GemCell: A generic platform for modeling multi-cellular biological systems

The mass and complexity of biological information requires computer-aided simulation and analysis to help scientists achieve understanding and guide experimentation. Although living organisms are composed of cells, actual genomic and proteomic data have not yet led to a satisfactory model of working cell in silico. We have set out to devise a user-friendly generic platform, GemCell, for Generic Executable Modeling of Cells, based on whole, functioning cells. Starting with the cell simplifies life, because all cells expresses essentially five generic types of behavior: replication, death, movement (including change of shape and adherence), export (secretion, signaling, etc.) and import (receiving signals, metabolites, phagocytosis, etc.). The details of these behaviors are specified in GemCell for particular kinds of cells as part of a database of biological specifics (the DBS), which specifies the cell properties and functions that depend on the cell’s history, state, environment, etc. The DBS is designed in an intuitive fashion, so users are able to easily insert their data of interest. The generic part of GemCell, built using Statecharts, is a fully dynamic model of a cell, its interactions with the environment and its resulting behavior, individually and collectively. Model specificity emerges from the DBS, so that model execution is carried out by the statecharts executing with the aid of specific data extracted from the DBS dynamically. Our long term goal is for GemCell to serve as a broadly applicable platform for biological modeling and analysis, supporting user-friendly in silico experimentation, animation, discovery of emergent properties, and hypothesis testing, for a wide variety of biological systems.     

On nonaqueous electrochemical behavior of titanium and Ti compounds

In this study, we examined the electrochemical behavior of titanium and Ti⁴⁺ compounds in THF solutions. Tetra butyl ammonium chloride (TBACl) was used as supporting electrolyte in order to increase the ionic conductivity of the solutions. Electrodeposition of pure titanium could not be obtained. A variety of analytical techniques have been used in conjunction with electrochemical methods in order to analyze the reduction process of Ti⁴⁺. These included Raman and UV-vis spectroscopy, ICP and CHNS elemental analyses. Ti⁴⁺ is being reduced to Ti³⁺ in TiCl₄/THF/TBACl solutions.In addition we show that metallic titanium can be electrochemically dissolved from an organo-metallic electrolyte solution comprising EtAlCl₂ and LiCl in THF. The product is Ti⁴⁺. While LiCl is insoluble in THF it reacts with EtAlCl₂ to form ionic species. Hence, these solutions possessed reasonable ionic conductivity.We could not obtain electroactive Ti⁴⁺ with TiBr₄ or TiI₄ as starting materials, in similar solutions.     

Equilibrium segregation of Ti to Au–sapphire interfaces

Equilibrium segregation of Ti to Au–sapphire interfaces was measured from dewetted Au(Ti) films on the (0001) surface of sapphire. Quantitative energy dispersive spectroscopy was used to determine a Ti excess at the Au–sapphire interface of 2.2 Ti atoms/nm², which together with an excess of 4.6 Ti atoms/nm² at the (0001) sapphire surface, is associated with a decrease in the solid–solid Au–sapphire interface energy. Quantitative high resolution transmission electron microscopy showed that the segregated Ti is distributed within a 1.54-nm thick intergranular film at the Au–sapphire interface, which is not a bulk phase but rather an equilibrium interface state. As a result, Ti segregation without the formation of a bulk reaction at the interface is associated with a decreased interface energy, improved wetting, and may be an important part of the total complex mechanism responsible for improved wetting and spreading in “reactive” braze systems.     

Destructive polyarthritis in Behcet's disease. Apropos of a case and review of the literature]

The authors report a case of a 37 years old man with Beh?et's disease since 7 years who develops a destructive chronic polyarthritis involving wrists, hands and one knee. The parallel evolution between recurrent orogenital ulceration and arthritis added to the absence of other associated destructive rheumatism permit to link this polyarthritis to Beh?et disease. In spite of the few reports, the occurrence of destructive arthritis can't exclude absolutely the diagnosis of this affection.     

Programming by predicates: a formal model for interactive synthesis

Acta Informatica - Program synthesis is the problem of computing from a specification a program that implements it. New and popular variations on the synthesis problem accept specifications in...     

Completeness for Symmetric Two-Party Functionalities: Revisited

Understanding the minimal assumptions required for carrying out cryptographic tasks is one of the fundamental goals of theoretic cryptography. A rich body of work has been dedicated to understanding the complexity of cryptographic tasks in the context of (semi-honest) secure two-party computation. Much of this work has focused on the characterization of trivial and complete functionalities (resp., functionalities that can be securely implemented unconditionally, and functionalities that can be used to securely compute all functionalities). Most previous works define reductions via an ideal implementation of the functionality; i.e., f reduces to g if one can implement f using a black-box (or oracle) that computes the function g and returns the output to both parties. Such a reduction models the computation of f as an atomic operation. However, in the real world, protocols proceed in rounds, and the output is not learned by the parties simultaneously. In this paper, we show that this distinction is significant. Specifically, we show that there exist symmetric functionalities (where both parties receive the same outcome) that are neither trivial nor complete under “black-box reductions,” and yet the existence of a constant-round protocol for securely computing such a functionality implies infinitely often oblivious transfer (meaning that it is secure for infinitely many values of the security parameter). In light of the above, we propose an alternative definitional infrastructure for studying the triviality and completeness of functionalities.     

Maternal N-Acetyl-Cysteine Prevents Neonatal Hypoxia-Induced Brain Injury in a Rat Model

Perinatal hypoxia is a major cause of infant brain damage, lifelong neurological disability, and infant mortality. N-Acetyl-Cysteine (NAC) is a powerful antioxidant that acts directly as a scavenger of free radicals. We hypothesized that maternal-antenatal and offspring-postnatal NAC can protect offspring brains from hypoxic brain damage.Sixty six newborn rats were randomized into four study groups. Group 1: Control (CON) received no hypoxic intervention. Group 2: Hypoxia (HYP)-received hypoxia protocol. Group 3: Hypoxia-NAC (HYP-NAC). received hypoxia protocol and treated with NAC following each hypoxia episode. Group 4: NAC Hypoxia (NAC-HYP) treated with NAC during pregnancy, pups subject to hypoxia protocol. Each group was evaluated for: neurological function (Righting reflex), serum proinflammatory IL-6 protein levels (ELISA), brain protein levels: NF-κB p65, neuronal nitric oxide synthase (nNOS), TNF-α, and IL-6 (Western blot) and neuronal apoptosis (histology evaluation with TUNEL stain). Hypoxia significantly increased pups brain protein levels compared to controls. NAC administration to dams or offspring demonstrated lower brain NF-κB p65, nNOS, TNF-α and IL-6 protein levels compared to hypoxia alone. Hypoxia significantly increased brain apoptosis as evidenced by higher grade of brain TUNEL reaction. NAC administration to dams or offspring significantly reduce this effect. Hypoxia induced acute sensorimotor dysfunction. NAC treatment to dams significantly attenuated hypoxia-induced acute sensorimotor dysfunction. Prophylactic NAC treatment of dams during pregnancy confers long-term protection to offspring with hypoxia associated brain injury, measured by several pathways of injury and correlated markers with pathology and behavior. This implies we may consider prophylactic NAC treatment for patients at risk for hypoxia during labor.     

On the Feasibility of Extending Oblivious Transfer

Oblivious transfer is one of the most basic and important building blocks in cryptography. As such, understanding its cost is of prime importance. Beaver (in: The 28th STOC, pp 479–488, 1996) showed that it is possible to obtain \(\mathsf{poly}(n)\) oblivious transfers given only n actual oblivious transfer calls and using one-way functions, where n is the security parameter. In addition, he showed that it is impossible to extend oblivious transfer information theoretically. The notion of extending oblivious transfer is important theoretically (to understand the complexity of computing this primitive) and practically (since oblivious transfers can be expensive and thus extending them using only one-way functions is very attractive). Despite its importance, very little is known about the feasibility of extending oblivious transfer, beyond the fact that it is impossible information theoretically. Specifically, it is not known whether or not one-way functions are actually necessary for extending oblivious transfer, whether or not it is possible to extend oblivious transfers with adaptive security, and whether or not it is possible to extend oblivious transfers when starting with \(O(\log n)\) oblivious transfers. In this paper, we address these questions and provide almost complete answers to all of them. We show that the existence of any oblivious transfer extension protocol with security for static semi-honest adversaries implies one-way functions, that an oblivious transfer extension protocol with adaptive security implies oblivious transfer with static security, and that the existence of an oblivious transfer extension protocol from only \(O(\log n)\) oblivious transfers implies oblivious transfer itself.