Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a real-time PCR method for detection and quantification of the parasitic protozoan Perkinsus olseni

The objective of this study was to develop a real-time PCR method for the rapid detection and quantification of the protozoan pathogen Perkinsus olseni using a TaqMan probe. For the standard, genomic DNA was extracted from 10 5 in vitro-cultured P. olseni trophozoites, and then 10-fold serial dilutions to the level of a single cell were prepared. To test the reliability of the technique, triplicates of genomic DNA were extracted from 5 × 10⁴ cells and 10-fold serial dilutions to the level of 5 cells were prepared. The standards and samples were analyzed in duplicate using an Exicycler TM 96 real-time quantitative thermal block. For quantification, the threshold cycle (CT) values of samples were compared with those obtained from standard dilutions. There was a strong linear relationship between the CT value and the log concentration of cells in the standard (r² = 0.996). Detection of DNA at a concentration as low as the equivalent of a single cell showed that the assay was sensitive enough to detect a single cell of P. olseni. The estimated number of P. olseni cells was similar to the original cell concentrations, indicating the reliability of P. olseni quantification by real-time PCR. Accordingly, the designed primers and probe may be used for the rapid detection and quantification of P. olseni from clam tissue, environmental water, and sediment samples.
Web service composition languages: old wine in New bottles?

Recently, several languages for Web service composition have emerged (e.g., BPEL4WS and WSCI). The goal of these languages is to glue Web services together in a process-oriented way. For this purpose, these languages typically borrow concepts from workflow management systems and embed these concepts in the so-called "Web services stack". Up to now, little or no effort has been dedicated to systematically evaluate the capabilities and limitations of these languages. BPEL4WS for example is said to combine the best of other standards for Web service composition such as WSFL (IBM) andXLANG (Microsoft), and allows for a mixture of block structured and graph structured process models. However, aspects such as the expressiveness, adequacy, orthogonality, and formal characterization of BPEL4WS (e.g. reachability) have not yet been systematically investigated. Although BPEL4WS is not a bad proposal, it is remarkable how much attention it receives while more fundamental issues such as semantics, expressiveness, and adequacy do not get the attention they deserve. Therefore, we advocate the use of more rigorous approaches to critically evaluate the so-called standards for Web services composition, and to learn from 25 years of experiences in the workflow/office automation domain.
MQD—Multiplex-Quadrature Detection in Multi-Dimensional NMR

With multiplex-quadrature detection (MQD) the tasks of coherence selection and quadrature separation in N-dimensional heteronuclear NMR experiments are merged. Thus the number of acquisitions required to achieve a desired resolution in the indirect dimensions is significantly reduced. The minimum number of transients per indirect data point, which have to be combined to give pure-phase spectra, is thus decreased by a factor (3/4)N−1. This reduction is achieved without adjustable parameters. We demonstrate the advantage by MQD 3D HNCO and HCCH-TOCSY spectra affording the same resolution and the same per-scan sensitivity as standard phase-cycled ones, but obtained in only 56 % of the usual time and by resolution improvements achieved in the same amount of time.
Spontaneous CD8 T Cell Responses against the Melanocyte Differentiation Antigen RAB38/NY-MEL-1 in Melanoma Patients1

The melanocyte differentiation Ag RAB38/NY-MEL-1 was identified by serological expression cloning (SEREX) and is expressed in the vast majority of melanoma lesions. The immunogenicity of RAB38/NY-MEL-1 has been corroborated previously by the frequent occurrence of specific Ab responses in melanoma patients. To elucidate potential CD8 T cell responses, we applied in vitro sensitization with overlapping peptides spanning the RAB38/NY-MEL-1 protein sequence and the reverse immunology approach. The identified peptide RAB38/NY-MEL-150–58 exhibited a marked response in ELISPOT assays after in vitro sensitization of CD8 T cells from HLA-A∗0201+ melanoma patients. In vitro digestion assays using purified proteasomes provided evidence of natural processing of RAB38/NY-MEL-150–58 peptide. Accordingly, monoclonal RAB38/NY-MEL-150–58-specific T cell populations were capable of specifically recognizing HLA-A2+ melanoma cell lines expressing RAB38/NY-MEL-1. Applying fluorescent HLA-A2/RAB38/NY-MEL-150–58 multimeric constructs, we were able to document a spontaneously developed memory/effector CD8 T cell response against this peptide in a melanoma patient. To elucidate the Ag-processing pathway, we demonstrate that RAB38/NY-MEL-150–58 is produced efficiently by the standard proteasome and the immunoproteasome. In addition to the identification of a RAB38/NY-MEL-1-derived immunogenic CD8 T cell epitope, this study is instrumental for both the onset and monitoring of future RAB38/NY-MEL-1-based vaccination trials.
Thermal error modelling of NC machine tools based on impulse response model

High accuracy of machine tool is the assurance of top-quality products in machining processes. Among the various errors related to machine tools, thermal errors have a significant effect on machining accuracy and directly determine the machined quality of the finished part with both the surface finish and the geometric shape. So, if we establish thermal error model accurately, the affection of thermal error would be eliminated through compensation. How to get the key temperature measuring points and robustness of the model is the main problem of thermal error modelling using traditional methods. Accordingly, the paper presents a novel method for searching key thermal point by means of infrared imaging system and modelling by system identification based on least square principle. The experiments of thermal error compensation have been conducted on a rotary table of five-axis Milling Center. The results show that the key points are selected simply and effectively and the compensation model has good adaptability, thus its prediction is accurate.
A Survey: Recent Development in Fractals

A brief review of chaotic dynamics and fractals is presented. Topics discussed include basic concepts, recent developments, and applications of fractals. Fractals are exotic graphics techniques, widely seen as a mathematical oddity only six years ago, hold promise for image compression. In this article I would like to report on some developments since the 1960s. This, however, is very far from a survey. I hope that by focusing on a couple of examples and a small sample of ideas I can convey to the general mathematics community a sense of some of the progress that has been made.
The Syntax of Programming Languages-A Survey

The syntactic rules for many programming languages have been expressed by formal grammars, generally variants of phrase-structure grammars. The syntactic analysis essential to translation of programming languages can be done entirely mechanically for such languages. Major problems remain in rendering analyzers efficient in use of space and time and in finding fully satisfactory formal grammars for present and future programming languages.
Biomarker Discovery in Non–Small Cell Lung Cancer: Integrating Gene Expression Profiling, Meta-analysis, and Tissue Microarray Validation

Purpose: Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis and therapy response. So far, the value of these multigene signatures in clinical practice is unclear, and the biologic importance of individual genes is difficult to assess, as the published signatures virtually do not overlap. Experimental Design: Here, we describe a novel single institute cohort, including 196 non–small lung cancers (NSCLC) with clinical information and long-term follow-up. Gene expression array data were used as a training set to screen for single genes with prognostic impact. The top 450 probe sets identified using a univariate Cox regression model (significance level P < 0.01) were tested in a meta-analysis including five publicly available independent lung cancer cohorts (n = 860). Results: The meta-analysis revealed 14 genes that were significantly associated with survival (P < 0.001) with a false discovery rate <1%. The prognostic impact of one of these genes, the cell adhesion molecule 1 (CADM1), was confirmed by use of immunohistochemistry on tissue microarrays from 2 independent NSCLC cohorts, altogether including 617 NSCLC samples. Low CADM1 protein expression was significantly associated with shorter survival, with particular influence in the adenocarcinoma patient subgroup. Conclusions: Using a novel NSCLC cohort together with a meta-analysis validation approach, we have identified a set of single genes with independent prognostic impact. One of these genes, CADM1, was further established as an immunohistochemical marker with a potential application in clinical diagnostics. Clin Cancer Res; 19(1); 194–204. ©2012 AACR.
The third-order term in the normal approximation for the AWGN channel

This paper shows that, under the average error probability formalism, the third-order term in the normal approximation for the additive white Gaussian noise channel with a maximal or equal power constraint is at least 1 over 2 log n+O(1). This improves on the lower bound by Polyanskiy-Poor-Verdú (2010) and matches the upper bound proved by the same authors.
Closed-form expressions vs. BIC: A comparison for speaker clustering

In this paper, the use of closed-form expressions is compared to the BIC approximation, with respect to speaker clustering. We first show that the particular BIC setting which is commonly used in this task, namely the approximation of the marginal - with respect to the model parameters - and conditional - with respect to the latent variables - likelihood, belongs to an exponential family, and hence admits a closed-form expression by attaching conjugate priors. We then formalize the role of the tuning parameter as a hyperparameter of the prior and finally we explain the several proposed setting - global, local and segmental - based on the strength of the prior. Experiments are carried out for the speaker clustering task and improvement over the BIC approximation is reported.
Dietary patterns and the risk of non-Hodgkin lymphoma

Abstract Objective Previous studies examining the role of single foods or nutrients in the aetiology of non-Hodgkin lymphoma (NHL) have produced inconsistent findings. Few studies have examined associations for dietary patterns, which may more accurately reflect patterns of consumption and the complexity of dietary intake. The objective of the present study was to examine whether dietary patterns identified by factor analysis were associated with NHL risk. Design Case–control. Setting Population-based sample residing in Nebraska from 1999 to 2002. Subjects A total of 336 cases and 460 controls. Results Factor analysis identified two major dietary patterns: (i) a ‘Meat, Fat and Sweets’ dietary pattern characterized by high intakes of French fries, red meat, processed meat, pizza, salty snacks, sweets and desserts, and sweetened beverages; and (ii) a ‘Fruit, Vegetables and Starch’ dietary pattern characterized by high intakes of vegetables, fruit, fish, and cereals and starches. In multivariable logistic regression models, the ‘Meat, Fat and Sweets’ dietary pattern was associated with an increased risk of overall NHL (ORQ4 v. Q1 = 3·6, 95 % CI 1·9, 6·8; P trend = 0·0004), follicular lymphoma (ORQ4 v. Q1 = 3·1, 95 % CI 1·2, 8·0; P trend = 0·01), diffuse large B-cell lymphoma (ORQ4 v. Q1 = 3·2, 95 % CI 1·1, 9·0; P trend = 0·09) and marginal zone lymphoma (ORQ4 v. Q1 = 8·2, 95 % CI 1·3, 51·2; P trend = 0·05). No association with overall or subtype-specific risk was detected for the ‘Fruit, Vegetables and Starch’ dietary pattern. No evidence of heterogeneity was detected across strata of age, sex, BMI, smoking status or alcohol consumption. Conclusions Our results suggest that a dietary pattern high in meats, fats and sweets may be associated with an increased risk of NHL.
Malware Analysis of WanaCry Ransomware

In this paper, we present some general observations on ransomwares. Furthermore we focus on the most recent and publicly covered development in the field, the ransomware WanaCry. We show how we analyzed the samples and what conclusions can be drawn from our results. Based on this information, we provide a number of preventive measures that users can take in order to protect their data and have their computers ransomware-free.
Scoring Semantic Annotations Returned by The NCBO Annotator

Semantic annotation using biomedical ontologies is required to enable data integration, interoperability, indexing and mining of biomedical data. When used to support semantic indexing the scoring and ranking of annotations become as important as provenance and metadata on the annotations themselves. In the biomedical domain, one broadly used service for annotations is the NCBO Annotator Web service, offered within the BioPortal platform and giving access to more than 350+ ontologies or terminologies. This paper presents a new scoring method for the NCBO Annotator allowing to rank the annotation results and enabling to use such scores for better indexing of the annotated data. By using a natural language processing-based term extraction measure, C-Value, we are able to enhance the original scoring algorithm which uses basic frequencies of the matches and in addition to positively discriminate multi-words term annotations. We show results obtained by comparing three different methods with a reference corpus of PubMed-MeSH manual annotations.
Aluminium nitride in steel

AbstractAluminium nitride (AlN) nucleates with difficulty in steel, unless precipitation is enhanced by thermal or mechanical treatments. This important characteristic determines the precipitation kinetics of AlN, and accounts for the wide variations in precipitate morphology achieved following different processing histories. The most significant effect of AlN in steel is on grain size control, which directly influences hardenability, hot ductility, texture development, and mechanical properties. In addition, the accompanying removal of nitrogen from solid solution affects the strain aging characteristics, weldability, mechanical properties, and creep performance. Aluminium nitride also exerts important second order effects through its influence on the precipitation of other alloy nitrides. The precipitation of AlN can cause embrittlement and cracking phenomena in castings, continuously cast products, ingots, and rolled or forged products, However, the basic mechanisms are well understood, and the occurre.
Efficient Web-based Facial Recognition System Employing 2DHOG

In this paper, a system for facial recognition to identify mi ssing and found people in Hajj and Umrah is described as a web portal. Explicitly, we present a novel algorithm for recognition and classifications of facial images based on applying 2DPCA to a 2D representation of the Histogram of oriented gradients (2D-HOG) which maintains the spatial relation between pixels of the input images. This algorithm allows a compact representation of the images which reduces the computational complexity and the storage requirments, while maintaining the highest reported recognition accuracy. This promotes this method for usage with very large datasets. Large dataset was collected for people in Hajj. Experimental results employing ORL, UMIST, JAFFE, and HAJJ datasets confirm these excellent properties.
Modeling and Optimal Operation of Distributed Battery Storage in Low Voltage Grids

Due to high power in-feed from photovoltaics, it can be expected that more battery systems will be installed in the distribution grid in near future to mitigate voltage violations and thermal line and transformer overloading. In this paper, we present a two-stage centralized model predictive control scheme for distributed battery storage that consists of a scheduling entity and a real-time control entity. To guarantee secure grid operation, we solve a robust multi-period optimal power flow (OPF) for the scheduling stage that minimizes battery degradation and maximizes photovoltaic utilization subject to grid constraints. The real-time controller solves a real-time OPF taking into account storage allocation profiles from the scheduler, a detailed battery model, and real-time measurements. To reduce the computational complexity of the controllers, we present a linearized OPF that approximates the nonlinear AC-OPF into a linear programming problem. Through a case study, we show, for two different battery technologies, that we can substantially reduce battery degradation when we incorporate a battery degradation model. A further finding is that we can reduce battery losses by 30% by using the detailed battery model in the real-time control stage.
On improving speech intelligibility in automotive hands-free systems

Due to its narrow acoustic bandwidth, typical telephone speech is poorly intelligible on a phoneme or syllable basis. Artificial bandwidth extension (ABWE) techniques intend to increase speech intelligibility by estimating and reconstructing higher frequency components up to 7kHz. Hands-free systems in automotive environments could especially benefit from that, since drivers are mentally stressed during telephone conversations. By improving speech intelligibility, their mental load may decrease. Thus driving safety and comfort increase. This paper presents a real-time ABWE implementation integrated into an automotive hands-free system. Its novelty is a phoneme-specific design that yields an improved performance on critical phonemes, especially /s/ and /z/. Hence, typical lisping effects of previous ABWE approaches are reduced. We performed informal listening tests on meaningless vowel-consonant-vowel (VCV) syllables demonstrating a significantly improved fricative intelligibility of ABWE speech vs. NB speech.
Measurement and analysis of IP network usage and behavior

Traffic, usage, and performance measurements are crucial to the design, operation and control of Internet protocol networks. This article describes a prototype infrastructure for the measurement, storage, and correlation of network data of different types and origins from AT&T's commercial IP network. We focus first on some novel aspects of the measurement infrastructure, then describe analyses that illustrate the power of joining different measured data sets for network planning and design.
Consistency maintenance in peer-to-peer file sharing networks

While the current generation of peer-to-peer networks share predominantly static files, future peer-to-peer networks will support sharing of files that are modified frequently by their users. We present techniques to maintain temporal consistency of replicated files in a peer-to-peer network. We consider the Gnutella P2P network and present techniques for maintaining consistency in Gnutella even when peers containing replicated files dynamically join and leave the network. An experimental evaluation of our techniques shows that: (i) a hybrid approach based on push and pull achieves high fidelity in highly dynamic P2P networks and (ii) the run-time overheads of our techniques are small, making them a practical choice for P2P networks.
Leveraging mediator cost models with heterogeneous data sources

Distributed systems require declarative access to diverse information sources. One approach to solving this heterogeneous distributed database problem is based on mediator architectures. In these architectures, mediators accept queries from users, process them with respect to wrappers, and return answers. Wrappers provide access to underlying sources. To efficiently process queries, the mediator must optimize the plan used for processing the query. In classical databases, cost-estimate based query optimization is effective. In a heterogeneous distributed databases, cost-estimate based query optimization is difficult to achieve because the underlying data sources do not export cost information. This paper describes a new method that permits the wrapper programmer to export cost estimates. For the wrapper programmer to describe all cost estimates may be impossible due to lack of information or burdensome due to the amount of information. We ease this responsibility of the wrapper programmer by leveraging the generic cost model of the mediator with specific cost estimates from the wrappers.
Spatial Multidimensional Sequence Clustering

Measurements at different time points and positions in large temporal or spatial databases requires effective and efficient data mining techniques. For several parallel measurements, finding clusters of arbitrary length and number of attributes, poses additional challenges. We present a novel algorithm capable of finding parallel clusters in different structural quality parameter values for river sequences used by hydrologists to develop measures for river quality improvements
From multidrug-resistant to extensively drug-resistant tuberculosis in Lisbon, Portugal: the stepwise mode of resistance acquisition.

OBJECTIVES The development and transmission of extensively drug-resistant (XDR) tuberculosis (TB) constitutes a serious threat to the effective control of TB in several countries. Here, in an attempt to further elucidate the dynamics of the acquisition of resistance to second-line drugs and investigate an eventual role for eis promoter mutations in aminoglycoside resistance, we have studied a set of multidrug-resistant (MDR)/XDR-TB isolates circulating in Lisbon, Portugal. METHODS Forty-four MDR-TB or XDR-TB isolates were genotyped and screened for mutations in genes associated with second-line drug resistance, namely tlyA, gyrA, rrs and eis. RESULTS The most prevalent mutations found in each gene were Ins755GT in tlyA, A1401G in rrs, G-10A in eis and S91P in gyrA. Additionally, two genetic clusters were found in this study: Lisboa3 and Q1. The characteristic mutational profile found among recent XDR-TB circulating in Lisbon was also found in MDR-TB strains isolated in the 1990s. Also investigated was the resistance level conferred by eis G-10A mutations, revealing that eis G-10A mutations may result in amikacin resistance undetectable by widely used phenotypic assays. CONCLUSIONS The analysis of the distribution of the mutations found by genetic clustering showed that in the Q1 cluster, two mutations, gyrA D94A and rrs A1401G, were enough to ensure development of XDR-TB from an MDR strain. Moreover, in the Lisboa3 cluster it was possible to elaborate a model in which the development of low-level kanamycin resistance was at the origin of the emergence of XDR-TB strains that can be discriminated by tlyA mutations.