Analysis of Bothrops jararacussu venomous gland transcriptome focusing on structural and functional aspects: I - gene expression profile of highly expressed phospholipases A(2)

Snake venom glands are a rich source of bioactive molecules such as peptides, proteins and enzymes that show important pharmacological activity leading to in local and systemic effects as pain, edema, bleeding and muscle necrosis. Most studies on pharmacologically active peptides and proteins from snake venoms have been concerned with isolation and structure elucidation through methods of classical biochemistry. As an attempt to examine the transcripts expressed in the venom gland of Bothrops jararacussu and to unveil the toxicological and pharmacological potential of its products at the molecular level, we generated 549 expressed sequence tags (ESTs) from a directional cDNA library. Sequences obtained from single-pass sequencing of randomly selected cDNA clones could be identified by similarities searches on existing databases, resulting in 197 sequences with significant similarity to phospholipase A(2) (PLA(2)), of which 83.2% were Lys49-PLA(2) homologs (BOJU-1), 0.1% were basic Asp49-PLA(2)s (BOJU-II) and 0.6% were acidic Asp49-PLA(2)s (BOJU-III). Adjoining this very abundant class of proteins we found 88 transcripts codifying for putative sequences of metalloproteases, which after clustering and assembling resulted in three full-length sequences: BOJUMET-I, BOJUMET-II and BOJUMET-III; as well as 25 transcripts related to C-type lectin like protein including a full-length cDNA of a putative galactose binding C-type lectin and a cluster of eight serine-proteases transcripts including a full-length cDNA of a putative serine protease. Among the full-length sequenced clones we identified a nerve growth factor (Bj-NGF) with 92% identity with a human NGF (NGHUBM) and an acidic phospholipase A2 (BthA-I-PLA(2)) displaying 85-93% identity with other snake venom toxins. Genetic distance among PLA(2)s from Bothrops species were evaluated by phylogenetic analysis. Furthermore, analysis of full-length putative Lys49-PLA(2) through molecular modeling showed conserved structural domains, allowing the characterization of those proteins as group II PLA(2)s. The constructed cDNA library provides molecular clones harboring sequences that can be used to probe directly the genetic material from gland venom of other snake species. Expression of complete cDNAs or their modified derivatives will be useful for elucidation of the structure-function relationships of these toxins and peptides of biotechnological interest. (C) 2004 Elsevier SAS. All rights reserved.

Effectiveness-ntu computation with a mathematical model for cross-flow heat exchangers

Due to the wide range of design possibilities, simple manufactured, low maintenance and low cost, cross-flow heat exchangers are extensively used in the petroleum, petrochemical, air conditioning, food storage, and others industries. In this paper a mathematical model for cross-flow heat exchangers with complex flow arrangements for determining epsilon -NTU relations is presented. The model is based on the tube element approach, according to which the heat exchanger outlet temperatures are obtained by discretizing the coil along the tube fluid path. In each cross section of the element, tube-side fluid temperature is assumed to be constant because the heat capacity rate ratio C*=Cmin/Cmax tends toward zero in the element. Thus temperature is controlled by effectiveness of a local element corresponding to an evaporator or a condenser-type element. The model is validated through comparison with theoretical algebraic relations for single-pass cross-flow arrangements with one or more rows. Very small relative errors are obtained showing the accuracy of the present model. epsilon -NTU curves for several complex circuit arrangements are presented. The model developed represents a useful research tool for theoretical and experimental studies on heat exchangers performance.

Photodegradation of dichloroacetic acid and 2,4-dichlorophenol by ferrioxalate/H2O2 system

The photo-Fenton process using potassium ferrioxalate as a mediator in the photodegradation reaction of organochloride compounds in an aqueous medium was investigated. The influence of parameters such as hydrogen peroxide and ferrioxalate concentrations and initial pH, was evaluated using dichloroacetic acid (DCA) as a model compound under black-light lamp irradiation. An upflow annular photoreactor, operating in a single pass or recirculating mode was used during photodegradation experiments with artificial light. The extent of the release of chloride ions was used to evaluate the photodegradation reaction. The optimum pH range observed was 2.5-2.8. The efficiency of DCA dechlorination increased with increasing concentrations of H2O2 and potassium ferrioxalate, reaching a plateau after the addition of 6 and 1.5 mmol/L of those reagents, respectively. The total organic carbon (TOC) content in DCA and 2,4-dichlorophenol (DCP) solutions was compared with the chloride released after photodegradation. The influence of natural solar light intensity, measured at 365 nm, was evaluated for the dechlorination of DCA on typical summer's days showing a linear dependency. The photodegradation of DCA using black-light lamp and solar irradiation was compared.

Caracterização mecânica e microestrutural do aço MARAGING 300, soldado a plasma e submetidas a reparos

Pós-graduação em Engenharia Mecânica - FEG

Desenvolvimento de uma EPS especificação de procedimento de soldagem para união de chapas de aço ASTM A131 com processo FCAW

In any welding process is of utmost importance by welders and responsible qualities of the area understand the process and the variables involved in it, in order to have maximum efficiency in welding both in terms of quality as the final cost , never forgetting, of course, the process conditions which the welder or welding operator shall be submitted. Therefore, we sought to understand the variables relevant to the welding process and develop an EPS (Welding Procedure Specification) as ASME IX for cored wire welding process (FCAW Specification AWS) with shielding gas and automated process for base material ASTM a 131, with 5/16 thick, using a single pass weld, for conditions with pre-and post-heating and the destructive testing for verification and analysis of the resulting weld bead

Caracterização de juntas soldadas em PAW e GTAW de chapas finas em aço maraging 300 submetidas a vários reparos

Pós-graduação em Engenharia Mecânica - FEG

Clearance of p-cresol sulfate and β-2-microglobulin from dialysate by commercially available sorbent technology

Dialysate regeneration by sorbents is an alternative to conventional single-pass dialysis. Little is known about the capacity of sorbents to clear dialysate of “middle molecules” and protein-bound uremic toxins. We studied p-cresol sulfate (PCS) and β-2-microglobulin (β2M) removal from dialysate by a sorbent: 1. PCS (40 mg PCS dissolved in 4 L of fresh dialysate) was recirculated through a sorbent cartridge (SORB Technology, Inc.) for analysis of PCS removal. 2. Spent peritoneal dialysate was recirculated on the “blood” side of a high-flux dialyzer. On the “dialysate” side of the membrane, bicarbonate dialysate was recirculated through a sorbent cartridge. β2M was measured in both streams. Two results are of particular importance for the use of regenerated fluid in chronic dialysis: 1. PCS was virtually completely removed from the dialysate. On average, PCS concentration was reduced to 1.4% of the starting concentration after 60 minutes. PCS extraction across the sorbent was nearly complete at any time. 2. β2M was on average reduced to 14.3% of the starting concentration after 60 minutes. Postsorbent concentrations were consistently below the validated range of the test method. We conclude that PCS and β2M are efficiently removed from the dialysate by commercially available sorbent technology. Spent peritoneal dialysis fluid can be cleared of β2M when circulated against sorbent-regenerated dialysate using a high-flux membrane.

Yellow laser light generation by frequency doubling of the output from a master oscillator fiber power amplifier system

We present a power-scalable approach for yellow laser-light generation based on standard Ytterbium (Yb) doped fibers. To force the cavity to lase at 1154 nm, far above the gain-maximum, measures must be taken to fulfill lasing condition and to suppress competing amplified spontaneous emission (ASE) in the high-gain region. To prove the principle we built a fiber-laser cavity and a fiber-amplifier both at 1154 nm. In between cavity and amplifier we suppressed the ASE by 70 dB using a fiber Bragg grating (FBG) based filter. Finally we demonstrated efficient single pass frequency doubling to 577 nm with a periodically poled lithium niobate crystal (PPLN). With our linearly polarized 1154 nm master oscillator power fiber amplifier (MOFA) system we achieved slope efficiencies of more than 15 % inside the cavity and 24 % with the fiber-amplifier. The frequency doubling followed the predicted optimal efficiency achievable with a PPLN crystal. So far we generated 1.5 W at 1154nm and 90 mW at 577 nm. Our MOFA approach for generation of 1154 nm laser radiation is power-scalable by using multi-stage amplifiers and large mode-area fibers and is therefore very promising for building a high power yellow laser-light source of several tens of Watt.

Cell-cell fusion induced by the Ig3 domain of receptor FGFRL1 in CHO cells.

FGFRL1 is a single-pass transmembrane protein with three extracellular Ig domains. When overexpressed in CHO cells or related cell types, it induces cell-cell fusion and formation of large, multinucleated syncytia. For this fusion-promoting activity, only the membrane-proximal Ig domain (Ig3) and the transmembrane domain are required. It does not matter whether the transmembrane domain is derived from FGFRL1 or from another receptor, but the distance of the Ig3 domain to the membrane is crucial. Fusion can be inhibited with soluble recombinant proteins comprising the Ig1-Ig2-Ig3 or the Ig2-Ig3 domains as well as with monoclonal antibodies directed against Ig3. Mutational analysis reveals a hydrophobic site in Ig3 that is required for fusion. If a single amino acid from this site is mutated, fusion is abolished. The site is located on a β-sheet, which is part of a larger β-barrel, as predicted by computer modeling of the 3D structure of FGFRL1. It is possible that this site interacts with a target protein of neighboring cells to trigger cell-cell fusion.

Abstraction-carrying code: a model for mobile code safety

Proof-Carrying Code (PCC) is a general approach to mobile code safety in which programs are augmented with a certificate (or proof). The intended benefit is that the program consumer can locally validate the certificate w.r.t. the "untrustcd" program by means of a certificate checker a process which should be much simpler, efficient, and automatic than generating the original proof. The practical uptake of PCC greatly depends on the existence of a variety of enabling technologies which allow both proving programs correct and replacing a costly verification process by an efficient checking proceduri on th( consumer side. In this work we propose Abstraction- Carrying Code (ACC), a novel approach which uses abstract interpretation as enabling technology. We argue that the large body of applications of abstract interpretation to program verification is amenable to the overall PCC scheme. In particular, we rely on an expressive class of safely policies which can be defined over different abstract domains. We use an abstraction (or abstract model) of the program computed by standard static analyzers as a certificate. The validity of the abstraction on ihe consumer side is checked in a single pass by a very efficient and specialized abstract-interpreter. We believe that ACC brings the expressiveness, flexibility and automation which is inherent in abstract interpretation techniques to the area of mobile code safety.

Reduced certificates for abstraction-carrying code

Abstraction-Carrying Code (ACC) has recently been proposed as a framework for mobile code safety in which the code supplier provides a program together with an abstraction whose validity entails compliance with a predefined safety policy. The abstraction plays thus the role of safety certifícate and its generation is carried out automatically by a fixed-point analyzer. The advantage of providing a (fixedpoint) abstraction to the code consumer is that its validity is checked in a single pass of an abstract interpretation-based checker. A main challenge is to reduce the size of certificates as much as possible while at the same time not increasing checking time. We introduce the notion of reduced certifícate which characterizes the subset of the abstraction which a checker needs in order to validate (and re-construct) the full certifícate in a single pass. Based on this notion, we instrument a generic analysis algorithm with the necessary extensions in order to identify the information relevant to the checker. We also provide a correct checking algorithm together with sufficient conditions for ensuring its completeness. The experimental results within the CiaoPP system show that our proposal is able to greatly reduce the size of certificates in practice.

Abstraction-carrying code

Proof-Carrying Code (PCC) is a general approach to mobile code safety in which programs are augmented with a certifícate (or proof). The practical uptake of PCC greatly depends on the existence of a variety of enabling technologies which allow both to prove programs correct and to replace a costly verification process by an efñcient checking procedure on the consumer side. In this work we propose Abstraction-Carrying Code (ACC), a novel approach which uses abstract interpretation as enabling technology. We argüe that the large body of applications of abstract interpretation to program verification is amenable to the overall PCC scheme. In particular, we rely on an expressive class of safety policies which can be defined over different abstract domains. We use an abstraction (or abstract model) of the program computed by standard static analyzers as a certifícate. The validity of the abstraction on the consumer side is checked in a single-pass by a very efficient and specialized abstract-interpreter. We believe that ACC brings the expressiveness, flexibility and automation which is inherent in abstract interpretation techniques to the área of mobile code safety. We have implemented and benchmarked ACC within the Ciao system preprocessor. The experimental results show that the checking phase is indeed faster than the proof generation phase, and that the sizes of certificates are reasonable.

On abstraction-carrying code and certificate-size reduction

Abstraction-Carrying Code (ACC) is a framework for mobile code safety in which the code supplier provides a program together with an abstraction (or abstract model of the program) whose validity entails compliance with a predefined safety policy. The abstraction plays thus the role of safety certificate and its generation is carried out automatically by a fixed-point analyzer. The advantage of providing a (fixed-point) abstraction to the code consumer is that its validity is checked in a single pass (i.e., one iteration) of an abstract interpretation-based checker. A main challenge to make ACC useful in practice is to reduce the size of certificates as much as possible, while at the same time not increasing checking time. Intuitively, we only include in the certificate the information which the checker is unable to reproduce without iterating. We introduce the notion of reduced certifícate which characterizes the subset of the abstraction which a checker needs in order to validate (and re-construct) the full certificate in a single pass. Based on this notion, we show how to instrument a generic analysis algorithm with the necessary extensions in order to identify the information relevant to the checker.

Abstract Interpretation-based verification/certification in the ciaoPP system

CiaoPP is the abstract interpretation-based preprocessor of the Ciao multi-paradigm (Constraint) Logic Programming system. It uses modular, incremental abstract interpretation as a fundamental tool to obtain information about programs. In CiaoPP, the semantic approximations thus produced have been applied to perform high- and low-level optimizations during program compilation, including transformations such as múltiple abstract specialization, parallelization, partial evaluation, resource usage control, and program verification. More recently, novel and promising applications of such semantic approximations are being applied in the more general context of program development such as program verification. In this work, we describe our extensión of the system to incorpórate Abstraction-Carrying Code (ACC), a novel approach to mobile code safety. ACC follows the standard strategy of associating safety certificates to programs, originally proposed in Proof Carrying- Code. A distinguishing feature of ACC is that we use an abstraction (or abstract model) of the program computed by standard static analyzers as a certifícate. The validity of the abstraction on the consumer side is checked in a single-pass by a very efficient and specialized abstractinterpreter. We have implemented and benchmarked ACC within CiaoPP. The experimental results show that the checking phase is indeed faster than the proof generation phase, and that the sizes of certificates are reasonable. Moreover, the preprocessor is based on compile-time (and run-time) tools for the certification of CLP programs with resource consumption assurances.

Abstraction carrying code and resource-awareness

Proof-Carrying Code (PCC) is a general approach to mobile code safety in which the code supplier augments the program with a certifícate (or proof). The intended benefit is that the program consumer can locally validate the certifícate w.r.t. the "untrusted" program by means of a certifícate checker—a process which should be much simpler, eíñcient, and automatic than generating the original proof. Abstraction Carrying Code (ACC) is an enabling technology for PCC in which an abstract model of the program plays the role of certifícate. The generation of the certifícate, Le., the abstraction, is automatically carried out by an abstract interpretation-based analysis engine, which is parametric w.r.t. different abstract domains. While the analyzer on the producer side typically has to compute a semantic fixpoint in a complex, iterative process, on the receiver it is only necessary to check that the certifícate is indeed a fixpoint of the abstract semantics equations representing the program. This is done in a single pass in a much more efficient process. ACC addresses the fundamental issues in PCC and opens the door to the applicability of the large body of frameworks and domains based on abstract interpretation as enabling technology for PCC. We present an overview of ACC and we describe in a tutorial fashion an application to the problem of resource-aware security in mobile code. Essentially the information computed by a cost analyzer is used to genérate cost certificates which attest a safe and efficient use of a mobile code. A receiving side can then reject code which brings cost certificates (which it cannot validate or) which have too large cost requirements in terms of computing resources (in time and/or space) and accept mobile code which meets the established requirements.