Miracle-dz/UniFAR-FTUs huggingface dataset:
Components of the Salmonella Flagellar Export Apparatus and Classification of Export Substrates

ABSTRACT Until now, identification of components of the flagellar protein export apparatus has been indirect. We have now identified these components directly by establishing whether mutants defective in putative export components could translocate export substrates across the cytoplasmic membrane into the periplasmic space. Hook-type proteins could be exported to the periplasm of rod mutants, indicating that rod protein export does not have to precede hook-type protein export and therefore that both types of proteins belong to a single export class, the rod/hook-type class, which is distinct from the filament-type class. Hook-capping protein (FlgD) and hook protein (FlgE) required FlhA, FlhB, FliH, FliI, FliO, FliP, FliQ, and FliR for their export to the periplasm. In the case of flagellin as an export substrate, because of the phenomenon of hook-to-filament switching of export specificity, it was necessary to use temperature-sensitive mutants and establish whether flagellin could be exported to the cell exterior following a shift from the permissive to the restrictive temperature. Again, FlhA, FlhB, FliH, FliI, and FliO were required for its export. No suitable temperature-sensitive fliQ or fliR mutants were available. FliP appeared not to be required for flagellin export, but we suspect that the temperature-sensitive FliP protein continued to function at the restrictive temperature if incorporated at the permissive temperature. Thus, we conclude that these eight proteins are general components of the flagellar export pathway. FliJ was necessary for export of hook-type proteins (FlgD and FlgE); we were unable to test whether FliJ is needed for export of filament-type proteins. We suspect that FliJ may be a cytoplasmic chaperone for the hook-type proteins and possibly also for FliE and the rod proteins. FlgJ was not required for the export of the hook-type proteins; again, because of lack of a suitable temperature-sensitive mutant, we were unable to test whether it was required for export of filament-type proteins. Finally, it was established that there is an interaction between the processes of outer ring assembly and of penetration of the outer membrane by the rod and nascent hook, the latter process being of course necessary for passage of export substrates into the external medium. During the brief transition stage from completion of rod assembly and initiation of hook assembly, the L ring and perhaps the capping protein FlgD can be regarded as bona fide export components, with the L ring being in a formal sense the equivalent of the outer membrane secretin structure of type III virulence factor export systems.
Automatic feedback using past queries: social searching?

The effect of using paat queries to improve automatic query expansion was examined in the TREC environment. Automatic feedback of documents identified from similar past queries was compared with standard top-document feedback and with no feedback. A new query similarity metric was used based on comparing result lists and using probability of relevance. Our top-document feedback method showed small improvements over no feedback method consistent with past studies. On recall-precision and average precision measures, past query feedback yielded performance superior to that of top-document feedback. The past query feedback method also lends itself to tunable thresholds such that better performance can be obtained by automatically deciding when, and when not, to apply the expansion. Automatic past-query feedback actually improved top document precision in this experiment.
Increasing Query Speed with Multithreaded Data Prefetching

The Info bright database engine stores data in column wise chunks in a highly compressed form. Access to data is slowed down by the necessity of fetching required chunks from disk and decompressing them. A pref etching mechanism is meant to perform these tasks shortly before a running query needs the data for processing. The pref etching implementation in Info bright is described and evaluated. An average speedup of 1.7 is reported. The speedup reaches 2.4 for some queries and generally is higher for long lasting queries for which the data fetching and decompression cost dominated the execution time. The limitations of the pref etching are presented on both system level and SQL query level.
A Naive Bayes approach for URL classification with supervised feature selection and rejection framework

Web page classification has become a challenging task due to the exponential growth of the World Wide Web. Uniform Resource Locator (URL)‐based web page classification systems play an important role, but high accuracy may not be achievable as URL contains minimal information. Nevertheless, URL‐based classifiers along with rejection framework can be used as a first‐level filter in a multistage classifier, and a costlier feature extraction from contents may be done in later stages. However, noisy and irrelevant features present in URL demand feature selection methods for URL classification. Therefore, we propose a supervised feature selection method by which relevant URL features are identified using statistical methods. We propose a new feature weighting method for a Naive Bayes classifier by embedding the term goodness obtained from the feature selection method. We also propose a rejection framework to the Naive Bayes classifier by using posterior probability for determining the confidence score. The proposed method is evaluated on the Open Directory Project and WebKB data sets. Experimental results show that our method can be an effective first‐level filter. McNemar tests confirm that our approach significantly improves the performance.
Effects of Sewage Sludge on Energy Content and Combustion Emissions of Energy Crops

This study was conducted to investigate the energy crop production suitability of sewage sludge as well as pollutant transfer from sewage sludge to feedstock of Miscanthus x giganteus and Arundo donax, with a focus on ash constituents and exhaust gaseous emissions. Dewatered sludge and natural field soil were filled into pots, and seedlings produced from rhizomes were planted in the pots, which were arranged under a completely randomized design with four replications. The soil treatments were fertilized with conventional fertilizer, while no external fertilizer was supplied for sludge treatments. Harvested plant samples were subjected to characterization. Both crop species produced sufficient biomass yield on either soil or sludge treatments. High heating values measured for plants cultivated on soil and sludge were insignificant and in the range of 17.95– 17.62 MJ kg and 17.31–18.05 MJ kg for M. x giganteus and A. donax, respectively. Sewage sludge significantly increased the plant macronutrients and heavy metal content of both species. Si was the dominant element in ash and was higher in A. donax plants. K and Ca were secondary high concentration elements, giving similar results for both plant species. Nitrogen concentrations in plant tissue provided by sewage sludge increased NOx emissions with a maximum increment observed at 10% with A. donax plants. SO2 emissions obtained were consistent with plant species but the emission concentrations were very small. The use of sewage sludge for energy crop cultivation confirmed that ash and air emissions hold great potential for both the energy crop production and waste minimizing alternative. © 2018 Friends Science Publishers
Magnetic and Magnetoresistance Behaviors of Solvent Extracted Particulate Iron/ Polyacrylonitrile Nanocomposites

Iron nanoparticle reinforced polyacrylonitrile (PAN) nanocomposites are fabricated by a facile and environmentally benign solvent extraction method. Fourier transform infrared (FT-IR), thermal gravimetric analysis (TGA), and differential scanning calorimetry (DSC) results indicate a strong interaction between the iron nanoparticles and the polymer matrix for the as-prepared polymer nanocomposites. The heat treatment induces the carbonization of the polymer matrix. High-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD) analysis show a protecting carbon shell surrounding the iron nanoparticles within the carbon matrix against the particle oxidation. The magnetic properties, electrical conductivity, and magnetic field dependent resistivity of heat-treated nanocomposites with different particle loadings are carried out in a physical properties measurement system by Quantum Design and by a standard four probe method. The saturation magnetization increases and the coercivity decrea.
Voice breaking in adolescent red-crowned cranes (Grus japonensis)

Summary Voice breaking is a process associated with puberty of human males that also occurs in adolescence in some birds. This study reports the jump-like vocal changes occurring during voice breaking in adolescent red-crowned cranes (Grus japonensis). We investigated acoustic parameters of chirp and trill calls during vocal ontogenesis from hatching to the age of 1.5 years in 17 male and 31 female captive red-crowned cranes and compared them with definitive calls of 5 male and 8 female conspecific adults. During voice breaking, trills and chirps of both sexes contained two non-overlapping independent fundamental frequencies: the upper one, representing the retained juvenile frequency, and the lower one, the newly attained adult frequency. Before voice breaking, the calls contained only the upper frequency, whereas after it only the lower one. Voice breaking occurred between the age of 7 and 11.5 months. We test whether sex, dates of birth and body mass gain are associated with voice breaking and speculate whether voice breaking triggers the disruption of the parent‐ chick bond or vice versa, or both events are driven by a third, yet unidentified trigger.
Improving PP Attachment Disambiguation in a Rule-based Parser

This paper deals with how to enhance the performance of a rule-based parser using statistical Information. PP (Prepositional Phrase) attachment ambiguity is one of the main ambiguities found in parsing. We therefore conducted some experiments on extracting statistical information for PP attachment from a corpus, and on applying such information to a rule-based parser. Two types of information are used: supervised learning data and unsupervised learning data. In this paper, we show how we apply these types of information and to what degree they contribute to the PP attachment as well as to the overall parsing performance. The final results show a 5.42% performance improvement in PP attachment, with an 8.7% error reduction ratio in the overall parsing performance.
Recent Developments in Index Number Theory and Practice

A surgical drill wherein a driven spindle is formed with an axial through bore and accommodates an axially movable clamping member which can either engage or release an elongated drilling tool. A nut is employed to move the clamping member between a first axial position in which the clamping member receives torque from the spindle and rotates the tool, and a second axial position in which the tool can be shifted axially of the clamping member and spindle so as to move a desired length of the tool beyond the spindle, to wit: a length which is sufficient to permit deeper penetration into a bone or the like but not enough to permit uncontrolled flexing of the tool. The axial length of the toll may exceed several times the axial length of the spindle.
THROMBOSIS AND HEMOSTASIS Platelet gene therapy corrects the hemophilic phenotype in immunocompromised hemophilia A mice transplanted with genetically manipulated human cord blood stem cells

Hemophilia A is a congenital bleeding disorder caused by a deficiency of factor VIII (FVIII). Protein replacement therapy using either plasma-derived or recombinant FVIII is effective for treating hemophilia A patients. However, it is expensive and requires frequent infusions owing to the short half-life of the protein. Furthermore, up to 35% of patients will develop anti-FVIII inhibitory antibodies, referred to as inhibitors, after exogenous FVIII replacement therapy. The clinical hallmark of inhibitor development in hemophilia A patients is failure to respond to routine replacement therapy for bleeding episodes. Gene therapy is an attractive strategy for treating hemophilia A. The goal of gene therapy is to introduce long-term expression of therapeutic levels of FVIII in vivo by genetically modifying the target cells resulting in a cure of the disease. Although substantial progress has been achieved in the past decade, potential development of an immune response to transgene product or vector remains a significant concern in genetic therapy. We have developed a novel clinically translatable platelet-targeted gene therapy approach using lentiviral gene delivery to hematopoietic stem cells (HSCs), in which FVIII expression is under the control of the platelet-specific glycoprotein IIb promoter (2bF8). Our previous studies have demonstrated that 2bF8 lentivirus (2bF8LV)-mediated platelet-specific gene therapy can efficiently introduce therapeutic levels of platelet FVIII in mice with hemophilia A that have no inhibitory or noninhibitory antibody development. Further studies have demonstrated that therapeutic levels of platelet FVIII are sustained while inhibitor titers decline with time after 2bF8 gene therapy in hemophilia A mice with preexisting anti-FVIII immunity. However, this approach has not been studied in human cells. Since our ultimate goal is to express FVIII in the platelets of patients with hemophilia A, the questions we addressed in this study included (1) whether human HSCs (hHSCs) can be transduced by 2bF8LV, (2) whether 2bF8LV-transduced hHSCs can normally give rise to blood cells including the platelet lineage, (3) whether 2bF8LV-mediated gene transfer can efficiently introduce FVIII expression in human platelets, and (4) whether human platelet– derived FVIII can correct the hemophilic bleeding diathesis. We demonstrate, for the first time, the feasibility of 2bF8LV gene delivery to hHSCs to introduce FVIII expression in human platelets
Skyline sets queries from databases with missing values

With the increase of data volume, advanced query operators, such as skyline queries, are necessary in order to help users to handle the huge amount of available data by identifying a set of interesting data objects. Skyline queries help us to filter unnecessary information efficiently and provide us clues for various decision making tasks. Most of the existing skyline algorithms can not preserve individual's privacy and are not well suited for data with outliers and frequently updated data. Considering these issues, earlier we have proposed skyline sets queries from databases where all dimensions are available for all data items. Let s be the number of objects in each set and n be the number of objects in the database. The number of sets in the database is nCs. Skyline sets query returns all skyline s-sets from nCs sets. We consider an efficient algorithm for computing “convex” skyline of the nCs sets. In this paper, we use the idea for skyline sets queries from databases with missing values and propose a method, namely, RBSSQ. RBSSQ method uses a replacement based approach and is applicable to the databases having any number of missing dimensions in the database objects. We have conducted several experiments in terms of computational cost and found that our proposed method can efficiently compute skyline sets from data items with missing values.
Human emotion recognition from body language of the head using soft computing techniques

When people interact with each other, they not only listen to what the other says, they react to facial expressions, gaze direction, and head movement. Human-computer interaction would be enhanced in a friendly and non-intrusive way if computers could understand and respond to users’ body language in the same way. This thesis aims to investigate new methods for human computer interaction by combining information from the body language of the head to recognize the emotional and cognitive states. We concentrated on the integration of facial expression, eye gaze and head movement using soft computing techniques. The whole procedure is done in two-stage. The first stage focuses on the extraction of explicit information from the modalities of facial expression, head movement, and eye gaze. In the second stage, all these information are fused by soft computing techniques to infer the implicit emotional states. In this thesis, the frequency of head movement (high frequency movement or low frequency movement) is taken into consideration as well as head nods and head shakes. A very high frequency head movement may show much more arousal and active property than the low frequency head movement which differs on the emotion dimensional space. The head movement frequency is acquired by analyzing the tracking results of the coordinates from the detected nostril points. Eye gaze also plays an important role in emotion detection. An eye gaze detector was proposed to analyze whether the subject's gaze direction was direct or averted. We proposed a geometrical relationship of human organs between nostrils and two pupils to achieve this task. Four parameters are defined according to the changes in angles and the changes in the proportion of length of the four feature points to distinguish avert gaze from direct gaze. The sum of these parameters is considered as an evaluation parameter that can be analyzed to quantify gaze level. The multimodal fusion is done by hybridizing the decision level fusion and the soft computing techniques for classification. This could avoid the disadvantages of the decision level fusion technique, while retaining its advantages of adaptation and flexibility. We introduced fuzzification strategies which can successfully quantify the extracted parameters of each modality into a fuzzified value between 0 and 1. These fuzzified values are the inputs for the fuzzy inference systems which map the fuzzy values into emotional states.
Systematic review of feedback mechanism improving safety in dynamic and static industry

Background Human resources is the most valuable and important resource. Behavior based safety (BBS) is one way the management can use to ensure safety. BBS aims at helping employees to identify and choose the safe behavior. BBS is based on the following four components: i. behavioral observation and feedback process, ii. formal review of observation data, iii. improvement goals; and iv. reinforcement for goal attainment and improvement. Objective This systematic review was aimed at studying the relationship between feedback mechanism and the reduced number of accidents, injuries and illness in dynamic and static industries. Methods – Eight articles using an inclusion and exclusion criteria were chosen. Epidemiological Appraisal Instrument (EAI) was used to assess the quality of all the accepted papers in the following areas: study description, subject selection, observation quality, data analysis and generalization of results. Results – The results showed that in both static and dynamic industries, feedback or combinations of feedback did reduce accidents, injuries and illness in workplace. Conclusion Feedback plays an important role in behavior modification. It increases the level of safety and in turn, reduces the number of accidents, incidents and claims that need to be paid by static or dynamic industries.
An user-friendly toolkit for heart rate variability analysis: Suitable for automatic analysis of episodes

In this work, a software package, called gHRV, and dedicated to the automatic analysis and study of the heart rate variability is presented. The software is provided with a graphical user interface, is both free and open source, and allows to perform both spectral and nonlinear analysis of several parameters related to the cardiac rhythm. To show the ease-of use, a detailed example employing a polysomnogram is presented, to study if differences in the various sleep stages can be found employing gHRV. As a result, the software has been proven to be potentially useful for discriminating among the previous mentioned stages, by analyzing the power in the different spectral bands, as well as other parameters.
On2Vec: Embedding-based Relation Prediction for Ontology Population

Populating ontology graphs represents a long-standing problem for the Semantic Web community. Recent advances in translation-based graph embedding methods for populating instance-level knowledge graphs lead to promising new approaching for the ontology population problem. However, unlike instance-level graphs, the majority of relation facts in ontology graphs come with comprehensive semantic relations, which often include the properties of transitivity and symmetry, as well as hierarchical relations. These comprehensive relations are often too complex for existing graph embedding methods, and direct application of such methods is not feasible. Hence, we propose On2Vec, a novel translation-based graph embedding method for ontology population. On2Vec integrates two model components that effectively characterize comprehensive relation facts in ontology graphs. The first is the Component-specific Model that encodes concepts and relations into low-dimensional embedding spaces without a loss of relational properties; the second is the Hierarchy Model that performs focused learning of hierarchical relation facts. Experiments on several well-known ontology graphs demonstrate the promising capabilities of On2Vec in predicting and verifying new relation facts. These promising results also make possible significant improvements in related methods.
Predictive Indexing for Fast Search

We tackle the computational problem of query-conditioned search. Given a machine-learned scoring rule and a query distribution, we build a predictive index by precomputing lists of potential results sorted based on an expected score of the result over future queries. The predictive index datastructure supports an anytime algorithm for approximate retrieval of the top elements. The general approach is applicable to webpage ranking, internet advertisement, and approximate nearest neighbor search. It is particularly effective in settings where standard techniques (e.g., inverted indices) are intractable. We experimentally find substantial improvement over existing methods for internet advertisement and approximate nearest neighbors.
AERMOD: A Dispersion Model for Industrial Source Applications. Part I: General Model Formulation and Boundary Layer Characterization.

Abstract The formulation of the American Meteorological Society (AMS) and U.S. Environmental Protection Agency (EPA) Regulatory Model (AERMOD) Improvement Committee’s applied air dispersion model is described. This is the first of two articles describing the model and its performance. Part I includes AERMOD’s characterization of the boundary layer with computation of the Monin–Obukhov length, surface friction velocity, surface roughness length, sensible heat flux, convective scaling velocity, and both the shear- and convection-driven mixing heights. These parameters are used in conjunction with meteorological measurements to characterize the vertical structure of the wind, temperature, and turbulence. AERMOD’s method for considering both the vertical inhomogeneity of the meteorological characteristics and the influence of terrain are explained. The model’s concentration estimates are based on a steady-state plume approach with significant improvements over commonly applied regulatory dispersion models. Co.