Miracle-dz/UniFAR-FTUs huggingface dataset:
Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications

We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text. We describe and evaluate our system, the clinical Text Analysis and Knowledge Extraction System (cTAKES), released open-source at http://www.ohnlp. org. The cTAKES builds on existing open-source technologies-the Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit. Its components, specifically trained for the clinical domain, create rich linguistic and semantic annotations. Performance of individual components: sentence boundary detector accuracy=0.949; tokenizer accuracy=0.949; part-of-speech tagger accuracy=0.936; shallow parser F-score=0.924; named entity recognizer and system-level evaluation F-score=0.715 for exact and 0.824 for overlapping spans, and accuracy for concept mapping, negation, and status attributes for exact and overlapping spans of 0.957, 0.943, 0.859, and 0.580, 0.939, and 0.839, respectively. Overall performance is discussed against five applications. The cTAKES annotations are the foundation for methods and modules for higher-level semantic processing of clinical free-text.
How to Thematically Segment Texts by using Lexical Cohesion?

This article outlines a quantitative method for segmenting texts into thematically coherent units. This method relies on a network of lexical collocations to compute the thematic coherence of the different parts of a text from the lexical cohesiveness of their words. We also present the results of an experiment about locating boundaries between a series of concatened texts.
Clerics die, doctors survive: A note on death risks among highly educated professionals

Aims: Mortality is strongly associated with education. We present relative death risks of men and women in 12 educational/ occupational groups in Sweden today, with a focus on individuals with higher education. Methods: Results from Cox regressions are reported for 12 educational groups with special emphasis on those with professional education, e.g. clerics, physicians, people with medical PhDs, and university teachers. The study is based on register data of the total Swedish population in the age group of 30—64 (n = 3,734,660). Results: There is a considerable variation in mortality between educational groups. Men with compulsory education run a risk that is more than three times higher than that of professors outside medicine, and other educational groups fall in between. Medical doctors and physicians have relatively low death risks compared to those with compulsory education — less than 50% among men and less than 60% among women — although professors in medicine deviate by having higher risks than their colleagues in other subjects. Those with a theological exam show higher risks of dying during the follow-up period compared to others of a similar educational level. Professors outside medicine experience the lowest death risks of all identified groups. Conclusions: Men and women with a professional education have comparatively low death risks, particularly low among medical doctors and university employees, while the clergy seems to experience relatively higher death risks than others with a similar level of education. These patterns may reflect the effects of education as well as the selection of men and women to higher education.
Sequences and consequences

The conversion of data into knowledge constitutes a great challenge for future biological research. The new science of Systems Biology claims to be able to solve the problem but I contend that this approach will fail because deducing models of function from the behaviour of a complex system is an inverse problem that is impossible to solve. In addition, one cannot easily escape into high-level holistic approaches, since the essence of all biological systems is that they are encoded as molecular descriptions in their genes and since genes are molecules and exert their functions through other molecules, the molecular explanation must constitute the core of understanding biological systems. We then solve the forward problem of computing the behaviour of the system from its components and their interactions. I propose that the correct level of abstraction is the cell and provide an outline of Cellmap, a design for a system to organize biological information.
Automatic organization for digital photographs with geographic coordinates

We describe PhotoCompas, a system that utilizes the time and location information embedded in digital photographs to automatically organize a personal photo collection. PhotoCompas produces browseable location and event hierarchies for the collection. These hierarchies are created using algorithms that interleave time and location to produce an organization that mimics the way people think about their photo collections. In addition, the algorithm annotates the generated hierarchy with geographical names. We tested our approach in case studies of three real-world collections and verified that the results are meaningful and useful for the collection owners.
Evidence for serotonin function as a neurochemical difference between fear and anxiety disorders in humans?

The relationships between serotonin and fear and anxiety disorders have been much studied yet many important questions remain, despite selective serotonin reuptake inhibitors having been the primary treatments for these disorders for some time. In order to explore this issue we performed a pooled analysis of six of our studies in remitted patients with a fear/anxiety disorder who were exposed to syndrome-specific aversive stimulation under acute tryptophan depletion. We based our analysis on the hypothesis that the inconsistencies observed in the studies could be predicted by Deakin and Graeff’s theory about the dual role of serotonin in responses to threats, whereby serotonin is critical to prevent fear (panic) but not anxiety. In accordance with this view, our results give support to a dissociation of the disorders traditionally grouped under fear and anxiety-related disorders in terms of different roles of serotonin in modulation of responses to aversive stimulation. Implications for future studies and psychiatric nosology are discussed.
Taxon sampling versus computational complexity and their impact on obtaining the Tree of Life

The scope of phylogenetic analysis has increased greatly in the last decade, with analyses of hundreds, if not thousands, of taxa becoming increasingly common in our efforts to reconstruct the tree of life and study large and species rich taxa. Through simulation, we investigated the potential to reconstruct ever larger portions of the tree of life using a variety of different methods
A Robust Optimization Approach for Planning the Transition to Plug-in Hybrid Electric Vehicles

This paper proposes a new technique to analyze the electricity and transport sectors within a single integrated framework to realize an environmentally and economically sustainable integration of plug-in hybrid electric vehicles (PHEVs) into the electric grid, considering the most relevant planning uncertainties. The method is based on a comprehensive robust optimization planning that considers the constraints of both the electricity grid and the transport sector. The proposed model is justified and described in some detail, applying it to the real case of Ontario, Canada, to determine Ontario's grid potential to support PHEVs for the planning horizon 2008-2025.
Enhancing Student Engagement through Personalized Motivations

A lack of appropriate engagement in online learning courses is a significant factor leading to poor performance and high dropout rates. This paper presents a framework that provides personalized motivations in the form of feedback, advices and reminders in order to enhance the engagement of students with online learning. It also describes the design, implementation and evaluation of the framework which has been used by over one hundred students. The paper focuses on how the framework by modelling and monitoring the level of engagement of students, it provides tailored motivations to stimulate and sustain their engagement. Finally, the paper compares the results from a previous student cohort (where no motivations were provided) to highlight how the framework has significantly increased the level of engagement of students.
Psychoacoustic quantities and their relevance for sound-quality optimization of switched reluctance machines

This paper gives a brief introduction to noise development in switched reluctance machines (SRMs) and presents psychoacoustic quantities that allow an objective evaluation of their sound quality by taking into account the characteristics of the human hearing system. The relevance of these quantities is determined by listening tests and statistical analyses. The goal of this work is to demonstrate that a successful acoustic optimization of a SRM should be performed based on both technical and psychoacoustic know-how
Compiling Causal Theories to Successor State Axioms and STRIPS-Like Systems

We describe a system for specifying the effects of actions. Unlike those commonly used in AI planning, our system uses an action description language that allows one to specify the effects of actions using domain rules, which are state constraints that can entail new action effects from old ones. Declaratively, an action domain in our language corresponds to a nonmonotonic causal theory in the situation calculus. Procedurally, such an action domain is compiled into a set of logical theories, one for each action in the domain, from which fully instantiated successor state-like axioms and STRIPS-like systems are then generated. We expect the system to be a useful tool for knowledge engineers writing action specifications for classical AI planning systems, GOLOG systems, and other systems where formal specifications of actions are needed.
Universally composable two-party and multi-party secure computation

We show how to securely realize any multi-party functionality in a universally composable way, regardless of the number of corrupted participants. That is, we consider a multi-party network with open communication and an adversary that can adaptively corrupt as many parties as it wishes. In this setting, our protocols allow any subset of the parties (with pairs of parties being a special case) to securely realize any desired functionality of their local inputs, and be guaranteed that security is preserved regardless of the activity in the rest of the network. This implies that security is preserved under concurrent composition of an unbounded number of protocol executions, it implies non-malleability with respect to arbitrary protocols, and more. Our constructions are in the common reference string model and make general intractability assumptions.
Controllers for running in the humanoid robot, HUBO

This paper discusses the controllers for running in the humanoid robot and verifies the validity of the proposed controllers via experiments. To realize running in a humanoid robot, the overall control structure is composed of an off-line controller and an on-line controller. The main purpose of the online controller is to maintain the dynamic stability while the humanoid robot runs. The on-line controller is composed of the posture balance control in the sagittal plane, the transient balance control in the frontal plane, and the swing ankle pitch compensator in the sagittal plane. These controllers were applied to the humanoid robot, HUBO, and it ran forward stably at a maximum speed of 3.24km/h.
Learning to share: narrowband-friendly wideband networks

Wideband technologies in the unlicensed spectrum can satisfy the ever-increasing demands for wireless bandwidth created by emerging rich media applications. The key challenge for such systems, however, is to allow narrowband technologies that share these bands (say, 802.11 a/b/g/n, Zigbee) to achieve their normal performance, without compromising the throughput or range of the wideband network. This paper presents SWIFT, the first system where high-throughput wideband nodes are shown in a working deployment to coexist with unknown narrowband devices, while forming a network of their own. Prior work avoids narrowband devices by operating below the noise level and limiting itself to a single contiguous unused band. While this achieves coexistence, it sacrifices the throughput and operating distance of the wideband device. In contrast, SWIFT creates high throughput wireless links by weaving together non-contiguous unused frequency bands that change as narrowband devices enter or leave the environment. This design principle of cognitive aggregation allows SWIFT to achieve coexistence, while operating at normal power, and thereby obtaining higher throughput and greater operating range. We implement SWIFT on a wideband hardware platform, and evaluate it in the presence of 802.11 devices. In comparison to a baseline that coexists with narrowband devices by operating below their noise level, SWIFT is equally narrowband-friendly but achieves 3.6-10.5x higher throughput and 6x greater range.
The Biometrics Grid: A Solution to Biometric Technologies

The biometrics grid can simplify resource management and access by making biometrics data as easy to access as Web pages via a Web browser. It tests user-designed modules, which are wrapped to Web services and deployed into a Web services container. Risk-resilient strategies are used for job scheduling. A case study of two biometrics recognition processes in voiceprint and face illustrates the process. The biometrics grid could benefit academic collaborations and improve biometric data sharing, as well as enhance biometric systems' efficiency in scientific research and commercial applications.
Conformational Altered p53 as an Early Marker of Oxidative Stress in Alzheimer's Disease

In order to study oxidative stress in peripheral cells of Alzheimer's disease (AD) patients, immortalized lymphocytes derived from two peculiar cohorts of patients, referring to early onset AD (EOSAD) and subjects harboured AD related mutation (ADmut), were used. Oxidative stress was evaluated measuring i) the typical oxidative markers, such as HNE Michel adducts, 3 Nitro-Tyrosine residues and protein carbonyl on protein extracts, ii) and the antioxidant capacity, following the enzymatic kinetic of superoxide dismutase (SOD), glutathione peroxidase (GPx) and glutathione reductase (GRD). We found that the signs of oxidative stress, measured as oxidative marker levels, were evident only in ADmut but not in EOSAD patients. However, oxidative imbalance in EOSAD as well as ADmut lymphocytes was underlined by a reduced SOD activity and GRD activity in both pathological groups in comparison with cells derived from healthy subjects. Furthermore, a redox modulated p53 protein was found conformational altered in both EOSAD and ADmut B lymphocytes in comparison with control cells. This conformational altered p53 isoform, named “unfolded p53”, was recognized by the use of two specific conformational anti-p53 antibodies. Immunoprecipitation experiments, performed with the monoclonal antibodies PAb1620 (that recognizes p53wt) and PAb240 (that is direct towards unfolded p53), and followed by the immunoblotting with anti-4-hydroxynonenal (HNE) and anti- 3-nitrotyrosine (3NT) antibodies, showed a preferential increase of nitrated tyrosine residues in unfolded p53 isoform comparing to p53 wt protein, in both ADmut and EOSAD. In addition, a correlation between unfolded p53 and SOD activity was further found. Thus this study suggests that ROS/RNS contributed to change of p53 tertiary structure and that unfolded p53 can be considered as an early marker of oxidative imbalance in these patients.
Polyhedral-Model Guided Loop-Nest Auto-Vectorization

Optimizing compilers strive to construct efficient executables by applying sequences of transformations. Additional transformations are constantly being devised, with various mutual interactions among them, thereby exacerbating the notoriously difficult phase-ordering problem --- that of deciding which transformations to apply and in which order. Fortunately, new infrastructures such as the polyhedral compilation framework host a variety of transformations, facilitating the efficient exploration and configuration of multiple transformation sequences. Many powerful optimizations, however, remain external to the polyhedral framework, with potential mutual interactions that need to be considered. In this paper we examine the interactions between loop transformations of the polyhedral compilation framework and subsequent vectorization optimizations targeting fine-grain SIMD data-level parallelism. Automatic vectorization involves many low-level, target-specific considerations and transformations, which currently exclude it from being part of the polyhedral framework. In order to consider potential interactions among polyhedral loop transformations and vectorization, we first model the performance impact of the different loop transformations and vectorization strategies, and then show how this cost model can be integrated seamlessly into the polyhedral representation. This predictive modelling then facilitates efficient exploration and educated decision making on how to best apply various polyhedral loop transformations while considering the subsequent effects of different vectorization schemes. Our work demonstrates the feasibility and benefit of tuning the polyhedral model in the context of vectorization. Experimental results confirm that our model has accurate predictions, providing speedups of over 2 on average over traditional innermost-loop vectorization on PowerPC970 and Cell-SPU SIMD platforms.
Adjacent Channel Interference Between Asynchronous TDD Cellular Networks

The increasing user density and higher data rate demands of future wireless networks are to be met with new technologies under the scope of IMT-Advanced. The required high data rates can be provided by wide transmission bandwidths and a high density of access points in local area scenarios. Care- fully coordinated network deployment and high performance RF front-ends are envisioned infeasible due to implied high costs. A major design challenge is then to handle the potentially severe adjacent channel interference arising among operators serving the same geographical area. This paper investigates the types of interference that form the major bottlenecks to the performance of time division duplex systems in such a scenario. This provides valuable input to system design pointing out the most detrimental interference types to be mitigated.
Bioactivity of volatile organic compounds produced by Pseudomonas tolaasii

Pseudomonas tolaasii is the main bacterial pathogen of several mushroom species. In this paper we report that strains of P. tolaasii produce volatile substances inducing in vitro mycelia growth inhibition of Pleurotus ostreatus and P. eryngii, and Agaricus bisporus and P. ostreatus basidiome tissue blocks brown discoloration. P. tolaasii strains produced the volatile ammonia but not hydrogen cyanide. Among the volatiles detected by GC–MS, methanethiol, dimethyl disulfide (DMDS), and 1-undecene were identified. The latter, when assayed individually as pure compounds, led to similar effects noticed when P. tolaasii volatiles natural blend was used on mushrooms mycelia and basidiome tissue blocks. Furthermore, the natural volatile mixture resulted toxic toward lettuce and broccoli seedling growth. In contrast, pure volatiles showed different activity according to their nature and/or doses applied. Indeed, methanethiol resulted toxic at all the doses used, while DMDS toxicity was assessed till a quantity of 1.25 μg, below which it caused, together with 1-undecene (≥10 μg), broccoli growth increase.
Enhancing Grid Security Using Workflows, Trusted Computing and Virtualisation

This paper highlights the need to meet both Grid user and resource provider security requirements, describing the rationale for securing Grid workflows: a set of tasks arranged into a logical order to process a Grid user’s dataset. An overview of a secure protocol using Trusted Computing technology is provided, which is further enhanced with platform virtualisation hardware and software. The proposed scheme allows the selection of trustworthy resource providers and gives confidentiality and integrity protection to the workflow, the Grid user’s processes and data. The scheme also detects any problems during workflow execution, collecting information that can be used for
Dosimetric Quantities and Neutron Spectra Outside the Shielding of Electron Accelerators

Typical neutron spectra as found at high energy electron accelerators outside concrete shielding of various thicknesses (at 90 degrees) have been calculated at three electron energies (100 MeV, 1 and 10 GeV) with the FLUKA Monte Carlo transport code. The results have provided useful information about neutron attenuation lengths and about the fraction of neutrons with energy larger than 20 MeV, not detectable by the usual radiation protection instruments.
Automatic Music Genre Classification Using a Hierarchical Clustering and a Language Model Approach

Automatic music genre classification has received a lot of attention from the Music Information Retrieval (MIR) community in the past years. Systems capable of discriminating music genres are essential for managing music databases. This paper presents a method for music genre classification based solely on the audio contents of the signal. The method relies on a language modeling approach and takes in account the temporal information of the music signals for genre classification. First, the music data is transformed into a sequence of symbols, and a model is derived for each genre by estimating n-grams from the training data. As a term o comparison, HMMs models for each musical genre were also implemented. Tests on different audio sets show that the proposed approach performs very well, and outperforms HMMs based methods.
A 0.5-50 GHz on-wafer, intermodulation, load-pull and power measurement system

A novel on-wafer, intermodulation, load-pull and power measurement system for characterizing devices and circuits for frequencies up to 50 GHz has been developed. The two-tone intermodulation measurement capabilities were added to an existing power and harmonic load-pull measurement system using the 50 GHz spectrum analyzer HP8565. Fundamental power levels and all measured intermodulation (IM) products are vector corrected to the probe tips of the DUT. A key feature of the described system are the vector corrected IM measurements and the capability to study the effects of load impedance on intermodulation. <<ETX>>