Comparing sentence-level features for authorship analysis in Portuguese

In this paper we compare the robustness of several types of stylistic markers to help discriminate authorship at sentence level. We train a SVM-based classifier using each set of features separately and perform sentence-level authorship analysis over corpus of editorials published in a Portuguese quality newspaper. Results show that features based on POS information, punctuation and word / sentence length contribute to a more robust sentence-level authorship analysis. © Springer-Verlag Berlin Heidelberg 2010.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.

RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.

AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).

Formalizing operator task analysis

Human operators are unique in their decision making capability, judgment and nondeterminism. Their sense of judgment, unpredictable decision procedures, susceptibility to environmental elements can cause them to erroneously execute a given task description to operate a computer system. Usually, a computer system is protected against some erroneous human behaviors by having necessary safeguard mechanisms in place. But some erroneous human operator behaviors can lead to severe or even fatal consequences especially in safety critical systems. A generalized methodology that can allow modeling and analyzing the interactions between computer systems and human operators where the operators are allowed to deviate from their prescribed behaviors will provide a formal understanding of the robustness of a computer system against possible aberrant behaviors by its human operators. We provide several methodology for assisting in modeling and analyzing human behaviors exhibited while operating computer systems. Every human operator is usually given a specific recommended set of guidelines for operating a system. We first present process algebraic methodology for modeling and verifying recommended human task execution behavior. We present how one can perform runtime monitoring of a computer system being operated by a human operator for checking violation of temporal safety properties. We consider the concept of a protection envelope giving a wider class of behaviors than those strictly prescribed by a human task that can be tolerated by a system. We then provide a framework for determining whether a computer system can maintain its guarantees if the human operators operate within their protection envelopes. This framework also helps to determine the robustness of the computer system under weakening of the protection envelopes. In this regard, we present a tool called Tutela that assists in implementing the framework. We then examine the ability of a system to remain safe under broad classes of variations of the prescribed human task. We develop a framework for addressing two issues. The first issue is: given a human task specification and a protection envelope, will the protection envelope properties still hold under standard erroneous executions of that task by the human operators? In other words how robust is the protection envelope? The second issue is: in the absence of a protection envelope, can we approximate a protection envelope encompassing those standard erroneous human behaviors that can be safely endured by the system? We present an extension of Tutela that implements this framework. The two frameworks mentioned above use Concurrent Game Structures (CGS) as models for both computer systems and their human operators. However, there are some shortcomings of this formalism for our uses. We add incomplete information concepts in CGSs to achieve better modularity for the players. We introduce nondeterminism in both the transition system and strategies of players and in the modeling of human operators and computer systems. Nondeterministic action strategies for players in \emph{i}ncomplete information \emph{N}ondeterministic CGS (iNCGS) is a more precise formalism for modeling human behaviors exhibited while operating a computer system. We show how we can reason about a human behavior satisfying a guarantee by providing a semantics of Alternating Time Temporal Logic based on iNCGS player strategies. In a nutshell this dissertation provides formal methodology for modeling and analyzing system robustness against both expected and erroneous human operator behaviors.

Sensory gating and its modulation by cannabinoids: electrophysiological, computational and mathematical analysis

Gating of sensory information can be assessed using an auditory conditioning-test paradigm which measures the reduction in the auditory evoked response to a test stimulus following an initial conditioning stimulus. Recording brainwaves from specific areas of the brain using multiple electrodes is helpful in the study of the neurobiology of sensory gating. In this paper, we use such technology to investigate the role of cannabinoids in sensory gating in the CA3 region of the rat hippocampus. Our experimental results show that application of the exogenous cannabinoid agonist WIN55,212-2 can abolish sensory gating. We have developed a phenomenological model of cannabinoid dynamics incorporated within a spiking neural network model of CA3 with synaptically interacting pyramidal and basket cells. Direct numerical simulations of this model suggest that the basic mechanism for this effect can be traced to the suppression of inhibition of slow GABAB synapses. Furthermore, by working with a simpler mathematical firing rate model we are able to show the robustness of this mechanism for the abolition of sensory gating.

Cost-effectiveness analysis of apixaban compared to low-molecular-weight heparins and vitamin k antagonists for treatment and secondary prevention of venous thromboembolism

Objective: Cost-effectiveness analysis of a 6-month treatment of apixaban (10 mg/12h, first 7 days; 5 mg/12h afterwards) for the treatment of the first event of venous thromboembolism (VTE) and prevention of recurrences, versus low-molecular-weight heparins/vitamin K antagonists treatment (LMWH/VKA). Material and methods: A lifetime Markov model with 13 health states was used for describing the course of the disease. Efficacy and safety data were obtained from AMPLIFY and AMPLIFY-EXT clinical trials; health outcomes were measured as life years gained (LYG) and quality-adjusted life years (QALY). The chosen perspective of this analysis has been the Spanish National Health System (NHS). Drugs, management of VTE and complications costs were obtained from several Spanish data sources (€, 2014). A 3% discount rate was applied to health outcomes and costs. Univariate and probabilistic sensitivity analyses (SA) were performed in order to assess the robustness of the results. Results: Apixaban was the most effective therapy with 7.182 LYG and 5.865 QALY, versus 7.160 LYG and 5.838 QALYs with LMWH/VKA. Furthermore, apixaban had a lower total cost (€13,374.70 vs €13,738.30). Probabilistic SA confirmed dominance of apixaban (led to better health outcomes with less associated costs) in 89% of the simulations. Conclusions: Apixaban 5 mg/12h versus LMWH/VKA was an efficient therapeutic strategy for the treatment and prevention of recurrences of VTE from the NHS perspective.

Adaptation of motor control to training and disuse : contribution of muscle synergy analysis and movement variability

The well-known degrees of freedom problem originally introduced by Nikolai Bernstein (1967) results from the high abundance of degrees of freedom in the musculoskeletal system. Such abundance in motor control have two sides: i) because it is unlikely that the Central Nervous System controls each degree of freedom independently, the complexity of the control needs to be reduced, and ii) because there are many options to perform a movement, a repetition of a given movement is never the same. It leads to two main topics in motor control and biomechanics: motor coordination and motor variability. The present thesis aimed to understand how motor systems behave and adapt under specific conditions. This thesis comprises three studies that focused on three topics of major interest in the field of sports sciences and medicine: expertise, injury risk and fatigue. The first study (expertise) has focused on the muscle coordination topic to further investigate the effect of expertise on the muscle synergistic organization, which ultimately may represent the underlying neural strategies. Studies 2 (excessive medial knee displacement) and 3 (fatigue) both aimed to better understand its impact on the dynamic local stability. The main findings of the present thesis suggest: 1) there is a great robustness in muscle synergistic organization between swimmers at different levels of expertise (study 1, chapter II), which ultimately indicate that differences in muscle coordination is mainly explained by peripheral adaptations; 2) injury risk factors such as excessive medial knee displacement (study 2, chapter III) and fatigue (study 3, chapter IV) alter the dynamic local stability of the neuromuscular system towards a more unstable state. This change in dynamic local stability represents a loss of adaptability in the neuromuscular system reducing the flexibility to adapt to a perturbation.

ANALYSIS OF POPULUS TREMULOIDES CLONAL VARIATION AND DELINEATION IN THE OTTAWA NATIONAL FOREST

The technique of delineating Populus tremuloides (Michx.) clonal colonies based on morphology and phenology has been utilized in many studies and forestry applications since the 1950s. Recently, the availability and robustness of molecular markers has challenged the validity of such approaches for accurate clonal identification. However, genetically sampling an entire stand is largely impractical or impossible. For that reason, it is often necessary to delineate putative genet boundaries for a more selective approach when genetically analyzing a clonal population. Here I re-evaluated the usefulness of phenotypic delineation by: (1) genetically identifying clonal colonies using nuclear microsatellite markers, (2) assessing phenotypic inter- and intraclonal agreement, and (3) determining the accuracy of visible characters to correctly assign ramets to their respective genets. The long-term soil productivity study plot 28 was chosen for analysis and is located in the Ottawa National Forest, MI (46° 37'60.0" N, 89° 12'42.7" W). In total, 32 genets were identified from 181 stems using seven microsatellite markers. The average genet size was 5.5 ramets and six of the largest were selected for phenotypic analyses. Phenotypic analyses included budbreak timing, DBH, bark thickness, bark color or brightness, leaf senescence, leaf serrations, and leaf length ratio. All phenotypic characters, except for DBH, were useful for the analysis of inter- and intraclonal variation and phenotypic delineation. Generally, phenotypic expression was related to genotype with multiple response permutation procedure (MRPP) intraclonal distance values ranging from 0.148 and 0.427 and an observed MRPP delta value=0.221 when the expected delta=0.5. The phenotypic traits, though, overlapped significantly among some clones. When stems were assigned into phenotypic groups, six phenotypic groups were identified with each group containing a dominant genotype or clonal colony. All phenotypic groups contained stems from at least two clonal colonies and no clonal colony was entirely contained within one phenotypic group. These results demonstrate that phenotype varies with genotype and stand clonality can be determined using phenotypic characters, but phenotypic delineation is less precise. I therefore recommend that some genetic identification follow any phenotypic delineation. The amount of genetic identification required for clonal confirmation is likely to vary based on stand and environmental conditions. Further analysis, however, is needed to test these findings in other forest stands and populations.

IMPROVED SAMPLE INTRODUCTION SYSTEMS FOR INDUCTIVELY COUPLED PLASMA OPTICAL EMISSION SPECTROMETRY AND THEIR APPLICATION TO THE ANALYSIS OF SIMPLE AND COMPLEX MATRICES

The objective of this thesis is to explore new and improved methods for greater sample introduction efficiency and enhanced analytical performance with inductively coupled plasma optical emission spectrometry (ICP-OES). Three projects are discussed in which the capabilities and applications of ICP-OES are expanded: 1. In the first project, a conventional ultrasonic nebuliser was modified to replace the heater/condenser with an infrared heated pre-evaporation tube. In continuation from previous works with pre-evaporation, the current work investigated the effects of heating with infrared block and rope heaters on two different ICP-OES instruments. Comparisons were made between several methods and setups in which temperatures were varied. By monitoring changes to sensitivity, detection limit, precision, and robustness, and analyzing two certified reference materials, a method with improved sample introduction efficiency and comparable analytical performance to a previous method was established. 2. The second project involved improvements to a previous work in which a multimode sample introduction system (MSIS) was modified by inserting a pre-evaporation tube between the MSIS and torch. The new work focused on applying an infrared heated ceramic rope for pre-evaporation. This research was conducted in all three MSIS modes (nebulisation mode, hydride generation mode, and dual mode) and on two different ICP-OES instruments, and comparisons were made between conventional setups in terms of sensitivity, detection limit, precision, and robustness. By tracking both hydride-forming and non-hydride forming elements, the effects of heating in combination with hydride generation were probed. Finally, optimal methods were validated by analysis of two certified reference materials. 3. A final project was completed in collaboration with ZincNyx Energy Solutions. This project sought to develop a method for the overall analysis of a 12 M KOH zincate fuel, which is used in green energy backup systems. By employing various techniques including flow injection analysis and standard additions, a final procedure was formulated for the verification of K concentration, as well as the measurement of additives (Al, Fe, Mg, In, Si), corrosion products (such C from CO₃²¯), and Zn particles both in and filtered from solution. Furthermore, the effects of exposing the potassium zincate electrolyte fuel to air were assessed.

A formal analysis of blockchain consensus

In this thesis, we analyse these protocols using PRISM+, our extension of the probabilistic model checker PRISM with blockchain types and operations upon them. This allows us to model the behaviour of key participants in the protocols and describe the protocols as a parallel composition of PRISM+ processes. Through our analysis of the Bitcoin model, we are able to understand how forks (where different nodes have different versions of the blockchain) occur and how they depend on specific parameters of the protocol, such as the difficulty of the cryptopuzzle and network communication delays. Our results corroborate the statement that considering confirmed the transactions in blocks at depth larger than 5 is reasonable because the majority of miners have consistent blockchains up-to that depth with probability of almost 1. We also study the behaviour of the Bitcoin network with churn miners (nodes that leave and rejoin the network) and with different topologies (linear topology, ring topology, tree topology and fully connected topology). PRISM+ is therefore used to analyse the resilience of Hybrid Casper when changing various basic parameters of the protocol, such as block creation rates and penalty determination strategies. We also study the robustness of Hybrid Casper against two known attacks: the Eclipse attack (where an attacker controls a significant portion of the network's nodes and can prevent other nodes from receiving new transactions) and the majority attack (where an attacker controls a majority of the network's nodes and can manipulate the blockchain to their advantage).

Analysis Of The Dna Fourier Transform-infrared Microspectroscopic Signature Using An All-reflecting Objective.

The Fourier transform-infrared (FT-IR) signature of dry samples of DNA and DNA-polypeptide complexes, as studied by IR microspectroscopy using a diamond attenuated total reflection (ATR) objective, has revealed important discriminatory characteristics relative to the PO2(-) vibrational stretchings. However, DNA IR marks that provide information on the sample's richness in hydrogen bonds have not been resolved in the spectral profiles obtained with this objective. Here we investigated the performance of an all reflecting objective (ARO) for analysis of the FT-IR signal of hydrogen bonds in DNA samples differing in base richness types (salmon testis vs calf thymus). The results obtained using the ARO indicate prominent band peaks at the spectral region representative of the vibration of nitrogenous base hydrogen bonds and of NH and NH2 groups. The band areas at this spectral region differ in agreement with the DNA base richness type when using the ARO. A peak assigned to adenine was more evident in the AT-rich salmon DNA using either the ARO or the ATR objective. It is concluded that, for the discrimination of DNA IR hydrogen bond vibrations associated with varying base type proportions, the use of an ARO is recommended.

Effect Of Platform Connection And Abutment Material On Stress Distribution In Single Anterior Implant-supported Restorations: A Nonlinear 3-dimensional Finite Element Analysis.

Although various abutment connections and materials have recently been introduced, insufficient data exist regarding the effect of stress distribution on their mechanical performance. The purpose of this study was to investigate the effect of different abutment materials and platform connections on stress distribution in single anterior implant-supported restorations with the finite element method. Nine experimental groups were modeled from the combination of 3 platform connections (external hexagon, internal hexagon, and Morse tapered) and 3 abutment materials (titanium, zirconia, and hybrid) as follows: external hexagon-titanium, external hexagon-zirconia, external hexagon-hybrid, internal hexagon-titanium, internal hexagon-zirconia, internal hexagon-hybrid, Morse tapered-titanium, Morse tapered-zirconia, and Morse tapered-hybrid. Finite element models consisted of a 4×13-mm implant, anatomic abutment, and lithium disilicate central incisor crown cemented over the abutment. The 49 N occlusal loading was applied in 6 steps to simulate the incisal guidance. Equivalent von Mises stress (σvM) was used for both the qualitative and quantitative evaluation of the implant and abutment in all the groups and the maximum (σmax) and minimum (σmin) principal stresses for the numerical comparison of the zirconia parts. The highest abutment σvM occurred in the Morse-tapered groups and the lowest in the external hexagon-hybrid, internal hexagon-titanium, and internal hexagon-hybrid groups. The σmax and σmin values were lower in the hybrid groups than in the zirconia groups. The stress distribution concentrated in the abutment-implant interface in all the groups, regardless of the platform connection or abutment material. The platform connection influenced the stress on abutments more than the abutment material. The stress values for implants were similar among different platform connections, but greater stress concentrations were observed in internal connections.

Is Thyroid Stunning Clinically Relevant? A Retrospective Analysis Of 208 Patients.

Current guidelines have advised against the performance of (131)I-iodide diagnostic whole body scintigraphy (dxWBS) to minimize the occurrence of stunning, and to guarantee the efficiency of radioiodine therapy (RIT). The aim of the study was to evaluate the impact of stunning on the efficacy of RIT and disease outcome. This retrospective analysis included 208 patients with differentiated thyroid cancer managed according to a same protocol and followed up for 12-159 months (mean 30 ± 69 months). Patients received RIT in doses ranging from 3,700 to 11,100 MBq (100 mCi to 300 mCi). Post-RIT-whole body scintigraphy images were performed 10 days after RIT in all patients. In addition, images were also performed 24-48 hours after therapy in 22 patients. Outcome was classified as no evidence of disease (NED), stable disease (SD) and progressive disease (PD). Thyroid stunning occurred in 40 patients (19.2%), including 26 patients with NED and 14 patients with SD. A multivariate analysis showed no association between disease outcome and the occurrence of stunning (p = 0.3476). The efficacy of RIT and disease outcome do not seem to be related to thyroid stunning.

Combined Analysis Of νμ Disappearance And νμ→νe Appearance In Minos Using Accelerator And Atmospheric Neutrinos.

We report on a new analysis of neutrino oscillations in MINOS using the complete set of accelerator and atmospheric data. The analysis combines the ν(μ) disappearance and ν(e) appearance data using the three-flavor formalism. We measure |Δm(32)(2)| = [2.28-2.46] × 10(-3) eV(2) (68% C.L.) and sin(2)θ(23) = 0.35-0.65 (90% C.L.) in the normal hierarchy, and |Δm(32)(2)| = [2.32-2.53] × 10(-3) eV(2) (68% C.L.) and sin(2)θ(23) = 0.34-0.67 (90% C.L.) in the inverted hierarchy. The data also constrain δ(CP), the θ(23} octant degeneracy and the mass hierarchy; we disfavor 36% (11%) of this three-parameter space at 68% (90%) C.L.

Phylogenetic Analysis Of The Microbial Community In Hypersaline Petroleum Produced Water From The Campos Basin.

In this work the archaea and eubacteria community of a hypersaline produced water from the Campos Basin that had been transported and discharged to an onshore storage facility was evaluated by 16S recombinant RNA (rRNA) gene sequence analysis. The produced water had a hypersaline salt content of 10 (w/v), had a carbon oxygen demand (COD) of 4,300 mg/l and contains phenol and other aromatic compounds. The high salt and COD content and the presence of toxic phenolic compounds present a problem for conventional discharge to open seawater. In previous studies, we demonstrated that the COD and phenolic content could be largely removed under aerobic conditions, without dilution, by either addition of phenol degrading Haloarchaea or the addition of nutrients alone. In this study our goal was to characterize the microbial community to gain further insight into the persistence of reservoir community members in the produced water and the potential for bioremediation of COD and toxic contaminants. Members of the archaea community were consistent with previously identified communities from mesothermic reservoirs. All identified archaea were located within the phylum Euryarchaeota, with 98 % being identified as methanogens while 2 % could not be affiliated with any known genus. Of the identified archaea, 37 % were identified as members of the strictly carbon-dioxide-reducing genus Methanoplanus and 59 % as members of the acetoclastic genus Methanosaeta. No Haloarchaea were detected, consistent with the need to add these organisms for COD and aromatic removal. Marinobacter and Halomonas dominated the eubacterial community. The presence of these genera is consistent with the ability to stimulate COD and aromatic removal with nutrient addition. In addition, anaerobic members of the phyla Thermotogae, Firmicutes, and unclassified eubacteria were identified and may represent reservoir organisms associated with the conversion hydrocarbons to methane.