Relationships between crown architecture and available irradiance in two cerrado species with different leaf phenologies

Structural differences between cerrado species with different leaf phenologies are linked to crown architecture, leaf production, and biomass allocation to shoots and leaves. The present study characterized crown structures and the patterns of biomass allocation to leaves and shoots in two woody cerrado species with contrasting leaf phenologies and quantified the irradiance reaching their leaves to determine the best period during the day for photosynthetic activity. The shoots and leaves of five individuals of both Annona coriacea (deciduous) and Hymenaea stigonocarpa (evergreen) were collected along a 50 m transect in a cerrado fragment within the urban perimeter of Catalão - GO, to determine their patterns of biomass allocation in their crowns. The evergreen H. stigonocarpa had significantly higher mean values of shoot inclination (SI), petiole length (PL), leaf area (LA), leaf display index (LDI), and individual leaf area per shoot (ILA), while the deciduous species A. coriacea had significantly higher leaf numbers (LN). The more complex crown of H. stigonocarpa had shoots in more erect positions (orthotropic), with intense self-shading within shoots; A. coriacea, on the other hand, had slanting (plagiotropic) shoots in the crown, allowing similar irradiance levels to all leaf surfaces. The production of plagiotropic shoots by the deciduous species (A. coriacea) is a strategy that enables its use of incident sunlight early in the morning and preventing excessive water loss or excessive irradiance. Hymenaea stigonocarpa (an evergreen), by contrast, had orthotropic shoots and uses intense self-shading as a strategy to avoid excessive irradiance, especially at midday. Differences in crown architectures between evergreen and deciduous species of cerrado sensu stricto can therefore be viewed as adaptations to the environmental light regime.

Potential of twenty exotic germplasms to improve Brazilian maize architecture

Temperate and temperate x tropical germplasms were introduced into the maize breeding of the Department of Genetics (ESALQ-USP). Twenty populations designated as P-1 to P-20 and a check population were evaluated in a randomized complete block design with two replications at Piracicaba, SP, Brazil. Plots were 2.0 m long, spaced 1.0 m apart, with 10 plants per plot after thinning. The following traits were evaluated: PH, plant height; EH, ear height; TB, tassel branch number; KW, 100 kernels weight; EL, ear length; ED, ear diameter; KR, kernels per row, and RN, number of rows of kernels. The means of the exotic populations showed a variation in performance for all traits. The population means were greater than check means for KW, EL, and KR. Populations P-9, P-10, P-12, and P-13 showed low relative ear placement values (EH/PH index), indicating that these materials could contribute to lower ear placement in local populations. P-1 and P-9 showed a high potential to reduce TB. The phenotypic correlation coefficients among populations were positive for most combinations, except for RN with PH, EH, TB, and KW. Predictions of 19 composite means were obtained for all traits.

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.

Stiffness based trajectory planning and feedforward based vibration suppression control of parallel robot machines

The dissertation proposes two control strategies, which include the trajectory planning and vibration suppression, for a kinematic redundant serial-parallel robot machine, with the aim of attaining the satisfactory machining performance. For a given prescribed trajectory of the robot's end-effector in the Cartesian space, a set of trajectories in the robot's joint space are generated based on the best stiffness performance of the robot along the prescribed trajectory. To construct the required system-wide analytical stiffness model for the serial-parallel robot machine, a variant of the virtual joint method (VJM) is proposed in the dissertation. The modified method is an evolution of Gosselin's lumped model that can account for the deformations of a flexible link in more directions. The effectiveness of this VJM variant is validated by comparing the computed stiffness results of a flexible link with the those of a matrix structural analysis (MSA) method. The comparison shows that the numerical results from both methods on an individual flexible beam are almost identical, which, in some sense, provides mutual validation. The most prominent advantage of the presented VJM variant compared with the MSA method is that it can be applied in a flexible structure system with complicated kinematics formed in terms of flexible serial links and joints. Moreover, by combining the VJM variant and the virtual work principle, a systemwide analytical stiffness model can be easily obtained for mechanisms with both serial kinematics and parallel kinematics. In the dissertation, a system-wide stiffness model of a kinematic redundant serial-parallel robot machine is constructed based on integration of the VJM variant and the virtual work principle. Numerical results of its stiffness performance are reported. For a kinematic redundant robot, to generate a set of feasible joints' trajectories for a prescribed trajectory of its end-effector, its system-wide stiffness performance is taken as the constraint in the joints trajectory planning in the dissertation. For a prescribed location of the end-effector, the robot permits an infinite number of inverse solutions, which consequently yields infinite kinds of stiffness performance. Therefore, a differential evolution (DE) algorithm in which the positions of redundant joints in the kinematics are taken as input variables was employed to search for the best stiffness performance of the robot. Numerical results of the generated joint trajectories are given for a kinematic redundant serial-parallel robot machine, IWR (Intersector Welding/Cutting Robot), when a particular trajectory of its end-effector has been prescribed. The numerical results show that the joint trajectories generated based on the stiffness optimization are feasible for realization in the control system since they are acceptably smooth. The results imply that the stiffness performance of the robot machine deviates smoothly with respect to the kinematic configuration in the adjacent domain of its best stiffness performance. To suppress the vibration of the robot machine due to varying cutting force during the machining process, this dissertation proposed a feedforward control strategy, which is constructed based on the derived inverse dynamics model of target system. The effectiveness of applying such a feedforward control in the vibration suppression has been validated in a parallel manipulator in the software environment. The experimental study of such a feedforward control has also been included in the dissertation. The difficulties of modelling the actual system due to the unknown components in its dynamics is noticed. As a solution, a back propagation (BP) neural network is proposed for identification of the unknown components of the dynamics model of the target system. To train such a BP neural network, a modified Levenberg-Marquardt algorithm that can utilize an experimental input-output data set of the entire dynamic system is introduced in the dissertation. Validation of the BP neural network and the modified Levenberg- Marquardt algorithm is done, respectively, by a sinusoidal output approximation, a second order system parameters estimation, and a friction model estimation of a parallel manipulator, which represent three different application aspects of this method.

JNK regulates dendrite and spine architecture in the central nervous system influencing spatial learning and motor tasks

JNK1 is a MAP-kinase that has proven a significant player in the central nervous system. It regulates brain development and the maintenance of dendrites and axons. Several novel phosphorylation targets of JNK1 were identified in a screen performed in the Coffey lab. These proteins were mainly involved in the regulation of neuronal cytoskeleton, influencing the dynamics and stability of microtubules and actin. These structural proteins form the dynamic backbone for the elaborate architecture of the dendritic tree of a neuron. The initiation and branching of the dendrites requires a dynamic interplay between the cytoskeletal building blocks. Both microtubules and actin are decorated by associated proteins which regulate their dynamics. The dendrite-specific, high molecular weight microtubule associated protein 2 (MAP2) is an abundant protein in the brain, the binding of which stabilizes microtubules and influences their bundling. Its expression in non-neuronal cells induces the formation of neurite-like processes from the cell body, and its function is highly regulated by phosphorylation. JNK1 was shown to phosphorylate the proline-rich domain of MAP2 in vivo in a previous study performed in the group. Here we verify three threonine residues (T1619, T1622 and T1625) as JNK1 targets, the phosphorylation of which increases the binding of MAP2 to microtubules. This binding stabilizes the microtubules and increases process formation in non-neuronal cells. Phosphorylation-site mutants were engineered in the lab. The non-phosphorylatable mutant of MAP2 (MAP2- T1619A, T1622A, T1625A) in these residues fails to bind microtubules, while the pseudo-phosphorylated form, MAP2- T1619D, T1622D, Thr1625D, efficiently binds and induces process formation even without the presence of active JNK1. Ectopic expression of the MAP2- T1619D, T1622D, Thr1625D in vivo in mouse brain led to a striking increase in the branching of cortical layer 2/3 (L2/3) pyramidal neurons, compared to MAP2-WT. The dendritic complexity defines the receptive field of a neuron and dictates the output to the postsynaptic cells. Previous studies in the group indicated altered dendrite architecture of the pyramidal neurons in the Jnk1-/- mouse motor cortex. Here, we used Lucifer Yellow loading and Sholl analysis of neurons in order to study the dendritic branching in more detail. We report a striking, opposing effect in the absence of Jnk1 in the cortical layers 2/3 and 5 of the primary motor cortex. The basal dendrites of pyramidal neurons close to the pial surface at L2/3 show a reduced complexity. In contrast, the L5 neurons, which receive massive input from the L2/3 neurons, show greatly increased branching. Another novel substrate identified for JNK1 was MARCKSL1, a protein that regulates actin dynamics. It is highly expressed in neurons, but also in various cancer tissues. Three phosphorylation target residues for JNK1 were identified, and it was demonstrated that their phosphorylation reduces actin turnover and retards migration of these cells. Actin is the main cytoskeletal component in dendritic spines, the site of most excitatory synapses in pyramidal neurons. The density and gross morphology of the Lucifer Yellow filled dendrites were characterized and we show reduced density and altered morphology of spines in the motor cortex and in the hippocampal area CA3. The dynamic dendritic spines are widely considered to function as the cellular correlate during learning. We used a Morris water maze to test spatial memory. Here, the wild-type mice outperformed the knock-out mice during the acquisition phase of the experiment indicating impaired special memory. The L5 pyramidal neurons of the motor cortex project to the spinal cord and regulate the movement of distinct muscle groups. Thus the altered dendrite morphology in the motor cortex was expected to have an effect on the input-output balance in the signaling from the cortex to the lower motor circuits. A battery of behavioral tests were conducted for the wild-type and Jnk1-/- mice, and the knock-outs performed poorly compared to wild-type mice in tests assessing balance and fine motor movements. This study expands our knowledge of JNK1 as an important regulator of the dendritic fields of neurons and their manifestations in behavior.

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

Gastroesophageal reflux episodes in asthmatic patients and their temporal relation with sleep architecture

Gastroesophageal reflux (GER) is common in asthma patients and can contribute to sleep disruption. The aim of the present study was to determine the time-related distribution of GER events together with their impact on sleep in asthmatic subjects with GER disease symptoms. The inclusion criteria were: 18-65 years, controlled moderate to severe asthma and GER-compatible clinical evidence. The exclusion criteria were: chronic obstructive lung disease, smoking, infections of the upper airways, use of oral corticosteroids, other co-morbidities, pregnancy, sleep-related disorders, night-time shift work, and the use of substances with impact on sleep. Asthmatic patients with nocturnal symptoms were excluded. All-night polysomnography and esophageal pH monitoring were recorded simultaneously. Of the 147 subjects selected, 31 patients and 31 controls were included. Seventeen patients were classified as DeMeester positive and 14 as DeMeester negative. Both groups displayed similar outcomes when general variables were considered. Sleep stage modification one minute prior to GER was observed in the DeMeester-positive group. Awakening was the most frequent occurrence at GER onset and during the 1-min period preceding 38% of the nocturnal GER. Sleep stage 2 was also prevalent and preceded 36% of GER events. In the DeMeester-negative group, awakening was the most frequent response before and during GER. Modifications in sleep stages, arousals or awakenings were associated with 75% of the total GER events analyzed during the period of one minute before and after the fall of esophageal pH below 4 in the DeMeester-positive group. These data provide evidence that sleep modifications precede the GER events in asthmatic patients.

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.

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.

Formal modelling for digital media distribution

Human beings have always strived to preserve their memories and spread their ideas. In the beginning this was always done through human interpretations, such as telling stories and creating sculptures. Later, technological progress made it possible to create a recording of a phenomenon; first as an analogue recording onto a physical object, and later digitally, as a sequence of bits to be interpreted by a computer. By the end of the 20th century technological advances had made it feasible to distribute media content over a computer network instead of on physical objects, thus enabling the concept of digital media distribution. Many digital media distribution systems already exist, and their continued, and in many cases increasing, usage is an indicator for the high interest in their future enhancements and enriching. By looking at these digital media distribution systems, we have identified three main areas of possible improvement: network structure and coordination, transport of content over the network, and the encoding used for the content. In this thesis, our aim is to show that improvements in performance, efficiency and availability can be done in conjunction with improvements in software quality and reliability through the use of formal methods: mathematical approaches to reasoning about software so that we can prove its correctness, together with the desirable properties. We envision a complete media distribution system based on a distributed architecture, such as peer-to-peer networking, in which different parts of the system have been formally modelled and verified. Starting with the network itself, we show how it can be formally constructed and modularised in the Event-B formalism, such that we can separate the modelling of one node from the modelling of the network itself. We also show how the piece selection algorithm in the BitTorrent peer-to-peer transfer protocol can be adapted for on-demand media streaming, and how this can be modelled in Event-B. Furthermore, we show how modelling one peer in Event-B can give results similar to simulating an entire network of peers. Going further, we introduce a formal specification language for content transfer algorithms, and show that having such a language can make these algorithms easier to understand. We also show how generating Event-B code from this language can result in less complexity compared to creating the models from written specifications. We also consider the decoding part of a media distribution system by showing how video decoding can be done in parallel. This is based on formally defined dependencies between frames and blocks in a video sequence; we have shown that also this step can be performed in a way that is mathematically proven correct. Our modelling and proving in this thesis is, in its majority, tool-based. This provides a demonstration of the advance of formal methods as well as their increased reliability, and thus, advocates for their more wide-spread usage in the future.

Changes in canola plant architecture and seed physiological quality in response to different sowing densities

The aim of this study was to evaluate changes in canola yield components and seed physiological quality in response to different sowing densities. The study was made in a greenhouse at the REIPESOL Company Technological Center, Madrid - Spain, with the commercial "Toccata" hybrid variety. The initial sowing density was 360,000 plants/ha and the plant population was later thinned down to include treatments of 250 and 180 thousand plants/ha. Harvested seeds were sent to the Seed Technology Center Laboratory (CATES) at the Madrid Polytechnic University (UPM) to evaluate changes in plant architecture and yield components, as well as the seed physiological quality of different plant parts. Results demonstrated that canola plants showed changes in morphology and yield components in response to different sowing densities. The population of 250,000 plants/ha showed the best seed yield demonstrating that maximum yield is directly related to a correct sowing density. The number of pods/plant was the most important component for increased seed yield/plant and seed yield/area. The spatial distribution of canola seeds in the plant and canola sowing density did not affect seed physiological quality.