Homology-based identification of capsid determinants that protect HIV1 from human TRIM5{alpha} restriction.

The tropism of retroviruses relies on their ability to exploit cellular factors for their replication as well as to avoid host-encoded inhibitory activities such as TRIM5α. N-tropic murine leukemia virus (MLV) is sensitive to human TRIM5α restriction, whereas human immunodeficiency virus type 1 (HIV1) escapes this antiviral factor. We showed previously that mutation of four critical amino acid residues within the capsid (CA) can render MLV resistant to huTRIM5α. Here, we exploit the high degree of conservation in the tertiary structure of retroviral capsids to map the corresponding positions on the HIV1 capsid. We then demonstrate that, by introducing changes at some of these positions, HIV1 becomes sensitive to huTRIM5α restriction, a phenomenon reinforced by additionally mutating the nearby cyclophilin A (CypA)-binding loop of the viral protein. These results indicate that retroviruses have evolved similar mechanisms to escape TRIM5α restriction, via the interference of structurally homologous determinants in the viral capsid.

Structural changes induced by daily music listening in the recovering brain after middle cerebral artery stroke: a voxel-based morphometry study

Music is a highly complex and versatile stimulus for the brain that engages many temporal, frontal, parietal, cerebellar, and subcortical areas involved in auditory, cognitive, emotional, and motor processing. Regular musical activities have been shown to effectively enhance the structure and function of many brain areas, making music a potential tool also in neurological rehabilitation. In our previous randomized controlled study, we found that listening to music on a daily basis can improve cognitive recovery and improve mood after an acute middle cerebral artery stroke. Extending this study, a voxel-based morphometry (VBM) analysis utilizing cost function masking was performed on the acute and 6-month post-stroke stage structural magnetic resonance imaging data of the patients (n = 49) who either listened to their favorite music [music group (MG), n = 16] or verbal material [audio book group (ABG), n = 18] or did not receive any listening material [control group (CG), n = 15] during the 6-month recovery period. Although all groups showed significant gray matter volume (GMV) increases from the acute to the 6-month stage, there was a specific network of frontal areas [left and right superior frontal gyrus (SFG), right medial SFG] and limbic areas [left ventral/subgenual anterior cingulate cortex (SACC) and right ventral striatum (VS)] in patients with left hemisphere damage in which the GMV increases were larger in the MG than in the ABG and in the CG. Moreover, the GM reorganization in the frontal areas correlated with enhanced recovery of verbal memory, focused attention, and language skills, whereas the GM reorganization in the SACC correlated with reduced negative mood. This study adds on previous results, showing that music listening after stroke not only enhances behavioral recovery, but also induces fine-grained neuroanatomical changes in the recovering brain.

Converter-flux-based current control of voltage source PWM rectifiers - analysis and implementation

Pulsewidth-modulated (PWM) rectifier technology is increasingly used in industrial applications like variable-speed motor drives, since it offers several desired features such as sinusoidal input currents, controllable power factor, bidirectional power flow and high quality DC output voltage. To achieve these features,however, an effective control system with fast and accurate current and DC voltage responses is required. From various control strategies proposed to meet these control objectives, in most cases the commonly known principle of the synchronous-frame current vector control along with some space-vector PWM scheme have been applied. Recently, however, new control approaches analogous to the well-established direct torque control (DTC) method for electrical machines have also emerged to implement a high-performance PWM rectifier. In this thesis the concepts of classical synchronous-frame current control and DTC-based PWM rectifier control are combined and a new converter-flux-based current control (CFCC) scheme is introduced. To achieve sufficient dynamic performance and to ensure a stable operation, the proposed control system is thoroughly analysed and simple rules for the controller design are suggested. Special attention is paid to the estimationof the converter flux, which is the key element of converter-flux-based control. Discrete-time implementation is also discussed. Line-voltage-sensorless reactive reactive power control methods for the L- and LCL-type line filters are presented. For the L-filter an open-loop control law for the d-axis current referenceis proposed. In the case of the LCL-filter the combined open-loop control and feedback control is proposed. The influence of the erroneous filter parameter estimates on the accuracy of the developed control schemes is also discussed. A newzero vector selection rule for suppressing the zero-sequence current in parallel-connected PWM rectifiers is proposed. With this method a truly standalone and independent control of the converter units is allowed and traditional transformer isolation and synchronised-control-based solutions are avoided. The implementation requires only one additional current sensor. The proposed schemes are evaluated by the simulations and laboratory experiments. A satisfactory performance and good agreement between the theory and practice are demonstrated.

Identification and characterization of a resistance gene analog (RGA) from the Caricaceae Dumort family

The majority of cloned resistance (R) genes characterized so far contain a nucleotide-binding site (NBS) and a leucine-rich repeat (LRR) domain, where highly conserved motifs are found. Resistance genes analogs (RGAs) are genetic markers obtained by a PCR-based strategy using degenerated oligonucleotide primers drawn from these highly conserved "motifs". This strategy has the advantage of the high degree of structural and amino acid sequence conservation that is observed in R genes. The objective of the present study was to search for RGAs in Carica papaya L. and Vasconcellea cauliflora Jacq. A. DC. Out of three combinations of primers tested, only one resulted in amplification. The amplified product was cloned in pCR2.1TOPO and than sequenced using M13 forward and reverse primers. Forty-eight clones were sequenced from each species. The 96 sequences generated for each species were cleaned of vector sequences and clustered using CAP3 assembler. From the GENEBANK, one RGA was identified in C. papaya showing a BlastX e-value of 2x10-61 to the gb|AAP45165.1| putative disease resistant protein RGA3 (Solanum bulbocastanum). To the extent of our knowledge this is the first report of a RGA in the Caricaceae Dumort family. Preliminary structural studies were performed to further characterize this putative NBS-LRR type protein. Efforts to search for other RGAs in papaya should continue, mostly to provide basis for the development of transgenic papaya with resistance to diseases.

Short communication.Wood identification based on their common name and their transversal surface anatomy. Application to the batch from the expedition of Ruiz and Pavon

Aim of study: To identify species of wood samples based on common names and anatomical analyses of their transversal surfaces (without microscopic preparations). Area of study: Spain and South America Material and methods: The test was carried out on a batch of 15 lumber samples deposited in the Royal Botanical Garden in Madrid, from the expedition by Ruiz and Pavon (1777-1811). The first stage of the methodology is to search and to make a critical analysis of the databases which list common nomenclature along with scientific nomenclature. A geographic filter was then applied to the information resulting from the samples with a more restricted distribution. Finally an anatomical verification was carried out with a pocket microscope with a magnification of x40, equipped with a 50 micrometers resolution scale. Main results: The identification of the wood based exclusively on the common name is not useful due to the high number of alternative possibilities (14 for “naranjo”, 10 for “ébano”, etc.). The common name of one of the samples (“huachapelí mulato”) enabled the geographic origin of the samples to be accurately located to the shipyard area in Guayaquil (Ecuador). Given that Ruiz y Pavon did not travel to Ecuador, the specimens must have been obtained by Tafalla. It was possible to determine correctly 67% of the lumber samples from the batch. In 17% of the cases the methodology did not provide a reliable identification. Research highlights: It was possible to determine correctly 67% of the lumber samples from the batch and their geographic provenance. The identification of the wood based exclusively on the common name is not useful.

A Gradient based algorithm for blind inversion of Wiener System using multi-variate score functions

A Wiener system is a linear time-invariant filter, followed by an invertible nonlinear distortion. Assuming that the input signal is an independent and identically distributed (iid) sequence, we propose an algorithm for estimating the input signal only by observing the output of the Wiener system. The algorithm is based on minimizing the mutual information of the output samples, by means of a steepest descent gradient approach.

Time to identify cardiac arrest and provide dispatch-assisted cardio-pulmonary resuscitation in a criteria-based dispatch system.

INTRODUCTION: Dispatch-assisted cardiopulmonary resuscitation (DA-CPR) plays a key role in out-of-hospital cardiac arrests. We sought to measure dispatchers' performances in a criteria-based system in recognizing cardiac arrest and delivering DA-CPR. Our secondary purpose was to identify the factors that hampered dispatchers' identification of cardiac arrests, the factors that prevented them from proposing DA-CPR, and the factors that prevented bystanders from performing CPR. METHODS AND RESULTS: We reviewed dispatch recordings for 1254 out-of-hospital cardiac arrests occurring between January 1, 2011 and December 31, 2013. Dispatchers correctly identified cardiac arrests in 71% of the reviewed cases and 84% of the cases in which they were able to assess for patient consciousness and breathing. The median time to recognition of the arrest was 60s. The median time to start chest compression was 220s. CONCLUSIONS: This study demonstrates that performances from a criteria-based dispatch system can be similar to those from a medical-priority dispatch system regarding out-of-hospital cardiac arrest (OHCA) time recognition and DA-CPR delivery. Agonal breathing recognition remains the weakest link in this sensitive task in both systems. It is of prime importance that all dispatch centers tend not only to implement DA-CPR but also to have tools to help them reach this objective, as today it should be mandatory to offer this service to the community. In order to improve benchmarking opportunities, we completed previously proposed performance standards as propositions.

Learning Preferences with Kernel-Based Methods

Learning of preference relations has recently received significant attention in machine learning community. It is closely related to the classification and regression analysis and can be reduced to these tasks. However, preference learning involves prediction of ordering of the data points rather than prediction of a single numerical value as in case of regression or a class label as in case of classification. Therefore, studying preference relations within a separate framework facilitates not only better theoretical understanding of the problem, but also motivates development of the efficient algorithms for the task. Preference learning has many applications in domains such as information retrieval, bioinformatics, natural language processing, etc. For example, algorithms that learn to rank are frequently used in search engines for ordering documents retrieved by the query. Preference learning methods have been also applied to collaborative filtering problems for predicting individual customer choices from the vast amount of user generated feedback. In this thesis we propose several algorithms for learning preference relations. These algorithms stem from well founded and robust class of regularized least-squares methods and have many attractive computational properties. In order to improve the performance of our methods, we introduce several non-linear kernel functions. Thus, contribution of this thesis is twofold: kernel functions for structured data that are used to take advantage of various non-vectorial data representations and the preference learning algorithms that are suitable for different tasks, namely efficient learning of preference relations, learning with large amount of training data, and semi-supervised preference learning. Proposed kernel-based algorithms and kernels are applied to the parse ranking task in natural language processing, document ranking in information retrieval, and remote homology detection in bioinformatics domain. Training of kernel-based ranking algorithms can be infeasible when the size of the training set is large. This problem is addressed by proposing a preference learning algorithm whose computation complexity scales linearly with the number of training data points. We also introduce sparse approximation of the algorithm that can be efficiently trained with large amount of data. For situations when small amount of labeled data but a large amount of unlabeled data is available, we propose a co-regularized preference learning algorithm. To conclude, the methods presented in this thesis address not only the problem of the efficient training of the algorithms but also fast regularization parameter selection, multiple output prediction, and cross-validation. Furthermore, proposed algorithms lead to notably better performance in many preference learning tasks considered.

A Method for Sky-Condition Classification from Ground-Based Solar Radiation Measurements

Identification of clouds from satellite images is now a routine task. Observation of clouds from the ground, however, is still needed to acquire a complete description of cloud conditions. Among the standard meteorologicalvariables, solar radiation is the most affected by cloud cover. In this note, a method for using global and diffuse solar radiation data to classify sky conditions into several classes is suggested. A classical maximum-likelihood method is applied for clustering data. The method is applied to a series of four years of solar radiation data and human cloud observations at a site in Catalonia, Spain. With these data, the accuracy of the solar radiation method as compared with human observations is 45% when nine classes of sky conditions are to be distinguished, and it grows significantly to almost 60% when samples are classified in only five different classes. Most errors are explained by limitations in the database; therefore, further work is under way with a more suitable database

Identification of acetates in elasmopalpulus lignosellus pheromone glands using a newly created mass spectral database and kóvats retention indices

Based on a specially created mass spectral database utilizing 23 tetradecenyl and 22 hexadecenyl acetate standards along with Kóvats retention indices obtained on a very polar stationary phase [poly (biscyanopropyl siloxane)] (SP 2340), (Z)-9-hexadecenyl acetate, (Z)-11-hexadecenyl acetate and (E)-8-hexadecenyl acetate were identified in active pheromone extracts of Elasmopalpus lignosellus. This identification was more efficient than our previous study using gas chromatography/mass spectrometry with a dimethyl disulfide derivative where we could only identify the first two acetates. The acetate composition of the pheromone gland differed from region to region in Brazil and from that from the Tifton (GA, USA) population, suggesting polymorphism or a different sub-species.

Genetic linkage map of Phaseolus vulgaris and identification of QTLs responsible for resistance to Xanthomonas axonopodis pv. phaseoli

Common bean (Phaseolus vulgaris) cultivars with a high degree of resistance to Xanthomonas axonopodis pv. phaseoli (Xap) are not available in Brazil. Despite many studies, a low degree of resistance to Xap continues to exist due to its complex genetic inheritance, which is not well known. The objectives of this research were to complement a common bean genetic map based on the cross between a susceptible genotype 'HAB-52' and a resistant genotype 'BAC-6', and to map and analyze genomic regions (quantitative trait loci – QTLs) related to Xap resistance. Eleven linkage groups were determined using 143 RAPD markers, covering 1,234.5 cM of the genome. This map was used to detect QTLs associated with Xap resistance on leaves and pods. The averages of disease severity on leaves (represented by the transformed disease index – TDI) and pods (represented by the diameter of lesion on pods – DLP) were added to the data of the linkage map. Five TDI QTLs and only one LDP QTL were detected. The TDI QTLs were placed in the A, B, G and J linkage groups, with phenotypic variations ranging from 12.7 to 71.6%. The DLP QTL explained 12.9% of the phenotypic variation and was mapped in a distinct linkage group. These results indicate that there are different genes involved in the control of resistance on leaves and pods.

Identification of Races of Selected Isolates of Uromyces appendiculatus from Minas Gerais (Brazil) Based on the new international classification system

Twelve single-pustule isolates of Uromyces appendiculatus, the etiological agent of common bean rust, were collected in the state of Minas Gerais, Brazil, and classified according to the new international differential series and the binary nomenclature system proposed during the 3rd Bean Rust Workshop. These isolates have been used to select rust-resistant genotypes in a bean breeding program conducted by our group. The twelve isolates were classified into seven different physiological races: 21-3, 29-3, 53-3, 53-19, 61-3, 63-3 and 63-19. Races 61-3 and 63-3 were the most frequent in the area. They were represented by five and two isolates, respectively. The other races were represented by just one isolate. This is the first time the new international classification procedure has been used for U. appendiculatus physiological races in Brazil. The general adoption of this system will facilitate information exchange, allowing the cooperative use of the results obtained by different research groups throughout the world. The differential cultivars Mexico 309, Mexico 235 and PI 181996 showed resistance to all of the isolates that were characterized. It is suggested that these cultivars should be preferentially used as sources for resistance to rust in breeding programs targeting development lines adapted to the state of Minas Gerais.

Detection of beetle damage in forests by X-ray CT image processing

Some beetle species can have devastating economic impacts on forest and nursery industries. A recent example is Anophophora glabripennis, a species of beetle known in the United States as the ''Asian Longhorrned beetle'', which has damaged many American forests, and is a threat which can unintentionally reach south American countries, including Brazil. This work presents a new method based on X-ray computerized tomography (CT) and image processing for beetle injury detection in forests. Its results show a set of images with correct identification of the location of beetles in living trees as well as damage evaluation with time.

Identification and characterization of new genes and pathways regulating spermatogonial cell fate

Spermatogenesis, i.e sperm production in the seminiferous tubules of the testis, is a complex process that takes over one month to complete. Life-long ability of sperm production ultimately lies in a small population of undifferentiated cells, called spermatogonial stem cells (SSCs). These cells give rise to differentiating spermatogonia, which are committed to mature into spermatozoa. SSCs represent a heterogeneous population of cells and many aspects of their basic biology are still unknown. Understanding the mechanisms behind the cell fate decision of these cells is important to gain more insights into the causes of infertility and testis cancer. In addition, an interesting new aspect is the use of testis-derived stem cells in regenerative medicine. Our data demonstrated that adult mouse testis houses a population of Nanog-expressing spermatogonia. Based on mRNA and protein analysis these cells are enriched in stage XII of the mouse seminiferous epithelial cycle. The cells derived from this stage have the highest capacity to give rise to ES cell-like cells which express Oct4 and Nanog. These cells are under tight non- GDNF regulation but their fate can be dictated by activating p21 signalling. Comparative studies suggested that these cells are regulated like ES cells. Taken together these data imply that pluripotent cells are present in the adult mammalian testis. CIP2A (cancerous inhibitor of PP2A) has been associated with tumour aggressiveness and poor prognosis. In the testis it is expressed by the descendants of stem cells, i.e. the spermatogonial progenitor cells. Our data suggest that CIP2A acts upstream of PLZF and is needed for quantitatively normal spermatogenesis. Classification of CIP2A as a cancer/testis gene makes it an attractive target for cancer therapy. Study on the CIP2A deficient mouse model demonstrates that systemic inhibition of CIP2A does not severely interfere with growth and development or tissue or organ function, except for the spermatogenic output. These data demonstrate that CIP2A is required for quantitatively normal spermatogenesis. Hedgehog (Hh) signalling is involved in the development and maintenance of many different tissues and organs. According to our data, Hh signalling is active at many different levels during rat spermatogenesis: in spermatogonia, spermatocytes and late elongating spermatids. Localization of Suppressor of Fused (SuFu), the negative regulator of the pathway, specifically in early elongating spermatids suggests that Hh signalling needs to be shut down in these cells. Introduction of Hh signalling inhibitor resulted in an increase in germ cell apoptosis. Follicle-stimulating hormone (FSH) and inhibition of receptor tyrosine kinases resulted in down-regulation of Hh signalling. These data show that Hh signalling is under endocrine and paracrine control and it promotes germ cell survival.

Damage control surgery: it's evolution over the last 20 years

In less than twenty years, what began as a concept for the treatment of exsanguinating truncal trauma patients has become the primary treatment model for numerous emergent, life threatening surgical conditions incapable of tolerating traditional methods. Its core concepts are relative straightforward and simple in nature: first, proper identification of the patient who is in need of following this paradigm; second, truncation of the initial surgical procedure to the minimal necessary operation; third, aggressive, focused resuscitation in the intensive care unit; fourth, definitive care only once the patient is optimized to tolerate the procedure. These simple underlying principles can be molded to a variety of emergencies, from its original application in combined major vascular and visceral trauma to the septic abdomen and orthopedics. A host of new resuscitation strategies and technologies have been developed over the past two decades, from permissive hypotension and damage control resuscitation to advanced ventilators and hemostatic agents, which have allowed for a more focused resuscitation, allowing some of the morbidity of this model to be reduced. The combination of the simple, malleable paradigm along with better understanding of resuscitation has proven to be a potent blend. As such, what was once an almost lethal injury (combined vascular and visceral injury) has become a survivable one.