Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancing MOEA with component-emphasizing mechanism for multi-objective optimization

Multi-objective optimization is an important and challenging topic in the field of industrial design and scientific research because real-world problems usually involve several conflicting objectives. Since a multi-objective evolutionary algorithms (MOEA) is able to obtain an approximation to the Pareto optimal set and provide substantial information of the tradeoff between objectives, it is becoming one of the most successful methods for multi-objective optimization. Usually, an MOEA generates new trial solutions (offspring) with some candidate decision vectors (parents) to search for the promising areas and make the population evolve towards the Pareto optimal set. Moreover, in the reproduction procedure, most of MOEAs view the decision vector as a whole, and do not recognize the effects of a single component on the new trial solutions. In this paper, we propose the component-emphasizing mechanism for enhancing the search ability of MOE As. In this mechanism, each component of a decision vector is viewed as an independent factor affecting the quality of the solution. Based on the mechanism, a new MOEA is presented. Finally, the performance of this new algorithm is compared with two other promising MOEAs, namely, NSGA-II and GDE3, on a set of test instances. The experimental results have shown that the proposed algorithm outperforms the others in solution quality and time cost. Keywords-MOEA; elite population; steady-state strategy; component-emphasizing mechanism;
Significance of cyclin B1 expression as an independent prognostic indicator of patients with squamous cell carcinoma of the esophagus.

PURPOSE Cyclin B1 plays an important role as a mitotic cyclin in the G(2)-M phase transition during the cell cycle. The aim of the present study was to elucidate the biological significance of cyclin B1 expression in squamous cell carcinoma (SCC) of the esophagus. EXPERIMENTAL DESIGN We analyzed immunohistochemically the expression of cyclin B1 in the tumor specimens from 120 patients with SCC of the esophagus that had been treated with surgical treatment without any preoperative therapies. RESULTS The positivity rate of cyclin B1 expression was 56.7% (68 of 120). One-, 3-, and 5-year survival rates in esophageal SCCs with cyclin B1 expression were 82.8, 61.6, and 50.7%, respectively, and they were significantly lower than those in esophageal SCCs without cyclin B1 expression (97.8, 85.5, and 78.6%, respectively; P = 0.005). Cyclin B1 expression was found to be an independent prognostic indicator in esophageal SCCs in a multivariate analysis. When immunostaining for cyclin B1 was classified as a nuclear dominant pattern and cytoplasmic dominant pattern, 1-, 3-, and 5-year survival rates in esophageal SCCs with nuclear dominant expression of cyclin B1 were 66.7, 47.9, and 28.7%, respectively, and they were significantly lower than those in esophageal SCCs with cytoplasmic dominant expression (92.5, 70.0, and 66.3%, respectively; P = 0.005). A multivariate analysis demonstrated that the nuclear dominant cyclin B1 expression was an independent prognosticator in patients with esophageal SCCs expressing cyclin B1. CONCLUSIONS Our results demonstrate that cyclin B1 expression, especially nuclear dominant expression, can be significant as a prognostic indicator in esophageal SCCs.
Common Spatio-Time-Frequency Patterns for Motor Imagery-Based Brain Machine Interfaces

For efficient decoding of brain activities in analyzing brain function with an application to brain machine interfacing (BMI), we address a problem of how to determine spatial weights (spatial patterns), bandpass filters (frequency patterns), and time windows (time patterns) by utilizing electroencephalogram (EEG) recordings. To find these parameters, we develop a data-driven criterion that is a natural extension of the so-called common spatial patterns (CSP) that are known to be effective features in BMI. We show that the proposed criterion can be optimized by an alternating procedure to achieve fast convergence. Experiments demonstrate that the proposed method can effectively extract discriminative features for a motor imagery-based BMI.
Primase-based whole genome amplification

In vitro DNA amplification methods, such as polymerase chain reaction (PCR), rely on synthetic oligonucleotide primers for initiation of the reaction. In vivo, primers are synthesized on-template by DNA primase. The bacteriophage T7 gene 4 protein (gp4) has both primase and helicase activities. In this study, we report the development of a primase-based Whole Genome Amplification (pWGA) method, which utilizes gp4 primase to synthesize primers, eliminating the requirement of adding synthetic primers. Typical yield of pWGA from 1 ng to 10 ng of human genomic DNA input is in the microgram range, reaching over a thousand-fold amplification after 1 h of incubation at 37°C. The amplification bias on human genomic DNA is 6.3-fold among 20 loci on different chromosomes. In addition to amplifying total genomic DNA, pWGA can also be used for detection and quantification of contaminant DNA in a sample when combined with a fluorescent reporter dye. When circular DNA is used as template in pWGA, 108-fold of amplification is observed from as low as 100 copies of input. The high efficiency of pWGA in amplifying circular DNA makes it a potential tool in diagnosis and genotyping of circular human DNA viruses such as human papillomavirus (HPV).
Assessment of Cramer-Rao lower bounds of WLAN user location estimation

The location estimation techniques based on wireless local area network (WLAN) have received increasing attention in recent years. To obtain location information, localization methods employing received signal strength (RSS) are widely used. This paper describes Cramer-Rao lower bounds (CRLB) of WLAN user location estimation in an auditorium. The physical layout of the auditorium is substantially different when comapared to the usual halls. The CRLBs are computed using real time radio signal strength measurements performed by user's mobile terminal. The distance error lower bound provides the reference for the accuracy of node localization. The numerical results shows that the mean location error is 1.95 m and is better as compared to the localization technique using linear least square estimate. The simulation results also demonstrate that the location accuracy improves for higher values of path loss exponent. Future directions of research are indicated.
The Effect of Electroacupuncture with Different Frequencies on Muscle Oxygenation in Humans

The aim of the present study was to investigate the effect of electroacupuncture (EA) with different frequencies on muscle oxygenation in humans. The subjects were 8 healthy male volunteers. Muscle oxygenation was measured using near-infrared spectroscopy (NIRS). Blood pressure (BP) and heart rate (HR) were monitored simultaneously. After baseline recording, EA was given for 15 min and recovery was measured for 20 minutes. The procedure of EA at 1 Hz, at 20 Hz, and at control followed in the same subjects. Tissue oxygenation index (TOI) decreased during EA at 20 Hz (P < 0.05) and increased during the recovery period. Normalized tissue hemoglobin index (nTHI) also decreased during EA at 20 Hz and increased during the recovery period (P < 0.05), whereas TOI and nTHI in the EA at 1 Hz did not change significantly throughout the experiment. The peak TOI and nTHI values at 20 Hz during the recovery period were higher than the values at 1 Hz and in the control (P < 0.05). BP and HR remained constant. These data suggest that the supply of oxygen to muscle decreased during EA at 20 Hz and increased after EA at 20 Hz, without any changes in HR and BP.
Imputation of Missing Data for the Pre-Elementary Education Longitudinal Study

In the Pre-Elementary Education Longitudinal Study (PEELS), imputation of item missing data was done using AutoImpute (AI) software, which uses semi-parametric modeling to form imputation classes. In this paper, we summarize PEELS experience with AI, investigate the bias aspect of the imputed data for the PEELS teacher questionnaire data, and study the variance estimation of imputed data using multiple imputation by AI. In the study of variance estimation, we look into the bias issue for the multiple imputation method and the performance of AI multiple imputation on domain estimation. PEELS is a longitudinal survey to study the preschool and early elementary school experiences of children with disability and their progression through early special education. The study took a nationally representative sample of about 3,000 children, consisting of three age cohorts, 3, 4, and 5 years of age at the start of the study in 2003–2004. The broad objectives of the study are to learn about the characteristics of children receiving special education and the preschool programs and services they receive. Also of interest are their transition from early intervention to preschool, from preschool to elementary school, their achievement results as they move from one program to another, and the factors that contribute to these results.
Rational Design of a Multiepitope Vaccine Encoding T-Lymphocyte Epitopes for Treatment of Chronic Hepatitis B Virus Infections

ABSTRACT Protein sequences from multiple hepatitis B virus (HBV) isolates were analyzed for the presence of amino acid motifs characteristic of cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes with the goal of identifying conserved epitopes suitable for use in a therapeutic vaccine. Specifically, sequences bearing HLA-A1, -A2, -A3, -A24, -B7, and -DR supertype binding motifs were identified, synthesized as peptides, and tested for binding to soluble HLA. The immunogenicity of peptides that bound with moderate to high affinity subsequently was assessed using HLA transgenic mice (CTL) and HLA cross-reacting H-2bxd (BALB/c × C57BL/6J) mice (HTL). Through this process, 30 CTL and 16 HTL epitopes were selected as a set that would be the most useful for vaccine design, based on epitope conservation among HBV sequences and HLA-based predicted population coverage in diverse ethnic groups. A plasmid DNA-based vaccine encoding the epitopes as a single gene product, with each epitope separated by spacer residues to enhance appropriate epitope processing, was designed. Immunogenicity testing in mice demonstrated the induction of multiple CTL and HTL responses. Furthermore, as a complementary approach, mass spectrometry allowed the identification of correctly processed and major histocompatibility complex-presented epitopes from human cells transfected with the DNA plasmid. A heterologous prime-boost immunization with the plasmid DNA and a recombinant MVA gave further enhancement of the immune responses. Thus, a multiepitope therapeutic vaccine candidate capable of stimulating those cellular immune responses thought to be essential for controlling and clearing HBV infection was successfully designed and evaluated in vitro and in HLA transgenic mice.
Quantitative analysis of chromatin proteomes in disease.

In the nucleus reside the proteomes whose functions are most intimately linked with gene regulation. Adult mammalian cardiomyocyte nuclei are unique due to the high percentage of binucleated cells,(1) the predominantly heterochromatic state of the DNA, and the non-dividing nature of the cardiomyocyte which renders adult nuclei in a permanent state of interphase. (2) Transcriptional regulation during development and disease have been well studied in this organ,(3-5) but what remains relatively unexplored is the role played by the nuclear proteins responsible for DNA packaging and expression, and how these proteins control changes in transcriptional programs that occur during disease. (6) In the developed world, heart disease is the number one cause of mortality for both men and women. (7) Insight on how nuclear proteins cooperate to regulate the progression of this disease is critical for advancing the current treatment options. Mass spectrometry is the ideal tool for addressing these questions as it allows for an unbiased annotation of the nuclear proteome and relative quantification for how the abundance of these proteins changes with disease. While there have been several proteomic studies for mammalian nuclear protein complexes,(8-13) until recently(14) there has been only one study examining the cardiac nuclear proteome, and it considered the entire nucleus, rather than exploring the proteome at the level of nuclear sub compartments. (15) In large part, this shortage of work is due to the difficulty of isolating cardiac nuclei. Cardiac nuclei occur within a rigid and dense actin-myosin apparatus to which they are connected via multiple extensions from the endoplasmic reticulum, to the extent that myocyte contraction alters their overall shape. (16) Additionally, cardiomyocytes are 40% mitochondria by volume(17) which necessitates enrichment of the nucleus apart from the other organelles. Here we describe a protocol for cardiac nuclear enrichment and further fractionation into biologically-relevant compartments. Furthermore, we detail methods for label-free quantitative mass spectrometric dissection of these fractions-techniques amenable to in vivo experimentation in various animal models and organ systems where metabolic labeling is not feasible.
Elektrotechniek ESAT-SCD ( SISTA ) / TR 05-Transportation Planning and Traffic Flow Models

In this paper, we focus on the different traffic flow models that exist in literature. Due to our frequently encountered confusion among traffic engineers and policy makers, this paper goes into more detail about transportation planning models on the one hand, and traffic flow models on the other hand. The former deal with households that make certain decisions which lead to transportation and the use of infrastructure, as opposed to the latter which explicitly describe the physical propagation of traffic flows in a road network. Our goal is not to give a full account (as that would be a dissertation of its own, given the broadness of the field), but rather to impose upon the reader a thorough feeling for the differences between transportation planning and traffic flow models. Because of the high course of progress over the last decade (or even during the last five years), this paper tries to chronicle both past models, as well as some of the latest developments in this area. PACS numbers: 89.40. -a
Hydrological Modelling For Quantification Of Coarse Scale Soil Moisture In Southern Africa

The prediction of hydrological dynamics is an important issue in the scientific community of hydrologists and modellers and essential for integrated water resources decision support. However, the utilization of hydrological models in regions with no or a limited amount of measured data is restricted. Remote sensing techniques provide the means to derive such information, e.g. land cover or soil moisture, over various space and time scales.
Pseudo-Relevance Feedback Driven for XML Query Expansion

Pseudo-relevance feedback has been perceived as an effective solution for automatic query expansion. However, a recent study has shown that traditional pseudo-relevance feedback may bring into topic drift and hence be harmful to the retrieval performance. It is often crucial to identify those good feedback documents from which useful expansion terms can be added to the query. Compared with traditional query expansion, XML query expansion needs not only content expansion but also considering structural expansion. This paper presents a solution for both identifying related documents and selecting good expansion information with new content and path constrains. Combined with XML semantic feature, a naive document similarity measurement is proposed in this paper. Based on this, kmedian clustering algorithm is firstly implemented and some related documents are found. Secondly, query expansion is only performed by two steps in the set of related documents, which key phrase extraction algorithm is carried out to expand original query in the first step and the second step is structural expansion based on the expanded key phrases. Finally a full-edged content-structure query expression which can represent user’s intention is formalized. Experimental results on IEEE CS collection show that the proposed method can reduce the topic drift effectively and obtain the better retrieval quality.
Caspase-2 functions upstream of mitochondria in endoplasmic reticulum stress-induced apoptosis by bortezomib in human myeloma cells

Multiple myeloma is an incurable plasma cell malignancy. The 26S proteasome inhibitor, bortezomib, selectively induces apoptosis in multiple myeloma cells; however, the mechanism by which this compound acts remains unknown. Here, we, using immunoblotting analysis, observed that the expression of BiP, CHOP, and XBP-1 is up-regulated in bortezomib-induced apoptosis in human multiple myeloma cell lines NCI-H929 and RPMI-8226/S, strongly suggesting that endoplasmic reticulum (ER) stress response or the unfolded protein response (UPR), a signaling pathway activated by the accumulation of unfolded proteins within ER, is initiated. In the meantime, we also showed that bortezomib inhibited classic ER stressor brefeldin A–induced up-regulation of prosurvival UPR components BiP and XBP-1, resulting in increased induction of apoptosis in multiple myeloma cell lines, raising the possibility that bortezomib induces apoptosis of multiple myeloma cells by means of evoking the severe ER stress but disrupting the prosurvival UPR required. Using caspase inhibitors and a RNA interference approach, we finally confirmed that bortezomib-triggered apoptosis in multiple myeloma cells is dependent on caspase-2 activation, which is associated with ER stress and required for release of cytochrome c, breakdown of mitochondrial transmembrane potential, and its downstream caspase-9 activation. Taken together, these data strongly suggest that caspase-2 can serve as a proximal caspase that functions upstream of mitochondrial signaling during ER stress-induced apoptosis by bortezomib in multiple myeloma cells. [Mol Cancer Ther 2008;7(8):2298–307]
Side-payment profitability depending on sensitivity of linear-demand to price of access and content

This note is concerned with the issue of sidepayments between content providers (CPs) and Internet service providers (ISPs) in a potentially not-neutral Internet. Previously, we found that side-payments were not profitable under communal demand response for different types of providers. Here, we consider different (though coupled) linear demand response to usage based prices applied by each provider type, and find conditions on demand sensitivities for overall profitability. The model is extended to account for competition among similar providers of the same type using a simple model of user loyalty to their existing provider.
Trace Metals and Hydrocarbons in Sediments of the Beaufort Lagoon, Northeast Arctic Alaska, Exposed to Long-term Natural Oil Seepage, Recent Anthropogenic Activities and Pristine Conditions

1 Background/Relevance to Framework Issues.3 Hypothesis And Objectives.5 Material And Methods . 5 Results.8 Discussion.8 Trace Metal Studies.9 Trace Metal Distribution Pattern:. 9 Acknowledgements.18 Publications and Talks Presented at International Conferences, Civic Bodies and CMI Annual Research Review.19 References.20 Executive Summary . 23
The social environment and the epigenome

The genome is programmed by the epigenome. Two of the fundamental components of the epigenome are chromatin structure and covalent modification of the DNA molecule itself by methylation. DNA methylation patterns are sculpted during development and it has been a long held belief that they remain stable after birth in somatic tissues. Recent data suggest that DNA methylation is dynamic later in life in postmitotic cells such as neurons and thus potentially responsive to different environmental stimuli throughout life. We hypothesize a mechanism linking the social environment early in life and long‐term epigenetic programming of behavior and responsiveness to stress and health status later in life. We will also discuss the prospect that the epigenetic equilibrium remains responsive throughout life and that therefore environmental triggers could play a role in generating interindividual differences in human behavior later in life. We speculate that exposures to different environmental toxins alters long‐established epigenetic programs in the brain as well as other tissues leading to late‐onset disease. Environ. Mol. Mutagen. , 2008. © 2007 Wiley‐Liss, Inc.
Automatic article extraction in old newspapers digitized collections

We present a complete method for article segmentation in old newspapers, which deals with complex layouts analysis of degraded documents. The designed workflow can process large amounts of documents and generates digital objects in METS/ALTO format in order to facilitate the indexing and the browsing of information in digital libraries. The analysis of the document image is performed by a two stages scheme. Pixels are labeled in a first stage with a Conditional Random Field model in order to intent to label the areas of interest with a low logical level. Then this first logical representation of the document content is analyzed in a second stage to get a higher logical representation including article segmentation and reading order. This top-level structural analysis relies on the generation of an article separation grid applied recursively on the document image, allowing analyzing any type of Manhattan page layout, even for complex structures with multiple columns and overlapping entities. This method which benefits from both a local analysis using a probabilistic model trained using machine learning procedures, and a more global structural analysis using recursive rules, is evaluated on a dataset of daily local press document images covering several time periods and different page layouts, to prove its effectiveness.
Evaluation of surface mounted PM machine's parameters on load conditions using Frozen Permeability Method. Part. I

This work deals with the influence of magnetic saturation on machine's parameters of a surface mounted permanent magnet synchronous machine driven by an ideal six-step three-phase inverter. In order to investigate and describe each machine's parameter, a review on Frozen Permeability Method is developed. Further, a general machine design characteristics are presented. At last, some simulation by means of finite element method with Frozen Permeability Method are carried out taking into account that the machine is driven by an ideal square current waveform. The results for line inductance, flux-linkage waveform and its harmonic contents are shown and analyzed.
Quantum Lightcone Fluctuations in Theories with Extra Dimensions

The effects of small extra dimensions upon quantum fluctuations of the lightcone are examined. We argue that compactified extra dimensions modify the quantum fluctuations of gravitational field so as to induce lightcone fluctuations. This phenomenon can be viewed as being related to the Casimir effect. The observable manifestation of the lightcone fluctuations is broadening of spectral lines from distant sources. In this paper, we further develop the formalism used to describe the lightcone fluctuations, and then perform explicit calculations for several models with flat extra dimensions. In the case of one extra compactified dimension, we find a large effect which places severe constraints on such models. When there is more than one compactified dimension, the effect is much weaker and does not place a meaningful constraint. We also discuss some brane worlds scenarios, in which gravitons satisfy Dirichlet or Neumann boundary conditions on parallel four-dimensional branes, separated by one or more flat extra dimensions.