthodox histidine kinase used in anoxic redox control. In order to resolve this issue we further analyse the mathematical model in order to identify discriminatory...

  7. MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations.

    Science.gov (United States)

    Ohmura, Itta; Morimoto, Gentaro; Ohno, Yousuke; Hasegawa, Aki; Taiji, Makoto

    2014-08-06

    We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s(-1) for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.

  8. The aging motor system as a model for plastic changes of GABA-mediated intracortical inhibition and their behavioral relevance.

    Science.gov (United States)

    Heise, Kirstin-F; Zimerman, Maximo; Hoppe, Julia; Gerloff, Christian; Wegscheider, Karl; Hummel, Friedhelm C

    2013-05-22

    Since GABAA-mediated intracortical inhibition has been shown to underlie plastic changes throughout the lifespan from development to aging, here, the aging motor system was used as a model to analyze the interdependence of plastic alterations within the inhibitory motorcortical network and level of behavioral performance. Double-pulse transcranial magnetic stimulation (dpTMS) was used to examine inhibition by means of short-interval intracortical inhibition (SICI) of the contralateral primary motor cortex in a sample of 64 healthy right-handed human subjects covering a wide range of the adult lifespan (age range 20-88 years, mean 47.6 ± 20.7, 34 female). SICI was evaluated during resting state and in an event-related condition during movement preparation in a visually triggered simple reaction time task. In a subgroup (N = 23), manual motor performance was tested with tasks of graded dexterous demand. Weak resting-state inhibition was associated with an overall lower manual motor performance. Better event-related modulation of inhibition correlated with better performance in more demanding tasks, in which fast alternating activation of cortical representations are necessary. Declining resting-state inhibition was associated with weakened event-related modulation of inhibition. Therefore, reduced resting-state inhibition might lead to a subsequent loss of modulatory capacity, possibly reflecting malfunctioning precision in GABAAergic neurotransmission; the consequence is an inevitable decline in motor function.

  9. Regulatory functions and pathological relevance of the MECP2 3′UTR in the central nervous system

    Directory of Open Access Journals (Sweden)

    Heather McGowan

    2015-01-01

    Full Text Available Methyl-CpG-binding protein 2 (MeCP2, encoded by the gene MECP2, is a transcriptional regulator and chromatin-remodeling protein, which is ubiquitously expressed and plays an essential role in the development and maintenance of the central nervous system (CNS. Highly enriched in post-migratory neurons, MeCP2 is needed for neuronal maturation, including dendritic arborization and the development of synapses. Loss-of-function mutations in MECP2 cause Rett syndrome (RTT, a debilitating neurodevelopmental disorder characterized by a phase of normal development, followed by the progressive loss of milestones and cognitive disability. While a great deal has been discovered about the structure, function, and regulation of MeCP2 in the time since its discovery as the genetic cause of RTT, including its involvement in a number of RTT-related syndromes that have come to be known as MeCP2-spectrum disorders, much about this multifunctional protein remains enigmatic. One unequivocal fact that has become apparent is the importance of maintaining MeCP2 protein levels within a narrow range, the limits of which may depend upon the cell type and developmental time point. As such, MeCP2 is amenable to complex, multifactorial regulation. Here, we summarize the role of the MECP2 3' untranslated region (UTR in the regulation of MeCP2 protein levels and how mutations in this region contribute to autism and other non-RTT neuropsychiatric disorders.

  10. The Use of System Codes in Scaling Studies: Relevant Techniques for Qualifying NPP Nodalizations for Particular Scenarios

    Directory of Open Access Journals (Sweden)

    V. Martinez-Quiroga

    2014-01-01

    Full Text Available System codes along with necessary nodalizations are valuable tools for thermal hydraulic safety analysis. Qualifying both codes and nodalizations is an essential step prior to their use in any significant study involving code calculations. Since most existing experimental data come from tests performed on the small scale, any qualification process must therefore address scale considerations. This paper describes the methodology developed at the Technical University of Catalonia in order to contribute to the qualification of Nuclear Power Plant nodalizations by means of scale disquisitions. The techniques that are presented include the so-called Kv-scaled calculation approach as well as the use of “hybrid nodalizations” and “scaled-up nodalizations.” These methods have revealed themselves to be very helpful in producing the required qualification and in promoting further improvements in nodalization. The paper explains both the concepts and the general guidelines of the method, while an accompanying paper will complete the presentation of the methodology as well as showing the results of the analysis of scaling discrepancies that appeared during the posttest simulations of PKL-LSTF counterpart tests performed on the PKL-III and ROSA-2 OECD/NEA Projects. Both articles together produce the complete description of the methodology that has been developed in the framework of the use of NPP nodalizations in the support to plant operation and control.

  11. Human Growth Hormone Delivery with a Microneedle Transdermal System: Preclinical Formulation, Stability, Delivery and PK of Therapeutically Relevant Doses

    Directory of Open Access Journals (Sweden)

    Mahmoud Ameri

    2014-05-01

    Full Text Available This study evaluated the feasibility of coating formulated recombinant human growth hormone (rhGH on a titanium microneedle transdermal delivery system, Zosano Pharma (ZP-hGH, and assessed preclinical patch delivery performance. Formulation rheology and surface activity were assessed by viscometry and contact angle measurement. rhGH liquid formulation was coated onto titanium microneedles by dip-coating and drying. The stability of coated rhGH was determined by size exclusion chromatography-high performance liquid chromatography (SEC-HPLC. Preclinical delivery and pharmacokinetic studies were conducted in female hairless guinea pigs (HGP using rhGH coated microneedle patches at 0.5 and 1 mg doses and compared to Norditropin® a commercially approved rhGH subcutaneous injection. Studies demonstrated successful rhGH formulation development and coating on microneedle arrays. The ZP-hGH patches remained stable at 40 °C for six months with no significant change in % aggregates. Pharmacokinetic studies showed that the rhGH-coated microneedle patches, delivered with high efficiency and the doses delivered indicated linearity with average Tmax of 30 min. The absolute bioavailability of the microneedle rhGH patches was similar to subcutaneous Norditropin® injections. These results suggest that ZP-transdermal microneedle patch delivery of rhGH is feasible and may offer an effective and patient-friendly alternative to currently marketed rhGH injectables.

  12. Human Growth Hormone Delivery with a Microneedle Transdermal System: Preclinical Formulation, Stability, Delivery and PK of Therapeutically Relevant Doses.

    Science.gov (United States)

    Ameri, Mahmoud; Kadkhodayan, Miryam; Nguyen, Joe; Bravo, Joseph A; Su, Rebeca; Chan, Kenneth; Samiee, Ahmad; Daddona, Peter E

    2014-05-15

    This study evaluated the feasibility of coating formulated recombinant human growth hormone (rhGH) on a titanium microneedle transdermal delivery system, Zosano Pharma (ZP)-hGH, and assessed preclinical patch delivery performance. Formulation rheology and surface activity were assessed by viscometry and contact angle measurement. rhGH liquid formulation was coated onto titanium microneedles by dip-coating and drying. The stability of coated rhGH was determined by size exclusion chromatography-high performance liquid chromatography (SEC-HPLC). Preclinical delivery and pharmacokinetic studies were conducted in female hairless guinea pigs (HGP) using rhGH coated microneedle patches at 0.5 and 1 mg doses and compared to Norditropin® a commercially approved rhGH subcutaneous injection. Studies demonstrated successful rhGH formulation development and coating on microneedle arrays. The ZP-hGH patches remained stable at 40 °C for six months with no significant change in % aggregates. Pharmacokinetic studies showed that the rhGH-coated microneedle patches, delivered with high efficiency and the doses delivered indicated linearity with average Tmax of 30 min. The absolute bioavailability of the microneedle rhGH patches was similar to subcutaneous Norditropin® injections. These results suggest that ZP-transdermal microneedle patch delivery of rhGH is feasible and may offer an effective and patient-friendly alternative to currently marketed rhGH injectables.

  13. CAST: a new program package for the accurate characterization of large and flexible molecular systems.

    Science.gov (United States)

    Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

    2014-09-15

    The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

  14. Self-consistent field theory based molecular dynamics with linear system-size scaling

    Energy Technology Data Exchange (ETDEWEB)

    Richters, Dorothee [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany); Kühne, Thomas D., E-mail: kuehne@uni-mainz.de [Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz (Germany); Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn (Germany)

    2014-04-07

    We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

  15. bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

    Science.gov (United States)

    Alexander, Nathan; Woetzel, Nils; Meiler, Jens

    2011-02-01

    Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

  16. Defining Health in the Era of Value-based Care: Lessons from England of Relevance to Other Health Systems.

    Science.gov (United States)

    Gentry, Sarah; Badrinath, Padmanabhan

    2017-03-06

    The demand for healthcare is rising due to aging populations, rising chronic disease prevalence, and technological innovations. There are currently more effective and cost-effective interventions available than can be afforded within limited budgets. A new way of thinking about the optimal use of resources is needed. Ensuring that available resources are used for interventions that provide outcomes that patient's most value, rather than a focus just on effectiveness and cost-effectiveness, may help to ensure that resources are used optimally. Value-based healthcare puts what patients value at the center of healthcare. It helps ensure that they receive the care that can provide them with outcomes they think are important and that limited resources are focused on high-value interventions. In order to do this, we need flexible definitions of 'health', personalized and tailored to patient values. We review the current status of value-based health care in England and identify lessons applicable to a variety of health systems. For this, we draw upon the work of the National Institute for Health and Care Excellence (NICE), the National Health Service (NHS), Right Care Initiative, and our local experience in promoting value-based health care for specific conditions in our region. Combining the best available evidence with open and honest dialogue between patients, clinicians, and others, whilst requiring considerable time and resources are essential to building a consensus around the value that allows the best use of limited budgets. Values have been present in healthcare since its beginnings. Placing value and values at the center of healthcare could help to ensure available resources are used to provide the greatest possible benefit to patients.

  17. Extensive Evaluation of the Conductor-like Screening Model for Real Solvents Method in Predicting Liquid-Liquid Equilibria in Ternary Systems of Ionic Liquids with Molecular Compounds.

    Science.gov (United States)

    Paduszyński, Kamil

    2018-04-12

    A conductor-like screening model for real solvents (COSMO-RS) is nowadays one of the most popular and commonly applied tools for the estimation of thermodynamic properties of complex fluids. The goal of this work is to provide a comprehensive review and analysis of the performance of this approach in calculating liquid-liquid equilibrium (LLE) phase diagrams in ternary systems composed of ionic liquid and two molecular compounds belonging to diverse families of chemicals (alkanes, aromatics, S/N-compounds, alcohols, ketones, ethers, carboxylic acid, esters, and water). The predictions are presented for extensive experimental database, including 930 LLE data sets and more than 9000 data points (LLE tie lines) reported for 779 unique ternary mixtures. An impact of the type of molecular binary subsystem on the accuracy of predictions is demonstrated and discussed on the basis of representative examples. The model's capability of capturing qualitative trends in the LLE distribution ratio and selectivity is also checked for a number of structural effects. Comparative analysis of two levels of quantum chemical theory (BP-TZVP-COSMO vs BP-TZVPD-FINE) for the input molecular data for COSMO-RS is presented. Finally, some general recommendations for the applicability of the model are indicated based on the analysis of the global performance as well as on the results obtained for systems relevant from the point of view of important separation problems.

  18. Molecular geometry

    CERN Document Server

    Rodger, Alison

    1995-01-01

    Molecular Geometry discusses topics relevant to the arrangement of atoms. The book is comprised of seven chapters that tackle several areas of molecular geometry. Chapter 1 reviews the definition and determination of molecular geometry, while Chapter 2 discusses the unified view of stereochemistry and stereochemical changes. Chapter 3 covers the geometry of molecules of second row atoms, and Chapter 4 deals with the main group elements beyond the second row. The book also talks about the complexes of transition metals and f-block elements, and then covers the organometallic compounds and trans

  19. A molecular dynamics simulation of sodium pentadecyl sulphonate (SPDS)/water system

    International Nuclear Information System (INIS)

    Arsenyan, L.H.; Poghosyan, A.H.; Shahinyan, A.A.

    2008-07-01

    We have carried out a molecular dynamics simulation of a sodium pentadecylsulfonate (SPDS)/water system consisting of 64PDS/1200water and 512PDS/9000water molecules, correspondingly. The overall simulation time for both cases reaches up to 60ns and the simulation was performed using the NAMD code with CHARMM27 force field. The main parameters of the system have been calculated and compared with available X-ray diffraction findings. For large system, after a couple of ns, we receive the molecule's hydrocarbon chains tilt in the opposite sense in layers and reducing the system size leads to the decrease of the average angle between bilayer normal and chain vector. At the end of 50ns of a simulation run we achieve the crystalline-like structure of hydrocarbon packing. For both cases, we obtain tilted hydrocarbon chains packing and the average angle between bilayer normal and chain vector is estimated to be about 13 deg. and 10 deg. (author)

  20. Molecular Mechanisms Underlying Renin-Angiotensin-Aldosterone System Mediated Regulation of BK Channels

    Directory of Open Access Journals (Sweden)

    Zhen-Ye Zhang

    2017-09-01

    Full Text Available Large-conductance calcium-activated potassium channels (BK channels belong to a family of Ca2+-sensitive voltage-dependent potassium channels and play a vital role in various physiological activities in the human body. The renin-angiotensin-aldosterone system is acknowledged as being vital in the body's hormone system and plays a fundamental role in the maintenance of water and electrolyte balance and blood pressure regulation. There is growing evidence that the renin-angiotensin-aldosterone system has profound influences on the expression and bioactivity of BK channels. In this review, we focus on the molecular mechanisms underlying the regulation of BK channels mediated by the renin-angiotensin-aldosterone system and its potential as a target for clinical drugs.

  1. Application range affected by software failures in safety relevant instrumentation and control systems of nuclear power plants; Auswirkungsbereiche von Softwarefehlern in sicherheitstechnisch wichtigen Einrichtungen von Kernkraftwerken

    Energy Technology Data Exchange (ETDEWEB)

    Jopen, Manuela; Mbonjo, Herve; Sommer, Dagmar; Ulrich, Birte

    2017-03-15

    This report presents results that have been developed within a BMUB-funded research project (Promotion Code 3614R01304). The overall objective of this project was to broaden the knowledge base of GRS regarding software failures and their impact in software-based instrumentation and control (I and C) systems. To this end, relevant definitions and terms in standards and publications (DIN, IEEE standards, IAEA standards, NUREG publications) as well as in the German safety requirements for nuclear power plants were analyzed first. In particular, it was found that the term ''software fault'' is defined differently and partly contradictory in the considered literature sources. For this reason, a definition of software fault was developed on the basis of the software life cycle of software-based I and C systems within the framework of this project, which takes into account the various aspects relevant to software faults and their related effects. It turns out that software failures result from latent faults in a software-based control system, which can lead to a non-compliant behavior of a software-based I and C system. Hereby a distinction should be made between programming faults and specification faults. In a further step, operational experience with software failures in software-based I and C systems in nuclear facilities and in nonnuclear sector was investigated. The identified events were analyzed with regard to their cause and impacts and the analysis results were summarized. Based on the developed definition of software failure and on the COMPSIS-classification scheme for events related to software based I and C systems, the COCS-classification scheme was developed to classify events from operating experience with software failures, in which the events are classified according to the criteria ''cause'', ''affected system'', ''impact'' and ''CCF potential''. This

  2. System characterization of neuronal excitability in the hippocampus and its relevance to observed dynamics of spontaneous seizure-like transitions

    Science.gov (United States)

    Zalay, Osbert C.; Serletis, Demitre; Carlen, Peter L.; Bardakjian, Berj L.

    2010-06-01

    Most forms of epilepsy are marked by seizure episodes that arise spontaneously. The low-magnesium/high-potassium (low-Mg2+/high-K+) experimental model of epilepsy is an acute model that produces spontaneous, recurring seizure-like events (SLEs). To elucidate the nature of spontaneous seizure transitions and their relationship to neuronal excitability, whole-cell recordings from the intact hippocampus were undertaken in vitro, and the response of hippocampal CA3 neurons to Gaussian white noise injection was obtained before and after treatment with various concentrations of low-Mg2+/high-K+ solution. A second-order Volterra kernel model was estimated for each of the input-output response pairs. The spectral energy of the responses was also computed, providing a quantitative measure of neuronal excitability. Changes in duration and amplitude of the first-order kernel correlated positively with the spectral energy increase following treatment with low-Mg2+/high-K+ solution, suggesting that variations in neuronal excitability are coded by the system kernels, in part by differences to the profile of the first-order kernel. In particular, kernel duration was more sensitive than amplitude to changes in spectral energy, and correlated more strongly with kernel area. An oscillator network model of the hippocampal CA3 was constructed to investigate the relationship of kernel duration to network excitability, and the model was able to generate spontaneous, recurrent SLEs by increasing the duration of a mode function analogous to the first-order kernel. Results from the model indicated that disruption to the dynamic balance of feedback was responsible for seizure-like transitions and the observed intermittency of SLEs. A physiological candidate for feedback imbalance consistent with the network model is the destabilizing interaction of extracellular potassium and paroxysmal neuronal activation. Altogether, these results (1) validate a mathematical model for epileptiform

  3. DEVELOPMENT OF SEPARATION SYSTEMS FOR POLYNUCLEAR AROMATIC HYDROCARBON ENVIRONMENTAL CONTAMINANTS USING MICELLAR ELECTROKINETIC CHROMATOGRAPHY WITH MOLECULAR MICELLES AND FREE ZONE ELECTROPHORESIS

    Science.gov (United States)

    Of four systems available from the literature, based on cyclodextrins, dioctylsulfosuccinate, bile salts, and molecular micelles consisting of oligomers of undecylenic acid, the most successful separation system in our hands is based on the molecular micelles, oligomers of sodiu...

  4. A Systems Biology Approach Reveals Converging Molecular Mechanisms that Link Different POPs to Common Metabolic Diseases.

    Science.gov (United States)

    Ruiz, Patricia; Perlina, Ally; Mumtaz, Moiz; Fowler, Bruce A

    2016-07-01

    A number of epidemiological studies have identified statistical associations between persistent organic pollutants (POPs) and metabolic diseases, but testable hypotheses regarding underlying molecular mechanisms to explain these linkages have not been published. We assessed the underlying mechanisms of POPs that have been associated with metabolic diseases; three well-known POPs [2,3,7,8-tetrachlorodibenzodioxin (TCDD), 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB 153), and 4,4´-dichlorodiphenyldichloroethylene (p,p´-DDE)] were studied. We used advanced database search tools to delineate testable hypotheses and to guide laboratory-based research studies into underlying mechanisms by which this POP mixture could produce or exacerbate metabolic diseases. For our searches, we used proprietary systems biology software (MetaCore™/MetaDrug™) to conduct advanced search queries for the underlying interactions database, followed by directional network construction to identify common mechanisms for these POPs within two or fewer interaction steps downstream of their primary targets. These common downstream pathways belong to various cytokine and chemokine families with experimentally well-documented causal associations with type 2 diabetes. Our systems biology approach allowed identification of converging pathways leading to activation of common downstream targets. To our knowledge, this is the first study to propose an integrated global set of step-by-step molecular mechanisms for a combination of three common POPs using a systems biology approach, which may link POP exposure to diseases. Experimental evaluation of the proposed pathways may lead to development of predictive biomarkers of the effects of POPs, which could translate into disease prevention and effective clinical treatment strategies. Ruiz P, Perlina A, Mumtaz M, Fowler BA. 2016. A systems biology approach reveals converging molecular mechanisms that link different POPs to common metabolic diseases. Environ

  5. Information theory and signal transduction systems: from molecular information processing to network inference.

    Science.gov (United States)

    Mc Mahon, Siobhan S; Sim, Aaron; Filippi, Sarah; Johnson, Robert; Liepe, Juliane; Smith, Dominic; Stumpf, Michael P H

    2014-11-01

    Sensing and responding to the environment are two essential functions that all biological organisms need to master for survival and successful reproduction. Developmental processes are marshalled by a diverse set of signalling and control systems, ranging from systems with simple chemical inputs and outputs to complex molecular and cellular networks with non-linear dynamics. Information theory provides a powerful and convenient framework in which such systems can be studied; but it also provides the means to reconstruct the structure and dynamics of molecular interaction networks underlying physiological and developmental processes. Here we supply a brief description of its basic concepts and introduce some useful tools for systems and developmental biologists. Along with a brief but thorough theoretical primer, we demonstrate the wide applicability and biological application-specific nuances by way of different illustrative vignettes. In particular, we focus on the characterisation of biological information processing efficiency, examining cell-fate decision making processes, gene regulatory network reconstruction, and efficient signal transduction experimental design. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. A state-of-the-art review of transportation systems evaluation techniques relevant to air transportation, volume 1. [urban planning and urban transportation using decision theory

    Science.gov (United States)

    Haefner, L. E.

    1975-01-01

    Mathematical and philosophical approaches are presented for evaluation and implementation of ground and air transportation systems. Basic decision processes are examined that are used for cost analyses and planning (i.e, statistical decision theory, linear and dynamic programming, optimization, game theory). The effects on the environment and the community that a transportation system may have are discussed and modelled. Algorithmic structures are examined and selected bibliographic annotations are included. Transportation dynamic models were developed. Citizen participation in transportation projects (i.e, in Maryland and Massachusetts) is discussed. The relevance of the modelling and evaluation approaches to air transportation (i.e, airport planning) is examined in a case study in St. Louis, Missouri.

  7. Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

    Science.gov (United States)

    Bolhuis, Peter

    Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

  8. Proteomic approach toward molecular backgrounds of drug resistance of osteosarcoma cells in spheroid culture system.

    Science.gov (United States)

    Arai, Kazuya; Sakamoto, Ruriko; Kubota, Daisuke; Kondo, Tadashi

    2013-08-01

    Chemoresistance is one of the most critical prognostic factors in osteosarcoma, and elucidation of the molecular backgrounds of chemoresistance may lead to better clinical outcomes. Spheroid cells resemble in vivo cells and are considered an in vitro model for the drug discovery. We found that spheroid cells displayed more chemoresistance than conventional monolayer cells across 11 osteosarcoma cell lines. To investigate the molecular mechanisms underlying the resistance to chemotherapy, we examined the proteomic differences between the monolayer and spheroid cells by 2D-DIGE. Of the 4762 protein species observed, we further investigated 435 species with annotated mass spectra in the public proteome database, Genome Medicine Database of Japan Proteomics. Among the 435 protein species, we found that 17 species exhibited expression level differences when the cells formed spheroids in more than five cell lines and four species out of these 17 were associated with spheroid-formation associated resistance to doxorubicin. We confirmed the upregulation of cathepsin D in spheroid cells by western blotting. Cathepsin D has been implicated in chemoresistance of various malignancies but has not previously been implemented in osteosarcoma. Our study suggested that the spheroid system may be a useful tool to reveal the molecular backgrounds of chemoresistance in osteosarcoma. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Molecular transformation, gene cloning, and gene expression systems for filamentous fungi

    Science.gov (United States)

    Gold, Scott E.; Duick, John W.; Redman, Regina S.; Rodriguez, Rusty J.

    2001-01-01

    This chapter discusses the molecular transformation, gene cloning, and gene expression systems for filamentous fungi. Molecular transformation involves the movement of discrete amounts of DNA into cells, the expression of genes on the transported DNA, and the sustainable replication of the transforming DNA. The ability to transform fungi is dependent on the stable replication and expression of genes located on the transforming DNA. Three phenomena observed in bacteria, that is, competence, plasmids, and restriction enzymes to facilitate cloning, were responsible for the development of molecular transformation in fungi. Initial transformation success with filamentous fungi, involving the complementation of auxotrophic mutants by exposure to sheared genomic DNA or RNA from wt isolates, occurred with low transformation efficiencies. In addition, it was difficult to retrieve complementing DNA fragments and isolate genes of interest. This prompted the development of transformation vectors and methods to increase efficiencies. The physiological studies performed with fungi indicated that the cell wall could be removed to generate protoplasts. It was evident that protoplasts could be transformed with significantly greater efficiencies than walled cells.

  10. Solar fuels generation and molecular systems: is it homogeneous or heterogeneous catalysis?

    Science.gov (United States)

    Artero, Vincent; Fontecave, Marc

    2013-03-21

    Catalysis is a key enabling technology for solar fuel generation. A number of catalytic systems, either molecular/homogeneous or solid/heterogeneous, have been developed during the last few decades for both the reductive and oxidative multi-electron reactions required for fuel production from water or CO(2) as renewable raw materials. While allowing for a fine tuning of the catalytic properties through ligand design, molecular approaches are frequently criticized because of the inherent fragility of the resulting catalysts, when exposed to extreme redox potentials. In a number of cases, it has been clearly established that the true catalytic species is heterogeneous in nature, arising from the transformation of the initial molecular species, which should rather be considered as a pre-catalyst. Whether such a situation is general or not is a matter of debate in the community. In this review, covering water oxidation and reduction catalysts, involving noble and non-noble metal ions, we limit our discussion to the cases in which this issue has been directly and properly addressed as well as those requiring more confirmation. The methodologies proposed for discriminating homogeneous and heterogeneous catalysis are inspired in part by those previously discussed by Finke in the case of homogeneous hydrogenation reaction in organometallic chemistry [J. A. Widegren and R. G. Finke, J. Mol. Catal. A, 2003, 198, 317-341].

  11. Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics

    Energy Technology Data Exchange (ETDEWEB)

    Tsourtis, Anastasios, E-mail: tsourtis@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, Crete (Greece); Pantazis, Yannis, E-mail: pantazis@math.umass.edu; Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-70013 Heraklion, Crete (Greece)

    2015-07-07

    In this paper, we present a parametric sensitivity analysis (SA) methodology for continuous time and continuous space Markov processes represented by stochastic differential equations. Particularly, we focus on stochastic molecular dynamics as described by the Langevin equation. The utilized SA method is based on the computation of the information-theoretic (and thermodynamic) quantity of relative entropy rate (RER) and the associated Fisher information matrix (FIM) between path distributions, and it is an extension of the work proposed by Y. Pantazis and M. A. Katsoulakis [J. Chem. Phys. 138, 054115 (2013)]. A major advantage of the pathwise SA method is that both RER and pathwise FIM depend only on averages of the force field; therefore, they are tractable and computable as ergodic averages from a single run of the molecular dynamics simulation both in equilibrium and in non-equilibrium steady state regimes. We validate the performance of the extended SA method to two different molecular stochastic systems, a standard Lennard-Jones fluid and an all-atom methane liquid, and compare the obtained parameter sensitivities with parameter sensitivities on three popular and well-studied observable functions, namely, the radial distribution function, the mean squared displacement, and the pressure. Results show that the RER-based sensitivities are highly correlated with the observable-based sensitivities.

  12. Improved Fab presentation on phage surface with the use of molecular chaperone coplasmid system.

    Science.gov (United States)

    Loh, Qiuting; Leong, Siew Wen; Tye, Gee Jun; Choong, Yee Siew; Lim, Theam Soon

    2015-05-15

    The low presentation efficiency of Fab (fragment antigen binding) fragments during phage display is largely due to the complexity of disulphide bond formation. This can result in the presentation of Fab fragments devoid of a light chain during phage display. Here we propose the use of a coplasmid system encoding several molecular chaperones (DsbA, DsbC, FkpA, and SurA) to improve Fab packaging. A comparison was done using the Fab fragment from IgG and IgD. We found that the use of the coplasmid during phage packaging was able to improve the presentation efficiency of the Fab fragment on phage surfaces. A modified version of panning using the coplasmid system was evaluated and was successful at enriching Fab binders. Therefore, the coplasmid system would be an attractive alternative for improved Fab presentation for phage display. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Molecular players involved in the interaction between beneficial bacteria and the immune system

    Directory of Open Access Journals (Sweden)

    Arancha eHevia

    2015-11-01

    Full Text Available The human gastrointestinal tract is a very complex ecosystem, in which there is a continuous interaction between nutrients, host cells, and microorganisms. The gut microbiota comprises trillions of microbes that have been selected during evolution on the basis of their functionality and capacity to survive in, and adapt to, the intestinal environment. Host bacteria and our immune system constantly sense and react to one another. In this regard, commensal microbes contribute to gut homeostasis, whereas the necessary responses are triggered against enteropathogens. Some representatives of our gut microbiota have beneficial effects on human health. Some of the most important roles of these microbes are to help to maintain the integrity of the mucosal barrier, to provide nutrients such as vitamins, or to protect against pathogens. In addition, the interaction between commensal microbiota and the mucosal immune system is crucial for proper immune function. This process is mainly performed via the pattern recognition receptors of epithelial cells, such as Toll-like or Nod-like receptors, which are able to recognize the molecular effectors that are produced by intestinal microbes. These effectors mediate processes that can ameliorate certain inflammatory gut disorders, discriminate between beneficial and pathogenic bacteria, or increase the number of immune cells or their pattern recognition receptors. This review intends to summarize the molecular players produced by probiotic bacteria, notably Lactobacillus and Bifidobacterium strains, but also other very promising potential probiotics, which affect the human immune system.

  14. Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

    Science.gov (United States)

    Stella, L.; Lorenz, C. D.; Kantorovich, L.

    2014-04-01

    The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

  15. Non-linear optical techniques and optical properties of condensed molecular systems

    Science.gov (United States)

    Citroni, Margherita

    2013-06-01

    Structure, dynamics, and optical properties of molecular systems can be largely modified by the applied pressure, with remarkable consequences on their chemical stability. Several examples of selective reactions yielding technologically attractive products can be cited, which are particularly efficient when photochemical effects are exploited in conjunction with the structural conditions attained at high density. Non-linear optical techniques are a basic tool to unveil key aspects of the chemical reactivity and dynamic properties of molecules. Their application to high-pressure samples is experimentally challenging, mainly because of the small sample dimensions and of the non-linear effects generated in the anvil materials. In this talk I will present results on the electronic spectra of several aromatic crystals obtained through two-photon induced fluorescence and two-photon excitation profiles measured as a function of pressure (typically up to about 25 GPa), and discuss the relationship between the pressure-induced modifications of the electronic structure and the chemical reactivity at high pressure. I will also present the first successful pump-probe infrared measurement performed as a function of pressure on a condensed molecular system. The system under examination is liquid water, in a sapphire anvil cell, up to 1 GPa along isotherms at 298 and 363 K. These measurements give a new enlightening insight into the dynamical properties of low- and high-density water allowing a definition of the two structures.

  16. Membrane Lipid Oscillation: An Emerging System of Molecular Dynamics in the Plant Membrane.

    Science.gov (United States)

    Nakamura, Yuki

    2018-03-01

    Biological rhythm represents a major biological process of living organisms. However, rhythmic oscillation of membrane lipid content is poorly described in plants. The development of lipidomic technology has led to the illustration of precise molecular profiles of membrane lipids under various growth conditions. Compared with conventional lipid signaling, which produces unpredictable lipid changes in response to ever-changing environmental conditions, lipid oscillation generates a fairly predictable lipid profile, adding a new layer of biological function to the membrane system and possible cross-talk with the other chronobiological processes. This mini review covers recent studies elucidating membrane lipid oscillation in plants.

  17. Molecular Thermodynamic Modeling and Design of Microencapsulation Systems for Drug Delivery

    DEFF Research Database (Denmark)

    Abildskov, Jens; O’Connell, John P.

    2011-01-01

    is based on fundamental thermodynamic relations and group contributions to properties of pure species (solvent, active ingredient and polymer) and their mixtures. The method is intended for pharmaceuticals with complex molecular structures, for which limited experimental information is known. Case studies......A systematic design strategy is given for computer-aided design of microparticle drug-delivery systems produced by solvent evaporation. In particular, design of solvents, polymer material, and external phase composition are considered for the case when the active ingredient is known. The procedure...... of solvent design are given....

  18. Studying the Impact of Spaceflight Environment on Immune Functions Using New Molecular Diagnostics System

    Science.gov (United States)

    Cohen, Luchino

    Immune functions are altered during space flights. Latent virus reactivation, reduction in the number of immune cells, decreased cell activation and increased sensitivity of astronauts to infections following their return on Earth demonstrate that the immune system is less efficient during space flight. The causes of this immune deficiency are not fully understood and this dysfunction during long-term missions could result in the appearance of opportunistic infections or a decrease in the immuno-surveillance mechanisms that eradicate cancer cells. Therefore, the immune functions of astronauts will have to be monitored continuously during long-term missions in space, using miniature and semi-automated diagnostic systems. The objectives of this project are to study the causes of space-related immunodeficiency, to develop countermeasures to maintain an optimal immune function and to improve our capacity to detect infectious diseases during space missions through the monitoring of astronauts' immune system. In order to achieve these objectives, an Immune Function Diagnostic System (IFDS) will be designed to perform a set of immunological assays on board spacecrafts or on planet-bound bases. Through flow cytometric assays and molecular biology analyses, this diagnostic system could improve medical surveillance of astronauts and could be used to test countermeasures aimed at preventing immune deficiency during space missions. The capacity of the instrument to assess cellular fluorescence and to quantify the presence of soluble molecules in biological samples would support advanced molecular studies in space life sciences. Finally, such diagnostic system could also be used on Earth in remote areas or in mobile hospitals following natural disasters to fight against infectious diseases and other pathologies.

  19. Profiles of Dialogue for Relevance

    Directory of Open Access Journals (Sweden)

    Douglas Walton

    2016-12-01

    Full Text Available This paper uses argument diagrams, argumentation schemes, and some tools from formal argumentation systems developed in artificial intelligence to build a graph-theoretic model of relevance shown to be applicable (with some extensions as a practical method for helping a third party judge issues of relevance or irrelevance of an argument in real examples. Examples used to illustrate how the method works are drawn from disputes about relevance in natural language discourse, including a criminal trial and a parliamentary debate.

  20. TCM grammar systems: an approach to aid the interpretation of the molecular interactions in Chinese herbal medicine.

    Science.gov (United States)

    Yan, Jing; Wang, Yun; Luo, Si-Jun; Qiao, Yan-Jiang

    2011-09-01

    Interpreting the molecular interactions in Chinese herbal medicine will help to understand the molecular mechanisms of Traditional Chinese medicines (TCM) and predict the new pharmacological effects of TCM. Yet, we still lack a method which could integrate the concerned pieces of parsed knowledge about TCM. To solve the problem, a new method named TCM grammar systems was proposed in the present article. The possibility to study the interactions of TCM at the molecular level using TCM grammar systems was explored using Herba Ephedrae Decoction (HED) as an example. A platform was established based on the formalism of TCM grammar systems. The related molecular network of Herba Ephedrae Decoction (HED) can be extracted automatically. The molecular network indicates that Beta2 adrenergic receptor, Glucocorticoid receptor and Interleukin12 are the relatively important targets for the anti-anaphylaxis asthma function of HED. Moreover, the anti-anaphylaxis asthma function of HED is also related with suppressing inflammation process. The results show the feasibility using TCM grammar systems to interpret the molecular mechanism of TCM. Although the results obtained depend on the database absolutely, recombination of existing knowledge in this method provides new insight for interpreting the molecular mechanism of TCM. TCM grammar systems could aid the interpretation of the molecular interactions in TCM to some extent. Moreover, it might be useful to predict the new pharmacological effects of TCM. The method is an in silico technology. In association with the experimental techniques, this method will play an important role in the understanding of the molecular mechanisms of TCM. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  1. Workable male sterility systems for hybrid rice: Genetics, biochemistry, molecular biology, and utilization.

    Science.gov (United States)

    Huang, Jian-Zhong; E, Zhi-Guo; Zhang, Hua-Li; Shu, Qing-Yao

    2014-12-01

    The exploitation of male sterility systems has enabled the commercialization of heterosis in rice, with greatly increased yield and total production of this major staple food crop. Hybrid rice, which was adopted in the 1970s, now covers nearly 13.6 million hectares each year in China alone. Various types of cytoplasmic male sterility (CMS) and environment-conditioned genic male sterility (EGMS) systems have been applied in hybrid rice production. In this paper, recent advances in genetics, biochemistry, and molecular biology are reviewed with an emphasis on major male sterility systems in rice: five CMS systems, i.e., BT-, HL-, WA-, LD- and CW- CMS, and two EGMS systems, i.e., photoperiod- and temperature-sensitive genic male sterility (P/TGMS). The interaction of chimeric mitochondrial genes with nuclear genes causes CMS, which may be restored by restorer of fertility (Rf) genes. The PGMS, on the other hand, is conditioned by a non-coding RNA gene. A survey of the various CMS and EGMS lines used in hybrid rice production over the past three decades shows that the two-line system utilizing EGMS lines is playing a steadily larger role and TGMS lines predominate the current two-line system for hybrid rice production. The findings and experience gained during development and application of, and research on male sterility in rice not only advanced our understanding but also shed light on applications to other crops.

  2. Fragment-orbital tunneling currents and electronic couplings for analysis of molecular charge-transfer systems.

    Science.gov (United States)

    Hwang, Sang-Yeon; Kim, Jaewook; Kim, Woo Youn

    2018-04-04

    In theoretical charge-transfer research, calculation of the electronic coupling element is crucial for examining the degree of the electronic donor-acceptor interaction. The tunneling current (TC), representing the magnitudes and directions of electron flow, provides a way of evaluating electronic couplings, along with the ability of visualizing how electrons flow in systems. Here, we applied the TC theory to π-conjugated organic dimer systems, in the form of our fragment-orbital tunneling current (FOTC) method, which uses the frontier molecular-orbitals of system fragments as diabatic states. For a comprehensive test of FOTC, we assessed how reasonable the computed electronic couplings and the corresponding TC densities are for the hole- and electron-transfer databases HAB11 and HAB7. FOTC gave 12.5% mean relative unsigned error with regard to the high-level ab initio reference. The shown performance is comparable with that of fragment-orbital density functional theory, which gave the same error by 20.6% or 13.9% depending on the formulation. In the test of a set of nucleobase π stacks, we showed that the original TC expression is also applicable to nondegenerate cases under the condition that the overlap between the charge distributions of diabatic states is small enough to offset the energy difference. Lastly, we carried out visual analysis on the FOTC densities of thiophene dimers with different intermolecular alignments. The result depicts an intimate topological connection between the system geometry and electron flow. Our work provides quantitative and qualitative grounds for FOTC, showing it to be a versatile tool in characterization of molecular charge-transfer systems.

  3. Radiopharmaceuticals: nanoparticles like multi-functional systems for the obtaining in vivo of molecular images; Radiofarmacos: nanoparticulas como sistemas multifuncionales para la obtencion in vivo de imagenes moleculares

    Energy Technology Data Exchange (ETDEWEB)

    Ferro F, G.; Ramirez de la Cruz, F. M.; Ocampo G, B. E.; Morales A, E.; Santos C, C. L.; Mendoza S, A. N., E-mail: guillermina.ferro@inin.gob.m [ININ, Departamento de Materiales Radiactivos, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico)

    2010-07-01

    The techniques of obtaining direct or indirect molecular images detect and register the space-temporary distribution of molecular or cellular processes for biochemical, biological, diagnostic and therapeutic applications. The advanced techniques of image like the nuclear magnetic resonance, the single photon emission computed tomography, the positron emission tomography and the images of optic fluorescence have been used successfully to detect these processes. On the other hand, the utility of the nanoparticles for any application is dependent of the physicochemical properties that present, being possible to modify their surface when making them react with different biomolecules what allows the formation of conjugates with specific molecular recognition. The joint of various protein molecules, peptides or oligonucleotides to the surface of a nanoparticle produce a multi-functional system able to increase the multivalent joints from the nanoparticles-biomolecules to their receivers for the obtaining of molecular images in vivo. The peptides stimulate, regulate or inhibit numerous functions of the life, acting mainly as information transmitters and activity coordinators of several tissues in the organism. The receivers of regulator peptides are over represented in numerous types of cancer cells and they are protein structures. These receivers have been used as white molecular of marked peptides, to locate primary malignant tumors and their metastasis, using the diagnostic techniques of molecular image mentioned above, which consist basically on the radio peptides use and conjugated peptides to fluoro chromes, to metallic nanoparticles and nano crystals. A summary of the work is presented carried out by the personnel of the Radio-active Materials and Chemistry Departments of the Instituto Nacional de Investigaciones Nucleares in this field. (Author)

  4. Molecular interactions in a surfactant-water-polyacrylamide system, according to densimetry, viscometry, conductometry, and spectroscopy data

    Science.gov (United States)

    Harutyunyan, R. S.

    2013-08-01

    Molecular interactions in a surfactant-polyacrylamide-water system are investigated. It is established that the interactions affect such physicochemical parameters of the system as viscosity, density, surface tension, conductivity, and critical micelle concentration. It is shown that in a polyacrylamide-water system, raising the polyacrylamide concentration to 0.02% causes conformational changes in its macromolecule.

  5. Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering; Caracterisation de la liaison hydrogene dans des systemes moleculaires d'interet biologique par diffusion de neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Cavillon, F

    2004-10-15

    This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N{sup 14}/N{sup 15}. The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules.

  6. Molecular Epidemiologic Typing Systems of Bacterial Pathogens: Current Issues and Perpectives

    Directory of Open Access Journals (Sweden)

    Struelens Marc J

    1998-01-01

    Full Text Available The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s ? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection. Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.

  7. Molecular – genetic variance of RH blood group system within human population of Bosnia and Herzegovina

    Directory of Open Access Journals (Sweden)

    Lejla Lasić

    2013-02-01

    Full Text Available There are two major theories for inheritance of Rh blood group system: Fisher - Race theory and Wiener theory. Aim of this study was identifying frequency of RHDCE alleles in Bosnian - Herzegovinian population and introduction of this method in screening for Rh phenotype in B&H since this type of analysis was not used for blood typing in B&H before. Rh blood group was typed by Polymerase Chain Reaction, using the protocols and primers previously established by other authors, then carrying out electrophoresis in 2-3% agarose gel. Percentage of Rh positive individuals in our sample is 84.48%, while the percentage of Rh negative individuals is 15.52%. Inter-rater agreement statistic showed perfect agreement (K=1 between the results of Rh blood system detection based on serological and molecular-genetics methods. In conclusion, molecular - genetic methods are suitable for prenatal genotyping and specific cases while standard serological method is suitable for high-throughput of samples.

  8. Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

    Science.gov (United States)

    van Heeswijk, Wally C.; Westerhoff, Hans V.

    2013-01-01

    SUMMARY We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now. PMID:24296575

  9. Thermal characterization of static and dynamical properties of the confined molecular systems interacting through dispersion force.

    Science.gov (United States)

    Ramos, Sergio Luis L M; Ogino, Michihiko; Oguni, Masaharu

    2015-01-28

    We investigated the thermal properties of liquid methylcyclohexane and racemic sec-butylcyclohexane, as representatives of a molecular system with only dispersion-force intermolecular interactions, confined in the pores (thickness/diameter d = 12, 6, 1.1 nm) of silica gels by adiabatic calorimetry. The results imply a heterogeneous picture for molecular aggregate under confinement consisting of an interfacial region and an inner pore one. In the vicinity of a glass-transition temperature T(g,bulk) of bulk liquid, two distinguishable relaxation phenomena were observed for the confined systems and their origins were attributed to the devitrification, namely glass transition, processes of (1) a layer of interfacial molecules adjacent to the pore walls and (2) the molecules located in the middle of the pore. A third glass-transition phenomenon was observed at lower temperatures and ascribed to a secondary relaxation process. The glass transition of the interfacial-layer molecules was found to proceed at temperatures rather above T(g,bulk), whereas that of the molecules located in the inner pore region occurred at temperatures below T(g,bulk). We discuss the reason why the molecules located in different places in the pores reveal the respectively different dynamical properties.

  10. Choice reaching with a LEGO arm robot (CoRLEGO): The motor system guides visual attention to movement-relevant information.

    Science.gov (United States)

    Strauss, Soeren; Woodgate, Philip J W; Sami, Saber A; Heinke, Dietmar

    2015-12-01

    We present an extension of a neurobiologically inspired robotics model, termed CoRLEGO (Choice reaching with a LEGO arm robot). CoRLEGO models experimental evidence from choice reaching tasks (CRT). In a CRT participants are asked to rapidly reach and touch an item presented on the screen. These experiments show that non-target items can divert the reaching movement away from the ideal trajectory to the target item. This is seen as evidence attentional selection of reaching targets can leak into the motor system. Using competitive target selection and topological representations of motor parameters (dynamic neural fields) CoRLEGO is able to mimic this leakage effect. Furthermore if the reaching target is determined by its colour oddity (i.e. a green square among red squares or vice versa), the reaching trajectories become straighter with repetitions of the target colour (colour streaks). This colour priming effect can also be modelled with CoRLEGO. The paper also presents an extension of CoRLEGO. This extension mimics findings that transcranial direct current stimulation (tDCS) over the motor cortex modulates the colour priming effect (Woodgate et al., 2015). The results with the new CoRLEGO suggest that feedback connections from the motor system to the brain's attentional system (parietal cortex) guide visual attention to extract movement-relevant information (i.e. colour) from visual stimuli. This paper adds to growing evidence that there is a close interaction between the motor system and the attention system. This evidence contradicts the traditional conceptualization of the motor system as the endpoint of a serial chain of processing stages. At the end of the paper we discuss CoRLEGO's predictions and also lessons for neurobiologically inspired robotics emerging from this work. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  11. Fluorescence-Raman Dual Modal Endoscopic System for Multiplexed Molecular Diagnostics

    Science.gov (United States)

    Jeong, Sinyoung; Kim, Yong-Il; Kang, Homan; Kim, Gunsung; Cha, Myeong Geun; Chang, Hyejin; Jung, Kyung Oh; Kim, Young-Hwa; Jun, Bong-Hyun; Hwang, Do Won; Lee, Yun-Sang; Youn, Hyewon; Lee, Yoon-Sik; Kang, Keon Wook; Lee, Dong Soo; Jeong, Dae Hong

    2015-03-01

    Optical endoscopic imaging, which was recently equipped with bioluminescence, fluorescence, and Raman scattering, allows minimally invasive real-time detection of pathologies on the surface of hollow organs. To characterize pathologic lesions in a multiplexed way, we developed a dual modal fluorescence-Raman endomicroscopic system (FRES), which used fluorescence and surface-enhanced Raman scattering nanoprobes (F-SERS dots). Real-time, in vivo, and multiple target detection of a specific cancer was successful, based on the fast imaging capability of fluorescence signals and the multiplex capability of simultaneously detected SERS signals using an optical fiber bundle for intraoperative endoscopic system. Human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) on the breast cancer xenografts in a mouse orthotopic model were successfully detected in a multiplexed way, illustrating the potential of FRES as a molecular diagnostic instrument that enables real-time tumor characterization of receptors during routine endoscopic procedures.

  12. Path integral molecular dynamics for exact quantum statistics of multi-electronic-state systems.

    Science.gov (United States)

    Liu, Xinzijian; Liu, Jian

    2018-03-14

    An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD), Liu et al. [J. Chem. Phys. 145, 024103 (2016)] and Zhang et al. [J. Chem. Phys. 147, 034109 (2017)], for quantum statistical mechanics when a single potential energy surface is involved. We first define an effective potential function that is numerically favorable for MES-PIMD and then derive corresponding estimators in MES-PIMD for evaluating various physical properties. Its application to several representative one-dimensional and multi-dimensional models demonstrates that MES-PIMD in principle offers a practical tool in either of the diabatic and adiabatic representations for studying exact quantum statistics of complex/large MES systems when the Born-Oppenheimer approximation, Condon approximation, and harmonic bath approximation are broken.

  13. Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

    Directory of Open Access Journals (Sweden)

    Peter Spijker

    2010-06-01

    Full Text Available Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.

  14. Integrating open-source software applications to build molecular dynamics systems.

    Science.gov (United States)

    Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

    2014-04-05

    Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

  15. Environmental Catastrophes in the Earth's History Due to Solar Systems Encounters with Giant Molecular Clouds

    Science.gov (United States)

    Pavlov, Alexander A.

    2011-01-01

    In its motion through the Milky Way galaxy, the solar system encounters an average density (>=330 H atoms/cubic cm) giant molecular cloud (GMC) approximately every 108 years, a dense (approx 2 x 103 H atoms/cubic cm) GMC every approx 109 years and will inevitably encounter them in the future. However, there have been no studies linking such events with severe (snowball) glaciations in Earth history. Here we show that dramatic climate change can be caused by interstellar dust accumulating in Earth's atmosphere during the solar system's immersion into a dense (approx ,2 x 103 H atoms/cubic cm) GMC. The stratospheric dust layer from such interstellar particles could provide enough radiative forcing to trigger the runaway ice-albedo feedback that results in global snowball glaciations. We also demonstrate that more frequent collisions with less dense GMCs could cause moderate ice ages.

  16. A quantum-mechanics molecular-mechanics scheme for extended systems.

    Science.gov (United States)

    Hunt, Diego; Sanchez, Veronica M; Scherlis, Damián A

    2016-08-24

    We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

  17. A quantum-mechanics molecular-mechanics scheme for extended systems

    International Nuclear Information System (INIS)

    Hunt, Diego; Scherlis, Damián A; Sanchez, Veronica M

    2016-01-01

    We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car–Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO 2 anatase (1 0 1) solid–liquid interface. This investigation suggests that the inclusion of a second monolayer of H 2 O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces. (paper)

  18. Nerve Regeneration in the Peripheral Nervous System versus the Central Nervous System and the Relevance to Speech and Hearing after Nerve Injuries

    Science.gov (United States)

    Gordon, Tessa; Gordon, Karen

    2010-01-01

    Schwann cells normally form myelin sheaths around axons in the peripheral nervous system (PNS) and support nerve regeneration after nerve injury. In contrast, nerve regeneration in the central nervous system (CNS) is not supported by the myelinating cells known as oligodendrocytes. We have found that: 1) low frequency electrical stimulation can be…

  19. A Silicon SPECT System for Molecular Imaging of the Mouse Brain.

    Science.gov (United States)

    Shokouhi, Sepideh; Fritz, Mark A; McDonald, Benjamin S; Durko, Heather L; Furenlid, Lars R; Wilson, Donald W; Peterson, Todd E

    2007-01-01

    We previously demonstrated the feasibility of using silicon double-sided strip detectors (DSSDs) for SPECT imaging of the activity distribution of iodine-125 using a 300-micrometer thick detector. Based on this experience, we now have developed fully customized silicon DSSDs and associated readout electronics with the intent of developing a multi-pinhole SPECT system. Each DSSD has a 60.4 mm × 60.4 mm active area and is 1 mm thick. The strip pitch is 59 micrometers, and the readout of the 1024 strips on each side gives rise to a detector with over one million pixels. Combining four high-resolution DSSDs into a SPECT system offers an unprecedented space-bandwidth product for the imaging of single-photon emitters. The system consists of two camera heads with two silicon detectors stacked one behind the other in each head. The collimator has a focused pinhole system with cylindrical-shaped pinholes that are laser-drilled in a 250 μm tungsten plate. The unique ability to collect projection data at two magnifications simultaneously allows for multiplexed data at high resolution to be combined with lower magnification data with little or no multiplexing. With the current multi-pinhole collimator design, our SPECT system will be capable of offering high spatial resolution, sensitivity and angular sampling for small field-of-view applications, such as molecular imaging of the mouse brain.

  20. Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

    Science.gov (United States)

    Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

    2015-12-03

    Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches.