Miracle-dz/UniFAR-FTUs huggingface dataset:
Bootstrapping structure using similarity

In this paper a new similarity-based learning algorithm, inspired by string edit-distance (Wagner and Fischer, 1974), is applied to the problem of bootstrapping structure from scratch. The algorithm takes a corpus of unannotated sentences as input and returns a corpus of bracketed sentences. The method works on pairs of unstructured sentences or sentences partially bracketed by the algorithm that have one or more words in common. It finds parts of sentences that are interchangeable (i.e. the parts of the sentences that are different in both sentences). These parts are taken as possible constituents of the same type. While this corresponds to the basic bootstrapping step of the algorithm, further structure may be learned from comparison with other (similar) sentences. We used this method for bootstrapping structure from the flat sentences of the Penn Treebank ATIS corpus, and compared the resulting structured sentences to the structured sentences in the ATIS corpus. Similarly, the algorithm was tested on the OVIS corpus. We obtained 86.04 % non-crossing brackets precision on the ATIS corpus and 89.39 % non-crossing brackets precision on the OVIS corpus.
Lane Departure Detection and Transmisson using Hough Transform Method

Vehicles need to be re-advancing by video transmission among vehicles for safety and cooperative deriving. The video images captured from camera could help the driver to monitor the surroundings as well as transmit the compressed images over vehicular communication network. Video over wireless communication has a lot of potential applications in intelligent transportation systems (ITS). Video streaming utilizes high bandwidth data links to transmit information. The high-bandwidth systems required larger equipment, better line-of-sight, and more complex mechanism for reliable transmit ion over the network. The intended platform for the system described in this study, is to develop a software defined algorithm for automatic video compression and transmission. The proposed algorithm is able to robustly find the left and right boundary of the lane using Hough Transform method and transmit over the network. Therefore the limitations of high-bandwidth equipment become more significant in a tactical scenario. The results show that the proposed method works well on marked roads and transmission in various lighting conditions. Streszczenie. W artykule przedstawiono algorytm kompresji i transmisji obrazow do zastosowania w komunikacji bezprzewodowej w sieci samochodowej. Przy pomocy transformacji Hough algorytm określa lewą i prawą granice pasa i przesyla dane do sieci. Przeprowadzono badania weryfikujące dzialanie algorytmu, ktore wykazaly jego skutecznośc na oznaczonych drogach przy roznych warunkach oświetlenia. (Zastosowanie transformacji Hough w detekcji wyjazdu z pasa i transmisji danych).
Immunophenotypes and Immune Markers Associated with Acute Promyelocytic Leukemia Prognosis

CD2+, CD34+, and CD56+ immunophenotypes are associated with poor prognoses of acute promyelocytic leukemia (APL). The present study aimed to explore the role of APL immunophenotypes and immune markers as prognostic predictors on clinical outcomes. A total of 132 patients with de novo APL were retrospectively analyzed. Immunophenotypes were determined by flow cytometry. Clinical features, complete remission (CR), relapse, and five-year overall survival (OS) rate were assessed and subjected to multivariate analyses. The CD13+CD33+HLA-DR-CD34− immunophenotype was commonly observed in patients with APL. Positive rates for other APL immune markers including cMPO, CD117, CD64, and CD9 were 68.7%, 26%, 78.4%, and 96.6%, respectively. When compared with patients with CD2− APL, patients with CD2+ APL had a significantly higher incidence of early death (50% versus 15.7%; P = 0.016), lower CR rate (50% versus 91.1%; P = 0.042), and lower five-year OS rate (41.7% versus 74.2%; P = 0.018). White blood cell (WBC) count before treatment was found to be the only independent risk factor of early death, CR failure, and five-year mortality rate. Flow cytometric immunophenotype analysis can facilitate prompt APL diagnosis. Multivariate analysis has demonstrated that WBC count before treatment is the only known independent risk factor that predicts prognosis for APL in this study population.
Implementation of a Parallel Algorithm for Protein Pairwise Alignment Using Reconfigurable Computing

This paper describes the design and implementation of a parallel pairwise alignment hardware, implemented in a FPGA device. This system is aimed at aligning pairs of proteins, using a dynamic programming algorithm. The alignment is done in parallel thanks to a pipelined approach. All functional blocks are described in detail. Experiments were done to access the performance of the system for up to pairs of 2000-amino acids-long proteins. Hardalign was compared with a similar algorithm implemented in software and running in a PC, resulting in a 1:10 speed-up ratio. Results encourage the continuity of the work, showing that reconfigurable computing can offer interesting solutions for bioinformatics problems
Repetitive Lumbar Punctures as Treatment for Normal Pressure Hydrocephalus

Selected normal pressure hydrocephalus (NPH) patients cannot be treated by shunt operation because of the procedure’s high complication rate. We have treated cases in which prolonged clinical improvement of NPH was experienced after one or two lumbar punctures (LPs). We evaluated the predictors of prolonged improvement of NPH symptoms by repeated LP. Thirty-one NPH patients were retrospectively evaluated (age 72.5 ± 5.8 years). Gait disturbance, urinary incontinence, and cognitive impairment were semiquantified. We divided the patients into three groups (non-responders, temporary responders, and prolonged responders) according to their responses after LP. We analyzed the characteristics of the groups. Gait disturbance (p = 0.046) and urinary incontinence (p = 0.040) scores and total NPH symptom score (p = 0.007) after cerebrospinal fluid drainage were more significantly improved in prolonged responders than in temporary responders. On multiple logistic regression analyses, total NPH score improvement was the only predictor of the prolonged responders (p = 0.03, odds ratio 0.148). Our study showed that some NPH patients could maintain favorable courses for at least 1 year after LP without shunt operation. Repeated LP could be an alternative treatment in selected NPH patients.
Hrd1 and ER-Associated Protein Degradation, ERAD, are Critical Elements of the Adaptive ER Stress Response in Cardiac Myocytes.

RATIONALE Hydroxymethyl glutaryl-coenzyme A reductase degradation protein 1 (Hrd1) is an endoplasmic reticulum (ER)-transmembrane E3 ubiquitin ligase that has been studied in yeast, where it contributes to ER protein quality control by ER-associated degradation (ERAD) of misfolded proteins that accumulate during ER stress. Neither Hrd1 nor ERAD has been studied in the heart, or in cardiac myocytes, where protein quality control is critical for proper heart function. OBJECTIVE The objective of this study were to elucidate roles for Hrd1 in ER stress, ERAD, and viability in cultured cardiac myocytes and in the mouse heart, in vivo. METHODS AND RESULTS The effects of small interfering RNA-mediated Hrd1 knockdown were examined in cultured neonatal rat ventricular myocytes. The effects of adeno-associated virus-mediated Hrd1 knockdown and overexpression were examined in the hearts of mice subjected to pressure overload-induced pathological cardiac hypertrophy, which challenges protein-folding capacity. In cardiac myocytes, the ER stressors, thapsigargin and tunicamycin increased ERAD, as well as adaptive ER stress proteins, and minimally affected cell death. However, when Hrd1 was knocked down, thapsigargin and tunicamycin dramatically decreased ERAD, while increasing maladaptive ER stress proteins and cell death. In vivo, Hrd1 knockdown exacerbated cardiac dysfunction and increased apoptosis and cardiac hypertrophy, whereas Hrd1 overexpression preserved cardiac function and decreased apoptosis and attenuated cardiac hypertrophy in the hearts of mice subjected to pressure overload. CONCLUSIONS Hrd1 and ERAD are essential components of the adaptive ER stress response in cardiac myocytes. Hrd1 contributes to preserving heart structure and function in a mouse model of pathological cardiac hypertrophy.
Responsiveness of cat area 17 after monocular inactivation: limitation of topographic plasticity in adult cortex.

1. Recordings were made from neurones in the splenial sulcus of normal adult cats and adult cats which had one eye inactivated by enucleation or photocoagulation of the optic disc. Two visually responsive regions were observed, corresponding to the peripheral representation of visual area 1 (V1) and the splenial visual area. In normal animals, responses to the ipsilateral eye in V1 were restricted to the medial half of the splenial sulcus, up to 45‐50 deg eccentricity. Thus, by inactivating the eye contralateral to the experimental hemisphere, we created a region in V1, 1‐2 mm wide, that lacked normal inputs. 2. In contrast to results from previous experiments where lesions were placed in the central retina, neurones in the deprived peripheral representation remained unresponsive to light stimuli for up to 12 h after deactivation of the contralateral eye. 3. In animals that were allowed to recover from the monocular deactivation for periods of 2 days to 16 months, there was rearrangement of the retinotopic maps. Receptive fields in regions of cortex that normally represented the monocular crescent were displaced to the temporal border of the binocular field of vision. However, most neurones in the deprived peripheral representation remained unresponsive to visual stimuli even more than 1 year after treatment. This is also in marked contrast with the extensive reorganization that is observed in the central representation of V1 after restricted retinal lesions. Analysis of the cortical magnification factor demonstrates that the change in visual topography is local, and does not involve an overall centro‐peripheral shift of the retinotopic map. 4. Among the neurones that did show displaced receptive fields, the response properties were clearly abnormal. They showed a notable lack of spontaneous activity, low firing rates and rapid habituation to repeated stimulation. 5. The low potential for reorganization of the monocular sector of V1 demonstrates that the capacity for plasticity of mature sensory representations varies with location in cortex. Even relatively small pieces of cortex, such as the monocular crescent representations, may not reorganize completely if certain conditions are not met. These results suggest the existence of natural boundaries that may limit the process of reorganization of sensory representations.
The Lived Experience of the Adolescent Sex Offender: A Phenomenological Case Study

ABSTRACT Treatment for adolescents with sexually maladaptive behaviors is a continuing intervention that is changing and developing as greater understanding about this population of adolescents is obtained. The majority of treatment programs for adolescent sexually maladaptive behavior contain programming components that include cognitive distortions/thinking errors. Interviews including a conceptual mapping exercise were conducted with four adolescents adjudicated to a secure care program for sexual behaviors. All four boys completed an interview and a conceptual map of their perceived experiences as an adolescent with sexual maladaptive behaviors. All interviews were audio recorded. Analysis of the interviews and conceptual mappings yielded five themes present in the boys’ experience as well as a consideration of the role early trauma may have in the establishment of cognitive distortion development. Contributing environmental and familial factors also play an important part in sustaining cognitive distortion. Main themes include: loss of responsible father or father figure, inability to regulate emotion, lack of personal and parental boundaries, and early exposure to pornography. The contributing influence of responsible male father figures may play an even greater role in the lives of young males than originally thought. How the adolescent inaccurately perceives his environment—in essence what he tells himself and continues to tell himself to make sense of his world—are building blocks in the development and continuation of thinking errors/cognitive distortions used to commit and justify sexual offending behaviors.
Qualitative Research Genres in the IS Literature: Emerging Issues and Potential Implications

In this opinion piece, we provide a critical commentary on the arena of qualitative research in IS. We reflect on why reviewer or editorial evaluations of manuscripts, with respect to methodological issues in qualitative studies, often come across as ''prejudiced. " By viewing the adoption of qualitative research in the IS discipline as an evolutionary process, and by highlighting key differences among genres of qualitative manuscripts, a number of implications for both authors and evaluators of qualitative manuscripts emerge
A primer for hybrid modeling and simulation

In dealing with complex systems, there is no single “best” possible modeling approach, as each specific system and modeling purpose has subtleties and specific needs. Consequently, in developing models that capture the complexity of real systems, it is useful to combine modeling approaches yielding what is referred to as a hybrid modeling approach. By combining different modeling paradigms, hybrid modeling and simulation provide a more comprehensive and holistic view of the system under investigation and a very powerful approach to understanding complexity. This paper discusses the uses and applications of hybrid modeling, general lessons related to how and when to use such an approach, and relevant tools.
ClusTop: A clustering-based topic modelling algorithm for twitter using word networks

Twitter is a popular microblogging service, where users frequently engage in discussions about various topics of interest, ranging from popular topics (e.g., music) to niche topics (e.g., politics). With the large amount of tweets, a key challenge is to automatically model and determine the discussion topics without having prior knowledge of the types and number of topics, or requiring the technical expertise to define various algorithmic parameters. For this purpose, we propose the Clustering-based Topic Modelling (ClusTop) algorithm that constructs various types of word network and automatically determines the discussion topics using community detection approaches. Unlike traditional topic models, ClusTop is able to automatically determine the appropriate number of topics and does not require numerous parameters to be set. The ClusTop algorithm is also able to capture the syntactic meaning in tweets via the use of bigrams, trigrams and other word combinations in constructing the word network graph. Using three Twitter datasets with labelled crises and events as topics, ClusTop has been shown to outperform various baselines in terms of topic coherence, pointwise mutual information, precision, recall and F-score.
Increased soil methane emissions and methanogenesis in oil contaminated areas

Crude oil exploration and related activities cause severe soil contamination and land degradation. However, how soil CH4 and CO2 fluxes respond to oil contamination is poorly understood. To address this question, we conducted in situ investigation of CH4 and CO2 emissions in the Shengli Oilfield, China. CH4 emissions from contaminated soils were 60–1,800 μg·m−2·hr−1, much higher than those from uncontaminated soils (29–33 μg·m−2·hr−1). CO2 fluxes of 2–78 mg·m−2·hr−1 were lower from contaminated soils compared with uncontaminated controls (78–104 mg·m−2·hr−1). The variance of CH4 and CO2 fluxes could be explained to 78.0% by soil properties and oil well age (p < .001) as suggested by the redundancy analysis and the variance partitioning analysis. On the basis of the Illumina MiSeq sequencing of the archaeal 16S rRNA gene, the relative abundance of methanogens over archaea increased by 8 times in contaminated soils compared with that in the uncontaminated soils, suggesting enhanced methanogenesis processes. The proportion of hydrogenotrophic methanogens over the total methanogens increased from 35% in the uncontaminated soil to 43% in the contaminated soils, consistent with the higher apparent fractionation factor (αC) in the stable isotope analysis. Both microbial and isotopic results suggested that the hydrogenotrophic methanogenesis relatively enhanced with the oil contamination, with less dominance of the acetoclastic methanogenesis. The dramatically increased CH4 emissions under oil contamination call for great attention as a potentially important anthropogenic source of CH4 in the atmosphere.
Low-cost and representative surrogate hydrological models. Part II - Use within calibration frameworks

This is a two-part work. In Part I, low-cost and representative reduced-fidelity models of two versions of the HYDROTEL hydrological model are constructed, using three types of surrogate models and their combination. Level of representativeness and CPU time ratios between original and surrogate models are evaluated to construct final reduced-fidelity models. Part II of this study focuses on the use of these models within an existing efficient calibration method: the hybrid DDS-MADS optimization approach. Based on this approach, this paper proposes a range of calibration frameworks exploiting reduced-fidelity models. The calibration frameworks are assessed and compared and results demonstrate that exploiting reduced-fidelity models within the hybrid DDS-MADS optimization approach decreases the overall computational time while maintaining the quality of the final solutions. The proposed framework provides a range of tradeoffs between computational time and objective function value. Depending on calibration objectives and optimization constraints, users can select the appropriate one.
Halloysite Nanotubes as Adsorptive Material for Phosphate Removal from Aqueous Solution

In this study, we were aiming at testing halloysite nanotubes as an efficient adsorbent for the removal of phosphate from agricultural runoff. Adsorption of phosphate onto powder and granular form of halloysite nanotubes has been examined by using the classical batch method and diffusion experiments at room temperature. Different forms of halloysite nanotubes were investigated to explore the effect of structure on the adsorption of phosphate. The maximum adsorption efficiency was obtained for powder halloysite nanotubes (79.5%) and granular form (94.7%). It is believed that the pore space of the granular halloysite nanotubes accommodates phosphorus in addition to physico-chemically bound phosphate at surfaces. The pseudo-first order and pseudo-second order model fitted well the experimental kinetic data for both powder and granular form of halloysite nanotubes. The fit of the Freundlich isotherm model was superior as compared with the Langmuir approach, implying that the halloysite nanotubes are heterogeneous because of multiple surface groups and different pore structures. The two forms of halloysite nanotube tested have the abundant potential for removal of phosphate from agriculture runoff. Additional investigations at the pilot scale are, however, required to draw definite conclusions.
Wnt ligand presentation and reception: from the stem cell niche to tissue engineering

Stem cells reside in niches where spatially restricted signals maintain a delicate balance between stem cell self-renewal and differentiation. Wnt family proteins are particularly suited for this role as they are modified by lipids, which constrain and spatially regulate their signalling range. In recent years, Wnt/β-catenin signalling has been shown to be essential for the self-renewal of a variety of mammalian stem cells. In this review, we discuss Wnt-responsive stem cells in their niche, and mechanisms by which Wnt ligands are presented to responsive cells. We also highlight recent progress in molecular visualization that has allowed for the monitoring of Wnt signalling within the stem cell compartment and new approaches to recapitulate this niche signalling in vitro. Indeed, new technologies that present Wnt in a localized manner and mimic the three-dimensional microenvironment of stem cells will advance our understanding of Wnt signalling in the stem cell niche. These advances will expand current horizons to exploit Wnt ligands in the rapidly evolving fields of tissue engineering and regenerative medicine.
On Different Models for Generating Random SAT Problems

In the last decade a lot of effort has been invested into both theoretical and experimental analysis of SAT phase transition. However, a deep theoretical understanding of this phenomenon is still lacking. Besides, many of experimental results are based on some assumptions that are not supported theoretically. In this paper we introduce the notion of SAT-equivalence and we prove that some restrictions often used in SAT experiments don't make an impact on location of a crossover point. We consider several fixed and random clause length SAT models and relations between them. We also discuss one new SAT model and report on a detected phase transition for it.
UvA-DARE (Digital Academic Repository) The entropy of a hole in spacetime

: We compute the gravitational entropy of “spherical Rindler space”, a time-dependent, spherically symmetric generalization of ordinary Rindler space, deﬁned with reference to a family of observers traveling along non-parallel, accelerated trajectories. All these observers are causally disconnected from a spherical region H (a “hole”) located at the origin of Minkowski space. The entropy evaluates to S = A / 4 G , where A is the area of the spherical acceleration horizon, which coincides with the boundary of H . We propose that S is the entropy of entanglement between quantum gravitational degrees of freedom supporting the interior and the exterior of the sphere H .
Lecture Notes Statistical and Machine Learning Information Theory Svm Neural Networks List of Figures

• Course plan: See Table of Contents (tentative). We will emphasize on knowing " why " and on statistical aspects instead of algorithms and programming. But still you have to know " how " by either writing your own implementation or modifying from others' code. • Grading policy: homework 30%, score for late homework= (full points) × 0.8 d , d : delay days. oral presentation 20% on assigned tasks (and your final project as well). final project 20%: choose your own data analysis problem and write up a short report and prepare for an oral presentation. The report should include – problem and data description, – methodology (related to this course), – data analysis, and – conclusion. – UCI Repository for machine learning is probably the most popular repository. – UCI KDD Archive. It is an online repository of large data sets which encompasses a wide variety of data types, analysis tasks, and application areas. – CiteSeer is a public search engine and digital library for scientific and academic papers in the fields of computer and information sciences. – Statlib for statistical software and data sets.