A model and an algebra for semi-structured and full-text queries

The need for a convergence between semi-structured data management and Information Retrieval techniques is manifest to the scientific community. In order to fulfil this growing request, W3C has recently proposed XQuery Full Text, an IR-oriented extension of XQuery. However, the issue of query optimization requires the study of important properties like query equivalence and containment; to this aim, a formal representation of document and queries is needed. The goal of this thesis is to establish such formal background. We define a data model for XML documents and propose an algebra able to represent most of XQuery Full-Text expressions. We show how an XQuery Full-Text expression can be translated into an algebraic expression and how an algebraic expression can be optimized.

Gene expression profile in newborn rat lungs after two days of recovery of mechanical ventilation.

BACKGROUND Preterm infants having immature lungs often require respiratory support, potentially leading to bronchopulmonary dysplasia (BPD). Conventional BPD rodent models based on mechanical ventilation (MV) present outcome measured at the end of the ventilation period. A reversible intubation and ventilation model in newborn rats recently allowed discovering that different sets of genes modified their expression related to time after MV. In a newborn rat model, the expression profile 48 h after MV was analyzed with gene arrays to detect potentially interesting candidates with an impact on BPD development. METHODS Rat pups were injected P4-5 with 2 mg/kg lipopolysaccharide (LPS). One day later, MV with 21 or 60% oxygen was applied during 6 h. Animals were sacrified 48 h after end of ventilation. Affymetrix gene arrays assessed the total gene expression profile in lung tissue. RESULTS In fully treated animals (LPS + MV + 60% O(2)) vs. controls, 271 genes changed expression significantly. All modified genes could be classified in six pathways: tissue remodeling/wound repair, immune system and inflammatory response, hematopoiesis, vasodilatation, and oxidative stress. Major alterations were found in the MMP and complement system. CONCLUSION MMPs and complement factors play a central role in several of the pathways identified and may represent interesting targets for BPD treatment/prevention.Bronchopulmonary dysplasia (BPD) is a chronic lung disease occurring in ~30% of preterm infants born less than 30 wk of gestation (1). Its main risk factors include lung immaturity due to preterm delivery, mechanical ventilation (MV), oxygen toxicity, chorioamnionitis, and sepsis. The main feature is an arrest of alveolar and capillary formation (2). Models trying to decipher genes involved in the pathophysiology of BPD are mainly based on MV and oxygen application to young mammals with immature lungs of different species (3). In newborn rodent models, analyses of lung structure and gene and protein expression are performed for practical reasons directly at the end of MV (4,5,6). However, later appearing changes of gene expression might also have an impact on lung development and the evolution towards BPD and cannot be discovered by such models. Recently, we developed a newborn rat model of MV using an atraumatic (orotracheal) intubation technique that allows the weaning of the newborn animal off anesthesia and MV, the extubation to spontaneous breathing, and therefore allows the evaluation of effects of MV after a ventilation-free period of recovery (7). Indeed, applying this concept of atraumatic intubation by direct laryngoscopy, we recently were able to show significant differences between gene expression changes appearing directly after MV compared to those measured after a ventilation-free interval of 48 h. Immediately after MV, inflammation-related genes showed a transitory modified expression, while another set of more structurally related genes changed their expression only after a delay of 2 d (7). Lung structure, analyzed by conventional 2D histology and also by 3D reconstruction using synchrotron x-ray tomographic microscopy revealed, 48 h after end of MV, a reduced complexity of lung architecture compared to the nonventilated rat lungs, similar to the typical findings in BPD. To extend these observations about late gene expression modifications, we performed with a similar model a full gene expression profile of lung tissue 48 h after the end of MV with either room air or 60% oxygen. Essentially, we measured changes in the expression of genes related to the MMPs and complement system which played a role in many of the six identified mostly affected pathways.

Clubroot (Plasmodiophora brassicae Woronin): an agricultural and biological challenge worldwide

Clubroot disease and the causal microbe Plasmodiophora brassicae offer abundant challenges to agriculturists and biological scientists. This microbe is well fitted for the environments which it inhabits. Plasmodiophora brassicae exists in soil as microscopic well protected resting spores and then grows actively and reproduces while shielded inside the roots of host plants. The pathogen is active outside the host for only short periods. Consequently, scientific studies are made challenging by the biological context of the host and pathogen and the technology required to investigate and understand that relationship. Controlling clubroot disease is a challenge for farmers, crop consultants and plant pathology practitioners because of the limited options which are available. Full symptom expression happens solely in members of the Brassicaceae family. Currently, only a few genes expressing strong resistance to P. brassicae are known and readily available. Agrochemical control is similarly limited by difficulties in molecule formulation which combines efficacy with environmental acceptability. Manipulation of husbandry encouraging improvements in soil structure, texture, nutrient composition and moisture content can reduce populations of P. brassicae. Integrating such strategies with rotation and crop management will reduce but not eliminate this disease. There are indications that forms of biological competition may be mobilised as additions to integrated control strategies. The aim of this review is to chart key themes in the development of scientific biological understanding of this host-pathogen relationship by offering signposts to grapple with clubroot disease which devastates crops and their profitability. Particular attention is given to the link between soil and nutrient chemistry and activity of this microbe.

Monodic temporal resolution

Until recently, First-Order Temporal Logic (FOTL) has been only partially understood. While it is well known that the full logic has no finite axiomatisation, a more detailed analysis of fragments of the logic was not previously available. However, a breakthrough by Hodkinson et al., identifying a finitely axiomatisable fragment, termed the monodic fragment, has led to improved understanding of FOTL. Yet, in order to utilise these theoretical advances, it is important to have appropriate proof techniques for this monodic fragment.In this paper, we modify and extend the clausal temporal resolution technique, originally developed for propositional temporal logics, to enable its use in such monodic fragments. We develop a specific normal form for monodic formulae in FOTL, and provide a complete resolution calculus for formulae in this form. Not only is this clausal resolution technique useful as a practical proof technique for certain monodic classes, but the use of this approach provides us with increased understanding of the monodic fragment. In particular, we here show how several features of monodic FOTL can be established as corollaries of the completeness result for the clausal temporal resolution method. These include definitions of new decidable monodic classes, simplification of existing monodic classes by reductions, and completeness of clausal temporal resolution in the case of monodic logics with expanding domains, a case with much significance in both theory and practice.

Mechanising first-order temporal resolution

First-order temporal logic is a concise and powerful notation, with many potential applications in both Computer Science and Artificial Intelligence. While the full logic is highly complex, recent work on monodic first-order temporal logics has identified important enumerable and even decidable fragments. Although a complete and correct resolution-style calculus has already been suggested for this specific fragment, this calculus involves constructions too complex to be of practical value. In this paper, we develop a machine-oriented clausal resolution method which features radically simplified proof search. We first define a normal form for monodic formulae and then introduce a novel resolution calculus that can be applied to formulae in this normal form. By careful encoding, parts of the calculus can be implemented using classical first-order resolution and can, thus, be efficiently implemented. We prove correctness and completeness results for the calculus and illustrate it on a comprehensive example. An implementation of the method is briefly discussed.

Monodic Temporal Resolution

First-order temporal logic is a coincise and powerful notation, with many potential applications in both Computer Science and Artificial Intelligence. While the full logic is highly complex, recent work on monodic first-order temporal logics have identified important enumerable and even decidable fragments. In this paper we present the first resolution-based calculus for monodic first-order temporal logic. Although the main focus of the paper is on establishing completeness result, we also consider implementation issues and define a basic loop-search algorithm that may be used to guide the temporal resolution system.

Handling Equality in Monodic Temporal Resolution

First-order temporal logic is a concise and powerful notation, with many potential applications in both Computer Science and Artificial Intelligence. While the full logic is highly complex, recent work on monodic first-order temporal logics has identified important enumerable and even decidable fragments including the guarded fragment with equality. In this paper, we specialise the monodic resolution method to the guarded monodic fragment with equality and first-order temporal logic over expanding domains. We introduce novel resolution calculi that can be applied to formulae in the normal form associated with the clausal resolution method, and state correctness and completeness results.

Towards the Implementation of First-Order Temporal Resolution: the Expanding Domain Case

First-order temporal logic is a concise and powerful notation, with many potential applications in both Computer Science and Artificial Intelligence. While the full logic is highly complex, recent work on monodic first-order temporal logics has identified important enumerable and even decidable fragments. In this paper, we develop a clausal resolution method for the monodic fragment of first-order temporal logic over expanding domains. We first define a normal form for monodic formulae and then introduce novel resolution calculi that can be applied to formulae in this normal form. We state correctness and completeness results for the method. We illustrate the method on a comprehensive example. The method is based on classical first-order resolution and can, thus, be efficiently implemented.

Implantação da técnica para diferenciação osteoblástica a partir de células tronco mesenquimais humanas derivadas do tecido adiposo

Pós-graduação em Fisiopatologia em Clínica Médica - FMB

Genetically determined chloride-sensitive hypertension and stroke

The stroke-prone spontaneously hypertensive rat (SHRSP) is a genetically determined model of “salt-sensitive” stroke and hypertension whose full phenotypic expression is said to require a diet high in Na+ and low in K+. We tested the hypothesis that dietary Cl− determines the phenotypic expression of the SHRSP. In the SHRSP fed a normal NaCl diet, supplementing dietary K+ with KCl exacerbated hypertension, whereas supplementing either KHCO3 or potassium citrate (KB/C) attenuated hypertension, when blood pressure (BP) was measured radiotelemetrically, directly and continually. Supplemental KCl, but not KB/C, induced strokes, which occurred in all and only those rats in the highest quartiles of both BP and plasma renin activity (PRA). PRA was higher with KCl than with KB/C. These observations demonstrate that with respect to both severity of hypertension and frequency of stroke the phenotypic expression of the SHRSP is (i) either increased or decreased, depending on whether the anionic component of the potassium salt supplemented is, or is not, Cl−; (ii) increased by supplementing Cl− without supplementing Na+, and despite supplementing K+; and hence (iii) both selectively Cl−-sensitive and Cl−-determined. The observations suggest that in the SHRSP selectively supplemented with Cl− the likelihood of stroke depends on the extent to which both BP and PRA increase.

Analysis of masked mutations in familial adenomatous polyposis

Familial adenomatous polyposis (FAP) is an autosomal-dominant disease characterized by the development of hundreds of adenomatous polyps of the colorectum. Approximately 80% of FAP patients can be shown to have truncating mutations of the APC gene. To determine the cause of FAP in the other 20% of patients, MAMA (monoallelic mutation analysis) was used to independently examine the status of each of the two APC alleles. Seven of nine patients analyzed were found to have significantly reduced expression from one of their two alleles whereas two patients were found to have full-length expression from both alleles. We conclude that more than 95% of patients with FAP have inactivating mutations in APC and that a combination of MAMA and standard genetic tests will identify APC abnormalities in the vast majority of such patients. That no APC expression from the mutant allele is found in some FAP patients argues strongly against the requirement for dominant negative effects of APC mutations. The results also suggest that there may be at least one additional gene, besides APC, that can give rise to FAP.

High-Performance WSe2 CMOS Technology and Integrated Circuits.

Because of their extraordinary structural and electrical properties, two dimensional materials are currently being pursued for applications such as thin-film transistors and integrated circuit. One of the main challenges that still needs to be overcome for these applications is the fabrication of air-stable transistors with industry-compatible complementary metal oxide semiconductor (CMOS) technology. In this work, we experimentally demonstrate a novel high performance air-stable WSe2 CMOS technology with almost ideal voltage transfer characteristic, full logic swing and high noise margin with different supply voltages. More importantly, the inverter shows large voltage gain (~38) and small static power (Pico-Watts), paving the way for low power electronic system in 2D materials.

Gene expression programming-fuzzy logic method for crop type classification

Crop type classification using remote sensing data plays a vital role in planning cultivation activities and for optimal usage of the available fertile land. Thus a reliable and precise classification of agricultural crops can help improve agricultural productivity. Hence in this paper a gene expression programming based fuzzy logic approach for multiclass crop classification using Multispectral satellite image is proposed. The purpose of this work is to utilize the optimization capabilities of GEP for tuning the fuzzy membership functions. The capabilities of GEP as a classifier is also studied. The proposed method is compared to Bayesian and Maximum likelihood classifier in terms of performance evaluation. From the results we can conclude that the proposed method is effective for classification.

A voltage-controlled ring oscillator using InP full enhancement-mode HEMT logic

A voltage-controlled ring oscillator (VCO) based on a full enhancement-mode InAIAs/InGaAs/InP high electron mobility transistor (HEMT) logic is proposed. An enhancement-mode HEMT (E-HEMT) is fabricated, whose threshold is demonstrated to be 10 mV. The model of the E-HEMT is established and used in the SPICE simulation of the VCO. The result proves that the full E-HEMT logic technology can be applied to the VCO. And compared with the HEMT DCFL technology, the complexity of our fabrication process is reduced and the reliability is improved.

A transglutaminase from Chinese shrimp (Fenneropenaeus chinensis), full-length cDNA cloning, tissue localization and expression profile after challenge

Transglutaminase can catalyze the cross-linking reaction between soluble clotting protein molecules from the plasma for prevention of excess blood loss from a wound and obstructing micro-organisms from invading the wound in crustaceans. A novel transglutaminase (FcTG) gene was cloned from hemocytes of Chinese shrimp Fenneropenaeus chinensis by 3' and 5' rapid amplification of cDNA ends (RACE) PCR. The full-length cDNA consists of 2972 bp, encoding 757 amino acids with a calculated molecular mass of 84.96 kDa and a theoretical isoelectric point of 5.61. FcTG contains a typical transglutaminase-like homologue (TGc domain: E-value = 1.94e-38). Three catalytic sites (Cys-324, His-391 and Asp-414) are present in this domain. The deduced amino acid sequence of FcTG showed high identity with black tiger shrimp TG, kuruma shrimp TG and crayfish TG. Transcripts of FcTG mRNA were mainly detected in gill, lymphoid organ and hemocytes by RT-PCR. RNA in situ hybridization further confirmed that FcTG was constitutively expressed in hemocytes both in the circulatory system and lymphoid organ. The variation of mRNA transcription level in hemocytes and lymphoid organ following injection of killed bacteria or infection with white spot syndrome virus (WSSV) was quantified by RT-PCR. The up-regulated expression of FcTG in shrimp lymphoid organ following injection of bacteria indicates that it is inducible and might be associated with bacterial challenge. (c) 2006 Elsevier Ltd. All rights reserved.