Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting phonon properties and thermal conductivity from anharmonic lattice dynamics calculations and molecular dynamics simulations

Two methods for predicting phonon frequencies and relaxation times are presented. The first is based on quasiharmonic and anharmonic lattice dynamics calculations, and the second is based on a combination of quasiharmonic lattice dynamics calculations and molecular dynamics simulations. These phonon properties are then used with the Boltzmann transport equation under the relaxation-time approximation to predict the lattice thermal conductivity. The validity of the low-temperature assumptions made in the lattice dynamics framework are assessed by comparing to thermal conductivities predicted by the Green-Kubo and direct molecular dynamics methods for a test system of Lennard-Jones argon. The predictions of all four methods are in agreement at low temperature 20 K. At temperatures of 40 K half the Debye temperature of Lennard-Jones argon and below, the thermal-conductivity predictions from the two methods that use lattice dynamics calculations are within about 30% of those made using the more accurate Green-Kubo and direct molecular dynamics methods. The thermal-conductivity predictions using the lattice dynamics techniques become inaccurate at high temperature above 40 K due to the approximations inherent in the lattice dynamics framework. We apply the results to assess the validity of i the isotropic approximation in modeling thermal transport and ii the common assertion that low-frequency phonons dominate thermal transport. Lastly, we suggest approximations that can be made within the lattice dynamics framework that allow the thermal conductivity of Lennard-Jones argon to be estimated using two orders of magnitude less computing effort than the Green-Kubo or direct molecular dynamics methods.
RNA processing and RNA tumor virus origin and evolution.

The results of molecular hybridization experiments with high-molecular-weight RNA isolated from RNA tumor viruses and DNA from normal cells suggest that RNA tumor virus genomes originate from cell genes. Some RNA tumor viruses (here called class 1) appear to have been generated in recent times in that their RNA is closely related in nucleotide sequence to certain cell genes (class 1 genes). A second class of RNA tumor viruses (here called class 2) is more distantly related to genomic information of normal cells. Structural properties of the RNA of RNA tumor viruses lead us to propose that the tumor virus RNA is originated when RNA transcripts of class 1 genes are processed by a mechanism we call "paraprocessing. " We postulate that RNA paraprocessing is normally used only at particular times during differentiation and is characterized by the cytoplasmic appearance of high-molecular-weight RNA chains containing terminal polyadenylic acid (200 residues). Paraprocessing of class 1 gene transcripts in committed or differentiated cells is considered to be aberrant in transcription that can lead to the generation of an RNA tumor virus genome. If the paraprocessed class 1 gene transcript codes for a reverse transcriptase, replication of the RNA becomes possible. Transfer of the replicating RNA to a new cell can result in genetic change such that the virus genome mutates, differing from the original progenitor genes. We propose that this genetic change causes class 1 viruses to become class 2. These ideas are applied to evidence concerning the biology of infection of RNA tumor viruses and concerning the involvement of RNA tumor viruses in human cancer. Genetic change can also occur during the origination of an RNA tumor virus genome by repeated reverse transcription and recombination (45) or by genetic alteration of particularly changeable cell genes ("hot spots") (43).
Evolutionary regional network modeling for efficient engineering optimization

This study presents a soft computing based optimization methodology, the evolutionary regional neural network modeling for engineering applications with sampling constraints. Engineering optimization often involves expensive experiment costs. Intelligent optimization advocates establishing a neural network model using small training samples such as orthogonal array to set up a surrogate model for the engineering system followed by an optimum search in the model to reduce optimization cost. However, scarce training samples might compromise modeling generality for a complex problem. Empirical rules suggest reliable predictions are likely restricted to the neighboring space of training samples, and interpolating designs are more reliable than extrapolating designs. To avoid imperfection of model due to small learning samples, an evolutionary regional network model is set up to confine the search of quasi-optimum using genetic algorithm. The constrained search in the regional network model provides a reliable quasi-optimum. The verification of the optimum is added to the learning samples to retrain the regional network model while the size and the distribution of reliable space will evolve intelligently during the optimization iteration using a fuzzy inference according to the prediction accuracy. An engineering case study, the optimal die gap parison programming of extrusion blow molding process for a uniform thickness, is presented to demonstrate the robustness and efficiency of the proposed methodology.
Multiple Similarity Queries: A Basic DBMS Operation for Mining in Metric Databases

Metric databases are databases where a metric distance function is defined for pairs of database objects. In such databases, similarity queries in the form of range queries or k-nearest-neighbor queries are the most important query types. In traditional query processing, single queries are issued independently by different users. In many data mining applications, however, the database is typically explored by iteratively asking similarity queries for answers of previous similarity queries. We introduce a generic scheme for such data mining algorithms and we investigate two orthogonal approaches, reducing I/O cost as well as CPU cost, to speed-up the processing of multiple similarity queries. The proposed techniques apply to any type of similarity query and to an implementation based on an index or using a sequential scan. Parallelization yields an additional impressive speed-up. An extensive performance evaluation confirms the efficiency of our approach.
European Conference on Information Systems ( ECIS ) 5-15-2012 ON THE VALUE OF INFORMATION-WHAT FACEBOOK USERS ARE WILLING TO PAY

In the age of Web 2.0 users contribute to platforms success by providing personal information by actively uploading information (e.g., messages, preferences, biographies) and also by leaving traces of their online behaviour as can be derived from their clicks, navigation paths, etc. While there is a market for trading such information among companies, there is little knowledge about how users actually value their personal information. In an online survey-based experiment we have asked 1.045 Facebook users how much they would be willing to pay for keeping their personal information. Surprisingly, 48.1 percent of participants are not willing to pay a single Euro, – thus, valuing their information at zero. Results indicate that people that show ‘spamming’ behaviour and users that use Facebook for ‘diary keeping’ are significantly more willing to pay a certain amount higher than zero to be able to keep their personal Facebook information. Interestingly, having analysed various kinds of user behaviour, the regression model still explains no more than 14.2 percent of variance. Additionally, this article discusses four different method manipulations for eliciting people’s willingness to pay for personal information and provides methodical guidance for future research in the field.
DETECTION OF INTRACELLULAR MARKERS IN AIRWAY INFLAMMATION A BIOCHEMICAL AND IMMUNOCYTOCHEMICAL STUDY IN INDUCED SPUTUM

6 ABBREVIATIONS APAAP alkaline phosphatase-anti-alkaline phosphatase AUC area under curve BAL bronchoalveolar lavage BSA bovine serum albumin BUD budesonide COPD chronic obstructive pulmonary disease CTAB N-cetyl-N,N,N,-trimethylammonium bromide DTE dithioerythritol DTT dithiothreitol EG2, EG1 monoclonal antibodies against ECP and/or EPX/EDN ECP eosinophil cationic protein EPO eosinophil peroxidase EPX/EDN eosinophil protein X/eosinophil-derived neurotoxin FA formaldehyde FEV 1 forced expiratory volume in one second GM-CSF granulocyte-macrophage colony-stimulating factor HNL human neutrophil lipocalin HSA human serum albumin IgG, IgE immunoglobulin G, immunoglobulin E IL-8 interleukin-8 kDa kiloDalton MBP major basic protein MGG May-Grünwald-Giemsa MPO myeloperoxidase NaCl sodium chloride OPF Ortho Permeafi x PAF platelet activating factor PBS phosphate-buffered saline PD 15 provocative dose of histamine causing a 15% reduction in FEV 1 (mg of histamine diphosphate) PD 20 FEV 1 provocative dose of histamine causing a 20% reduction in FEV 1 (mg of histamine diphosphate) PEF peak expiratory fl ow PFA paraformaldehyde PLP periodate-lysine-paraformaldehyde ROC receiver-operating characteristic SD standard deviation TER terbutaline 7 ORIGINAL PUBLICATIONS This thesis is based on the following original publications, referred to in the text by the Roman numeral concerned. I Metso T, Rytilä P, Peterson C, Haahtela T. Granulocyte markers in induced sputum in patients with respiratory disorders and healthy persons obtained by two sputum-processing methods. Cell-specifi c markers for eosi-nophils and neutrophils in sputum and bronchoalveolar lavage of patients with respiratory conditions and healthy persons. Eosinophil cationic protein in induced sputum as a marker of infl ammation in asthmatic children. Some unpublished results are also reported and discussed. 8 ABSTRACT Characteristic features in asthma and chronic obstructive pulmonary disease (COPD) are airfl ow limitation and bronchial infl ammation. During airway infl ammation, increased numbers of activated cells (e.g. eosinophils and neutrophils) associated with infl ammation are found in bronchial mucosa, in bronchoalveolar lavage (BAL) fl uid, in sputum, and, in severe cases, in blood. Both eosinophils and neutrophils contain various mediators in their intracellular granules. When such cells are activated, various types of harmful mediator are released into the immediate environment. Until recently, investigation of airway infl ammation has mainly relied on monitoring of lung function. However, numerous bronchial biopsy and BAL fl uid studies have revealed that airway infl ammation can occur in the absence of bronchial hyper-reactivity, if respiratory disease is mild or clinically well controlled. Cellular and biochemical accompaniments of airway infl ammation have been widely studied by investigation of BAL fl uid and bronchial …
Use of folic acid supplements and risk of cleft lip and palate in infants: a population-based cohort study.

BACKGROUND Orofacial clefts occur when the lips or the roof of the mouth do not fuse properly during the early weeks of pregnancy. There is strong evidence that periconceptional use of folic acid can prevent neural tube defects but its effect on oral clefts has generated debate. AIM To identify factors associated with suboptimal periconceptional use of folic acid and its potential effect on oral clefts. DESIGN AND SETTING The population-based infant cohort of the national Growing Up in Ireland study, which consists of 11 134 9-month-old infants. METHOD Data collection comprised questionnaires conducted by interviewers with parents in parents' homes. Characteristics of mothers who did or did not take folic acid before and during pregnancy, as well as the effect of folic acid use on the prevalence of cleft lip and palate were recorded. RESULTS The prevalence of cleft lip and palate was 1.98 (95% confidence interval [CI] = 1.31 to 2.99) per 1000 9-month-olds. The odds ratio for cleft lip was 4.36-fold higher (95% CI = 1.55 to 12.30, P = 0.005) for infants of mothers who did not take folic acid during the first 3 months of pregnancy, when compared with those who did have a folate intake during the first trimester. Folic acid use was suboptimal in 36.3% (95% CI = 35.4 to 37.2) of the sample. CONCLUSION These findings support the hypothesis that taking folic acid may partially prevent cleft lip and palate. They are particularly relevant for GPs, because they are usually the first port of call for women before and during early pregnancy.
Runtime pointer disambiguation

To optimize code effectively, compilers must deal with memory dependencies. However, the state-of-the-art heuristics available in the literature to track memory dependencies are inherently imprecise and computationally expensive. Consequently, the most advanced code transformations that compilers have today are ineffective when applied on real-world programs. The goal of this paper is to solve this conundrum through dynamic disambiguation of pointers. We provide different ways to determine at runtime when two memory locations can overlap. We then produce two versions of a code region: one that is aliasing-free - hence, easy to optimize - and another that is not. Our checks let us safely branch to the optimizable region. We have applied these ideas on Polly-LLVM, a loop optimizer built on top of the LLVM compilation infrastructure. Our experiments indicate that our method is precise, effective and useful: we can disambiguate every pair of pointer in the loop intensive Polybench benchmark suite. The result of this precision is code quality: the binaries we generate are 10% faster than those that Polly-LLVM produces without our optimization, at the -O3 optimization level of LLVM.
KEN06138 Reflections on the interactive whiteboard phenomenon: a synthesis of research from the UK

It is unusual to focus educational research on a particular piece of equipment, but the interactive whiteboard (IWB) seems to have a pedagogical and cultural status which makes it different from other new pieces of ICT equipment. It particular, it has been enthusiastically adopted by nearly all the teachers who have one installed in their classrooms, and is sought after by most of the teachers who do not currently have access to one. A group of researchers has formed within BERA New Technologies SIG, covering several projects in the UK which have been funded to investigate, directly or indirectly, the impact of the IWB on teaching and learning. On behalf of the BERA group, this paper reviews recent research concerning the use of IWBs and: analyses the nature of the medium characterises the associated pedagogies synthesises some roles for the IWB discusses what we have found concerning the potential of the technology for supporting ‘engaging pedagogies’; It also considers the effects of national policy contexts on our work in the UK, raises issues for other countries and helps to generate questions concerning what we do not yet know.
Programming language techniques for modular router congurations

This paper applies programming language techniques to a high-level system description, both to optimize the system and to prove useful properties about it. The system in question is Click, a modular software router framework [13]. Click routers are built from components called elements. Elements are written in C++, but the user creates a configuration using a simple, declarative data flow language. This language is amenable to data flow analysis and other conventional programming language techniques. Applied to a router configuration, these techniques have high-level results—for example, optimizing the router or verifying its high-level properties. This paper describes several programming language techniques that have been useful in practice, including optimization tools that remove virtual function calls from router definitions and remove redundant parts of adjacent routers. We also present performance results for an extensively optimized standards-compliant IP router. On conventional PC hardware, this router can forward up to 456,000 64-byte packets per second.
Robust Jacobian Estimation for Uncalibrated Visual Servoing

This paper addresses robust estimation of the uncalibrated visual-motor Jacobian for an image-based visual servoing (IBVS) system. The proposed method does not require knowledge of model or system parameters and is robust to outliers caused by various visual tracking errors, such as occlusion or mis-tracking. Previous uncalibrated methods are not robust to outliers and assume that the visual-motor data belong to the underlying model. In unstructured environments, this assumption may not hold. Outliers to the visual-motor model may deteriorate the Jacobian, which can make the system unstable or drive the arm in the wrong direction. We propose to apply a statistically robust M-estimator to reject the outliers. We compare the quality of the robust Jacobian estimation with the least squares-based estimation. The effect of outliers on the estimation quality is studied through MATLAB simulations and eye-in-hand visual servoing experiments using a WAM arm. Experimental results show that the Jacobian estimated by robust M-estimation is robust when up to 40% of the visualmotor data are outliers.
A Role for the Tec Family Tyrosine Kinase Txk in T Cell Activation and Thymocyte Selection

Recent data indicate that several members of the Tec family of protein tyrosine kinases function in antigen receptor signal transduction. Txk, a Tec family protein tyrosine kinase, is expressed in both immature and mature T cells and in mast cells. By overexpressing Txk in T cells throughout development, we found that Txk specifically augments the phospholipase C (PLC)-γ1–mediated calcium signal transduction pathway upon T cell antigen receptor (TCR) engagement. Although Txk is structurally different from inducible T cell kinase (Itk), another Tec family member expressed in T cells, expression of the Txk transgene could partially rescue defects in positive selection and signaling in itk − / − mice. Conversely, in the itk +/+ (wild-type) background, overexpression of Txk inhibited positive selection of TCR transgenic thymocytes, presumably due to induction of cell death. These results identify a role for Txk in TCR signal transduction, T cell development, and selection and suggest that the Tec family kinases Itk and Txk perform analogous functions.
Using EM for Text Classification on Arabic

Text classification is getting more attention and there is an increased need for text classification technique that provides automatic, fast, and accurate semi-supervised classification with the least human interaction with such systems. In our work we incorporated a well experimented technique for classification that makes use of the famous EM algorithm in training the classifier to be more effective on Arabic language.
Coupling of Flagellar Gene Expression to Flagellar Assembly in Salmonella enterica Serovar Typhimurium andEscherichia coli

SUMMARY How do organisms assess the degree of completion of a large structure, especially an extracellular structure such as a flagellum? Bacteria can do this. Mutants that lack key components needed early in assembly fail to express proteins that would normally be added at later assembly stages. In some cases, the regulatory circuitry is able to sense completion of structures beyond the cell surface, such as completion of the external hook structure. In Salmonella and Escherichia coli, regulation occurs at both transcriptional and posttranscriptional levels. One transcriptional regulatory mechanism involves a regulatory protein, FlgM, that escapes from the cell (and thus can no longer act) through a complete flagellum and is held inside when the structure has not reached a later stage of completion. FlgM prevents late flagellar gene transcription by binding the flagellum-specific transcription factor ς28. FlgM is itself regulated in response to the assembly of an incomplete flagellum known as the hook-basal body intermediate structure. Upon completion of the hook-basal body structure, FlgM is exported through this structure out of the cell. Inhibition of ς28-dependent transcription is relieved, and genes required for the later assembly stages are expressed, allowing completion of the flagellar organelle. Distinct posttranscriptional regulatory mechanisms occur in response to assembly of the flagellar type III secretion apparatus and of ring structures in the peptidoglycan and lipopolysaccharide layers. The entire flagellar regulatory pathway is regulated in response to environmental cues. Cell cycle control and flagellar development are codependent. We discuss how all these levels of regulation ensure efficient assembly of the flagellum in response to environmental stimuli.
Automatic Identification of Comparative Effectiveness Research from Medline Citations to Support Clinicians' Treatment Information Needs

UNLABELLED Online knowledge resources such as Medline can address most clinicians' patient care information needs. Yet, significant barriers, notably lack of time, limit the use of these sources at the point of care. The most common information needs raised by clinicians are treatment-related. Comparative effectiveness studies allow clinicians to consider multiple treatment alternatives for a particular problem. Still, solutions are needed to enable efficient and effective consumption of comparative effectiveness research at the point of care. OBJECTIVE Design and assess an algorithm for automatically identifying comparative effectiveness studies and extracting the interventions investigated in these studies. METHODS The algorithm combines semantic natural language processing, Medline citation metadata, and machine learning techniques. We assessed the algorithm in a case study of treatment alternatives for depression. RESULTS Both precision and recall for identifying comparative studies was 0.83. A total of 86% of the interventions extracted perfectly or partially matched the gold standard. CONCLUSION Overall, the algorithm achieved reasonable performance. The method provides building blocks for the automatic summarization of comparative effectiveness research to inform point of care decision-making.