Structure and dynamics of aqueous 2-propanol: A THz-TDS, NMR and neutron diffraction study

Aqueous liquid mixtures, in particular, those involving amphiphilic species, play an important role in many physical, chemical and biological processes. Of particular interest are alcohol/water mixtures; however, the structural dynamics of such systems are still not fully understood. Herein, a combination of terahertz time-domain spectroscopy (THz-TDS) and NMR relaxation time analysis has been applied to investigate 2-propanol/water mixtures across the entire composition range; while neutron diffraction studies have been carried out at two specific concentrations. Excellent agreement is seen between the techniques with a maximum in both the relative absorption coefficient and the activation energy to molecular motion occurring at ∼90 mol% H₂O. Furthermore, this is the same value at which well-established excess thermodynamic functions exhibit a maximum/minimum. Additionally, both neutron diffraction and THz-TDS have been used to provide estimates of the size of the hydration shell around 2-propanol in solution. Both methods determine that between 4 and 5 H₂O molecules per 2-propanol are found in the 2-propanol/water clusters at 90 mol% H₂O. Based on the acquired data, a description of the structure of 2-propanol/water across the composition range is presented.

Molecular structure and functional analysis of runx3 in zebrafish

Tese de doutoramento, Ciências Biomédicas, Universidade do Algarve, Departamento de Ciências Biomédicas e Medicina, 2014

Impact of a cis-associated gene expression SNP on chromosome 20q11.22 on bipolar disorder susceptibility, hippocampal structure and cognitive performance.

BackgroundBipolar disorder is a highly heritable polygenic disorder. Recent enrichment analyses suggest that there may be true risk variants for bipolar disorder in the expression quantitative trait loci (eQTL) in the brain.AimsWe sought to assess the impact of eQTL variants on bipolar disorder risk by combining data from both bipolar disorder genome-wide association studies (GWAS) and brain eQTL.MethodTo detect single nucleotide polymorphisms (SNPs) that influence expression levels of genes associated with bipolar disorder, we jointly analysed data from a bipolar disorder GWAS (7481 cases and 9250 controls) and a genome-wide brain (cortical) eQTL (193 healthy controls) using a Bayesian statistical method, with independent follow-up replications. The identified risk SNP was then further tested for association with hippocampal volume (n = 5775) and cognitive performance (n = 342) among healthy individuals.ResultsIntegrative analysis revealed a significant association between a brain eQTL rs6088662 on chromosome 20q11.22 and bipolar disorder (log Bayes factor = 5.48; bipolar disorder P = 5.85×10(-5)). Follow-up studies across multiple independent samples confirmed the association of the risk SNP (rs6088662) with gene expression and bipolar disorder susceptibility (P = 3.54×10(-8)). Further exploratory analysis revealed that rs6088662 is also associated with hippocampal volume and cognitive performance in healthy individuals.ConclusionsOur findings suggest that 20q11.22 is likely a risk region for bipolar disorder; they also highlight the informative value of integrating functional annotation of genetic variants for gene expression in advancing our understanding of the biological basis underlying complex disorders, such as bipolar disorder.

Some Implications of the Zero Lower Bound on Interest Rates for the Term Structure and Monetary Policy

In an economy where cash can be stored costlessly (in nominal terms), the nominal interest rate is bounded below by zero. This paper derives the implications of this nonnegativity constraint for the term structure and shows that it induces a nonlinear and convex relation between short- and long-term interest rates. As a result, the long-term rate responds asymmetrically to changes in the short-term rate, and by less than predicted by a benchmark linear model. In particular, a decrease in the short-term rate leads to a decrease in the long-term rate that is smaller in magnitude than the increase in the long-term rate associated with an increase in the short-term rate of the same size. Up to the extent that monetary policy acts by affecting long-term rates through the term structure, its power is considerably reduced at low interest rates. The empirical predictions of the model are examined using data from Japan.

Investigation of the structure and dynamics of the centromeric epigenetic mark

Le centromère est le site chromosomal où le kinetochore se forme, afin d’assurer une ségrégation fidèles des chromosomes et ainsi maintenir la ploïdie appropriée lors de la mitose. L’identité du centromere est héritée par un mécanisme épigénétique impliquant une variante de l’histone H3 nommée centromere protein-A (CENP-A), qui remplace l’histone H3 au niveau de la chromatine du centromère. Des erreurs de propagation de la chromatine du centromère peuvent mener à des problèmes de ségrégation des chromosomes, pouvant entraîner l’aneuploïdie, un phénomène fréquemment observé dans le cancer. De plus, une expression non-régulée de CENP-A a aussi été rapportée dans différentes tumeurs humaines. Ainsi, plusieurs études ont cherchées à élucider la structure et le rôle de la chromatine contenant CENP-A dans des cellules en prolifération. Toutefois, la nature moléculaire de CENP-A en tant que marqueur épigénétique ainsi que ces dynamiques à l'extérieur du cycle cellulaire demeurent des sujets débat. Dans cette thèse, une nouvelle méthode de comptage de molécules uniques à l'aide de la microscopie à réflexion totale interne de la fluorescence (TIRF) sera décrite, puis exploitée afin d'élucider la composition moléculaire des nucléosomes contenant CENP-A, extraits de cellules en prolifération. Nous démontrons que les nucléosomes contenant CENP-A marquent les centromères humains de façon épigénétique à travers le cycle cellulaire. De plus, nos données démontrent que la forme prénucléosomale de CENP-A, en association avec la protéine chaperon HJURP existe sous forme de monomère et de dimère, ce qui reflète une étape intermédiaire de l'assemblage de nucléosomes contenant CENP-A. Ensuite, des analyses quantitatives de centromères lors de différenciation myogénique, et dans différents tissus adultes révèlent des changements globaux qui maintiennent la marque épigénétique dans une forme inactive suite à la différentiation terminale. Ces changements incluent une réduction du nombre de points focaux de CENP-A, un réarrangement des points dans le noyau, ainsi qu'une réduction importante de la quantité de CENP-A. De plus, nous démontrons que lorsqu'une dédifférenciation cellulaire est induite puis le cycle cellulaire ré-entamé, le phénotype "différencié" décrit ci-haut est récupéré, et les centromères reprennent leur phénotype "prolifératif". En somme, cet oeuvre décrit la composition structurale sous-jacente à l'identité épigénétique des centromères de cellules humaines lors du cycle cellulaire, et met en lumière le rôle de CENP-A à l'extérieur du cycle cellulaire.

Diversification In Employment Structure And Status Of Rural Women Workers In Ernakulam District

The basic objective of the present study has been to observe the process and pattern of employment diversification among the rural women workers in Ernakulam district. The evidences are that the women workers in the rural areas of the state are being increasingly diversified into the tertiary sector. The clear cut evidence for the fact that in Kerala non-agricultural employment of rural women is increasing with more and more of them getting diversified into the tertiary sector. The women get more self esteem and recognition in terms of the work being done by them. In the urban areas of the state as a poverty eradicating measure the Kerala government has already introduced a new scheme under the banner of Kudumbasree. Another fact noticed in the study that the sectoral shift of women workers has posed a grave problem to the agricultural sector. The reluctance of workers to do manual jobs on land and the prevalence of high wages among the agricultural labours has left many a cultivable area fallow or has induced farmers to shift to less labour –intensive crops. The situation is expected to worsen in future as even the high wages fail to attract the young generation to this sector. To conclude the study has fulfilled all its objectives, viz; highlighting the rural employment structure in Kerala, examining the process, pattern, determinants and consequences of diversification among rural women workers in the sample villages. Being the first of its kind at the micro level in the state it contributes to the available literature in the area enriching the database that is crucially lacking for devising projects at the village and block-level. There exists ample scope for future research of similar nature in an urban background where the secondary data-sources are hinding towards a reversal of trends from non-agriculture to agriculture.

Geophysical Constraints on Structure and Tectonics of the Eastern Arabian Sea and the Adjoining West Coast of India with Special Reference to the Kerala Basin

The main objective of the present study is to model the gravity fields in terms of lithospheric structure below the western continental margin of India (WCMI) identify zones of crustal mass anomalies and attempt to infer the location of Ocean Continent transition in the Arabian Sea. In this study, the area starting from the western shield margin to the region covering the deep oceanic parts of the Arabian Sea which is bounded by Carlsberg and Cerg and Central Indian ridges in the south, eastern part of the Indus Cone in the west and falling between 630E and 800E longitudes, and 50N - 240N latitudes has been considered. The vast amount of seismic reflection and refraction data in the form of crustal velocities, basement configuration and crustal thicknesses available for the west coast as well as the eastern Arabian Sea has been utilized for this purpose

Implications of Hydrobiology and Nutrient dynamics on trophic structure and interactions in Cochin backwaters

In the present thesis entitled” Implications of Hydrobiology and Nutrient dynamics on Trophic structure and Interactions in Cochin backwaters”, an attempt has been made to assess the influence of general hydrography, nutrients and other environmental factors on the abundance, distribution and trophic interactions in Cochin backwater system. The study was based on five seasonal sampling campaigns carried out at 15 stations spread along the Cochin backwater system. The thesis is presented in the following 5 chapters. Salient features of each chapter are summarized below: Chapter 1- General Introduction: Provides information on the topic of study, environmental factors, back ground information, the significance, review of literature, aim and scope of the present study and its objectives.Chapter 2- Materials and Methods: This chapter deals with the description of the study area and the methodology adopted for sample collection and analysis. Chapter 3- General Hydrograhy and Sediment Characteristics: Describes the environmental setting of the study area explaining seasonal variation in physicochemical parameters of water column and sediment characteristics. Data on hydrographical parameters, nitrogen fractionation, phosphorus fractionation and biochemical composition of the sediment samples were assessed to evaluate the trophic status. Chapter 4- Nutrient Dynamics on Trophic Structure and Interactions: Describes primary, secondary and tertiary production in Cochin backwater system. Primary production related to cell abundance, diversity of phytoplankton that varies seasonally, concentration of various pigments and primary productivitySecondary production refers to the seasonal abundance of zooplankton especially copepod abundance and tertiary production deals with seasonal fish landings, gut content analysis and proximate composition of dominant fish species. The spatiotemporal variation, interrelationships and trophic interactions were evaluated by statistical methods. Chapter 5- Summary: The results and findings of the study are summarized in the fifth chapter of the thesis.

Electronic structure and properties of Cu2O

The structural and electronic properties of Cu2O have been investigated using the periodic Hartree-Fock method and a posteriori density-functional corrections. The lattice parameter, bulk modulus, and elastic constants have been calculated. The electronic structure of and bonding in Cu2O are analyzed and compared with x-ray photoelectron spectroscopy spectra, showing a good agreement for the valence-band states. To check the quality of the calculated electron density, static structure factors and Compton profiles have been calculated, showing a good agreement with the available experimental data. The effective electron and hole masses have been evaluated for Cu2O at the center of the Brillouin zone. The calculated interaction energy between the two interpenetrated frameworks in the cuprite structure is estimated to be around -6.0 kcal/mol per Cu2O formula. The bonding between the two independent frameworks has been analyzed using a bimolecular model and the results indicate an important role of d10-d10 type interactions between copper atoms.

Analysis of the electronic structure, hyperfine structure, and volume isotope shifts in the low lying states of BA I and BA II

Relativistic multi-configuration Dirac Fock (MCDF) wavefunctions coupled to good angular momentum J have been calculated for low lying states of Ba I and Ba II. These wavefunctions are compared with semiempirical ones derived from experimental atomic energy levels. It is found that significantly better agreement is obtained when close configurations are included in the MCDF wavefunctions. Calculations of the electronic part of the field isotope shift lead to very good agreement with electronic factors derived from experimental data. Furthermore, the slopes of the lines in a King plot analysis of many of the optical lines are predicted accurately by these calculations. However, the MCDF wavefunctions seem not to be of sufficient accuracy to give agreement with the experimental magnetic dipole and electric quadrupole hyperfine structure constants.

Electronic structure and properties of the group 4, 5 and 6 highest chlorides including elements 104, 105, and 106

Results of the Dirac-Slater discrete variational calculations for the group 4, 5, and 6 highest chlorides including elements 104, 105, and 106 have shown that the groups are not identical with respect to trends in the electronic structure and bonding. The charge density distribution data show that notwithstanding the basic increase in covalency within the groups this increase diminishes in going from group 4 to group 6. As a result, E106Cl_6 will be less stable toward thermal decomposition than WCl_6, which is confirmed by an estimated low E106-Cl bond energy. \delta H_form equal to -90.3 ± 6 kcal/rnol is obtained for E106Cl_6 in the gas phase, which is indicative of a very low stability of this compound. The stability of the maximum oxidation state is shown to decrease in the direction E104(+4) > E105(+5) > E106(+6).

3D Simultaneous Inversion for Seismic Structure and Local Hypocenters in Germany under Consideration of Seismic Anisotropy in the Upper Mantel

The main task of this work has been to investigate the effects of anisotropy onto the propagation of seismic waves along the Upper Mantle below Germany and adjacent areas. Refraction- and reflexion seismic experiments proved the existence of Upper Mantle anisotropy and its influence onto the propagation of Pn-waves. By the 3D tomographic investigations that have been done here for the crust and the upper mantle, considering the influence of anisotropy, a gap for the investigations in Europe has been closed. These investigations have been done with the SSH-Inversionprogram of Prof. Dr. M. Koch, which is able to compute simultaneously the seismic structure and hypocenters. For the investigation, a dataset has been available with recordings between the years 1975 to 2003 with a total of 60249 P- and 54212 S-phase records of 10028 seismic events. At the beginning, a precise analysis of the residuals (RES, the difference between calculated and observed arrivaltime) has been done which confirmed the existence of anisotropy for Pn-phases. The recognized sinusoidal distribution has been compensated by an extension of the SSH-program by an ellipse with a slow and rectangular fast axis with azimuth to correct the Pn-velocities. The azimuth of the fast axis has been fixed by the application of the simultaneous inversion at 25° - 27° with a variation of the velocities at +- 2.5 about an average value at 8 km/s. This new value differs from the old one at 35°, recognized in the initial residual analysis. This depends on the new computed hypocenters together with the structure. The application of the elliptical correction has resulted in a better fit of the vertical layered 1D-Model, compared to the results of preceding seismological experiments and 1D and 2D investigations. The optimal result of the 1D-inversion has been used as initial starting model for the 3D-inversions to compute the three dimensional picture of the seismic structure of the Crust and Upper Mantle. The simultaneous inversion has showed an optimization of the relocalization of the hypocenters and the reconstruction of the seismic structure in comparison to the geology and tectonic, as described by other investigations. The investigations for the seismic structure and the relocalization have been confirmed by several different tests. First, synthetic traveltime data are computed with an anisotropic variation and inverted with and without anisotropic correction. Further, tests with randomly disturbed hypocenters and traveltime data have been proceeded to verify the influence of the initial values onto the relocalization accuracy and onto the seismic structure and to test for a further improvement by the application of the anisotropic correction. Finally, the results of the work have been applied onto the Waldkirch earthquake in 2004 to compare the isotropic and the anisotropic relocalization with the initial optimal one to verify whether there is some improvement.

Adaptive Real-time Anomaly-based Intrusion Detection using Data Mining and Machine Learning Techniques

Die zunehmende Vernetzung der Informations- und Kommunikationssysteme führt zu einer weiteren Erhöhung der Komplexität und damit auch zu einer weiteren Zunahme von Sicherheitslücken. Klassische Schutzmechanismen wie Firewall-Systeme und Anti-Malware-Lösungen bieten schon lange keinen Schutz mehr vor Eindringversuchen in IT-Infrastrukturen. Als ein sehr wirkungsvolles Instrument zum Schutz gegenüber Cyber-Attacken haben sich hierbei die Intrusion Detection Systeme (IDS) etabliert. Solche Systeme sammeln und analysieren Informationen von Netzwerkkomponenten und Rechnern, um ungewöhnliches Verhalten und Sicherheitsverletzungen automatisiert festzustellen. Während signatur-basierte Ansätze nur bereits bekannte Angriffsmuster detektieren können, sind anomalie-basierte IDS auch in der Lage, neue bisher unbekannte Angriffe (Zero-Day-Attacks) frühzeitig zu erkennen. Das Kernproblem von Intrusion Detection Systeme besteht jedoch in der optimalen Verarbeitung der gewaltigen Netzdaten und der Entwicklung eines in Echtzeit arbeitenden adaptiven Erkennungsmodells. Um diese Herausforderungen lösen zu können, stellt diese Dissertation ein Framework bereit, das aus zwei Hauptteilen besteht. Der erste Teil, OptiFilter genannt, verwendet ein dynamisches "Queuing Concept", um die zahlreich anfallenden Netzdaten weiter zu verarbeiten, baut fortlaufend Netzverbindungen auf, und exportiert strukturierte Input-Daten für das IDS. Den zweiten Teil stellt ein adaptiver Klassifikator dar, der ein Klassifikator-Modell basierend auf "Enhanced Growing Hierarchical Self Organizing Map" (EGHSOM), ein Modell für Netzwerk Normalzustand (NNB) und ein "Update Model" umfasst. In dem OptiFilter werden Tcpdump und SNMP traps benutzt, um die Netzwerkpakete und Hostereignisse fortlaufend zu aggregieren. Diese aggregierten Netzwerkpackete und Hostereignisse werden weiter analysiert und in Verbindungsvektoren umgewandelt. Zur Verbesserung der Erkennungsrate des adaptiven Klassifikators wird das künstliche neuronale Netz GHSOM intensiv untersucht und wesentlich weiterentwickelt. In dieser Dissertation werden unterschiedliche Ansätze vorgeschlagen und diskutiert. So wird eine classification-confidence margin threshold definiert, um die unbekannten bösartigen Verbindungen aufzudecken, die Stabilität der Wachstumstopologie durch neuartige Ansätze für die Initialisierung der Gewichtvektoren und durch die Stärkung der Winner Neuronen erhöht, und ein selbst-adaptives Verfahren eingeführt, um das Modell ständig aktualisieren zu können. Darüber hinaus besteht die Hauptaufgabe des NNB-Modells in der weiteren Untersuchung der erkannten unbekannten Verbindungen von der EGHSOM und der Überprüfung, ob sie normal sind. Jedoch, ändern sich die Netzverkehrsdaten wegen des Concept drif Phänomens ständig, was in Echtzeit zur Erzeugung nicht stationärer Netzdaten führt. Dieses Phänomen wird von dem Update-Modell besser kontrolliert. Das EGHSOM-Modell kann die neuen Anomalien effektiv erkennen und das NNB-Model passt die Änderungen in Netzdaten optimal an. Bei den experimentellen Untersuchungen hat das Framework erfolgversprechende Ergebnisse gezeigt. Im ersten Experiment wurde das Framework in Offline-Betriebsmodus evaluiert. Der OptiFilter wurde mit offline-, synthetischen- und realistischen Daten ausgewertet. Der adaptive Klassifikator wurde mit dem 10-Fold Cross Validation Verfahren evaluiert, um dessen Genauigkeit abzuschätzen. Im zweiten Experiment wurde das Framework auf einer 1 bis 10 GB Netzwerkstrecke installiert und im Online-Betriebsmodus in Echtzeit ausgewertet. Der OptiFilter hat erfolgreich die gewaltige Menge von Netzdaten in die strukturierten Verbindungsvektoren umgewandelt und der adaptive Klassifikator hat sie präzise klassifiziert. Die Vergleichsstudie zwischen dem entwickelten Framework und anderen bekannten IDS-Ansätzen zeigt, dass der vorgeschlagene IDSFramework alle anderen Ansätze übertrifft. Dies lässt sich auf folgende Kernpunkte zurückführen: Bearbeitung der gesammelten Netzdaten, Erreichung der besten Performanz (wie die Gesamtgenauigkeit), Detektieren unbekannter Verbindungen und Entwicklung des in Echtzeit arbeitenden Erkennungsmodells von Eindringversuchen.

Geostatistics for constrained variables: positive data, compositions and probabilities. Applications to environmental hazard monitoring

Aquesta tesi estudia com estimar la distribució de les variables regionalitzades l'espai mostral i l'escala de les quals admeten una estructura d'espai Euclidià. Apliquem el principi del treball en coordenades: triem una base ortonormal, fem estadística sobre les coordenades de les dades, i apliquem els output a la base per tal de recuperar un resultat en el mateix espai original. Aplicant-ho a les variables regionalitzades, obtenim una aproximació única consistent, que generalitza les conegudes propietats de les tècniques de kriging a diversos espais mostrals: dades reals, positives o composicionals (vectors de components positives amb suma constant) són tractades com casos particulars. D'aquesta manera, es generalitza la geostadística lineal, i s'ofereix solucions a coneguts problemes de la no-lineal, tot adaptant la mesura i els criteris de representativitat (i.e., mitjanes) a les dades tractades. L'estimador per a dades positives coincideix amb una mitjana geomètrica ponderada, equivalent a l'estimació de la mediana, sense cap dels problemes del clàssic kriging lognormal. El cas composicional ofereix solucions equivalents, però a més permet estimar vectors de probabilitat multinomial. Amb una aproximació bayesiana preliminar, el kriging de composicions esdevé també una alternativa consistent al kriging indicador. Aquesta tècnica s'empra per estimar funcions de probabilitat de variables qualsevol, malgrat que sovint ofereix estimacions negatives, cosa que s'evita amb l'alternativa proposada. La utilitat d'aquest conjunt de tècniques es comprova estudiant la contaminació per amoníac a una estació de control automàtic de la qualitat de l'aigua de la conca de la Tordera, i es conclou que només fent servir les tècniques proposades hom pot detectar en quins instants l'amoni es transforma en amoníac en una concentració superior a la legalment permesa.

A singular vector perspective of 4DVAR: The spatial structure and evolution of baroclinic weather systems

The extent to which the four-dimensional variational data assimilation (4DVAR) is able to use information about the time evolution of the atmosphere to infer the vertical spatial structure of baroclinic weather systems is investigated. The singular value decomposition (SVD) of the 4DVAR observability matrix is introduced as a novel technique to examine the spatial structure of analysis increments. Specific results are illustrated using 4DVAR analyses and SVD within an idealized 2D Eady model setting. Three different aspects are investigated. The first aspect considers correcting errors that result in normal-mode growth or decay. The results show that 4DVAR performs well at correcting growing errors but not decaying errors. Although it is possible for 4DVAR to correct decaying errors, the assimilation of observations can be detrimental to a forecast because 4DVAR is likely to add growing errors instead of correcting decaying errors. The second aspect shows that the singular values of the observability matrix are a useful tool to identify the optimal spatial and temporal locations for the observations. The results show that the ability to extract the time-evolution information can be maximized by placing the observations far apart in time. The third aspect considers correcting errors that result in nonmodal rapid growth. 4DVAR is able to use the model dynamics to infer some of the vertical structure. However, the specification of the case-dependent background error variances plays a crucial role.