iNucs:Inter-nucleosome interactions

[Motivation] Deciphering nucleosome–nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. [Results] We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools

Mitigation of Moral Hazard and Adverse Selection in Venture Capital Financing: The Influence of the Country’s Institutional Setting

A venture capitalist (VC) needs to trade off benefits and costs when attempting to mitigate agency problems in their investor-investee relationship. We argue that signals of ventures complement the VC’s capacity to screen and conduct a due diligence during the pre-investment phase, but its attractiveness may diminish in institutional settings supporting greater transparency. Similarly, whereas a VC may opt for contractual covenants to curb potential opportunism by ventures in the post-investment phase, this may only be effective in settings supportive of shareholder rights enforcement. Using an international sample of VC contracts, our study finds broad support for these conjectures. It delineates theoretical and practical implications for how investors can best deploy their capital in different institutional settings whilst nurturing their relationships with entrepreneurs

Effects of Transmitters and Amyloid-Beta Peptide on Calcium Signals in Rat Cortical Astrocytes: Fura-2AM Measurements and Stochastic Model Simulations

BACKGROUND: To better understand the complex molecular level interactions seen in the pathogenesis of Alzheimer's disease, the results of the wet-lab and clinical studies can be complemented by mathematical models. Astrocytes are known to become reactive in Alzheimer's disease and their ionic equilibrium can be disturbed by interaction of the released and accumulated transmitters, such as serotonin, and peptides, including amyloid- peptides (A). We have here studied the effects of small amounts of A25-35 fragments on the transmitter-induced calcium signals in astrocytes by Fura-2AM fluorescence measurements and running simulations of the detected calcium signals. METHODOLOGY/PRINCIPAL FINDINGS: Intracellular calcium signals were measured in cultured rat cortical astrocytes following additions of serotonin and glutamate, or either of these transmitters together with A25-35. A25-35 increased the number of astrocytes responding to glutamate and exceedingly increased the magnitude of the serotonin-induced calcium signals. In addition to A25-35-induced effects, the contribution of intracellular calcium stores to calcium signaling was tested. When using higher stimulus frequency, the subsequent calcium peaks after the initial peak were of lower amplitude. This may indicate inadequate filling of the intracellular calcium stores between the stimuli. In order to reproduce the experimental findings, a stochastic computational model was introduced. The model takes into account the major mechanisms known to be involved in calcium signaling in astrocytes. Model simulations confirm the principal experimental findings and show the variability typical for experimental measurements. CONCLUSIONS/SIGNIFICANCE: Nanomolar A25-35 alone does not cause persistent change in the basal level of calcium in astrocytes. However, even small amounts of A25-35, together with transmitters, can have substantial synergistic effects on intracellular calcium signals. Computational modeling further helps in understanding the mechanisms associated with intracellular calcium oscillations. Modeling the mechanisms is important, as astrocytes have an essential role in regulating the neuronal microenvironment of the central nervous system

Cherenkov radiation emitted by ultrafast laser pulses and the generation of coherent polaritons

We report on the generation of coherent phonon polaritons in ZnTe, GaP and LiTaO$_{3}$ using ultrafast optical pulses. These polaritons are coupled modes consisting of mostly far-infrared radiation and a small phonon component, which are excited through nonlinear optical processes involving the Raman and the second-order susceptibilities (difference frequency generation). We probe their associated hybrid vibrational-electric field, in the THz range, by electro-optic sampling methods. The measured field patterns agree very well with calculations for the field due to a distribution of dipoles that follows the shape and moves with the group velocity of the optical pulses. For a tightly focused pulse, the pattern is identical to that of classical Cherenkov radiation by a moving dipole. Results for other shapes and, in particular, for the planar and transient-grating geometries, are accounted for by a convolution of the Cherenkov field due to a point dipole with the function describing the slowly-varying intensity of the pulse. Hence, polariton fields resulting from pulses of arbitrary shape can be described quantitatively in terms of expressions for the Cherenkov radiation emitted by an extended source. Using the Cherenkov approach, we recover the phase-matching conditions that lead to the selection of specific polariton wavevectors in the planar and transient grating geometry as well as the Cherenkov angle itself. The formalism can be easily extended to media exhibiting dispersion in the THz range. Calculations and experimental data for point-like and planar sources reveal significant differences between the so-called superluminal and subluminal cases where the group velocity of the optical pulses is, respectively, above and below the highest phase velocity in the infrared.Comment: 13 pages, 11 figure

Prescrição e preparo de medicamentos sem formulação adequada para crianças: um estudo de base hospitalar

Este trabalho teve como objetivo identificar medicamentos cuja forma ou formulação farmacêutica representa um problema em pediatria (Medicamento Problema - MP), bem como analisar as estratégias empregadas pelos médicos, para sua utilização nas crianças e os riscos envolvidos. Trata-se de um estudo descritivo, que tem como base um inquérito com pediatras de um hospital de referência do SUS em Fortaleza-Ceará, conduzido para identificação dos MPs em julho-agosto de 2004; uma análise das prescrições contendo adaptação de formas sólidas e uma observação direta do preparo dos medicamentos, que foram conduzidas em dezembro de 2004 e janeiro de 2005, respectivamente. Os medicamentos foram agrupados pela classificação ATC e pelo cálculo de frequências das variáveis. Os pediatras (N=48, 98%) identificaram: 16 produtos sem forma injetável, 32 injetáveis necessários em concentrações menores e 30 MP sem formulação líquida para uso oral. Foram analisadas 89 prescrições contendo adaptação de formas sólidas, envolvendo 119 itens de medicamentos; todas continham inadequações, sendo a principal a partição de comprimidos. As doses prescritas corresponderam ao preconizado em 33,6% dos casos. Adaptações foram realizadas em local inadequado, por profissional não qualificado e sem as boas práticas. Concluindo, a carência de formulações apropriadas ao uso pediátrico repercute na prática médica e é agravada pela inexistência de condições adequadas para a manipulação de medicamentos por farmacêuticos, nos hospitais brasileiros.This work aimed to identify medicines whose form or pharmaceutical formula presents a problem to pediatrics (Problem Medication - PM), the strategies employed by doctors to use them in children, and the potential risks involved. Descriptive study: based on a survey with pediatricians from a SUS (Public Health System) reference hospital in Fortaleza-CE (Northeastern Brazil), in order to identify PMs, from July to August 2004; an analysis of prescriptions containing modification of medicines in the solid forms; and a follow-up of medicinal preparations, developed in December 2004 and January 2005, respectively. The medications were grouped by an anatomic, therapeutic and chemical classification and by means of a calculation of variables frequency. The pediatricians (N=48, 98% of the total) identified as PMs: 16 products without an injectable form; 32 in an injectable form that should be presented in lesser concentrations; and 30 without a liquid formula for oral use. Eighty two (82) prescriptions containing modifications of solid forms, involving 111 medicinal items were analyzed, all of which contained inadequacies; the main one being the partition of pills. In 33.6% of the cases, the prescribed doses were in accordance with that generally recommended. The modifications were carried out in inadequate places, by nonqualified professionals and without the use of best practices. The lack of appropriate formulae for pediatric use has an impact on medical practices. It is aggravated by the lack of appropriate conditions for medicines manipulation by pharmacists, in Brazilian hospitals, and this impact involves risks to patients