Miracle-dz/UniFAR-FTUs huggingface dataset:
Structured puncturing for rate-compatible B-LDPC codes with dual-diagonal parity structure

In this paper, we propose a generalized formula for generating puncturing patterns for block-type low-density parity check (B-LDPC) codes with dual-diagonal parity structure. The proposed formula distributes punctured bits uniformly in the zigzag edge connections, as well as maximizes the minimum recovery speed and the reliability of each punctured node. Also, the proposed puncturing can be applied to any B-LDPC code with dual-diagonal parity structure and can provide efficient bitwise puncturing patterns even when the number of puncturing bits is not equal to an integer multiple of the block size. Simulation results show that the proposed punctured B-LDPC codes are better than existing punctured B-LDPC codes and even dedicated B-LDPC codes used in commercial standards.
Concept Maps for Integrating Modeling Techniques for the Analysis and Re-Design of Partly-Autonomous Interactive Systems

Socio-Technical Systems (STS) such as Air Traffic Management Systems (ATM) are considered as complex as they encompass interactions involving humans and machines deeply influenced by environmental aspects (e.g. weather conditions) and by the overall organizational structure in which they are deployed in. Within such STS, interactive systems are omnipresent allowing operators to interact with the underlying system. Such interactive systems must be both usable (i.e. enabling users to perform their tasks efficiently and effectively while ensuring a certain level of operator satisfaction) and resilient to adverse events including software malfunctions (e.g. automation degradation) as well as interaction related problems (e.g. human errors or interactive system failures). Current techniques, methods and tools do not allow to model STSs as a whole and thus to analyze both usability and resilience properties. This paper proposes a multi-models based approach for the modelling and the analysis of partly-autonomous interactive systems for assessing their resilience and usability. The approach integrates 3 modelling techniques: Functional Resonance Analysis Method (FRAM) (focused on organizational functions), Human-centered Assessment and Modelling to Support Task Engineering for Resilient Systems (HAMSTERS) (centered on human goals and activities) and Interactive Cooperative Objects (ICO) (dedicated to the modelling of interactive systems). The principles of the multi-models approach is illustrated on an example for carefully showing the extensions proposed to the selected modelling techniques and how they integrate together. A case study dealing with aircraft route change due to bad weather conditions demonstrates the scalability and benefits of the approach.
A Longitudinal Examination of American Business Ethics: Clark’s Scales Revisited

In recent years the issue of ethics and ethical standards has become a significant topic in the United States (Akaah, 1990; Lysonski and Gaidis, 1991; Robertson and Anderson, 1989). It appears that many Americans feel that their country's moral values and ethical standards are deteriorating in correlation with the decay of their cultural and social institutions. It is claimed that self-interest, increased concentra tion on short-term earnings, and lawsuits much too frequently become the prevalent approach in business and social interactions.
Clinicians' perceptions of the problem of antimicrobial resistance in health care facilities.

BACKGROUND Many clinicians do not comply with guidelines regarding antimicrobial resistance (AR). In response, the Centers for Disease Control and Prevention developed a national Campaign to Prevent Antimicrobial Resistance in Healthcare Settings that presents 4 strategies and 12 evidence-based steps. METHODS To assess clinicians' perceptions of AR, barriers and facilitators to preventing AR, and how best to reach clinicians, a questionnaire and 4 focus groups were conducted after presentation of the Campaign at 4 Pittsburgh Regional Healthcare Initiative hospitals. RESULTS One hundred seventeen clinicians completed the questionnaire; 28 participated in the focus groups. Clinicians were significantly more likely to perceive that AR was a problem nationally than in their own institution (95% vs 77%; P<.001) or practice (95% vs 65%; P =.002), consistent with focus group results (93% nationally vs 46% institution or practice). The 3 Campaign steps with the most barriers to implementation were "Treat infection, not colonization" (35%), "Stop treatment when infection is cured or unlikely" (35%), and "Practice antimicrobial control" (33%). Clinicians in the focus groups cited the additional barriers of the health care culture, lack of knowledge, and the nursing shortage; facilitators included education, information technology, and consults. Computer programs, posters, and local data were suggested for reaching clinicians about AR. CONCLUSIONS Clinicians perceive AR to be a complex national problem but less relevant to their own institution or practice. Providing clinicians with information and steps for preventing AR, as in the Campaign, may affect their perceptions of the problem and motivate them to take actions to ensure patient safety.
Resource Discovery in Activity-Based Sensor Networks

This paper proposes a service discovery protocol for sensor networks that is specifically tailored for human-centered pervasive environments and scales well to large sensor networks, such as those deployed for medical care in major incidents and hospitals. It uses the high-level concept of computational activities (logical bundles of data and resources) to give sensors in activity-based sensor networks (ABSNs) knowledge about their usage even at the network layer. ABSN redesigns classical service discovery protocols to include a logical structuring of the network for a more applicable discovery scheme. Noting that in practical settings activity-based sensor patches are localized, ABSN designs a fully distributed, hybrid discovery protocol based on extended zone routing protocol (EZRP), proactive in a neighbourhood zone and reactive outside, so that any query among the sensors of one activity is routed through the network with minimum overhead, guided by the bounds of that activity. Compared to EZRP, ABSN lowers the network overhead of the discovery process, while keeping discovery latency close to optimal.
A domain swap approach reveals a role of the plant wall-associated kinase 1 (WAK1) as a receptor of oligogalacturonides

Oligogalacturonides (OGs) released from the plant cell wall are active both as damage-associated molecular patterns (DAMPs) for the activation of the plant immune response and regulators of plant growth and development. Members of the Wall-Associated Kinase (WAK) family are candidate receptors of OGs, due to their ability to bind in vitro these oligosaccharides. Because lethality and redundancy have hampered the study of WAKs by reverse genetics, we have adopted a chimeric receptor approach to elucidate the role of Arabidopsis WAK1. In a test-of-concept study, we first defined the appropriate chimera design and demonstrated that the Arabidopsis pattern recognition receptor (PRR) EFR is amenable to the construction of functional and resistance-conferring chimeric receptors carrying the ectodomain of another Arabidopsis PRR, FLS2. After, we analyzed chimeras derived from EFR and WAK1. Our results show that, upon stimulation with OGs, the WAK1 ectodomain is capable of activating the EFR kinase domain. On the other hand, upon stimulation with the cognate ligand elf18, the EFR ectodomain activates the WAK1 kinase, triggering defense responses that mirror those normally activated by OGs and are effective against fungal and bacterial pathogens. Finally, we show that transgenic plants overexpressing WAK1 are more resistant to Botrytis cinerea.
Practical Tools to Implement Massive Parallel Pyrosequencing of PCR Products in Next Generation Molecular Diagnostics

Despite improvements in terms of sequence quality and price per basepair, Sanger sequencing remains restricted to screening of individual disease genes. The development of massively parallel sequencing (MPS) technologies heralded an era in which molecular diagnostics for multigenic disorders becomes reality. Here, we outline different PCR amplification based strategies for the screening of a multitude of genes in a patient cohort. We performed a thorough evaluation in terms of set-up, coverage and sequencing variants on the data of 10 GS-FLX experiments (over 200 patients). Crucially, we determined the actual coverage that is required for reliable diagnostic results using MPS, and provide a tool to calculate the number of patients that can be screened in a single run. Finally, we provide an overview of factors contributing to false negative or false positive mutation calls and suggest ways to maximize sensitivity and specificity, both important in a routine setting. By describing practical strategies for screening of multigenic disorders in a multitude of samples and providing answers to questions about minimum required coverage, the number of patients that can be screened in a single run and the factors that may affect sensitivity and specificity we hope to facilitate the implementation of MPS technology in molecular diagnostics.
Overcoming the winner's curse: estimating penetrance parameters from case-control data.

Genomewide association studies are now a widely used approach in the search for loci that affect complex traits. After detection of significant association, estimates of penetrance and allele-frequency parameters for the associated variant indicate the importance of that variant and facilitate the planning of replication studies. However, when these estimates are based on the original data used to detect the variant, the results are affected by an ascertainment bias known as the "winner's curse. " The actual genetic effect is typically smaller than its estimate. This overestimation of the genetic effect may cause replication studies to fail because the necessary sample size is underestimated. Here, we present an approach that corrects for the ascertainment bias and generates an estimate of the frequency of a variant and its penetrance parameters. The method produces a point estimate and confidence region for the parameter estimates. We study the performance of this method using simulated data sets and show that it is possible to greatly reduce the bias in the parameter estimates, even when the original association study had low power. The uncertainty of the estimate decreases with increasing sample size, independent of the power of the original test for association. Finally, we show that application of the method to case-control data can improve the design of replication studies considerably.
Phylogeny-Based Species Delimitation In Philippine Slender Skinks (Reptilia: Squamata: Scincidae) III: Taxonomic Revision of the Brachymeles Gracilis Complex, With Descriptions of Three New Species

Abstract: Species diversity in skinks in the genus Brachymeles recently has undergone a state of flux, with numerous taxonomic discoveries over the past few years. Newly available, robust data sets from morphological data and molecular sequences have revealed that taxonomic diversity within this unique group of lizards is substantially underestimated. In this third recent monographic revision of a major Brachymeles clade, we review the medium-sized, pentadactyl species of the Brachymeles gracilis Complex (now known to include B. pathfinderi) and describe three new species in this unique clade of endemic Philippine lizards. For more than three decades B. gracilis has been recognized as a single polytypic, “widespread” species. The species' wide geographic range has persisted as a result of weak sampling, morphologically similar body sizes, scale pigmentation, and patterns of scalation among populations. However, previous authors have noted morphological variation between populations on different islands, as well as in geographically different subregions across the large southern island of Mindanao in the Philippines. Our new data build on these observations and extend them to inference of species boundaries. We evaluate both morphological and genetic data to define species limits in B. gracilis and its close relatives, and our data indicate that the “widespread” species B. gracilis is actually a complex of at least six distinct lineages. In order to clarify the status of B. suluensis (a species collected only once, in 1918) we redescribe this enigmatic taxon. Phylogenetic analyses of available B. gracilis sampling reveal that some of these lineages are not each others' closest relatives, but are all genetically distinct. All but two of the taxa we define possess allopatric geographic ranges and differ from their congeners by numerous diagnostic characters of external morphology, and therefore should be recognized as full species in accordance with any lineage-based species concept. Over the past 3 yr, the species diversity of the genus Brachymeles has increased by 125%.
A 20-800 MHz relaxation oscillator with automatic swing control

An automatic swing control (ASC) feedback for relaxation voltage-controlled oscillators (VCO) dynamically monitors capacitor voltage swing and adjusts threshold voltage of the oscillator to maintain the swing at a constant level, providing wide linear frequency range. The ASC-VCO is implemented in 14 GHz f/sub T/ bipolar technology. The circuit has a frequency sweep range from 20 MHz up to 800 MHz, with the upper frequency limit dictated by the value of the delay. The bipolar process offers n-p-n transistors with 14 GHz cut-off frequency and lateral p-n-p transistors with 60 MHz cut-off frequency. The chip consists of the following blocks: a relaxation oscillator with ASC feedback, a voltage-to-current converter, a bandgap voltage generator, trimming circuitry and temperature compensation circuitry.
Re-examining the Effectiveness of Manual Review

Recent studies have found that automated retrieval methods in ediscovery are not only cheaper than manual review, but are al so as or more reliable. We argue that these studies, while sugge tive, are not conclusive. There is a high variability in the qualit y of unsupervised manual reviewers, as data from the TREC Legal Tra ck shows. The best manual reviewers are as reliable as automate d methods, and a properly supervised manual review may be more reliable than automation. We show the effectiveness of the s imple review management approach of observing the proportions fo und relevant between reviewers. Finally, we describe the exper imental protocol necessary for a more conclusive comparison of m anual and automated review.
A parallel collision-avoidance algorithm for robot manipulators

Throughout the world, researchers are improving robots to enable them to do more complex tasks with less human intervention. One aspect of this research is the complex path planning problem. The authors' approach combines potential fields, which guide a robot through Cartesian space, and a parallel genetic algorithm, which calculates suitable joint variables for the robot's trajectory.
Cannabinoids for epilepsy.

BACKGROUND Marijuana appears to have anti-epileptic effects in animals. It is not currently known if it is effective in patients with epilepsy. Some states in the United States of America have explicitly approved its use for epilepsy. OBJECTIVES To assess the efficacy and safety of cannabinoids when used as monotherapy or add-on treatment for people with epilepsy. SEARCH METHODS We searched the Cochrane Epilepsy Group Specialized Register (9 September 2013), Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library (2013, Issue 8), MEDLINE (Ovid) (9 September 2013), ISI Web of Knowledge (9 September 2013), CINAHL (EBSCOhost) (9 September 2013), and ClinicalTrials.gov (9 September 2013). In addition, we included studies we personally knew about that were not found by the searches, as well as searched the references in the identified studies. SELECTION CRITERIA Randomized controlled trials (RCTs) whether blinded or not. DATA COLLECTION AND ANALYSIS Two authors independently selected trials for inclusion and extracted the data. The primary outcome investigated was seizure freedom at one year or more, or three times the longest interseizure interval. Secondary outcomes included responder rate at six months or more, objective quality of life data, and adverse events. MAIN RESULTS We found four randomized trial reports that included a total of 48 patients, each of which used cannabidiol as the treatment agent. One report was an abstract and another was a letter to the editor. Anti-epileptic drugs were continued in all studies. Details of randomisation were not included in any study report. There was no investigation of whether the control and treatment participant groups were the same or different. All the reports were low quality.The four reports only answered the secondary outcome about adverse effects. None of the patients in the treatment groups suffered adverse effects. AUTHORS' CONCLUSIONS No reliable conclusions can be drawn at present regarding the efficacy of cannabinoids as a treatment for epilepsy. The dose of 200 to 300 mg daily of cannabidiol was safely administered to small numbers of patients generally for short periods of time, and so the safety of long term cannabidiol treatment cannot be reliably assessed.
Randomized Phase II Trial of Inhaled Budesonide versus Placebo in High-Risk Individuals with CT Screen–Detected Lung Nodules

Screening CT identifies small peripheral lung nodules, some of which may be pre- or early invasive neoplasia. Secondary end point analysis of a previous chemoprevention trial in individuals with bronchial dysplasia showed reduction in size of peripheral nodules by inhaled budesonide. We performed a randomized, double-blind, placebo-controlled phase IIb trial of inhaled budesonide in current and former smokers with CT-detected lung nodules that were persistent for at least 1 year. A total of 202 individuals received inhaled budesonide, 800 μg twice daily or placebo for 1 year. The primary endpoint was the effect of treatment on target nodule size in a per person analysis after 1 year. The per person analysis showed no significant difference between the budesonide and placebo arms (response rate 2% and 1%, respectively). Although the per lesion analysis revealed a significant effect of budesonide on regression of existing target nodules (P = 0.02), the appearance of new lesions was similar in both groups and thus the significance was lost in the analysis of all lesions. The evaluation by nodule type revealed a nonsignificant trend toward regression of nonsolid and partially solid lesions after budesonide treatment. Budesonide was well tolerated, with no unexpected side effects identified. Treatment with inhaled budesonide for 1 year did not significantly affect peripheral lung nodule size. There was a trend toward regression of nonsolid and partially solid nodules after budesonide treatment. Because a subset of these nodules is more likely to represent precursors of adenocarcinoma, additional follow-up is needed. Cancer Prev Res; 4(1); 34–42. ©2010 AACR.
Effect of HCl on Starch Structure and Properties of Starch-based Wood Adhesives

Starch-based adhesive was prepared from corn starch and polyvinyl alcohol (PVA) as raw materials by acid hydrolysis with HCl. The starch was hydrolyzed with different amounts of HCl and characterized using Fourier transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy, and thermal gravimetric analysis. The results indicated that different amounts of HCl affected hydrogen bonds, the amount of free hydroxyl groups, crystalline structure, compatibility between starch and PVA, thermal stability, and bond strength. The crystallinity decreased by 13.7% when the amount of acid was 33% compared with untreated starch. The bond strength reached its maximum of 1.35 MPa when the acid content was 23%. The initial decomposition temperature of starch decreased after acid hydrolysis. It was also noted that corrosion of the starch surface increased with increasing acid content.
PREDICTION OF PARTICLE GROWTH DURING MELT SPRAY GRANULATION USING A FIVE-FLUID CFD-PBE APPROACH

The process of fluidized bed spray granulation unites the steps of solid formation and product formulation in one apparatus and is used to produce granules out of a liquid. Thereby, a melt is atomized into small droplets and sprayed into the fluidized bed, which consists of seed particles of the same material. Droplets deposit on the particles near the spray zone and form a film which solidifies in the cold fluidization air. Layer-by-layer, granulate products with defined particle sizes are formed. In a previous investigation, Li et al. (2011) developed a model using computational fluid dynamics (CFD) and population balance equations (PBE) to predict the development of particle size distributions (PSD) in fluidized bed spray systems. Thereby, they focused on low solution spray flow rates (< 5 kg/h per nozzle) and small specific bed masses (< 40 kg/m2). The aim of this work is to extend this model and to apply it to industrial melt granulation processes with high spray flow rates (> 100 kg/h per nozzle) and high specific bed masses (> 200 kg/m2). Using this CFD-PBE model, it is possible to predict the development of PSD in melt granulation processes using PBE. For such predictions, it is necessary to evaluate internal process variables, e.g. size-dependent growth rates of the granules, as a function of the current state of the process. This can be obtained using a two-dimensional rotationally symmetric CFD multiphase batch model with one nozzle at its centre. A five-fluid model is solved for short process times (~ s) considering fluid dynamics, particle growth due to drop deposition and energy equations. Extracting size-dependent and timeand spaceaveraged particle growth rates, the PBE can finally be solved to predict the particle size distribution for long process times (~ min). The numerical results are validated with experimental data of a melt spray granulation process in batch mode.
The determinants of the molecular substitution process in turtles

Neutral rates of molecular evolution vary across species, and this variation has been shown to be related to biological traits. One of the first patterns to be observed in vertebrates has been an inverse relationship between body mass (BM) and substitution rates. The effects of three major life‐history traits (LHT) that covary with BM – metabolic rate, generation time and longevity (LON) – have been invoked to explain this relationship. However, most of the theoretical and empirical evidence supporting this relationship comes from endothermic vertebrates, that is, mammals and birds, in which the environmental conditions, especially temperature, do not have a direct impact on cellular and molecular biology. We analysed the variations in mitochondrial and nuclear rates of synonymous substitution across 224 turtle species and examined their correlation with two LHT (LON and BM) and two environmental variables [latitude (LAT) and habitat]. Our analyses indicate that in turtles, neutral rates of molecular evolution are hardly correlated with LON or BM. Rather, both the mitochondrial and nuclear substitution rates are significantly correlated with LAT – faster evolution in the tropics – and especially so for aquatic species. These results question the generality of the relationships reported in mammals and birds and suggest that environmental factors might be the strongest determinants of the mutation rate in ectotherms.