LLukas22/scidocs huggingface dataset:
Compact architecture for high-throughput regular expression matching on FPGA

In this paper we present a novel architecture for high-speed and high-capacity regular expression matching (REM) on FPGA. The proposed REM architecture, based on nondeterministic finite automaton (RE-NFA), efficiently constructs regular expression matching engines (REME) of arbitrary regular patterns and character classes in a uniform structure, utilizing both logic slices and block memory (BRAM) available on modern FPGA devices. The resulting circuits take advantage of synthesis and routing optimizations to achieve high operating speed and area efficiency. The uniform structure of our RE-NFA design can be stacked in a simple way to produce multi-character input circuits to scale up throughput further. An n-state m-character input REME takes only O (n X log2 m) time to construct and occupies no more than O (n X m) logic units. The REMEs can be staged and pipelined in large numbers to achieve high parallelism without sacrificing clock frequency.
 Using the proposed RE-NFA architecture, we are able to implement 3 copies of two-character input REMEs, each with 760 regular expressions, 18715 states and 371 character classes, onto a single Xilinx Virtex 4 LX-100-12 device. Each copy processes 2 characters per clock cycle at 300 MHz, resulting in a concurrent throughput of 14.4 Gbps for 760 REMEs. Compared with the automatic NFA-to-VHDL REME compilation [13], our approach achieves over 9x throughput efficiency (Gbps*state/LUT). Compared with state-of-the-art REMEs on FPGA, our approach also indicates up to 70% better throughput efficiency.
2 Maturity Models in Business Process Management

Purpose – Maturity models are a prospering approach to improving a company’s processes and business process management (BPM) capabilities. In fact, the number of corresponding maturity models is such high that practitioners and scholars run the risk of losing track. We therefore provide a systematic in-depth review of BPM maturity models. Design/methodology/approach – The paper follows the accepted research process for literature reviews. We analyze a sample of 10 BPM maturity models according to a framework of general design principles. The framework particularly focuses on the applicability and usefulness of maturity models. Findings – The analyzed maturity models sufficiently address basic design principles as well as principles for a descriptive purpose of use. The design principles for a prescriptive use, however, are hardly met. Thus, BPM maturity models provide limited guidance for identifying desirable maturity levels and for implementing improvement measures. Research limitations/implications – We are confident that this review covers the majority of publicly available BPM maturity models. As the number of corresponding maturity models seems to be constantly growing, exhaustiveness can hardly be guaranteed. Our results stimulate future research. Inter alia, adopters from industry require more elaborate support by means of ready-to-use and adaptable instruments for maturity assessment and improvement. We also reaffirm the need for maturity model consolidation in the field of BPM. Originality/value – As existing literature reviews focus on process improvement or BPM in general, our findings extend current knowledge. They also increase transparency. Our results provide guidance for scholars and practitioners involved in the design, enhancement, or application of BPM maturity models.
Automatic Semantic Content Removal by Learning to Neglect

We introduce a new system for automatic image content removal and inpainting. Unlike traditional inpainting algorithms, which require advance knowledge of the region to be filled in, our system automatically detects the area to be removed and infilled. Region segmentation and inpainting are performed jointly in a single pass. In this way, potential segmentation errors are more naturally alleviated by the inpainting module. The system is implemented as an encoder-decoder architecture, with two decoder branches, one tasked with segmentation of the foreground region, the other with inpainting. The encoder and the two decoder branches are linked via neglect nodes, which guide the inpainting process in selecting which areas need reconstruction. The whole model is trained using a conditional GAN strategy. Comparative experiments show that our algorithm outperforms state-of-the-art inpainting techniques (which, unlike our system, do not segment the input image and thus must be aided by an external segmentation module.)
PICO, PICOS and SPIDER: a comparison study of specificity and sensitivity in three search tools for qualitative systematic reviews

BACKGROUND
Qualitative systematic reviews are increasing in popularity in evidence based health care. Difficulties have been reported in conducting literature searches of qualitative research using the PICO search tool. An alternative search tool, entitled SPIDER, was recently developed for more effective searching of qualitative research, but remained untested beyond its development team.


METHODS
In this article we tested the 'SPIDER' search tool in a systematic narrative review of qualitative literature investigating the health care experiences of people with Multiple Sclerosis. Identical search terms were combined into the PICO or SPIDER search tool and compared across Ovid MEDLINE, Ovid EMBASE and EBSCO CINAHL Plus databases. In addition, we added to this method by comparing initial SPIDER and PICO tools to a modified version of PICO with added qualitative search terms (PICOS).


RESULTS
Results showed a greater number of hits from the PICO searches, in comparison to the SPIDER searches, with greater sensitivity. SPIDER searches showed greatest specificity for every database. The modified PICO demonstrated equal or higher sensitivity than SPIDER searches, and equal or lower specificity than SPIDER searches. The modified PICO demonstrated lower sensitivity and greater specificity than PICO searches.


CONCLUSIONS
The recommendations for practice are therefore to use the PICO tool for a fully comprehensive search but the PICOS tool where time and resources are limited. Based on these limited findings the SPIDER tool would not be recommended due to the risk of not identifying relevant papers, but has potential due to its greater specificity.
A new resource for incremental, dependency and semantic parsing

Abstract. We introduce LTAG-spinal, a novel variant of traditional Lexicalized Tree Adjoining Grammar (LTAG) with desirable linguistic, computational and statistical properties. Unlike in traditional LTAG, subcategorization frames and the argument-adjunct distinction are left underspecified in LTAG-spinal. LTAG-spinal with adjunction constraints is weakly equivalent to LTAG. The LTAG-spinal formalism is used to extract an LTAG-spinal Treebank from the Penn Treebank with Propbank annotation. Based on Propbank annotation, predicate coordination and LTAG adjunction structures are successfully extracted. The LTAG-spinal Treebank makes explicit semantic relations that are implicit or absent from the original PTB. LTAG-spinal provides a very desirable resource for statistical LTAG parsing, incremental parsing, dependency parsing, and semantic parsing. This treebank has been successfully used to train an incremental LTAG-spinal parser and a bidirectional LTAG dependency parser.
Local opinion leaders: effects on professional practice and health care outcomes.

BACKGROUND
Clinical practice is not always evidence-based and, therefore, may not optimise patient outcomes. Opinion leaders disseminating and implementing 'best evidence' is one method that holds promise as a strategy to bridge evidence-practice gaps.


OBJECTIVES
To assess the effectiveness of the use of local opinion leaders in improving professional practice and patient outcomes.


SEARCH STRATEGY
We searched Cochrane EPOC Group Trials Register, the Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, HMIC, Science Citation Index, Social Science Citation Index, ISI Conference Proceedings and World Cat Dissertations up to 5 May 2009. In addition, we searched reference lists of included articles.


SELECTION CRITERIA
Studies eligible for inclusion were randomised controlled trials investigating the effectiveness of using opinion leaders to disseminate evidence-based practice and reporting objective measures of professional performance and/or health outcomes.


DATA COLLECTION AND ANALYSIS
Two review authors independently extracted data from each study and assessed its risk of bias. For each trial, we calculated the median risk difference (RD) for compliance with desired practice, adjusting for baseline where data were available. We reported the median adjusted RD for each of the main comparisons.


MAIN RESULTS
We included 18 studies involving more than 296 hospitals and 318 PCPs. Fifteen studies (18 comparisons) contributed to the calculations of the median adjusted RD for the main comparisons. The effects of interventions varied across the 63 outcomes from 15% decrease in compliance to 72% increase in compliance with desired practice. The median adjusted RD for the main comparisons were: i) Opinion leaders compared to no intervention, +0.09; ii) Opinion leaders alone compared to a single intervention, +0.14; iii) Opinion leaders with one or more additional intervention(s) compared to the one or more additional intervention(s), +0.10; iv) Opinion leaders as part of multiple interventions compared to no intervention, +0.10. Overall, across all 18 studies the median adjusted RD was +0.12 representing a 12% absolute increase in compliance in the intervention group.


AUTHORS' CONCLUSIONS
Opinion leaders alone or in combination with other interventions may successfully promote evidence-based practice, but effectiveness varies both within and between studies. These results are based on heterogeneous studies differing in terms of type of intervention, setting, and outcomes measured. In most of the studies the role of the opinion leader was not clearly described, and it is therefore not possible to say what the best way is to optimise the effectiveness of opinion leaders.
Implementation of a Three-Phase Capacitor-Clamped Active Power Filter Under Unbalanced Condition

A capacitor-clamped voltage-source inverter for active power filter operation under balanced and unbalanced conditions is proposed to suppress current harmonics and compensate the reactive power generated from the nonlinear loads. The adopted voltage-source inverter is based on a three-level capacitor-clamped topology to reduce the voltage stress of power semiconductors. Two control loops are used in the control scheme to achieve harmonic and reactive currents compensation and to regulate the inverter dc side voltage. In the adopted inverter, the neutral point voltage is compensated by a voltage compensator to obtain the balanced capacitor voltages on the dc side. In order to control the flying capacitor voltages, two redundant states in each inverter leg can be selected to compensate the flying capacitor to obtain a better voltage waveform with low harmonic contents on the ac terminals. The balanced and sinusoidal line currents are drawn from the ac source under the balanced and unbalanced conditions. The feasibility of the proposed scheme is confirmed through experimental results
Pharmacokinetic interactions between lersivirine and zidovudine, tenofovir disoproxil fumarate/emtricitabine and abacavir/lamivudine.

BACKGROUND
To investigate pharmacokinetic interactions associated with coadministration of lersivirine with zidovudine, tenofovir disoproxil fumarate (DF)/emtricitabine (Truvada(®)) or abacavir/lamivudine (Epzicom(®)/Kivexa(®)).


METHODS
Three Phase I, open, crossover studies with two (studies 1 and 3) or three (study 2) treatment periods were conducted in healthy individuals. In study 1, individuals received zidovudine and placebo or zidovudine and lersivirine on days 1-14. In study 2, individuals received lersivirine and tenofovir DF/emtricitabine, lersivirine and placebo or tenofovir DF/emtricitabine and placebo on days 1-10. In study 3, individuals received abacavir/lamivudine only in period 1 (5 days) and abacavir/lamivudine and lersivirine in period 2 (10 days). Blood samples were taken on days 1-14 (study 1) or day of final dose (studies 2 and 3) and analysed using high performance liquid chromatography/dual mass spectrometry. Pharmacokinetic parameters were calculated by standard non-compartmental methods.


RESULTS
When coadministered with lersivirine, zidovudine exposure increased by 35%, and exposure of its metabolite zidovudine-glucuronide decreased by 19%. Following coadministration of lersivirine and tenofovir DF/emtricitabine, tenofovir exposure increased by 30%, and lersivirine exposure decreased by 12%. Coadministration of lersivirine and abacavir/lamivudine increased abacavir exposure by 27% and decreased lamivudine exposure by 8%. Adverse events were predominantly mild in these Phase I studies.


CONCLUSIONS
Coadministration of lersivirine with zidovudine, tenofovir DF/emtricitabine or abacavir/lamivudine influenced the systemic exposure of all nucleoside reverse transcriptase inhibitor agents investigated (except for lamivudine; emtricitabine pharmacokinetics were not assessed). Changes were not considered clinically meaningful for zidovudine and abacavir. The clinical relevance of the effect on tenofovir pharmacokinetics is currently unknown.
Bioremediation of acidic oily sludge-contaminated soil by the novel yeast strain Candida digboiensis TERI ASN6.

BACKGROUND, AIM, AND SCOPE
Primitive wax refining techniques had resulted in almost 50,000 tonnes of acidic oily sludge (pH 1-3) being accumulated inside the Digboi refinery premises in Assam state, northeast India. A novel yeast species Candida digboiensis TERI ASN6 was obtained that could degrade the acidic petroleum hydrocarbons at pH 3 under laboratory conditions. The aim of this study was to evaluate the degradation potential of this strain under laboratory and field conditions.


MATERIALS AND METHODS
The ability of TERI ASN6 to degrade the hydrocarbons found in the acidic oily sludge was established by gravimetry and gas chromatography-mass spectroscopy. Following this, a feasibility study was done, on site, to study various treatments for the remediation of the acidic sludge. Among the treatments, the application of C. digboiensis TERI ASN6 with nutrients showed the highest degradation of the acidic oily sludge. This treatment was then selected for the full-scale bioremediation study conducted on site, inside the refinery premises.


RESULTS
The novel yeast strain TERI ASN6 could degrade 40 mg of eicosane in 50 ml of minimal salts medium in 10 days and 72% of heneicosane in 192 h at pH 3. The degradation of alkanes yielded monocarboxylic acid intermediates while the polycyclic aromatic hydrocarbon pyrene found in the acidic oily sludge yielded the oxygenated intermediate pyrenol. In the feasibility study, the application of TERI ASN6 with nutrients showed a reduction of solvent extractable total petroleum hydrocarbon (TPH) from 160 to 28.81 g kg(-1) soil as compared to a TPH reduction from 183.85 to 151.10 g kg(-1) soil in the untreated control in 135 days. The full-scale bioremediation study in a 3,280-m(2) area in the refinery showed a reduction of TPH from 184.06 to 7.96 g kg(-1) soil in 175 days.


DISCUSSION
Degradation of petroleum hydrocarbons by microbes is a well-known phenomenon, but most microbes are unable to withstand the low pH conditions found in Digboi refinery. The strain C. digboiensis could efficiently degrade the acidic oily sludge on site because of its robust nature, probably acquired by prolonged exposure to the contaminants.


CONCLUSIONS
This study establishes the potential of novel yeast strain to bioremediate hydrocarbons at low pH under field conditions.


RECOMMENDATIONS AND PERSPECTIVES
Acidic oily sludge is a potential environmental hazard. The components of the oily sludge are toxic and carcinogenic, and the acidity of the sludge further increases this problem. These results establish that the novel yeast strain C. digboiensis was able to degrade hydrocarbons at low pH and can therefore be used for bioremediating soils that have been contaminated by acidic hydrocarbon wastes generated by other methods as well.
Sex differences in aortic valve calcification measured by multidetector computed tomography in aortic stenosis.

BACKGROUND
Aortic valve calcification (AVC) is the intrinsic mechanism of valvular obstruction leading to aortic stenosis (AS) and is measurable by multidetector computed tomography. The link between sex and AS is controversial and that with AVC is unknown.


METHODS AND RESULTS
We prospectively performed multidetector computed tomography in 665 patients with AS (aortic valve area, 1.05±0.35 cm(2); mean gradient, 39±19 mm Hg) to measure AVC and to assess the impact of sex on the AVC-AS severity link in men and women. AS severity was comparable between women and men (peak aortic jet velocity: 4.05±0.99 versus 3.93±0.91 m/s, P=0.11; aortic valve area index: 0.55±0.20 versus 0.56±0.18 cm(2)/m(2); P=0.46). Conversely, AVC load was lower in women versus men (1703±1321 versus 2694±1628 arbitrary units; P<0.0001) even after adjustment for their smaller body surface area or aortic annular area (both P<0.0001). Thus, odds of high-AVC load were much greater in men than in women (odds ratio, 5.07; P<0.0001). Although AVC showed good associations with hemodynamic AS severity in men and women (all r>0.67; P<0.0001), for any level of AS severity measured by peak aortic jet velocity or aortic valve area index, AVC load, absolute or indexed, was higher in men versus women (all P≤0.01).


CONCLUSIONS
In this large AS population, women incurred similar AS severity than men for lower AVC loads, even after indexing for their smaller body size. Hence, the relationship between valvular calcification process and AS severity differs in women and men, warranting further pathophysiological inquiry. For AS severity diagnostic purposes, interpretation of AVC load should be different in men and in women.
Sobolevicanthus transvaalensis n.sp. (Cestoda: Hymenolepididae) from the Cape Teal (Anas capensis Gmelin, 1789)

Sobolevicanthus transvaalensis n.sp. is described from the Cape Teal, Anas capensis Gmelin, 1789, collected in the Republic of South Africa. The new species possesses 8 skrjabinoid hooks 78–88 μm long (mean 85 μm) and a short claviform cirrus-sac 79–143 μm long and resembles S. javanensis (Davis, 1945) and S. terraereginae (Johnston, 1913). It can be distinguished from S. javanensis by its shorter cirrus-sac and smaller cirrus diameter, and by differences in the morphology of the accessory sac and vagina and in their position relative to the cirrus-sac. It can be separated from S. terraereginae on the basis of cirrus length and diameter. The basal diameter of the cirrus in S. terraereginae is three times that in S. transvaalensis. ac]19830414
Vision-guided Robot System for Picking Objects by Casting Shadows

We present a complete vision guided robot system for model based 3D pose estimation and picking of singulated 3D objects. Our system employs a novel vision sensor consisting of a video camera surrounded by eight flashes (light emitting diodes). By capturing images under different flashes and observing the shadows, depth edges or silhouettes in the scene are obtained. The silhouettes are segmented into different objects and each silhouette is matched across a database of object silhouettes in different poses to find the coarse 3D pose. The database is pre-computed using a Computer Aided Design (CAD) model of the object. The pose is refined using a fully projective formulation [ACB98] of Lowe’s model based pose estimation algorithm [Low91, Low87]. The estimated pose is transferred to robot coordinate system utilizing the handeye and camera calibration parameters, which allows the robot to pick the object. Our system outperforms conventional systems using 2D sensors with intensity-based features as well as 3D sensors. We handle complex ambient illumination conditions, challenging specular backgrounds, diffuse as well as specular objects, and texture-less objects, on which traditional systems usually fail. Our vision sensor is capable of computing depth edges in real time and is low cost. Our approach is simple and fast for practical implementation. We present real experimental results using our custom designed sensor mounted on a robot arm to demonstrate the effectiveness of our technique. International Journal of Robotics Research This work may not be copied or reproduced in whole or in part for any commercial purpose. Permission to copy in whole or in part without payment of fee is granted for nonprofit educational and research purposes provided that all such whole or partial copies include the following: a notice that such copying is by permission of Mitsubishi Electric Research Laboratories, Inc.; an acknowledgment of the authors and individual contributions to the work; and all applicable portions of the copyright notice. Copying, reproduction, or republishing for any other purpose shall require a license with payment of fee to Mitsubishi Electric Research Laboratories, Inc. All rights reserved. Copyright c ©Mitsubishi Electric Research Laboratories, Inc., 2009 201 Broadway, Cambridge, Massachusetts 02139
Early hepatitis C viral kinetics correlate with long-term outcome in patients receiving high dose induction followed by combination interferon and ribavirin therapy.

BACKGROUND/AIMS
The majority of patients with genotype 1 do not respond to interferon (IFN) plus ribavirin. Limited data exist on the use of induction followed by combination therapy.


METHODS
In this prospective study of 28 patients infected with genotype 1, randomization involved either daily or twice daily high dose IFN for 6 weeks, followed by standard therapy of 3 million units three times a week in combination with ribavirin for an additional 42 weeks. Hepatitis C virus (HCV) RNA was quantitated before and frequently during treatment.


RESULTS
The best correlate of response was delta (the infected cell loss rate). Sixteen patients continued on the study because they had at least a 2 log drop in their HCV RNA levels by week 12; all but one were PCR negative for HCV RNA at 48 weeks, and 14 of these 16 patients continued to be PCR negative at 72 weeks. Both African-Americans in our trial failed to respond to therapy, and differences were evident during the induction phase.


CONCLUSIONS
This randomized study of induction IFN therapy followed by combination IFN plus ribavirin yielded the highest rate of sustained response (50%) reported to date in chronically HCV-infected patients with genotype 1. The predictive value of the infected cell loss rate needs to be evaluated prospectively in larger studies, particularly in patients receiving pegylated IFN.