Miracle-dz/UniFAR-FTUs huggingface dataset:
Active and passive stabilization of body pitch in insect flight

Flying insects have evolved sophisticated sensory–motor systems, and here we argue that such systems are used to keep upright against intrinsic flight instabilities. We describe a theory that predicts the instability growth rate in body pitch from flapping-wing aerodynamics and reveals two ways of achieving balanced flight: active control with sufficiently rapid reactions and passive stabilization with high body drag. By glueing magnets to fruit flies and perturbing their flight using magnetic impulses, we show that these insects employ active control that is indeed fast relative to the instability. Moreover, we find that fruit flies with their control sensors disabled can keep upright if high-drag fibres are also attached to their bodies, an observation consistent with our prediction for the passive stability condition. Finally, we extend this framework to unify the control strategies used by hovering animals and also furnish criteria for achieving pitch stability in flapping-wing robots.
Multimodal observational assessment of quality and productivity benefits from the implementation of wireless technology for out of hours working

Objectives The authors investigated if a wireless system of call handling and task management for out of hours care could replace a standard pager-based system and improve markers of efficiency, patient safety and staff satisfaction. Design Prospective assessment using both quantitative and qualitative methods, including interviews with staff, a standard satisfaction questionnaire, independent observation, data extraction from work logs and incident reporting systems and analysis of hospital committee reports. Setting A large teaching hospital in the UK. Participants Hospital at night co-ordinators, clinical support workers and junior doctors handling approximately 10 000 tasks requested out of hours per month. Outcome measures Length of hospital stay, incidents reported, co-ordinator call logging activity, user satisfaction questionnaire, staff interviews. Results Users were more satisfied with the new system (satisfaction score 62/90 vs 82/90, p=0.0080). With the new system over 70 h/week of co-ordinator time was released, and there were fewer untoward incidents related to handover and medical response (OR=0.30, p=0.02). Broad clinical measures (cardiac arrest calls for peri-arrest situations and length of hospital stay) improved significantly in the areas covered by the new system. Conclusions The introduction of call handling software and mobile technology over a medical-grade wireless network improved staff satisfaction with the Hospital at Night system. Improvements in efficiency and information flow have been accompanied by a reduction in untoward incidents, length of stay and peri-arrest calls.
Massilia solisilvae sp. nov., Massilia terrae sp. nov. and Massilia agilis sp. nov., isolated from forest soil in South Korea by using a newly developed culture method.

Using a newly developed culture method for not yet cultured soil bacteria, three Gram-stain-negative, aerobic, non-spore-forming, motile, and rod-shaped bacteria (strain designated J18T, J11T and J9T) were isolated from forest soil at Kyonggi University, South Korea. Isolates were subjected to a taxonomic study by using a polyphasic approach. According to a phylogenetic tree based on 16S rRNA gene sequences, strains J18T, J11T and J9T belonged to the genus Massilia and clustered with Massilia haematophila CCUG 38318T (similarity range: 97.6~98.0 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, and the genomic DNA G+C contents of strains J18T, J11T and J9T were 63.4, 68.7 and 64.5 mol%, respectively. The major polyamines were putrescine and 2-hydroxyputescine, which were detected in all three strains. DNA-DNA between the three tested strains and the reference strains much lower than 70 %, the recommended threshold value for the delineation of genomic species. The predominant respiratory quinine was ubiquinone-8 (Q-8) and the major cellular fatty acids were Summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C16 : 0. On the basis of phenotypic and genotypic data and DNA-DNA hybridization results, the three isolates are considered to represent three novel species of the genus Massilia, for which the names Massilia solisilvae sp. nov. for type strain J18T (=KEMB 9005-366T=JCM 31607T), Massilia terrae sp. nov. for type strain J11T (=KEMB 9005-360T=JCM 31606T) and Massilia agilis sp. nov. for type strain J9T (=KEMB 9005-359T=JCM 31605T) are proposed.
Expression and purification of Manduca sexta prophenoloxidase-activating proteinase precursor (proPAP) from baculovirus-infected insect cells.

Analogous to human thrombin, prophenoloxidase-activating proteinase (PAP) is a terminal enzyme of a serine proteinase cascade in the tobacco hornworm Manduca sexta. In order to purify and study the activating enzyme for PAP from this insect, we produced the zymogen of PAP (proPAP) in a bacterial expression system. The affinity-purified protein was then used as an antigen to generate a specific rabbit antiserum. Immunoblot analysis indicated that the proPAP was present at a low level in Manduca larval hemolymph, but was induced by six- to eightfold in larvae that had been injected with Escherichia coli or Micrococcus lysodeikticus. To produce the native proenzyme for functional analyses, we constructed a recombinant baculovirus to infect Spodoptera frugiperda Sf21 cells. ProPAP was secreted into the medium at a low concentration of approximately 0.37 mg/liter under the optimal conditions. We then developed a simple, efficient scheme to enrich and purify this protein, which involves two lectin affinity and one HPLC ion-exchange chromatographic steps. Immunoblot analysis following SDS-polyacrylamide gel electrophoresis indicated that the recombinant proPAP is nearly identical in mobility to the zymogen from Manduca hemolymph. After the purified proPAP was added to the larval hemolymph, it was readily activated by an unknown proteinase in the presence of M. lysodeikticus.
Knowledge Representation and Query in Semantic MediaWiki: A Formal Study

Semantic wikis extend conventional wikis, which allow users to collaboratively generate data, through semantic web technologies. This allows wiki-based information to be annotated with metadata for facilitating automated search, querying, propagation and inference. Se- mantic wikis have recently attained wide adoption and, with this, formal research on their functionality (e.g., inference and concept modeling) is starting to be conducted. In this paper, we present a formal analysis of the semantic technologies in an emerging semantic wiki framework called Semantic MediaWiki (SMW). In particular, we deflne a RDF- like model theoretical semantics for the SMW modeling language, and a closed world, minimal Herbrand model semantics for the SMW query language by a reduction to positive logic programs. We discover that the entailment problem in SMW is NL-complete thus is highly tractable, and query answering in SMW is P-complete in general and is in L if subqueries are disallowed. We show that such a formalization allows us to discover some rather powerful usages of SMW, such as entailment in- ference, and to extend SMW with some frequently needed features, like negation as failure.
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible and used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. This freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.
Effect of a light-emitting diode on composite polymerization shrinkage and hardness.

PURPOSE This study evaluated the effect of light-emitting diodes (LEDs) on polymerization shrinkage and bottom-to-top hardness ratios of composites. MATERIALS AND METHODS Six LEDs (Elipar FreeLight, 3M ESPE, St. Paul, MN, USA; Versalux, Centrix, Shelton, CT, USA; Ultra-Lume LED2, Ultradent, South Jordan, UT, USA; Zap LED only, CMS-Dental/Soft-Core Texas, North Richland Hills, TX, USA; Zap dual light; and L.E. Demetron I, Kerr Manufacturing Inc., Orange, CA, USA) and a quartz-tungsten-halogen (QTH) light (Optilux 501, Kerr Manufacturing Inc.) were tested. Ten specimens each of a microhybrid (Point 4, Kerr Manufacturing, Inc.) and a hybrid (Filtek Z250, 3M ESPE, St. Paul, MN, USA) composite, measuring 2 mm thick by 5 mm in diameter, were polymerized using each of the lights. Linear shrinkage was recorded using a contactless displacement instrument. Ten specimens were also polymerized with each light to determine the Knoop hardness number (KHN) at the top and bottom surfaces. RESULTS For the microhybrid, Zap dual light had the least volumetric shrinkage 2.08% (+/- 0.33) and Elipar FreeLight had the highest 3.02% (+/- 0.73). There was no significant difference (p < or = .05) in shrinkage for the LEDs when compared with the Optilux 501. The hybrid showed the least amount of shrinkage with the L.E. Demetron I, 1.42% (+/- 0.12), and the greatest with the Zap dual light, 2.47% (+/- 0.31). The Ultra-Lume LED2 (p < or = .05) and Zap LED and dual light (p < or = .001) had significantly greater shrinkage than did the Optilux 501. Zap LED had the lowest depth of cure with a bottom KHN of 11.46 (+/- 2.71) and 33.62 (+/- 3.57) for the microhybrid and hybrid, respectively. The L.E. Demetron I had the highest bottom hardness value for the microhybrid, with a value of 40.65 (+/- 1.50). The Optilux 501 had the highest bottom hardness value for the hybrid, with a value of 62.03 (+/- 0.82). The Zap LED and dual light and Versalux lights had significantly lower bottom-to-top hardness ratios than did the QTH (p < or = .001) with the microhybrid. CONCLUSIONS There was no statistically significant difference in shrinkage for the microhybrid with any of the lights tested. The hybrid, however, showed significantly less shrinkage with the halogen compared with the Ultra-Lume LED2 and Zap LED and dual light. All LEDs had equal or lower bottom hardness values than did the QTH, except for L.E. Demetron I with the microhybrid.
Ambiguity-driven Interaction in Robot-to-Human Teaching

The transfer of task knowledge is ubiquitous in our daily lives, where various types of interaction occur. Such an interactive task knowledge transfer, however, requires that an instructor and a learner to be at the same place and time. If we use a robot to mediate between them, such limitations can be eliminated. This paper focuses on human-to-robot teaching, in which a robot instructor interactively teaches a human learner how to achieve a task. We develop an ambiguity-driven formulation of interactive teaching based on the Dempster-Shafer theory. We implemented an experimental system for blocks world tasks as a proof-of-concept and show our preliminary results.
Musca domestica, a window on the evolution of sex-determining mechanisms in insects.

The genetic cascades regulating sex determination of the housefly, Musca domestica, and the fruitfly, Drosophila melanogaster, appear strikingly different. The bifunctional switch gene doublesex, however, is present at the bottom of the regulatory cascades of both species, and so is transformer-2, one of the genetic elements required for the sex-specific regulation of doublesex. The upstream regulators are different: Drosophila utilizes Sex-lethal to coordinate the control of sex determination and dosage compensation, i.e., the process that equilibrates the difference of two X chromosomes in females versus one X chromosome in males. In the housefly, Sex-lethal is not involved in sex determination, and dosage compensation, if existent at all, is not coupled with sexual differentiation. This allows for more adaptive plasticity in the housefly system. Accordingly, natural housefly populations can vary greatly in their mechanism of sex determination, and new types can be generated in the laboratory.
Formal definitions for usable access control rule sets from goals to metrics

Access control policies describe high level requirements for access control systems. Access control rule sets ideally translate these policies into a coherent and manageable collection of Allow/Deny rules. Designing rule sets that reflect desired policies is a difficult and time-consuming task. The result is that rule sets are difficult to understand and manage. The goal of this paper is to provide means for obtaining usable access control rule sets, which we define as rule sets that (i) reflect the access control policy and (ii) are easy to understand and manage. In this paper, we formally define the challenges that users face when generating usable access control rule sets and provide formal tools to handle them more easily. We started our research with a pilot study in which specialists were interviewed. The objective was to list usability challenges regarding the management of access control rule sets and verify how those challenges were handled by specialists. The results of the pilot study were compared and combined with results from related work and refined into six novel, formally defined metrics that are used to measure the security and usability aspects of access control rule sets. We validated our findings with two user studies, which demonstrate that our metrics help users generate statistically significant better rule sets.
Novel composite W ber structures to provide drug / protein delivery for medical implants and tissue regeneration

A novel class of bioresorbable composite (core/shell) Wber structures loaded with bioactive agents was developed and studied. These unique polymeric structures are designed to combine good mechanical properties with a desired controlled release proWle, in order to serve as scaVolds for tissue regeneration applications and as basic elements of medical implants. These core/shell Wber structures were formed by “coating” core polymer Wbers with drug/protein-containing poly(DL-lactic-co-glycolic acid) porous structures. The shell preparation (“coating”) was performed by the freeze-drying of water-in-oil emulsions. Both water soluble and water insoluble agents can be incorporated in these structures and their activity is preserved, since the Wber fabrication requires neither high temperatures nor harsh solvents in the vicinity of the bioactive agents. Examples for release proWles of protein (horseradish peroxidase) and drug (paclitaxel) are presented. We have demonstrated that appropriate selection of the emulsion’s parameters can yield a variety of new core/shell Wber structures with desirable drug/protein release behavior. This will lead to the engineering of new implants and scaVolds, and will advance the Weld of tissue regeneration and medical implants. © 2006 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
What can machine translation learn from speech recognition?

The performance of machine translation technology after 50 years of development leaves much to be desired. There is a high demand for well performing and cheap MT systems for many language pairs and domains, which automatically adapt to rapidly changing terminology. We argue that for successful MT systems it will be crucial to apply data-driven methods, especially statistical machine translation. In addition, it will be very important to establish common test environments. This includes the availability of large parallel training corpora, well defined test corpora and standardized evaluation criteria. Thereby research results can be compared and this will open the possibility for more competition in MT research.
Visualizing the Evaluation of Distance Measures

This paper describes the development and use of an interface for visually evaluating distance measures. The combination of multidimensional scaling plots, histograms and tables allows for different stages of overview and detail. The interdisciplinary project Rule-based search in text databases with nonstandard orthography develops a fuzzy full text search engine and uses distance measures for historical text document retrieval. This engine should provide easier text access for experts as well as interested amateurs.
Contrasting interleukin 2 binding properties of the alpha (p55) and beta (p70) protein subunits of the human high-affinity interleukin 2 receptor

In this report, we have investigated the kinetics of IL-2 binding to the alpha (p55) and beta (p70) IL-2 binding proteins and compared these properties with ligand binding to the high-affinity IL-2-R. The association and dissociation of IL-2 to the alpha (p55) chain occurred with very rapid kinetics (t 1/2 = 4-10 s). In contrast, IL-2 association to, and dissociation from the beta (p70) chain occurred at a greatly reduced rate (t 1/2 = 40-50 min and 200-400 min, respectively). Measurements of IL-2 binding to the high-affinity receptor revealed an interesting composite of these binding properties with a rapid association rate (t 1/2 = 30-45 s) resembling the alpha (p55) chain and a slow dissociation rate (t 1/2 = 270-300 min) similar to the beta (p70) chain. These findings provide additional support for the model of the high-affinity IL-2-R as a heterodimeric membrane complex composed of both the alpha (p55) and beta (p70) subunits and suggest that high-affinity IL-2 binding may involve a conformational change in structure of either or possibly both of the receptor chains. These results highlight the important and perhaps different role played by each subunit in the formation of functional high-affinity IL-2-R.
From Targets to Treatments: A Review of Molecular Targets in Pancreatic Neuroendocrine Tumors

Pancreatic neuroendocrine tumors (pancreatic NET) are relatively rare, slowly growing tumors, although their incidence is increasing, and patients may survive for several years with metastatic disease. Apart from symptomatic relief, there have been few treatment options for these tumors in the past. More recently, investigators have explored the potential of molecularly targeted agents in treating pancreatic NET, with some success. In this review, we consider the data supporting exploitation of different targets in pancreatic NET, including peptide receptors, receptor tyrosine kinases (involved in tumor angiogenesis and more directly supporting tumor growth), and intracellular targets, such as the mammalian target of rapamycin (mTOR), which has a central role in regulating cell growth, metabolism, and apoptosis. Probably due to the paucity of pancreatic NET, many clinical trials to date have included heterogeneous NET populations, and there are few randomized studies of this specific patient population. Very recently, promising results have been achieved in placebo-controlled, phase III trials with the multitargeted tyrosine kinase inhibitor, sunitinib, and the mTOR inhibitor, everolimus. These agents have been approved or are currently being reviewed by authorities for use in patients with pancreatic NET. Here we review potential molecular targets in pancreatic NET and summarize the available data for targeted agents from phase II and III trials open to patients with this tumor.
Secretless Security Structures

We introduce the N-variant systems framework for protecting vulnerable services from attack. Our approach employs artificial diversity techniques. However, instead of relying on keeping secrets like previous approaches, we use an architectural framework to provide a high degree of assurance without needing any secrets. By designing variants that satisfy disjoint sets of possible attack preconditions, and ensuring that an attacker must compromise all variants simultaneously, we can obtain provable security against classes of attacks. In this paper, we present the N-variant systems framework, identify types of variation that may be used to provide immunity against particular attack classes, describe a prototype implementation of a simple example of an N-variant system based on partitioning the space of valid addresses, and discuss issues involved in making our approach secure and practical for complex servers.
Contexts as Abstraction of Grouping

This paper presents a framework of context-centered digital course libraries founded on the Topic Maps paradigm and used for developing an authoring environment for building such libraries. We explore the idea of using contexts to support more efficient information search. The notion of context is perceived as abstraction of grouping of domain concepts and resources based on the existing semantic relationships between them. The suggested framework implies a layered information structure of the library content consisting of three layers, each capturing a different aspect of the information space conceptual, resource-related, and contextual. The proposed model of context is used for context representation in the TM4L environment, which enables the creation, maintenance, and use of ontologyaware courseware based on Topic Maps.
Biotemplated Synthesis of Gold Nanoparticle–Bacteria Cellulose Nanofiber Nanocomposites and Their Application in Biosensing

Bacteria cellulose (BC) nanofibers are used as robust biotemplates for the facile fabrication of novel gold nanoparticle (NP)–bacteria cellulose nanofiber (Au–BC) nanocomposites via a one‐step method. The BC nanofibers are uniformly coated with Au NPs in aqueous suspension using poly(ethyleneimine) (PEI) as the reducing and linking agent. With the addition of different halides, Au–BC nanocomposites with different Au shell thicknesses are formed, and a possible formation mechanism is proposed by taking into account the special role played by PEI. A novel H2O2 biosensor is constructed using the obtained Au–BC nanocomposites as excellent support for horseradish peroxidase (HRP) immobilization, which allows the detection of H2O2 with a detection limit lower than 1 µM. The Au–BC nanocomposites could be further used for the immobilization of many other enzymes, and thus, may find potential applications in bioelectroanalysis and bioelectrocatalysis.