Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 2 INFORMATION EXTRACTION FROM TEXT

Information extraction is the task of finding structured information from unstructured or semi-structured text. It is an important task in text mining and has been extensively studied in various research communities including natural language processing, information retrieval and Web mining. It has a wide range of applications in domains such as biomedical literature mining and business intelligence. Two fundamental tasks of information extraction are named entity recognition and relation extraction. The former refers to finding names of entities such as people, organizations and locations. The latter refers to finding the semantic relations such as FounderOf and HeadquarteredIn between entities. In this chapter we provide a survey of the major work on named entity recognition and relation extraction in the past few decades, with a focus on work from the natural language processing community.
Green energy from marine algae: biogas production and composition from the anaerobic digestion of Irish seaweed species

Marine algae have emerged as an alternative feedstock for the production of a number of renewable fuels, including biogas. In addition to energy potential, other characteristics make them attractive as an energy source, including their ability to absorb carbon dioxide (CO2), higher productivity rates than land-based crops and the lack of water use or land competition. For Ireland, biofuels from marine algae can play an important role by reducing imports of fossil fuels as well as providing the necessary energy in rural communities. In this study, five potential seaweed species common in Irish waters, Saccorhiza polyschides, Ulva sp. , Laminaria digitata, Fucus serratus and Saccharina latissima, were co-digested individually with bovine slurry. Batch reactors of 120 ml and 1000 ml were set up and incubated at 35°C to investigate their suitability for production of biogas. Digesters fed with S. latissima produced the maximum methane yield (335 ml g volatile solids−1 (gVS−1)) followed by S. polyschides with 255 ml gVS−1. L. digitata produced 246 ml gVS−1 and the lowest yields were from the green seaweed Ulva sp. 191 ml gVS−1. The methane and CO2 percentages ranged between 50–72% and 10–45%, respectively. The results demonstrated that the seaweed species investigated are good feedstocks candidates for the production of biogas and methane as a source of energy. Their use on a large-scale process will require further investigation to increase yields and reduce production costs.
Lines of least resistance and genetic architecture of house mouse (Mus musculus) mandible shape

Evolution along “lines of least resistance (LLR)” is a well‐established phenomenon, which is ultimately based on variational properties of the developmental system. However, it has remained unclear which aspects of development are responsible for observed distributions of variation. This article suggests that house mouse mandible shape may present an opportunity for future research in this field. The genetic architecture of mouse mandible shape has been investigated in the laboratory, and its evolution has been surveyed in studies on natural variation. Here, I ask whether evolutionary diversification of mandible shape follows “LLR” by comparing principal directions of genetic and evolutionary variation, and I assess the potential contribution of specific genomic regions to evolutionary divergence along these directions. The role of two aspects of development, QTL number (presumably reflecting mutational target size) and canalization, is comparatively assessed. Overall, our results demonstrate a strong tendency of genetic and evolutionary systems to vary along similar directions, suggesting that mandible shape evolves along LLR at the level of populations, subspecies and species. At the level of genetic factors, effects bearing similarity to directions of evolution are significantly overrepresented, providing support for the mutational target size hypothesis. A role for canalization is not supported by a clear correlation between directions of evolution and size of genetic effects; however, the evidence for canalization remains ambiguous. These results provide some insights into how the developmental system may shape the variational properties of genetic systems and thus influence the direction of evolution.
Lifecycle of neural semantic parsing

Humans are born with the ability to learn to perceive, comprehend and communicate with language. Computing machines, on the other hand, only understand programming languages. To bridge the gap between humans and computers, deep semantic parsers convert natural language utterances into machine-understandable logical forms. The technique has a wide range of applications ranging from spoken dialogue systems and natural language interfaces. This thesis focuses on neural network-based semantic parsing. Traditional semantic parsers function with a domain-specific grammar that pairs utterances and logical forms, and parse with a CKY-like algorithm in polynomial time. Recent advances in neural semantic parsing reformulate the task as a sequenceto-sequence learning problem. Neural semantic parsers parse a sentence in linear time, and reduce the need for domain-specific assumptions, grammar learning, and extensive feature engineering. But this modeling flexibility comes at a cost since it is no longer possible to interpret how meaning composition is performed, given that logical forms are structured objects (trees or graphs). Such knowledge plays a critical role in understanding modeling limitations so as to build better semantic parsers. Moreover, the sequence-to-sequence learning problem is fairly unconstrained, both in terms of the possible derivations to consider and in terms of the target logical forms which can be ill-formed or unexecutable. The first contribution of this thesis is an improved neural semantic parser, which produces syntactically valid logical forms following a transition system and grammar constrains. The transition system integrates the generation of domain-general (i.e., valid tree-structures and language-specific predicates) and domain-specific aspects (i.e., domain-specific predicates and entities) in a unified way. The model employs various neural attention mechanisms to handle mismatches between natural language and formal language—a central challenge in semantic parsing. Training data to semantic parsers typically consists of utterances paired with logical forms. Another challenge of semantic parsing concerns the annotation of logical forms, which is labor-intensive. To write down the correct logical form of an utterance, one not only needs to have expertise in the semantic formalism, but also has to ensure the logical form matches the utterance semantics. We tackle this challenge in two ways. On the one hand, we extend the neural semantic parser to a weakly-supervised setting within a parser-ranker framework. The weakly-supervised setup uses training data of utterance-denotation (e.g., question-answer) pairs, which are much easier to obtain and therefore allow to scale semantic parsers to complex domains. Our framework
Pilot Trial Results from a Virtual Reality System Designed to Enhance Recovery of Skilled Arm and Hand Movements after Stroke

Rehabilitation programs designed to develop skill in upper extremity (UE) function after stroke require learner-centered opportunities for active problem solving. Virtual realty (VR) provides a unique environment where the presentation of stimuli can be systematically controlled to enable an optimal level of challenge by progressing task difficulty as performance improves. We describe four VR tasks that were developed and tested to improve skilled arm and hand movements in individuals with hemiparesis. Two participants post-stroke with different levels of motor severity attended 12 training sessions lasting 1 to 2 hours each over a 3-week period. Behavioral measures and questionnaires were administered pre-, mid-, and post-training. The less impaired participant averaged more time on task, practiced a greater number of blocks per session, and progressed at a faster rate over sessions than the more impaired participant. Differences in functional outcomes for these two cases can be explained in part by which tasks were practiced, the level of task difficulty applied during practice, and the amount of repetition included in practice
A linear stochastic state space model for electrocardiograms

This paper proposes a linear stochastic state space model for electrocardiogram signal processing and analysis. The model is obtained as a discretized version of Wiener process acceleration model. The model is combined with a fixed-lag Rauch-Tung-Striebel smoother to perform on-line signal denoising, feature extraction, and beat classification. The results indicate that the proposed approach outperforms a conventional FIR filter in terms of improved signal-to-noise ratio, and that the approach can be used for highly accurate online classification of normal beats and premature ventricular contractions. The benefits of the model include the possibility to use closed-form solutions to the optimal filtering and smoothing problems, quick adaptation to sudden changes in beat morphology and heart rate, simple and fast initialization, preprocessing-free operation, intuitive interpretation of the system state, and more.
Institutions and Culture

How and why does distant political and economic history shape the functioning of current institutions? This paper argues that individual values and convictions about the scope of application of norms of good conduct provide the "missing link". Evidence from a variety of sources points to two main findings. First, individual values consistent with generalized (as opposed to limited) morality are widespread in societies that were ruled by non-despotic political institutions in the distant past. Second, well functioning institutions are often observed in countries or regions where individual values are consistent with generalized morality, and under different identifying assumptions this suggests a causal effect from values to institutional outcomes. The paper ends with a discussion of the implications for future research.
Japanese Argument Reordering Based on Dependency Structure for Statistical Machine Translation

While phrase-based statistical machine translation systems prefer to translate with longer phrases, this may cause errors in a free word order language, such as Japanese, in which the order of the arguments of the predicates is not solely determined by the predicates and the arguments can be placed quite freely in the text. In this paper, we propose to reorder the arguments but not the predicates in Japanese using a dependency structure as a kind of reordering. Instead of a single deterministically given permutation, we generate multiple reordered phrases for each sentence and translate them independently. Then we apply a re-ranking method using a discriminative approach by Ranking Support Vector Machines (SVM) to re-score the multiple reordered phrase translations. In our experiment with the travel domain corpus BTEC, we gain a 1.22% BLEU score improvement when only 1-best is used for re-ranking and 4.12% BLEU score improvement when n-best is used for Japanese-English translation. key words: predicate-argument structure, reordering, paraphrasing, reranking, statistical machine translation
Sheaf Semantics for Physically Motivated Network Description with Applications

Aalto University, P.O. Box 11000, FI-00076 Aalto www.aalto. fi Author Author(s): Kari Visala Name of the publication Sheaf Semantics for Physically Motivated Network Description with Applications Publisher School of Science Unit Department of Computer Science and Engineering Series Aalto University publication series SCIENCE + TECHNOLOGY 10/2014 Field of research Network and protocol modeling
GFDM with Different Subcarrier Bandwidths

This paper proposes a generalized frequency division multiplexing (GFDM) modulation scheme that transmits a signal with different subcarrier bandwidths. In a receiver, the GFDM signal is demodulated by using a zero forcing (ZF) algorithm or a minimum mean square error (MMSE) algorithm and the BER performance of these algorithms is related to the condition number of a modulation matrix. This matrix can be optimized by adjusting the roll-off factor of subcarrier filters. It is shown that the performance of the proposed GFDM is about 0.02 dB better than that with a roll-off factor of 0 at a BER of 10^(-3) on an AWGN channel. On the other hand, on the multipath fading channels, the BER performance improves as the subcarrier bandwidth increases because of frequency diversity.
Adaptive beamformer incorporating with element directivity

High frame rate ultrasound is an emerging technique for medical ultrasound imaging. However, spatial resolution and contrast are degraded compared to conventional beamforming using focused transmit beams. In the present study, a kind of minimum variance beamformer, namely, amplitude and phase estimation (APES) beamformer, was examined for improvement of the spatial resolution. The APES beamformer estimates the desired signal, i.e., echo from the focal point, using delay-and-sum beamforming without considering the element directivity and removes it from the spatial covariance matrix. By omitting the element directivity, the error in estimation of the desired signal increases and, as a result, more part of the desired signal remains in the spatial covariance matrix. Consequently, sub-array averaging is necessary for further suppressing the desired signal contained in the spatial covariance matrix. In the present study, the APES beamformer was modified so as to consider the element directivity in estimation of the desired signal. Also, the proposed APES beamforming was further modified to be applied to outputs of sub-aperture beamforming to reduce dimension of the spatial covariance matrix. In the present study, the effect of the element directivity on APES beamforming was evaluated by a basic experiment using a phantom. In parallel beamforming with the conventional DAS, lateral spatial resolution, which was evaluated from the lateral full width at half maximum of the amplitude profile of an echo from a fine wire, was 0.50 mm. Using conventional APES, the lateral spatial resolution was improved to 0.26 mm. Lateral spatial resolution was further improved to 0.25 mm using the modified APES. In both APES beamforming, sub-array averaging was not used, and outputs from 6 sub-apertures were processed. Also in B-mode imaging of a carotid artery, undesired echoes are suppressed significantly by the modified APES.
Dynamic Interaction Between a Two-phase Submarine Landslide and a Fluid Reservoir

Gravitational flows, such as subaerial and submarine landslides, debris avalanches and pyroclastic flows are often the sources of super tsunamis. Here, the general two-phase debris flow model proposed by Pudasaini (2012) is applied to study subaerial and submarine debris flows, and the tsunami generated by the debris impact at reservoirs. The model, which includes three fundamentally new and dominant physical aspects such as enhanced non-Newtonian viscous stress, virtual mass, and generalized drag, constitutes the most generalized two-phase physical-mathematical mass flow model to date. Threedimensional, high-resolution simulation results are presented in case when a real two-phase debris mass hits a fluid reservoir that consists of different solid concentrations. Simulations are performed for different time slices and different parameter values. An innovative formulation is employed that provides an opportunity, within a single framework, to simultaneously simulate the sliding two-phase debris/landslide, reservoir, debris impact at reservoir, tsunami generation, amplification and propagation, mixing and separation between the solid and fluid phases. The results show formation and propagation of very special solidand fluid-structures in the reservoir, propagation of the submarine debris mass and turbidity currents, tsunami impacts at coastal lines, and complex interactions between the subaerial, tsunami and submarine debris waves, and reservoir walls. The employed modeling and simulation techniques can adequately describe the dynamics of solid-fluid mixture flows and particle transports in submarine environments, coastal regions, mountain lakes, rivers, reservoirs, and hydroelectric power plants. The simulation results show that the amount of grain in the reservoir plays a significant role in controlling the overall dynamics of the tsunami waves, and submarine debris flow. These findings substantially increase the understanding of three-dimensional complex multi-phase systems and flows and allow for the proper modeling of landslide and debris induced tsunami, dynamics of turbidity currents and sediment transports, with associated applications to engineering and hazard mitigation plans.
Dietary approaches to stop hypertension diet and obesity: A cross-sectional study of Iranian children and adolescents

BACKGROUND Few studies have investigated the effects of dietary approaches to stop hypertension (DASH) diet on obesity in children. The present study was conducted to examine adherence to the DASH diet in relation to obesity in children and adolescents, Isfahan, Iran. METHODS A cross-sectional study was carried out among 456 children aged 11-18 years who were selected by random cluster sampling method. Dietary intakes were assessed using a validated Food Frequency Questionnaire (FFQ). The DASH score was constructed based on food items emphasized or minimized in the DASH diet. Anthropometric measurements were conducted based on standard protocols. General and abdominal obesity were defined based on body mass index ≥ 95th percentiles and waist: height ratio of more than 0.5, respectively. RESULTS Higher adherence to DASH diet was inversely associated with general obesity (odds ratioT1 vs. T3 3.34, 95% confidence interval 1.28-8.75); however, after controlling for confounding factors, this association disappeared. Furthermore, higher adherence to DASH diet was negatively associated with central obesity in children, but the relation was not statistically significant. CONCLUSION We concluded that there was an inverse nonsignificant association between adherence to DASH diet and general obesity indices after adjustment for potential confounders. Further, well-designed randomized clinical trial studies are suggested to find out the effect of DASH diet on obesity obviously.
Optimizing a random system of cascaded video processing modules by parallel evolution modeling

Video processing algorithms tend to improve over time in terms of image quality while increasing in implementation complexity. Generally, video algorithms are developed and evaluated in isolation from the video processing system of which they will be a part, in a consumer product. The final image quality obtained by that system, however, strongly depends on the interaction of its constituent algorithms. Current methods for optimizing the overall image quality are ad-hoc, time consuming and do not guarantee the best possible result. We propose a rapid and reliable method for fine-tuning composite video processing systems based on genetic algorithms (GA). The GA method evolves toward a system configuration that gives the best image quality, driven by an objective video quality metric.
Blink Rate, Blink Amplitude, and Tear Film Integrity during Dynamic Visual Display Terminal Tasks

Purpose: The present study aimed at investigating the influence of the level of dynamism of two different visual display terminal tasks on spontaneous eyeblink rate, blink amplitude, and tear film integrity. Material and Methods: A total of 25 healthy, young volunteers participated in the study. Blink rate and blink amplitude were recorded in silent primary gaze conditions and while subjects were playing two computer games of similar cognitive demands but different rate of visual information presentation. For each experimental condition, tear volume was evaluated by measuring meniscus height and with the red phenol thread test. Fluorescein and non-invasive break-up time tests, as well as the observation of interference patterns and the estimation of the dry area extension, were employed to assess tear stability. Results: Statistically significant differences were revealed in blink rate (F = 595.85, p < 0.001) and blink amplitude (χ2 = 34.00, p < 0.001), with blink rate during fast- and slow-paced game play decreasing to almost 1/3 and 1/2 of baseline levels, respectively, and with a larger percentage of incomplete blinks during dynamic tasks. Fluorescein and non-invasive break-up time tests and dry area extension were able to differentiate between experimental conditions in general (F = 408.42, p < 0.001; F = 163.49, p < 0.001; χ2 = 20.74, p < 0.001), as well as between fast- and slow-paced games, thus suggesting that tear quality was more affected than tear volume. Conclusions: Blink rate, blink amplitude, and tear film stability were compromised during the most dynamic visual display terminal task, suggesting a negative influence of not only the cognitive aspects of the task, but also of the rate at which new visual information is presented. Frequent breaks and blinking awareness training are recommended for visual display terminal users requiring prolonged periods of visually demanding dynamic computer play or work.
Advances and Applications of Ion Torrent Personal Genome Machine in Cutaneous Squamous Cell Carcinoma Reveal Novel Gene Mutations

The Ion Torrent Personal Genome Machine (Ion PGM) is a semiconductor-based sequencing technology that is high quality, scalable, and economic. Its applications include genomic sequencing, drug resistance testing, microbial characterization, and targeted sequencing in cancer studies. However, little is known about the application of Ion PGM in cutaneous squamous cell carcinoma (cSCC). We therefore investigated the utility and validity of Ion PGM in cSCC and also gained a better understanding of the underlying molecular biology of cSCC. We detected novel gene mutations (KDR, FGFR2, and EGFR) in two cSCC patients. Moreover, we validated these mutations by pyrosequencing and Sanger sequencing. Our results indicated that the mutation screen using Ion PGM is consistent with traditional sequencing methods. Notably, these identified mutations were present at significantly higher rates in high-risk cSCC. Our results demonstrate a method to detect targetable genes in high-risk cSCC, and suggest that Ion PGM may enable therapeutic decision-making and future potential targets for personalized therapies in cSCC.
Comparison Analysis of Outdoor Channel Characteristics at 28 GHz and 2 GHz Using 3D Ray-Tracing Technique

Broadband wireless systems operating in millimeter wave (mmWave) frequency band has been used for short-range wireless communication and point-to- point wireless backhaul. Due to lack of research work on outdoor radio propagation characteristics in mmWave frequency band, the question of feasibility of cellular communication including long-range and non-line of sight (NLoS) environments in mmWave frequency band is unanswered. In this paper, we investigate the radio propagation characteristics at 28 GHz and 2 GHz using 3D ray-tracing simulation based on Manhattan-like grid model. LoS and NLoS results of outdoor radio propagation characteristics considering beamforming effects at 28 GHz are provided. Results of 2 GHz in the same geometry are also provided. In LoS environment, the radio propagation with 25 dBi beamforming gain at 28 GHz has similar characteristics with 2 GHz. In NLoS environment, even if the transmitter has 25 dBi beamforming gain at 28 GHz, the received power is 10 to 25 dB lower than 2 GHz. The received power loss because of narrow beam usage at 28 GHz is negligible in both LoS and NLoS environments.