Shape and chemically anisotropic colloidal particles: A theoretical study of their structure, phase behavior, and slow dynamics

A detailed non-equilibrium state diagram of shape-anisotropic particle fluids is constructed. The effects of particle shape are explored using Naive Mode Coupling Theory (NMCT), and a single particle Non-linear Langevin Equation (NLE) theory. The dynamical behavior of non-ergodic fluids are discussed. We employ a rotationally frozen approach to NMCT in order to determine a transition to center of mass (translational) localization. Both ideal and kinetic glass transitions are found to be highly shape dependent, and uniformly increase with particle dimensionality. The glass transition volume fraction of quasi 1- and 2- dimensional particles fall monotonically with the number of sites (aspect ratio), while 3-dimensional particles display a non-monotonic dependence of glassy vitrification on the number of sites. Introducing interparticle attractions results in a far more complex state diagram. The ideal non-ergodic boundary shows a glass-fluid-gel re-entrance previously predicted for spherical particle fluids. The non-ergodic region of the state diagram presents qualitatively different dynamics in different regimes. They are qualified by the different behaviors of the NLE dynamic free energy. The caging dominated, repulsive glass regime is characterized by long localization lengths and barrier locations, dictated by repulsive hard core interactions, while the bonding dominated gel region has short localization lengths (commensurate with the attraction range), and barrier locations. There exists a small region of the state diagram which is qualified by both glassy and gel localization lengths in the dynamic free energy. A much larger (high volume fraction, and high attraction strength) region of phase space is characterized by short gel-like localization lengths, and long barrier locations. The region is called the attractive glass and represents a 2-step relaxation process whereby a particle first breaks attractive physical bonds, and then escapes its topological cage. The dynamic fragility of fluids are highly particle shape dependent. It increases with particle dimensionality and falls with aspect ratio for quasi 1- and 2- dimentional particles. An ultralocal limit analysis of the NLE theory predicts universalities in the behavior of relaxation times, and elastic moduli. The equlibrium phase diagram of chemically anisotropic Janus spheres and Janus rods are calculated employing a mean field Random Phase Approximation. The calculations for Janus rods are corroborated by the full liquid state Reference Interaction Site Model theory. The Janus particles consist of attractive and repulsive regions. Both rods and spheres display rich phase behavior. The phase diagrams of these systems display fluid, macrophase separated, attraction driven microphase separated, repulsion driven microphase separated and crystalline regimes. Macrophase separation is predicted in highly attractive low volume fraction systems. Attraction driven microphase separation is charaterized by long length scale divergences, where the ordering length scale determines the microphase ordered structures. The ordering length scale of repulsion driven microphase separation is determined by the repulsive range. At the high volume fractions, particles forgo the enthalpic considerations of attractions and repulsions to satisfy hard core constraints and maximize vibrational entropy. This results in site length scale ordering in rods, and the sphere length scale ordering in Janus spheres, i.e., crystallization. A change in the Janus balance of both rods and spheres results in quantitative changes in spinodal temperatures and the position of phase boundaries. However, a change in the block sequence of Janus rods causes qualitative changes in the type of microphase ordered state, and induces prominent features (such as the Lifshitz point) in the phase diagrams of these systems. A detailed study of the number of nearest neighbors in Janus rod systems reflect a deep connection between this local measure of structure, and the structure factor which represents the most global measure of order.

Elucidating the interactions between the adhesive and transcriptioanl functions of beta-catenin in normal and cancerous cells

Wnt signalling is involved in a wide range of physiological and pathological processes. The presence of an extracellular Wnt stimulus induces cytoplasmic stabilisation and nuclear translocation of beta-catenin, a protein that also plays an essential role in cadherin-mediated adhesion. Two main hypotheses have been proposed concerning the balance between beta-catenin's adhesive and transcriptional functions: either beta-catenin's fate is determined by competition between its binding partners, or Wnt induces folding of beta-catenin into a conformation allocated preferentially to transcription. The experimental data supporting each hypotheses remain inconclusive. In this paper we present a new mathematical model of the Wnt pathway that incorporates beta-catenin's dual function. We use this model to carry out a series of in silico experiments and compare the behaviour of systems governed by each hypothesis. Our analytical results and model simulations provide further insight into the current understanding of Wnt signalling and, in particular, reveal differences in the response of the two modes of interaction between adhesion and signalling in certain in silico settings. We also exploit our model to investigate the impact of the mutations most commonly observed in human colorectal cancer. Simulations show that the amount of functional APC required to maintain a normal phenotype increases with increasing strength of the Wnt signal, a result which illustrates that the environment can substantially influence both tumour initiation and phenotype.

Agonistic interactions elicit rapid changes in brain nonapeptide levels in zebrafish

The teleost fish nonapeptides, arginine vasotocin (AVT) and isotocin (IT), have been implicated in the regulation of social behavior. These peptides are expected to be involved in acute and transient changes in social context, in order to be efficient in modulating the expression of social behavior according to changes in the social environment. Here we tested the hypothesis that short-term social interactions are related to changes in the level of both nonapeptides across different brain regions. For this purpose we exposed male zebrafish to two types of social interactions: (1) real opponent interactions, from which a Winner and a Loser emerged; and (2) mirror-elicited interactions, that produced individuals that did not experience a change in social status despite expressing similar levels of aggressive behavior to those of participants in real-opponent fights. Non-interacting individuals were used as a reference group. Each social phenotype (i.e. Winners, Losers, Mirror-fighters) presented a specific brain profile of nonapeptides when compared to the reference group. Moreover, the comparison between the different social phenotypes allowed to address the specific aspects of the interaction (e.g. assessment of opponent aggressive behavior vs. self-assessment of expressed aggressive behavior) that are linked with neuropeptide responses. Overall, agonistic interactions seem to be more associated with the changes in brain AVT than IT, which highlights the preferential role of AVT in the regulation of aggressive behavior already described for other species.

Sensitivity and specificity of the Gastrointestinal Short Form Questionnaire in diagnosis of gastroesophageal reflux disease

Introduction: Gastrointestinal Short Form Questionnaire (GSFQ) is a questionnaire for gastroesophageal reflux disease (GERD) diagnosis, with a version in Spanish language, not yet compared to an objective test. Aims: To establish GSFQ diagnostic performance against 24-hour pH monitoring carried out in two tertiary care hospitals. Methods: Consecutive adult patients with typical GERD symptoms (heartburn, regurgitation) referred for pH monitoring fulfilled the GSFQ (score range 0-30, proportional to probability of GERD). Diagnosis of GERD was established when acid exposure time in distal esophagus was superior to 4.5% or symptom association probability was greater than 95%. Receiver-operator characteristic (ROC) curves were calculated and best cut-off score determined, with corresponding sensitivity, specificity and likelihood ratios (LR) (95% confidence interval for each). Results: One hundred and fifty-two patients were included (59.9% women, age 47.9 ± 13.9; 97.4% heartburn; 71.3% regurgitation). pH monitoring was abnormal in 65.8%. Mean GSFQ score was 11.2 ± 6. Area under ROC was 56.5% (47.0-65.9%). Optimal cut-off score was 13 or greater: sensitivity 40% (30.3-50.3%), specificity 71.2% (56.9-82.9%), positive LR 1.39 (0.85-2.26) and negative LR 0.84 (0.67-1.07). Exclusion of questions 1 and 3 of the original GSFQ, easily interpreted as referred to dyspepsia and not GERD, improved only marginally the diagnostic performance: AUROC 59.1%. Conclusion: The GSFQ does not predict results of pH monitoring in patients with typical symptoms in a tertiary care setting.

MULTI-BAND BOSE HUBBARD MODELS AND EFFECTIVE THREE-BODY INTERACTIONS

Experiments with ultracold atoms in optical lattice have become a versatile testing ground to study diverse quantum many-body Hamiltonians. A single-band Bose-Hubbard (BH) Hamiltonian was first proposed to describe these systems in 1998 and its associated quantum phase-transition was subsequently observed in 2002. Over the years, there has been a rapid progress in experimental realizations of more complex lattice geometries, leading to more exotic BH Hamiltonians with contributions from excited bands, and modified tunneling and interaction energies. There has also been interesting theoretical insights and experimental studies on “un- conventional” Bose-Einstein condensates in optical lattices and predictions of rich orbital physics in higher bands. In this thesis, I present our results on several multi- band BH models and emergent quantum phenomena. In particular, I study optical lattices with two local minima per unit cell and show that the low energy states of a multi-band BH Hamiltonian with only pairwise interactions is equivalent to an effec- tive single-band Hamiltonian with strong three-body interactions. I also propose a second method to create three-body interactions in ultracold gases of bosonic atoms in a optical lattice. In this case, this is achieved by a careful cancellation of two contributions in the pair-wise interaction between the atoms, one proportional to the zero-energy scattering length and a second proportional to the effective range. I subsequently study the physics of Bose-Einstein condensation in the second band of a double-well 2D lattice and show that the collision aided decay rate of the con- densate to the ground band is smaller than the tunneling rate between neighboring unit cells. Finally, I propose a numerical method using the discrete variable repre- sentation for constructing real-valued Wannier functions localized in a unit cell for optical lattices. The developed numerical method is general and can be applied to a wide array of optical lattice geometries in one, two or three dimensions.

Effect of the cation on the interactions between alkyl methyl imidazolium chloride ionic liquids and water

A systematic study of the interactions between water and alkyl methyl imidazolium chloride ionic liquids at 298.2 K, based on activity coefficients estimated from water activity measurements in the entire solubility range, is presented. The results show that the activity coefficients of water in the studied ILs are controlled by the hydrophilicity of the cation and the cation-anion interaction. To achieve a deeper understanding on the interactions between water and the ILs, COSMO-RS and FTIR spectroscopy were also applied. COSMO-RS was used to predict the activity coefficient of water in the studied ionic liquids along with the excess enthalpies, suggesting the formation of complexes between three molecules of water and one IL molecule. On the basis of quantum-chemical calculations, it is found that cation-anion interaction plays an important role upon the ability of the IL anion to interact with water. The changes in the peak positions/band areas of OH vibrational modes of water as a function of IL concentration were investigated, and the impact of the cation on the hydrogen-bonding network of water is identified and discussed.

Transcatheter Closure of Atrial Septal Defects in a Center With Limited Resources: Outcomes and Short Term Follow-Up

Background: Transcatheter closure of atrial septal defects (ASD) has been accepted world-wide as an alternative to surgical closure with excellent results. This interventional, non-surgical technique plays an important role in the treatment of ASD mostly in the developing world where resources are limited. Objectives: To report the outcomes and short term follow-up of transcatheter closure of ASD over a 12-year period at our institution with limited resources. Patients and Methods: This retrospective study included all patients with the diagnosis of secundum ASD and significant shunting (Qp/Qs > 1.5:1) as well as dilated right atrium and right ventricle who had transcatheter closure at Integrated Cardiovascular Center (PJT), Dr. Cipto Mangunkusumo Hospital between October 2002 and October 2014. One hundred fifty-two patients enrolled in this study were candidates for device closure. Right and left heart cardiac catheterization was performed before the procedure. All patients underwent physical examination, ECG, chest X-ray and transthoracal echocardiography (TTE) prior to device implantation. Results: A total of 152 patients with significant ASD underwent device implantation. Subjects’ age ranged from 0.63 to 69.6 years, with median 9.36 years and mean 16.30 years. They consisted of 33 (21.7%) males and 119 (78.3%) females, with mean body weight of 29.9 kg (range 8 to 75; SD 18.2). The device was successfully implanted in 150 patients where the majority of cases received the Amplatzer septal occluder (147/150; 98%) and the others received the Heart Lifetech ASD occluder (3/150, 2%), whereas two other cases were not suitable for device closure and we decided for surgical closure. The mean ASD size was 19.75 (range 14 - 25) mm. During the procedure, 5 (4.9%) patients had bradycardia and 3 (2.9%) patients had supraventricular tachycardia (SVT), all of which resolved. Conclusions: In our center with limited facilities and manpower, transcatheter closure of atrial septal defect was effective and safe as an alternative treatment to surgery. The outcome and short-term follow-up revealed excellent results, but long-term follow-up is needed.

Generation and screening of natural product-like compounds for antibiotic discovery

Avec l’apparition de plus en plus de souches de bactérie résistante aux antibiotiques, le développement de nouveaux antibiotiques est devenu une important problématique pour les agences de santé. C’est pour cela que la création de nouvelles plateformes pour accélérer la découverte de médicaments est devenu un besoin urgent. Dans les dernières décennies, la recherche était principalement orientée sur la modification de molécules préexistantes, la méta-analyse d’organismes produisant des molécules activent et l’analyse de librairies moléculaires pour trouver des molécules synthétiques activent, ce qui s’est avéré relativement inefficace. Notre but était donc de développer de nouvelles molécules avec des effets thérapeutiques de façon plus efficace à une fraction du prix et du temps comparé à ce qui se fait actuellement. Comme structure de base, nous avons utilisé des métabolites secondaires qui pouvaient altérer le fonctionnement des protéines ou l’interaction entre deux protéines. Pour générer ces molécules, j’ai concentré mes efforts sur les terpènes, une classe de métabolites secondaires qui possède un large éventail d’activités biologiques incluant des activités antibactériennes. Nous avons développé un système de chromosome artificiel de levure (YAC) qui permet à la fois l’assemblage directionnel et combinatoire de gènes qui permet la création de voies de biosynthèse artificielles. Comme preuve de concept, j’ai développé des YACs qui contiennent les gènes pour l’expression des enzymes impliquées dans la biosynthèse de la -carotène et de l’albaflavenone et produit ces molécules avec un haut rendement. Finalement, Des YACs produits à partir de librairies de gènes ont permis de créer une grande diversité de molécules.

DOING MORE WITH SHORT PERIOD DATA: DETERMINING MAGNITUDES FROM CLIPPED AND OVER-RUN SEISMIC DATA AT MOUNT ST. HELENS

How can we calculate earthquake magnitudes when the signal is clipped and over-run? When a volcano is very active, the seismic record may saturate (i.e., the full amplitude of the signal is not recorded) or be over-run (i.e., the end of one event is covered by the start of a new event). The duration, and sometimes the amplitude, of an earthquake signal are necessary for determining event magnitudes; thus, it may be impossible to calculate earthquake magnitudes when a volcano is very active. This problem is most likely to occur at volcanoes with limited networks of short period seismometers. This study outlines two methods for calculating earthquake magnitudes when events are clipped and over-run. The first method entails modeling the shape of earthquake codas as a power law function and extrapolating duration from the decay of the function. The second method draws relations between clipped duration (i.e., the length of time a signal is clipped) and the full duration. These methods allow for magnitudes to be determined within 0.2 to 0.4 units of magnitude. This error is within the range of analyst hand-picks and is within the acceptable limits of uncertainty when quickly quantifying volcanic energy release during volcanic crises. Most importantly, these estimates can be made when data are clipped or over-run. These methods were developed with data from the initial stages of the 2004-2008 eruption at Mount St. Helens. Mount St. Helens is a well-studied volcano with many instruments placed at varying distances from the vent. This fact makes the 2004-2008 eruption a good place to calibrate and refine methodologies that can be applied to volcanoes with limited networks.

Generation and screening of natural product-like compounds for antibiotic discovery

Avec l’apparition de plus en plus de souches de bactérie résistante aux antibiotiques, le développement de nouveaux antibiotiques est devenu une important problématique pour les agences de santé. C’est pour cela que la création de nouvelles plateformes pour accélérer la découverte de médicaments est devenu un besoin urgent. Dans les dernières décennies, la recherche était principalement orientée sur la modification de molécules préexistantes, la méta-analyse d’organismes produisant des molécules activent et l’analyse de librairies moléculaires pour trouver des molécules synthétiques activent, ce qui s’est avéré relativement inefficace. Notre but était donc de développer de nouvelles molécules avec des effets thérapeutiques de façon plus efficace à une fraction du prix et du temps comparé à ce qui se fait actuellement. Comme structure de base, nous avons utilisé des métabolites secondaires qui pouvaient altérer le fonctionnement des protéines ou l’interaction entre deux protéines. Pour générer ces molécules, j’ai concentré mes efforts sur les terpènes, une classe de métabolites secondaires qui possède un large éventail d’activités biologiques incluant des activités antibactériennes. Nous avons développé un système de chromosome artificiel de levure (YAC) qui permet à la fois l’assemblage directionnel et combinatoire de gènes qui permet la création de voies de biosynthèse artificielles. Comme preuve de concept, j’ai développé des YACs qui contiennent les gènes pour l’expression des enzymes impliquées dans la biosynthèse de la -carotène et de l’albaflavenone et produit ces molécules avec un haut rendement. Finalement, Des YACs produits à partir de librairies de gènes ont permis de créer une grande diversité de molécules.

Pelvic floor muscle training versus no treatment, or inactive control treatments, for urinary incontinence in women : a short version Cochrane systematic review with meta-analysis

Background Pelvic floor muscle training (PFMT) is a commonly used physical therapy for women with urinary incontinence (UI). Objectives To determine the effects of PFMT for women with UI in comparison to no treatment, placebo or other inactive control treatments. Search Methods Cochrane Incontinence Group Specialized Register, (searched 15 April 2013). Selection Criteria Randomized or quasi-randomized trials in women with stress, urgency or mixed UI (based on symptoms, signs, or urodynamics). Data Collection and Analysis At least two independent review authors carried out trial screening, selection, risk of bias assessment and data abstraction. Trials were subgrouped by UI diagnosis. The quality of evidence was assessed by adopting the (GRADE) approach. Results Twenty-one trials (1281 women) were included; 18 trials (1051 women) contributed data to the meta-analysis. In women with stress UI, there was high quality evidence that PFMT is associated with cure (RR 8.38; 95% CI 3.68 to 19.07) and moderate quality evidence of cure or improvement (RR 17.33; 95% CI 4.31 to 69.64). In women with any type of UI, there was also moderate quality evidence that PFMT is associated with cure (RR 5.5; 95% CI 2.87–10.52), or cure and improvement (RR 2.39; 95% CI 1.64–3.47). Conclusions The addition of seven new trials did not change the essential findings of the earlier version of this review. In this iteration, using the GRADE quality criteria strengthened the recommendations for PFMT and a wider range of secondary outcomes (also generally in favor of PFMT) were reported.

Theoretical and experimental study on electron interactions with chlorobenzene: Shape resonances and differential cross sections

In this work, we report theoretical and experimental cross sections for elastic scattering of electrons by chlorobenzene (ClB). The theoretical integral and differential cross sections (DCSs) were obtained with the Schwinger multichannel method implemented with pseudopotentials (SMCPP) and the independent atom method with screening corrected additivity rule (IAM-SCAR). The calculations with the SMCPP method were done in the static-exchange (SE) approximation, for energies above 12 eV, and in the static-exchange plus polarization approximation, for energies up to 12 eV. The calculations with the IAM-SCAR method covered energies up to 500 eV. The experimental differential cross sections were obtained in the high resolution electron energy loss spectrometer VG-SEELS 400, in Lisbon, for electron energies from 8.0 eV to 50 eV and angular range from 7 degrees to 110 degrees. From the present theoretical integral cross section (ICS) we discuss the low-energy shape-resonances present in chlorobenzene and compare our computed resonance spectra with available electron transmission spectroscopy data present in the literature. Since there is no other work in the literature reporting differential cross sections for this molecule, we compare our theoretical and experimental DCSs with experimental data available for the parent molecule benzene. Published by AIP Publishing.

Exoplanet atmospheres Characterization Observatory payload short-wave infrared channel: EChO SWiR

EChO (Exoplanet atmospheres Characterization Observatory), a proposal for exoplanets exploration space mission, is considered the next step for planetary atmospheres characterization. It would be a dedicated observatory to uncover a large selected sample of planets spanning a wide range of masses (from gas giants to super-Earths) and orbital temperatures (from hot to habitable). All targets move around stars of spectral types F, G, K, and M. EChO would provide an unprecedented view of the atmospheres of planets in the solar neighbourhood. The consortium formed by various institutions of different countries proposed as ESA M3 an integrated spectrometer payload for EChO covering the wavelength interval 0.4 to 16 µm. This instrument is subdivided into 4 channels: a visible channel, which includes a fine guidance system (FGS) and a VIS spectrometer, a near infrared channel (SWiR), a middle infrared channel (MWiR), and a long wave infrared module (LWiR). In addition, it contains a common set of optics spectrally dividing the wavelength coverage and injecting the combined light of parent stars and their exoplanets into the different channels. The proposed payload meets all of the key performance requirements detailed in the ESA call for proposals as well as all scientific goals. EChO payload is based on different spectrometers covering the spectral range mentioned above. Among them, SWiR spectrometer would work from 2.45 microns to 5.45 microns. In this paper, the optical and mechanical designs of the SWiR channel instrument are reported on.

“Step by step”: high frequency short-distance epizoochorous dispersal of aquatic macrophytes

Aquatic macrophytes can successfully colonise and re-colonise areas separated by space and time. The mechanisms underlying such “mobility” are not well understood, but it has often been hypothesised that epizoochory (external dispersal) plays an important role. Yet, there is only limited, and mostly anecdotal, evidence concerning successful epizoochorous dispersal of aquatic macrophytes, particularly in the case of short-distance dispersal. Here we examine in situ and ex situ dispersal of aquatic macrophytes, including three invasive alien species. A high frequency of Lemna minor Linnaeus dispersal was observed in situ, and this was linked to bird-mediated epizoochory. We concluded that wind had no effect on dispersal. Similarly, in an ex situ examination Lemna minuta Kunth and Azolla filiculoides Lamarck, were found to be dispersed with a high frequency by mallard ducks (Anas platyrhynchos). No dispersal was measured for Elodea nuttalli (Planchon) H. St. John. It is concluded that short-distance or “stepping-stone” dispersal via bird-mediated epizoochory can occur with high frequencies, and therefore can play an important role in facilitating colonisation, range expansion and biological invasion of macrophytes.

Pelvic floor muscle training versus no treatment, or inactive control treatments, for urinary incontinence in women : a short version Cochrane systematic review with meta-analysis

Background Pelvic floor muscle training (PFMT) is a commonly used physical therapy for women with urinary incontinence (UI). Objectives To determine the effects of PFMT for women with UI in comparison to no treatment, placebo or other inactive control treatments. Search Methods Cochrane Incontinence Group Specialized Register, (searched 15 April 2013). Selection Criteria Randomized or quasi-randomized trials in women with stress, urgency or mixed UI (based on symptoms, signs, or urodynamics). Data Collection and Analysis At least two independent review authors carried out trial screening, selection, risk of bias assessment and data abstraction. Trials were subgrouped by UI diagnosis. The quality of evidence was assessed by adopting the (GRADE) approach. Results Twenty-one trials (1281 women) were included; 18 trials (1051 women) contributed data to the meta-analysis. In women with stress UI, there was high quality evidence that PFMT is associated with cure (RR 8.38; 95% CI 3.68 to 19.07) and moderate quality evidence of cure or improvement (RR 17.33; 95% CI 4.31 to 69.64). In women with any type of UI, there was also moderate quality evidence that PFMT is associated with cure (RR 5.5; 95% CI 2.87–10.52), or cure and improvement (RR 2.39; 95% CI 1.64–3.47). Conclusions The addition of seven new trials did not change the essential findings of the earlier version of this review. In this iteration, using the GRADE quality criteria strengthened the recommendations for PFMT and a wider range of secondary outcomes (also generally in favor of PFMT) were reported.