Working towards the invisible repository

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Use of RAPD-PCR to identify true hybrid plants from crosses between closely related progenitors

RAPD-PCR molecular markers were used to identify common bean and soybean hybrid plants derived from crosses between closely related progenitors, with no apparent phenotypic differences. Primers OP-F12 and OP-0O3 were used to identify true hybrids derived from crosses between common bean cultivars Rudá (A 285) and AN 910408, and soybean cultivars Cristalina and Bossier, respectively. Each primer generated one polymorphic DNA band which was present in the male progenitor and absent in the female progenitor. As RAPD bands are normally inherited as dominant characters, the presence of these bands in the F1 plants confirmed their status.

Multivariate genetic divergence and hybrid performance of cacao (Theobroma cacao L.)

Genetic distances among cacao cultivars were calculated through multivariate analysis, using the D2 statistic, to examine racial group classification and to assess heterotic hybrids. A 5 x 5 complete diallel was evaluated. Over a five-year period (1986-1990), five cultivars of the S1 generation, pertaining to the Lower Amazon Forastero and Trinitario racial groups and 20 crosses between the corresponding S0 parents were analyzed, based upon five yield components - number of healthy and collected fruits per plant (NHFP and NCFP), wet seed weight per plant and per fruit (WSWP and WSWF), and percentage of diseased fruits per plant (PDFP). The diversity analysis suggested a close relationship between the Trinitario and Lower Amazon Forastero groups. A correlation coefficient (r) was calculated to determine the association between genetic diversity and heterosis. Genetic distance of parents by D2 was found to be linearly related to average performance of hybrids for WSWP and WSWF (r = 0.68, P < 0.05 and r = 0.76, P < 0.05, respectively). The heterotic performance for the same components was also correlated with D2, both with r = 0.66 (P < 0.05). A relationship between genetic divergence and combining ability effects was suggested because the most divergent cultivar exhibited a high general combining ability, generating the best performing hybrids. Results indicated that genetic diversity estimates can be useful in selecting parents for crosses and in assessing relationships among cacao racial groups.

Minimizing Circulating Current in Parallel-Connected Photovoltaic Inverters

Parallel-connected photovoltaic inverters are required in large solar plants where it is not economically or technically reasonable to use a single inverter. Currently, parallel inverters require individual isolating transformers to cut the path for the circulating current. In this doctoral dissertation, the problem is approached by attempting to minimize the generated circulating current. The circulating current is a function of the generated common-mode voltages of the parallel inverters and can be minimized by synchronizing the inverters. The synchronization has previously been achieved by a communication link. However, in photovoltaic systems the inverters may be located far apart from each other. Thus, a control free of communication is desired. It is shown in this doctoral dissertation that the circulating current can also be obtained by a common-mode voltage measurement. A control method based on a short-time switching frequency transition is developed and tested with an actual photovoltaic environment of two parallel inverters connected to two 5 kW solar arrays. Controls based on the measurement of the circulating current and the common-mode voltage are generated and tested. A communication-free method of controlling the circulating current between parallelconnected inverters is developed and verified.

Polysiloxane/PVA-glutaraldehyde hybrid composite as solid phase for immunodetections by ELISA

We developed an efficient method to prepare a hybrid inorganic-organic composite based on polyvinyl alcohol (PVA) and polysiloxane using the sol-gel disc technique. Antigen obtained from Yersinia pestis was covalently immobilized onto these discs with glutaraldehyde and used as solid phase in ELISA for antibody detection in serum of rabbits experimentally immunized with plague. Using 1.25 µg antigen per disc, a peroxidase conjugate dilution of 1:4,000 and a serum dilution of 1:200 were adequate for the establishment of the procedure. These values are similar to those used for PVA-glutaraldehyde discs, plasticized filter paper discs and the polyaniline-Dacron composite discs. This procedure is comparable to that which utilizes the adsorption of the antigen to conventional PVC plates, with the amount of antigen being one fourth that employed in conventional PVC plates (5 µg/well). In addition to the performance of the polysiloxane/PVA-glutaraldehyde disc as a matrix for immunodetection, its easy synthesis and low cost are additional advantages for commercial application.

Presence of the RHD pseudogene and the hybrid RHD-CE-Ds gene in Brazilians with the D-negative phenotype

The molecular basis for RHD pseudogene or RHDpsi is a 37-bp insertion in exon 4 of RHD. This insertion, found in two-thirds of D-negative Africans, appears to introduce a stop codon at position 210. The hybrid RHD-CE-Ds, where the 3' end of exon 3 and exons 4 to 8 are derived from RHCE, is associated with the VS+V- phenotype, and leads to a D-negative phenotype in people of African origin. We determined whether Brazilian blood donors of heterogeneous ethnic origin had RHDpsi and RHD-CE-Ds. DNA from 206 blood donors were tested for RHDpsi by a multiplex PCR that detects RHD, RHDpsi and the C and c alleles of RHCE. The RHD genotype was determined by comparison of size of amplified products associated with the RHD gene in both intron 4 and exon 10/3'-UTR. VS was determined by amplification of exon 5 of RHCE, and sequencing of PCR products was used to analyze C733G (Leu245Val). Twenty-two (11%) of the 206 D-negative Brazilians studied had the RHDpsi, 5 (2%) had the RHD-CE-Ds hybrid gene associated with the VS+V- phenotype, and 179 (87%) entirely lacked RHD. As expected, RHD was deleted in all the 50 individuals of Caucasian descent. Among the 156 individuals of African descent, 22 (14%) had inactive RHD and 3% had the RHD-CE-Ds hybrid gene. These data confirm that the inclusion of two different multiplex PCR for RHD is essential to test the D-negative Brazilian population in order to avoid false-positive typing of polytransfused patients and fetuses.

pp-Blast: a "pseudo-parallel" Blast

We have developed a software called pp-Blast that uses the publicly available Blast package and PVM (parallel virtual machine) to partition a multi-sequence query across a set of nodes with replicated or shared databases. Benchmark tests show that pp-Blast running in a cluster of 14 PCs outperformed conventional Blast running in large servers. In addition, using pp-Blast and the cluster we were able to map all human cDNAs onto the draft of the human genome in less than 6 days. We propose here that the cost/benefit ratio of pp-Blast makes it appropriate for large-scale sequence analysis. The source code and configuration files for pp-Blast are available at http://www.ludwig.org.br/biocomp/tools/pp-blast.

The Arctic Ocean between Greenland and Nova Zemla and between the 60th and 82d parallel of latitude from Swedish, Danish, British, Russian and German surveys and explorations up to 1871

Kartta kuuluu A. E. Nordenskiöldin kokoelmaan

Virtual Runtime Application Partitions for Resource Management in Massively Parallel Architectures

This thesis presents a novel design paradigm, called Virtual Runtime Application Partitions (VRAP), to judiciously utilize the on-chip resources. As the dark silicon era approaches, where the power considerations will allow only a fraction chip to be powered on, judicious resource management will become a key consideration in future designs. Most of the works on resource management treat only the physical components (i.e. computation, communication, and memory blocks) as resources and manipulate the component to application mapping to optimize various parameters (e.g. energy efficiency). To further enhance the optimization potential, in addition to the physical resources we propose to manipulate abstract resources (i.e. voltage/frequency operating point, the fault-tolerance strength, the degree of parallelism, and the configuration architecture). The proposed framework (i.e. VRAP) encapsulates methods, algorithms, and hardware blocks to provide each application with the abstract resources tailored to its needs. To test the efficacy of this concept, we have developed three distinct self adaptive environments: (i) Private Operating Environment (POE), (ii) Private Reliability Environment (PRE), and (iii) Private Configuration Environment (PCE) that collectively ensure that each application meets its deadlines using minimal platform resources. In this work several novel architectural enhancements, algorithms and policies are presented to realize the virtual runtime application partitions efficiently. Considering the future design trends, we have chosen Coarse Grained Reconfigurable Architectures (CGRAs) and Network on Chips (NoCs) to test the feasibility of our approach. Specifically, we have chosen Dynamically Reconfigurable Resource Array (DRRA) and McNoC as the representative CGRA and NoC platforms. The proposed techniques are compared and evaluated using a variety of quantitative experiments. Synthesis and simulation results demonstrate VRAP significantly enhances the energy and power efficiency compared to state of the art.

Readout architectures for hybrid pixel detector readout chips

The original contribution of this thesis to knowledge are novel digital readout architectures for hybrid pixel readout chips. The thesis presents asynchronous bus-based architecture, a data-node based column architecture and a network-based pixel matrix architecture for data transportation. It is shown that the data-node architecture achieves readout efficiency 99% with half the output rate as a bus-based system. The network-based solution avoids “broken” columns due to some manufacturing errors, and it distributes internal data traffic more evenly across the pixel matrix than column-based architectures. An improvement of > 10% to the efficiency is achieved with uniform and non-uniform hit occupancies. Architectural design has been done using transaction level modeling (TLM) and sequential high-level design techniques for reducing the design and simulation time. It has been possible to simulate tens of column and full chip architectures using the high-level techniques. A decrease of > 10 in run-time is observed using these techniques compared to register transfer level (RTL) design technique. Reduction of 50% for lines-of-code (LoC) for the high-level models compared to the RTL description has been achieved. Two architectures are then demonstrated in two hybrid pixel readout chips. The first chip, Timepix3 has been designed for the Medipix3 collaboration. According to the measurements, it consumes < 1 W/cm^2. It also delivers up to 40 Mhits/s/cm^2 with 10-bit time-over-threshold (ToT) and 18-bit time-of-arrival (ToA) of 1.5625 ns. The chip uses a token-arbitrated, asynchronous two-phase handshake column bus for internal data transfer. It has also been successfully used in a multi-chip particle tracking telescope. The second chip, VeloPix, is a readout chip being designed for the upgrade of Vertex Locator (VELO) of the LHCb experiment at CERN. Based on the simulations, it consumes < 1.5 W/cm^2 while delivering up to 320 Mpackets/s/cm^2, each packet containing up to 8 pixels. VeloPix uses a node-based data fabric for achieving throughput of 13.3 Mpackets/s from the column to the EoC. By combining Monte Carlo physics data with high-level simulations, it has been demonstrated that the architecture meets requirements of the VELO (260 Mpackets/s/cm^2 with efficiency of 99%).

Effects of conventional vs high-dose rocuronium on the QTc interval during anesthesia induction and intubation in patients undergoing coronary artery surgery: a randomized, double-blind, parallel trial

Myocardial ischemia, as well as the induction agents used in anesthesia, may cause corrected QT interval (QTc) prolongation. The objective of this randomized, double-blind trial was to determine the effects of high- vs conventional-dose bolus rocuronium on QTc duration and the incidence of dysrhythmias following anesthesia induction and intubation. Fifty patients about to undergo coronary artery surgery were randomly allocated to receive conventional-dose (0.6 mg/kg, group C, n=25) or high-dose (1.2 mg/kg, group H, n=25) rocuronium after induction with etomidate and fentanyl. QTc, heart rate, and mean arterial pressure were recorded before induction (T0), after induction (T1), after rocuronium (just before laryngoscopy; T2), 2 min after intubation (T3), and 5 min after intubation (T4). The occurrence of dysrhythmias was recorded. In both groups, QTc was significantly longer at T3 than at baseline [475 vs 429 ms in group C (P=0.001), and 459 vs 434 ms in group H (P=0.005)]. The incidence of dysrhythmias in group C (28%) and in group H (24%) was similar. The QTc after high-dose rocuronium was not significantly longer than after conventional-dose rocuronium in patients about to undergo coronary artery surgery who were induced with etomidate and fentanyl. In both groups, compared with baseline, QTc was most prolonged at 2 min after intubation, suggesting that QTc prolongation may be due to the nociceptive stimulus of intubation.

Metronomic chemotherapy in the neoadjuvant setting: results of two parallel feasibility trials (TraQme and TAME) in patients with HER2+ and HER2− locally advanced breast cancer

Neoadjuvant chemotherapy has practical and theoretical advantages over adjuvant chemotherapy strategy in breast cancer (BC) management. Moreover, metronomic delivery has a more favorable toxicity profile. The present study examined the feasibility of neoadjuvant metronomic chemotherapy in two cohorts [HER2+ (TraQme) and HER2− (TAME)] of locally advanced BC. Twenty patients were prospectively enrolled (TraQme, n=9; TAME, n=11). Both cohorts received weekly paclitaxel at 100 mg/m2 during 8 weeks followed by weekly doxorubicin at 24 mg/m2 for 9 weeks in combination with oral cyclophosphamide at 100 mg/day (fixed dose). The HER2+ cohort received weekly trastuzumab. The study was interrupted because of safety issues. Thirty-six percent of patients in the TAME cohort and all patients from the TraQme cohort had stage III BC. Of note, 33% from the TraQme cohort and 66% from the TAME cohort displayed hormone receptor positivity in tumor tissue. The pathological complete response rates were 55% and 18% among patients enrolled in the TraQme and TAME cohorts, respectively. Patients in the TraQme cohort had more advanced BC stages at diagnosis, higher-grade pathological classification, and more tumors lacking hormone receptor expression, compared to the TAME cohort. The toxicity profile was also different. Two patients in the TraQme cohort developed pneumonitis, and in the TAME cohort we observed more hematological toxicity and hand-foot syndrome. The neoadjuvant metronomic chemotherapy regimen evaluated in this trial was highly effective in achieving a tumor response, especially in the HER2+ cohort. Pneumonitis was a serious, unexpected adverse event observed in this group. Further larger and randomized trials are warranted to evaluate the association between metronomic chemotherapy and trastuzumab treatment.

HYBRID ARTIFICIAL NEURAL NETWORK APPLIEDTO MODELING SCFE OF BASIL AND ROSEMARY OILS

This work presents the results of a Hybrid Neural Network (HNN) technique as applied to modeling SCFE curves obtained from two Brazilian vegetable matrices. A series Hybrid Neural Network was employed to estimate the parameters of the phenomenological model. A small set of SCFE data of each vegetable was used to generate an extended data set, sufficient to train the network. Afterwards, other sets of experimental data, not used in the network training, were used to validate the present approach. The series HNN correlates well the experimental data and it is shown that the predictions accomplished with this technique may be promising for SCFE purposes.

Implementing Green IT approach for transferring Big Data over Parallel Data Link

The whole research of the current Master Thesis project is related to Big Data transfer over Parallel Data Link and my main objective is to assist the Saint-Petersburg National Research University ITMO research team to accomplish this project and apply Green IT methods for the data transfer system. The goal of the team is to transfer Big Data by using parallel data links with SDN Openflow approach. My task as a team member was to compare existing data transfer applications in case to verify which results the highest data transfer speed in which occasions and explain the reasons. In the context of this thesis work a comparison between 5 different utilities was done, which including Fast Data Transfer (FDT), BBCP, BBFTP, GridFTP, and FTS3. A number of scripts where developed which consist of creating random binary data to be incompressible to have fair comparison between utilities, execute the Utilities with specified parameters, create log files, results, system parameters, and plot graphs to compare the results. Transferring such an enormous variety of data can take a long time, and hence, the necessity appears to reduce the energy consumption to make them greener. In the context of Green IT approach, our team used Cloud Computing infrastructure called OpenStack. It’s more efficient to allocated specific amount of hardware resources to test different scenarios rather than using the whole resources from our testbed. Testing our implementation with OpenStack infrastructure results that the virtual channel does not consist of any traffic and we can achieve the highest possible throughput. After receiving the final results we are in place to identify which utilities produce faster data transfer in different scenarios with specific TCP parameters and we can use them in real network data links.