Bounded seas

Abstract Imprecise manipulation of source code (semi-parsing) is useful for tasks such as robust parsing, error recovery, lexical analysis, and rapid development of parsers for data extraction. An island grammar precisely defines only a subset of a language syntax (islands), while the rest of the syntax (water) is defined imprecisely. Usually water is defined as the negation of islands. Albeit simple, such a definition of water is naive and impedes composition of islands. When developing an island grammar, sooner or later a language engineer has to create water tailored to each individual island. Such an approach is fragile, because water can change with any change of a grammar. It is time-consuming, because water is defined manually by an engineer and not automatically. Finally, an island surrounded by water cannot be reused because water has to be defined for every grammar individually. In this paper we propose a new technique of island parsing —- bounded seas. Bounded seas are composable, robust, reusable and easy to use because island-specific water is created automatically. Our work focuses on applications of island parsing to data extraction from source code. We have integrated bounded seas into a parser combinator framework as a demonstration of their composability and reusability.

Extraction of the s-wave pi N scattering lengths from data on pionic atoms

For many years a combined analysis of pionic hydrogen and deuterium atoms has been known as a good tool to extract information on the isovector and especially on the isoscalar s-wave pN scattering length. However, given the smallness of the isoscalar scattering length, the analysis becomes useful only if the pion–deuteron scattering length is controlled theoretically to a high accuracy comparable to the experimental precision. To achieve the required few-percent accuracy one needs theoretical control over all isospin-conserving three-body pNN !pNN operators up to one order before the contribution of the dominant unknown (N†N)2pp contact term. This term appears at next-to-next-to-leading order in Weinberg counting. In addition, one needs to include isospin-violating effects in both two-body (pN) and three-body (pNN) operators. In this talk we discuss the results of the recent analysis where these isospin-conserving and -violating effects have been carefully taken into account. Based on this analysis, we present the up-to-date values of the s-wave pN scattering lengths.

A Concept of Semantics Extraction from Web Data by Induction of Fuzzy Ontologies

Traditionally, ontologies describe knowledge representation in a denotational, formalized, and deductive way. In addition, in this paper, we propose a semiotic, inductive, and approximate approach to ontology creation. We define a conceptual framework, a semantics extraction algorithm, and a first proof of concept applying the algorithm to a small set of Wikipedia documents. Intended as an extension to the prevailing top-down ontologies, we introduce an inductive fuzzy grassroots ontology, which organizes itself organically from existing natural language Web content. Using inductive and approximate reasoning to reflect the natural way in which knowledge is processed, the ontology’s bottom-up build process creates emergent semantics learned from the Web. By this means, the ontology acts as a hub for computing with words described in natural language. For Web users, the structural semantics are visualized as inductive fuzzy cognitive maps, allowing an initial form of intelligence amplification. Eventually, we present an implementation of our inductive fuzzy grassroots ontology Thus,this paper contributes an algorithm for the extraction of fuzzy grassroots ontologies from Web data by inductive fuzzy classification.

Lake ice phenology from AVHRR data for European lakes: An automated two-step extraction method

Several lake ice phenology studies from satellite data have been undertaken. However, the availability of long-term lake freeze-thaw-cycles, required to understand this proxy for climate variability and change, is scarce for European lakes. Long time series from space observations are limited to few satellite sensors. Data of the Advanced Very High Resolution Radiometer (AVHRR) are used in account of their unique potential as they offer each day global coverage from the early 1980s expectedly until 2022. An automatic two-step extraction was developed, which makes use of near-infrared reflectance values and thermal infrared derived lake surface water temperatures to extract lake ice phenology dates. In contrast to other studies utilizing thermal infrared, the thresholds are derived from the data itself, making it unnecessary to define arbitrary or lake specific thresholds. Two lakes in the Baltic region and a steppe lake on the Austrian–Hungarian border were selected. The later one was used to test the applicability of the approach to another climatic region for the time period 1990 to 2012. A comparison of the extracted event dates with in situ data provided good agreements of about 10 d mean absolute error. The two-step extraction was found to be applicable for European lakes in different climate regions and could fill existing data gaps in future applications. The extension of the time series to the full AVHRR record length (early 1980 until today) with adequate length for trend estimations would be of interest to assess climate variability and change. Furthermore, the two-step extraction itself is not sensor-specific and could be applied to other sensors with equivalent near- and thermal infrared spectral bands.

Multicentre validation study of nucleic acids extraction from FFPE tissues

In most pathology laboratories worldwide, formalin-fixed paraffin embedded (FFPE) samples are the only tissue specimens available for routine diagnostics. Although commercial kits for diagnostic molecular pathology testing are becoming available, most of the current diagnostic tests are laboratory-based assays. Thus, there is a need for standardized procedures in molecular pathology, starting from the extraction of nucleic acids. To evaluate the current methods for extracting nucleic acids from FFPE tissues, 13 European laboratories, participating to the European FP6 program IMPACTS (www.impactsnetwork.eu), isolated nucleic acids from four diagnostic FFPE tissues using their routine methods, followed by quality assessment. The DNA-extraction protocols ranged from homemade protocols to commercial kits. Except for one homemade protocol, the majority gave comparable results in terms of the quality of the extracted DNA measured by the ability to amplify differently sized control gene fragments by PCR. For array-applications or tests that require an accurately determined DNA-input, we recommend using silica based adsorption columns for DNA recovery. For RNA extractions, the best results were obtained using chromatography column based commercial kits, which resulted in the highest quantity and best assayable RNA. Quality testing using RT-PCR gave successful amplification of 200 bp-250 bp PCR products from most tested tissues. Modifications of the proteinase-K digestion time led to better results, even when commercial kits were applied. The results of the study emphasize the need for quality control of the nucleic acid extracts with standardised methods to prevent false negative results and to allow data comparison among different diagnostic laboratories.

Automatic extraction of femur contours from calibrated fluoroscopic images

Automatic identification and extraction of bone contours from X-ray images is an essential first step task for further medical image analysis. In this paper we propose a 3D statistical model based framework for the proximal femur contour extraction from calibrated X-ray images. The automatic initialization is solved by an estimation of Bayesian network algorithm to fit a multiple component geometrical model to the X-ray data. The contour extraction is accomplished by a non-rigid 2D/3D registration between a 3D statistical model and the X-ray images, in which bone contours are extracted by a graphical model based Bayesian inference. Preliminary experiments on clinical data sets verified its validity

Parameter-free extraction of the functional network topology from intracranial EEG recordings: a time-resolved study of graph properties in focal onset seizures

Rationale: Focal onset epileptic seizures are due to abnormal interactions between distributed brain areas. By estimating the cross-correlation matrix of multi-site intra-cerebral EEG recordings (iEEG), one can quantify these interactions. To assess the topology of the underlying functional network, the binary connectivity matrix has to be derived from the cross-correlation matrix by use of a threshold. Classically, a unique threshold is used that constrains the topology [1]. Our method aims to set the threshold in a data-driven way by separating genuine from random cross-correlation. We compare our approach to the fixed threshold method and study the dynamics of the functional topology. Methods: We investigate the iEEG of patients suffering from focal onset seizures who underwent evaluation for the possibility of surgery. The equal-time cross-correlation matrices are evaluated using a sliding time window. We then compare 3 approaches assessing the corresponding binary networks. For each time window: * Our parameter-free method derives from the cross-correlation strength matrix (CCS)[2]. It aims at disentangling genuine from random correlations (due to finite length and varying frequency content of the signals). In practice, a threshold is evaluated for each pair of channels independently, in a data-driven way. * The fixed mean degree (FMD) uses a unique threshold on the whole connectivity matrix so as to ensure a user defined mean degree. * The varying mean degree (VMD) uses the mean degree of the CCS network to set a unique threshold for the entire connectivity matrix. * Finally, the connectivity (c), connectedness (given by k, the number of disconnected sub-networks), mean global and local efficiencies (Eg, El, resp.) are computed from FMD, CCS, VMD, and their corresponding random and lattice networks. Results: Compared to FMD and VMD, CCS networks present: *topologies that are different in terms of c, k, Eg and El. *from the pre-ictal to the ictal and then post-ictal period, topological features time courses that are more stable within a period, and more contrasted from one period to the next. For CCS, pre-ictal connectivity is low, increases to a high level during the seizure, then decreases at offset. k shows a ‘‘U-curve’’ underlining the synchronization of all electrodes during the seizure. Eg and El time courses fluctuate between the corresponding random and lattice networks values in a reproducible manner. Conclusions: The definition of a data-driven threshold provides new insights into the topology of the epileptic functional networks.

Hard thermal loop benchmark for the extraction of the nonperturbative QQ[over ¯] potential

The extraction of the finite temperature heavy quark potential from lattice QCD relies on a spectral analysis of the Wilson loop. General arguments tell us that the lowest lying spectral peak encodes, through its position and shape, the real and imaginary parts of this complex potential. Here we benchmark this extraction strategy using leading order hard-thermal loop (HTL) calculations. In other words, we analytically calculate the Wilson loop and determine the corresponding spectrum. By fitting its lowest lying peak we obtain the real and imaginary parts and confirm that the knowledge of the lowest peak alone is sufficient for obtaining the potential. Access to the full spectrum allows an investigation of spectral features that do not contribute to the potential but can pose a challenge to numerical attempts of an analytic continuation from imaginary time data. Differences in these contributions between the Wilson loop and gauge fixed Wilson line correlators are discussed. To better understand the difficulties in a numerical extraction we deploy the maximum entropy method with extended search space to HTL correlators in Euclidean time and observe how well the known spectral function and values for the real and imaginary parts are reproduced. Possible venues for improvement of the extraction strategy are discussed.

New method for porewater extraction from claystone and determination of transport properties with results for Opalinus Clay (Switzerland)

A new technique to porewater extraction from claystone employs advective displacement of the in situ porewater by traced artificial porewater. Monitoring of tracer breakthrough yields species-specific transport properties. Results for Opalinus Clay from the Mont Terri Research Laboratory indicate that the chemical disturbances due to the method are minimal, and the observed significant differences in transport properties for Br– and 2H are in agreement with existing data. Sampling times are 2–4 months, and observation of tracer breakthrough takes 12–24 months at hydraulic conductivity of ∼10-13 m/s.

Extraction of spin periods of space debris from optical light curves

The population of space debris increased drastically during the last years. These objects have become a great threat for active satellites. Because the relative velocities between space debris and satellites are high, space debris objects may destroy active satellites through collisions. Furthermore, collisions involving massive objects produce large number of fragments leading to significant growth of the space debris population. The long term evolution of the debris population is essentially driven by so-called catastrophic collisions. An effective remediation measure in order to stabilize the population in Low Earth Orbit (LEO) is therefore the removal of large, massive space debris. To remove these objects, not only precise orbits, but also more detailed information about their attitude states will be required. One important property of an object targeted for removal is its spin period, spin axis orientation and their change over time. Rotating objects will produce periodic brightness variations with frequencies which are related to the spin periods. Such a brightness variation over time is called a light curve. Collecting, but also processing light curves is challenging due to several reasons. Light curves may be undersampled, low frequency components due to phase angle and atmospheric extinction changes may be present, and beat frequencies may occur when the rotation period is close to a multiple of the sampling period. Depending on the method which is used to extract the frequencies, also method-specific properties have to be taken into account. The astronomical Institute of the University of Bern (AIUB) light curve database will be introduced, which contains more than 1,300 light curves acquired over more than seven years. We will discuss properties and reliability of different time series analysis methods tested and currently used by AIUB for the light curve processing. Extracted frequencies and reconstructed phases for some interesting targets, e.g. GLONASS satellites, for which also SLR data were available for the period confirmation, will be presented. Finally we will present the reconstructed phase and its evolution over time of a High-Area-to-Mass-Ratio (HAMR) object, which AIUB observed for several years.

A prospective, randomized, controlled study using OsseoSpeed™ implants placed in maxillary fresh extraction socket: soft tissues response

PURPOSE The aim of this work was to study the peri-implant soft tissues response, by evaluating both the recession and the papilla indexes, of patients treated with implants with two different configurations. In addition, data were stratified by tooth category, smoking habit and thickness of buccal bone wall. MATERIALS AND METHODS The clinical trial was designed as a prospective, randomized-controlled multicenter study. Adults in need of one or more implants replacing teeth to be removed in the maxilla within the region 15-25 were recruited. Following tooth extraction, the site was randomly allocated to receive either a cylindrical or conical/cylindrical implant. The following parameters were studied: (i) Soft tissue recession (REC) measured by comparing the gingival zenith (GZ) score at baseline (permanent restoration) with that of the yearly follow-up visits over a period of 3 years (V1, V2 and V3). (ii) Interdental Papilla Index (PI): PI measurements were performed at baseline and compared with that of the follow-up visits. In addition, data were stratified by different variables: tooth category: anterior (incisors and canine) and posterior (first and second premolar); smoking habit: patient smoker (habitual or occasional smoker at inclusion) or non-smoker (non-smoker or ex-smoker at inclusion) and thickness of buccal bone wall (TB): TB ≤ 1 mm (thin buccal wall) or TB > 1 mm (thick buccal wall). RESULTS A total of 93 patients were treated with 93 implants. At the surgical re-entry one implant was mobile and then removed; moreover, one patient was lost to follow-up. Ninety-one patients were restored with 91 implant-supported permanent single crowns. After the 3-year follow-up, a mean gain of 0.23 mm of GZ was measured; moreover, 79% and 72% of mesial and distal papillae were classified as >50%/ complete, respectively. From the stratification analysis, not significant differences were found between the mean GZ scores of implants with TB ≤ 1 mm (thin buccal wall) and TB > 1 mm (thick buccal wall), respectively (P < 0.05, Mann-Whitney U-test) at baseline, at V1, V2 and V3 follow-up visits. Also, the other variables did not seem to influence GZ changes over the follow-up period. Moreover, a re-growth of the interproximal mesial and distal papillae was the general trend observed independently from the variables studied. CONCLUSIONS Immediate single implant treatment may be considered a predictable option regarding soft tissue stability over a period of 3 years of follow-up. An overall buccal soft tissue stability was observed during the GZ changes from the baseline to the 3 years of follow-up with a mean GZ reduction of 0.23 mm. A nearly full papillary re-growth can be detectable over a minimum period of 2 years of follow-up for both cylindrical and conical/cylindrical implants. Both the interproximal papilla filling and the midfacial mucosa stability were not influenced by variables such as type of fixture configuration, tooth category, smoke habit, and thickness of buccal bone wall of ≤ 1 mm (thin buccal wall).

The timing of extraction of non-restorable first permanent molars: a systematic review.

AIM To identify the ideal timing of first permanent molar extraction to reduce the future need for orthodontic treatment. MATERIALS AND METHODS A computerised database and subsequent manual search was performed using Medline database, Embase and Ovid, covering the period from January 1946 to February 2013. Two reviewers (JE and ME) extracted the data independently and evaluated if the studies matched the inclusion criteria. Inclusion criteria were specification of the follow-up with clinical examination or analysis of models, specification of the chronological age or dental developmental stage at the time of extraction, no treatment in between, classification of the treatment result into perfect, good, average and poor. The search was limited to human studies and no language limitations were set. RESULTS The search strategy resulted in 18 full-text articles, of which 6 met the inclusion criteria. By pooling the data from maxillary sites, good to perfect clinical outcome was estimated in 72% (95% confidence interval 63%-82%). Extractions at the age of 8-10.5 years tended to show better spontaneous clinical outcomes compared to the other age groups. By pooling the data from mandibular sites, extractions performed at the age of 8-10.5 and 10.5-11.5 years showed significantly superior spontaneous clinical outcome with a probability of 50% and 59% likelihood, respectively, to achieve good to perfect clinical result (p<0.05) compared to the other age groups (<8 years of age: 34%, >11.5 years of age: 44%). CONCLUSION Prevention of complications after first permanent molars extractions is an important issue. The overall success rate of spontaneous clinical outcome for maxillary extraction of first permanent molars was superior to mandibular extraction. Extractions of mandibular first permanent molars should be performed between 8 and 11.5 years of age in order to achieve a good spontaneous clinical outcome. For the extraction in the maxilla, no firm conclusions concerning the ideal extraction timing could be drawn.

A multinational case-control study on childhood brain tumours, anthropogenic factors, birth characteristics and prenatal exposures: A validation of interview data.

Little is known about the aetiology of childhood brain tumours. We investigated anthropometric factors (birth weight, length, maternal age), birth characteristics (e.g. vacuum extraction, preterm delivery, birth order) and exposures during pregnancy (e.g. maternal: smoking, working, dietary supplement intake) in relation to risk of brain tumour diagnosis among 7-19 year olds. The multinational case-control study in Denmark, Sweden, Norway and Switzerland (CEFALO) included interviews with 352 (participation rate=83.2%) eligible cases and 646 (71.1%) population-based controls. Interview data were complemented with data from birth registries and validated by assessing agreement (Cohen's Kappa). We used conditional logistic regression models matched on age, sex and geographical region (adjusted for maternal age and parental education) to explore associations between birth factors and childhood brain tumour risk. Agreement between interview and birth registry data ranged from moderate (Kappa=0.54; worked during pregnancy) to almost perfect (Kappa=0.98; birth weight). Neither anthropogenic factors nor birth characteristics were associated with childhood brain tumour risk. Maternal vitamin intake during pregnancy was indicative of a protective effect (OR 0.75, 95%-CI: 0.56-1.01). No association was seen for maternal smoking during pregnancy or working during pregnancy. We found little evidence that the considered birth factors were related to brain tumour risk among children and adolescents.