Grid warehousing of molecular dynamics protein unfolding data

With the increasing awareness of protein folding disorders, the explosion of genomic information, and the need for efficient ways to predict protein structure, protein folding and unfolding has become a central issue in molecular sciences research. Molecular dynamics computer simulations are increasingly employed to understand the folding and unfolding of proteins. Running protein unfolding simulations is computationally expensive and finding ways to enhance performance is a grid issue on its own. However, more and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. This paper describes efforts to provide a grid-enabled data warehouse for protein unfolding data. We outline the challenge and present first results in the design and implementation of the data warehouse.

Grid computing solutions for distributed repositories of protein folding and unfolding simulations

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data and a data warehouse. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular we look at two aspects, first how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories --- this is an important and challenging aspect of P-found because the data volumes involved are too large to be centralised. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling new scientific discoveries.

P-found: grid-enabling distributed repositories of protein folding and unfolding simulations for data mining

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform data mining and other analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data that is used to populate the second component, and a data warehouse that contains important molecular properties. These properties may be used for data mining studies. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular, we look at two aspects: firstly, how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories — this is an important and challenging aspect of P-found, due to the large data volumes involved and the desire of scientists to maintain control of their own data. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling scientific discovery.

Quantifying the relationship between temperature regulation in the ear and floret development stage in wheat (Triticum aestivum L.) under heat and drought stress

Thermal imaging is a valuable tool for the elucidation of gas exchange dynamics between a plant and its environment. The presence of stomata in wheat glumes and awns offers an opportunity to assess photosynthetic activity of ears up to and during flowering. The knowledge of spatial and temporal thermodynamics of the wheat ear may provide insight into interactions between floret developmental stage (FDS), temperature depression (TD) and ambient environment, with potential to be used as a high-throughput screening tool for breeders. A controlled environment study was conducted using six spring wheat (Triticum aestivum L.) genotypes of the elite recombinant inbred line Seri/Babax. Average ear temperature (AET) was recorded using a hand held infrared camera and gas exchange was measured by enclosing ears in a custom built cuvette. FDS was monitored and recorded daily throughout the study. Plants were grown in pots and exposed to a combination of two temperature and two water regimes. In the examined wheat lines, TD varied from 0.1°C to 0.6°C according to the level of stress imposed. The results indicated that TD does not occur at FDS F3, the peak of active flowering, but during the preceding stages prior to pollen release and stigma maturity (F1-F2). These findings suggest that ear temperature during the early stages of anthesis, prior to pollen release and full extension of the stigma, are likely to be the most relevant for identifying heat stress tolerant genotypes.

Mandibulofacial Syndrome With Growth and Mental Retardation, Microcephaly, Ear Anomalies With Skin Tags, and Cleft Palate in a Mother and Her Son: Autosomal Dominant or X-Linked Syndrome?

We report on a Brazilian mother and her son affected with mandibulofacial dysostosis, growth and mental retardation, microcephaly, first branchial arch anomalies, and cleft palate. To date only three males and one female, all sporadic cases, with a similar condition have been reported. This article describes the first familial case with this rare condition indicating autosomal dominant or X-linked inheritance. (C) 2009 Wiley-Liss, Inc.

Structural stability and reversible unfolding of recombinant porcine S100A12

Porcine S100A12 is a member of the S100 proteins, family of small acidic calcium-binding proteins characterized by the presence of two EF-hand motifs. These proteins are involved in many cellular events such as the regulation of protein phosphorylation, enzymatic activity, protein-protein interaction, Ca(2+) homeostasis, inflammatory processes and intermediate filament polymerization. In addition, members of this family bind Zn(2+) or Ca(2+) with cooperative effect on binding. In this study, the gene sequence encoding porcine S100A12 was obtained by the synthetic gene approach using E. coli codon bias. Additionally, we report a thermodynamic study of the recombinant S100A12 using circular dichroism, fluorescence and isothermal titration calorimetry. The results of urea and temperature induced unfolding and refolding processes indicated a reversible two-state process. Also, the ANS fluorescence studies showed that in presence of divalent ions the protein exposes hydrophobic sites which could facilitate the interaction with other proteins and trigger the physiological responses. (c) 2008 Elsevier B.V. All rights reserved.

Is the unfolding of the group discussion off-pattern? Improving coordination support in educational forums using mobile devices

A forum is a valuable tool to foster reflection in an in-depth discussion; however, it forces the course mediator to continually pay close attention in order to coordinate learners` activities. Moreover, monitoring a forum is time consuming given that it is impossible to know in advance when new messages are going to be posted. Additionally, a forum may be inactive for a long period and suddenly receive a burst of messages forcing forum mediators to frequently log on in order to know how the discussion is unfolding to intervene whenever it is necessary. Mediators also need to deal with a large amount of messages to identify off-pattern situations. This work presents a piece of action research that investigates how to improve coordination support in a forum using mobile devices for mitigating mediator`s difficulties in following the status of a forum. Based on summarized information extracted from message meta-data, mediators consult visual information summaries on PDAs and receive textual notifications in their mobile phone. This investigation revealed that mediators used the mobile-based coordination support to keep informed on what is taking place within the forum without the need to log on their desktop computer. (C) 2009 Elsevier Ltd. All rights reserved.

Implementação da rotina de unfolding para determinação de distribuição de tamanho de grãos esféricos via distribuição de interceptos lineares e de área de seção

Na unfolding method of linear intercept distributions and secction área distribution was implemented for structures with spherical grains. Although the unfolding routine depends on the grain shape, structures with spheroidal grains can also be treated by this routine. Grains of non-spheroidal shape can be treated only as approximation. A software was developed with two parts. The first part calculates the probability matrix. The second part uses this matrix and minimizes the chi-square. The results are presented with any number of size classes as required. The probability matrix was determined by means of the linear intercept and section area distributions created by computer simulation. Using curve fittings the probability matrix for spheres of any sizes could be determined. Two kinds of tests were carried out to prove the efficiency of the Technique. The theoretical tests represent ideal cases. The software was able to exactly find the proposed grain size distribution. In the second test, a structure was simulated in computer and images of its slices were used to produce the corresponding linear intercept the section area distributions. These distributions were then unfolded. This test simulates better reality. The results show deviations from the real size distribution. This deviations are caused by statistic fluctuation. The unfolding of the linear intercept distribution works perfectly, but the unfolding of section area distribution does not work due to a failure in the chi-square minimization. The minimization method uses a matrix inversion routine. The matrix generated by this procedure cannot be inverted. Other minimization method must be used

Relationships between physical, morphological, and physiological characteristics of seeds developed at different positions of the ear of two maize (Zea mays L.) hybrids

Maize seeds developed at different portions of the ear of two hybrids (one, a large seeded, and the other a small seeded hybrid) were compared as to physical positions, morphological, and physiological characteristics viewing to gain information to be used during seed conditioning. The number of positions in the ear were 10, starting at the proximal and ending at the distal end. For the sake of simplification, the data were combined to refer to seeds of the proximal, the central and the distal sectors of an ear. Measurements made of the seeds as to shape (length, width, and thickness) and as to size (1,000 seeds weight) indicated that the round seeds growing at the distal sector are significantly smaller (mainly when thickness is considered) and lighter than those growing at the proximal sector. on the other hand, determinations of the physiological quality indicated that the round-proximal and the central seeds are equivalent and both significantly superior to the round-distal ones, Considering these significant differences as to size, shape, and physiological quality, a proposition of suppressing part of the round-distal from the totallity of the round seeds during the operations of seed conditioning is made.

Association between ear creases and peripheral arterial disease

INTRODUCTION: Peripheral arterial disease is a severe manifestation of atherosclerosis that can lead to critical ischemia of the lower limbs and is also associated with high cardiovascular risk. Diagonal lobular and anterior tragal ear creases have been associated with coronary artery disease, but they have not yet been investigated in patients with peripheral arterial disease.OBJECTIVES: To evaluate the prevalence of ear creases among patients with peripheral arterial disease of the lower limbs, compared with patients without documented atherosclerotic disease.METHODS: Cross-sectional study including 60 male patients with peripheral arterial disease of the lower limbs and 60 dermatologic outpatients matched for age and gender. The associations were adjusted for other risk factors by conditional logistic regression.RESULTS: The prevalence of diagonal and anterior tragal ear creases was higher among cases (73% vs. 25% and 80% vs. 43%, respectively) than controls; these associations remained significant even when adjusting for other known risk factors of atherosclerosis (odds ratio = 8.1 and 4.1, respectively).CONCLUSIONS: Ear creases are independently associated with peripheral arterial disease and may be an external marker for risk identification.

Rehabilitation with ear prosthesis linked to osseointegrated implants

Background: The absence of an ear, which can be the result of a congenital malformation, surgical tumour resection or traumatic injury, is a significant aesthetic problem. Attachment of ear prostheses with adhesives can cause local irritation for the wearer and affect the colour of the prostheses. Use of implants in craniofacial reconstruction can improve the retention and stability of prostheses giving to patient greater comfort and security relative to adhesive attachment.Objective: The aim of this report was to present a clinical case of a mutilated patient who was rehabilitated by means of installing an ear prosthesis fixed through osseointegrated implants.Materials and methods: The patient had two implants installed in the mastoid region that were linked by a bar, and a clip-type system was used. The ear prosthesis was constructed from medical-use silicone, pigmented to match the patient's skin colour and linked to the retention system.Conclusion: The patient's rehabilitation was satisfactory from both a functional and an aesthetic point of view, making it possible for the patient to return to a normal social life and regain lost self-esteem.

Mouse ear edema modulation by different propolis ethanol extracts

The anti-inflammatory activity of 14 commercial ethanol extracts of propolis were evaluated, using a mouse ear inflammation model induced by arachidonic acid. Indometacin was also assayed as standard anti-inflammatory agent. Different activities were observed and discussed. This model could be used to assess the anti-inflammatory quality of propolis extracts and facilitate their posological usage on skin edema resulting from wounds.