Miracle-dz/UniFAR-FTUs huggingface dataset:
A wavelet-based filtering approach to functional bipartite ranking

It is the purpose of this paper to investigate the bipartite ranking task from the perspective of functional data analysis (FDA). Precisely, given a collection of independent copies of a (possibly sampled) random curve X = (X(t))t∊[0,1] taking its values in a function space X, with a locally smooth autocorrelation structure and to which a binary label Y ∊ {−1, +1} is randomly assigned, the goal is to learn a scoring functions: X → R with optimal ROC curve. Based on nonlinear wavelet-based approximation, it is shown how to select compact finite dimensional representations of the input curves in order to build accurate ranking rules, using recent advances in the ranking problem for multivariate data with binary feedback.
Multi-Block Joint Optimization for the Peak-to-Average Power Ratio Reduction of FBMC-OQAM Signals

Recently, the filter bank multicarrier with offset quadrature amplitude modulation (FBMC-OQAM) has attracted increasing attention. However, most peak-to-average power ratio (PAPR) reduction schemes developed for orthogonal frequency division multiplexing (OFDM) signals are not effective for FBMC-OQAM signals, due to the overlapping structure of FBMC-OQAM signals. In this paper, we propose an improved partial transmit sequence (PTS) scheme by employing multi-block joint optimization (MBJO) for the PAPR reduction of FBMC-OQAM signals, called as MBJO-PTS scheme. In PTS scheme, one data block is divided into several subblocks and each subblock is multiplied by a phase rotation factor for the subblock. The PTS scheme searches over all combinations of allowed phase factors to lower the PAPR. Unlike existing PAPR reduction schemes of independently optimizing the data blocks, the MBJO-based scheme exploits the overlapping structure of the FBMC-OQAM signal and jointly optimizes multiple data blocks. Moreover, we develop two algorithms for the optimization problem in the MBJO-PTS scheme, including a dynamic programming (DP) algorithm to guarantee the optimal solution and avoid exhaustive search. Theoretical analysis and simulations show that the proposed MBJO-PTS scheme could provide a significant PAPR reduction in the FBMC-OQAM system, by exploiting the overlapping structure of the FBMC-OQAM signal. Employing the proposed DP algorithm, the FBMC-OQAM system with the proposed MBJO-PTS scheme even outperforms the OFDM system with the conventional PTS scheme by 0.9 dB at CCDF of 10-3 in PAPR reduction, under the same number of subcarriers, modulation type and PTS parameters given in Section V.
Classifying SSH encrypted traffic with minimum packet header features using genetic programming

The classification of Encrypted Traffic, namely Secure Shell (SSH), on the fly from network TCP traffic represents a particularly challenging application domain for machine learning. Solutions should ideally be both simple - therefore efficient to deploy - and accurate. Recent advances to teambased Genetic Programming provide the opportunity to decompose the original problem into a subset of classifiers with non-overlapping behaviors, in effect providing further insight into the problem domain and increasing the throughput of solutions. Thus, in this work we have investigated the identification of SSH encrypted traffic based on packet header features without using IP addresses, port numbers and payload data. Evaluation of C4.5 and AdaBoost - representing current best practice - against the Symbiotic Bid-based (SBB) paradigm of team-based Genetic Programming (GP) under data sets common and independent from the training condition indicates that SBB based GP solutions are capable of providing simpler solutions without sacrificing accuracy.
Model-based analysis of N-glycosylation in Chinese hamster ovary cells

The Chinese hamster ovary (CHO) cell is the gold standard for manufacturing of glycosylated recombinant proteins for production of biotherapeutics. The similarity of its glycosylation patterns to the human versions enable the products of this cell line favorable pharmacokinetic properties and lower likelihood of causing immunogenic responses. Because glycan structures are the product of the concerted action of intracellular enzymes, it is difficult to predict a priori how the effects of genetic manipulations alter glycan structures of cells and therapeutic properties. For that reason, quantitative models able to predict glycosylation have emerged as promising tools to deal with the complexity of glycosylation processing. For example, an earlier version of the same model used in this study was used by others to successfully predict changes in enzyme activities that could produce a desired change in glycan structure. In this study we utilize an updated version of this model to provide a comprehensive analysis of N-glycosylation in ten Chinese hamster ovary (CHO) cell lines that include a wild type parent and nine mutants of CHO, through interpretation of previously published mass spectrometry data. The updated N-glycosylation mathematical model contains up to 50,605 glycan structures. Adjusting the enzyme activities in this model to match N-glycan mass spectra produces detailed predictions of the glycosylation process, enzyme activity profiles and complete glycosylation profiles of each of the cell lines. These profiles are consistent with biochemical and genetic data reported previously. The model-based results also predict glycosylation features of the cell lines not previously published, indicating more complex changes in glycosylation enzyme activities than just those resulting directly from gene mutations. The model predicts that the CHO cell lines possess regulatory mechanisms that allow them to adjust glycosylation enzyme activities to mitigate side effects of the primary loss or gain of glycosylation function known to exist in these mutant cell lines. Quantitative models of CHO cell glycosylation have the potential for predicting how glycoengineering manipulations might affect glycoform distributions to improve the therapeutic performance of glycoprotein products.
AZF1 Is a Glucose-Dependent Positive Regulator of CLN3 Transcription in Saccharomyces cerevisiae

ABSTRACT Transcription of the CLN3 G1 cyclin in Saccharomyces cerevisiae is positively regulated by glucose in a process that involves a set of DNA elements with the sequence AAGAAAAA (A2GA5). To identify proteins that interact with these elements, we used a 1-hybrid approach, which yielded a nuclear zinc finger protein previously identified as Azf1. Gel shift and chromatin immunoprecipitation experiments show that Azf1 binds to the A2GA5 CLN3 regulatory sequences in vitro and in vivo, thus identifying a transcriptional regulatory protein for CLN3 and a DNA sequence target for Azf1. We show that glucose-induced expression of a reporter gene driven by the A2GA5 CLN3 regulatory sequences is dependent upon the presence of AZF1. Furthermore, deletion of AZF1 markedly reduces the transcriptional induction of CLN3 by glucose. In addition, Azf1 can induce reporter expression in a glucose-specific manner when artificially tethered to a promoter via the DNA-binding domain from Gal4. We conclude that AZF1 is a glucose-dependent transcription factor that interacts with the CLN3 A2GA5 repeats to play a positive role in the regulation of CLN3 mRNA expression by glucose.
Training an integrated sentence planner on user dialogue

An appealing methodology for natural language generation in dialogue systems is to train the system to match a target corpus. We show how users can provide such a corpus as a natural side effect of interacting with a prototype system, when the system uses mixed-initiative interaction and a reversible architecture to cover a domain familiar to users. We experiment with integrated problems of sentence planning and realization in a referential communication task. Our model learns general and context-sensitive patterns to choose descriptive content, vocabulary, syntax and function words, and improves string match with user utterances to 85.8% from a handcrafted baseline of 54.4%.
Implementing a heavy hitter detection on the NetFPGA OpenFlow switch

Heavy hitter detection is an important task in many network security and traffic measurement applications. In this work, we implement a heavy hitter detection accelerator based on the Count-Min sketch algorithm inside the NetFPGA-10G OpenFlow switch. By using only a small amount of extra memory and logic resources, the OpenFlow switch is capable of detecting the heavy hitter flows accurately without the intervention of the host CPU and the OpenFlow controller. The sketch data structure and identified heavy hitter list can be sent to the controller for further advanced processing.
Multigene Families in Trypanosoma cruzi and Their Role in Infectivity

ABSTRACT The Trypanosoma cruzi genome contains the most widely expanded content (∼12,000 genes) of the trypanosomatids sequenced to date. This expansion is reflected in the high number of repetitive sequences and particularly in the large quantity of genes that make up its multigene families. Recently it was discovered that the contents of these families vary between phylogenetically unrelated strains. We review the basic characteristics of trans-sialidases and mucins as part of the mechanisms of immune evasion of T. cruzi and as ligands and factors involved in the cross talk between the host cell and the parasite. We also show recently published data describing two new multigene families, DGF-1 and MASP, that form an important part of the scenario representing the complex biology of T. cruzi.
Diffraction gratings for neutrons from polymers and holographic polymer-dispersed liquid crystals

We discuss the applicability of holographically recorded gratings in photopolymers and holographic polymer-dispersed liquid crystals as neutron optical elements. An experimental investigation of their properties for light and neutrons with different grating spacings and grating thicknesses is performed. The angular dependences of the diffraction efficiencies for those gratings are interpreted in terms of a rigorous coupled wave analysis. Starting from the obtained results we work out the lines for the production of an optimized neutron optical diffraction grating, i.e. high diffraction efficiency in the Bragg diffraction regime with moderate angular selectivity.
Role Play: Theory and Practice

Introduction An Epistemological Context for the Use of Role Play An Overview of Current Role Play Practice Role Play Practice Today Focusing Specifically on Technique Reflections upon Extant Definitions of Role Play Redefining Role Play and General Methodological and Technical Considerations On Involvement, Engagement and Technique in Role Plays Conceptual Underpinnings of Three Key Induction Principles Overview of Practical Implications for Good Induction Practical Overview of Induction Principles Afterword Concluding Remarks
The metalloproteinase ADAM‐12 regulates bronchial epithelial cell proliferation and apoptosis

Abstract. Objectives: The ADAMs (a disintegrin and metalloproteinase) enzymes compose a family of membrane‐bound proteins characterized by their multi‐domain structure and ADAM‐12 expression is elevated in human non‐small cell lung cancers. The aim of this study was to investigate the roles played by ADAM‐12 in critical steps of bronchial cell transformation during carcinogenesis. Materials and methods: To assess the role of ADAM‐12 in tumorigenicity, BEAS‐2B cells were transfected with a plasmid encoding human full‐length ADAM‐12 cDNA, and then the effects of ADAM‐12 overexpression on cell behaviour were explored. Treatment of clones with heparin‐binding epidermal growth factor (EGF)‐like growth factor (HB‐EGF) neutralizing antibodies as well as an EGFR inhibitor allowed the dissection of mechanisms regulating cell proliferation and apoptosis. Results: Overexpression of ADAM‐12 in BEAS‐2B cells promoted cell proliferation. ADAM‐12 overexpressing clones produced higher quantities of HB‐EGF in their culture medium which may rely on membrane‐bound HB‐EGF shedding by ADAM‐12. Targeting HB‐EGF activity with a neutralizing antibody abrogated enhanced cell proliferation in the ADAM‐12 overexpressing clones. In sharp contrast, targeting of amphiregulin, EGF or transforming growth factor‐α failed to influence cell proliferation; moreover, ADAM‐12 transfectants were resistant to etoposide‐induced apoptosis and the use of a neutralizing antibody against HB‐EGF activity restored rates of apoptosis to be similar to controls.Conclusions: ADAM‐12 contributes to enhancing HB‐EGF shedding from plasma membranes leading to increased cell proliferation and reduced apoptosis in this bronchial epithelial cell line.
Generic Object Detection using AdaBoost

Boosting has been shown to be an effective technique for face detection. This paper explores the implementation of a real-time object detection system as described by Viola and Jones. The system is initially tested on the problem of face detection and then applied to the problem of aircraft detection. Initial results show that detecting aircraft with high accuracy comes at the cost of many false detections. Reducing the number of false positives requires more training and possibly more complex classifiers.
Ratio-based decisions and the quantitative analysis of cDNA microarray images.

Gene expression can be quantitatively analyzed by hybridizing fluor-tagged mRNA to targets on a cDNA micro-array. Comparison of gene expression levels arising from co-hybridized samples is achieved by taking ratios of average expression levels for individual genes. In an image-processing phase, a method of image segmentation identifies cDNA target sites in a cDNA micro-array image. The resulting cDNA target sites are analyzed based on a hypothesis test and confidence interval to quantify the significance of observed differences in expression ratios. In particular, the probability density of the ratio and the maximum-likelihood estimator for the distribution are derived, and an iterative procedure for signal calibration is developed.
The Extensive Challenges of Internet Application Measurement

The Internet has grown dramatically and evolved significantly over the past 10 years. Although this growth provides new opportunities and many value-added services for millions of Internet users, this growth also presents ongoing challenges to networking researchers, for whom the study of the Internet itself is the raison d'etre. Other than the network link speed, there are many technical challenges that make the monitoring of Internet applications difficult. To illustrate this point, this article presents several practical examples drawn from our experiences in Internet application measurement and monitoring
Long-term secular trend of skeletal maturation of Taiwanese children between agricultural (1960s) and contemporary (after 2000s) generations using the Tanner-Whitehouse 3 (TW3) method

Abstract Background: The Tanner-Whitehouse (TW) method is one of the well-known techniques in determining the bone age. Objective: According to the objectivity of TW3, the secular trend was investigated to discover whether the skeletal maturation of Taiwanese children between two generations was different. Subjects and methods: The large-scale database of Taiwan was collected. The first group, called mid-1960s, included 265 boys and 295 girls in the agricultural generation (between 1966 and 1967). The second group, called mid-2000s, includes 114 boys and 616 girls in the contemporary generation (after 2000s). The bone age was determined by three radiologists using the carpals-only system of the TW3 method and by two physicians using the Greulich and Pyle method. A comparison of the means (independent-samples t-test) was applied by examining the difference of the children’s skeletal maturation between the two generations in the same chronological age. The significant difference was considered while the p-value was 0.05 or less (95% confidence interval). Results: A significant difference of the mean bone age (by, on average, three radiologists using the TW3 method) between the mid-1960s and mid-2000s in the same gender and chronological age was presented by the independent-samples t-test (p<0.001 with 95% confidence interval), and the bone age, determined by the TW3 method, of the mid-2000s group was higher than that of the mid-1960s group. This scenario corresponded with the children’s bone age determined by pediatricians. Besides, it deserved to notice that the bone age of boys in the mid-2000s was larger than that of the girls in the mid-1960s. Furthermore, by comparing the environmental condition, we suspect that the difference of bone age of children between the two generations was attributed to the discrepancy in nutrition and socioeconomic variation during the four decades in Taiwan. Conclusion: The study presents that the secular trend of skeletal maturation of children in the mid-2000s is faster than that in the mid-1960s.
Distributed control for an anthropomimetic robot

Major progress in robotics turns today's humanoid robots into ever safer, more robust, and more agile agents by the moment. However, it is still a long way until robots can safely operate in open environments. Especially in the area of service robotics, the need arises for robots to work flexibly in a human centered environment. One way towards this goal is to incorporate more and more of the mechanisms that can be found in humans for our robots. In this work we would like to propose a bio-inspired control architecture for an equally bio-inspired — namely anthropomimetic — humanoid robot. To achieve this, the human motor control system is analyzed and copied at a structural level. This results in a distributed control infrastructure that is capable of reducing the complexity of the control task by off-loading parts of the control problem into the robot's limbs. Finally, we will prove the fact that it is possible to control an anthropomimetic robot with a large number of degrees of freedom with the proposed control architecture.
Bioeffects of Low‐Intensity Ultrasound In Vitro

Objective. The purpose of this study was to evaluate the potential molecular mechanism of low‐intensity ultrasound‐induced apoptosis by analyzing protein profile alteration in response to ultrasound exposure. Methods. Human hepatocarcinoma SMMC‐7721 cells were used in this study. Cell viability was measured by a trypan blue dye exclusion test. Morphologic changes were examined by light microscopy. Apoptosis was assessed by phosphatidylserine externalization and DNA fragmentation. The pattern of the mitochondrial membrane potential decrease was determined by flow cytometry. Protein profile alteration was analyzed by comparative proteomics based on 2‐dimensional polyacrylamide gel electrophoresis and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. Results. Low‐intensity ultrasound (3.0 W/cm2, 1 minute, cells incubated for 6 hours after ultrasound exposure) induced early apoptosis (mean ± SD, 26.5% ± 6.2%) significantly (P < .05) with minimal lysis in human hepatocarcinoma cells in vitro. On a molecular level, several proteins, eg, cellular tumor antigen protein 53, BH3‐interacting domain death agonist, apoptosis regulator Bcl‐2, and heme oxygenase 1 were identified as responding to ultrasound irradiation, suggesting that mitochondrial dysfunction and oxidative stresses were involved in ultrasound‐induced apoptosis. It was also assumed that mitofilin‐regulated crista remodeling may be a potential channel of mitochondrial membrane permeabilization pore formation involved in low‐intensity ultrasound‐induced apoptosis. Conclusions. This study suggests that 2 potential molecular signaling pathways are involved in ultrasound‐induced apoptosis. It is a first step toward low‐intensity ultrasound‐induced apoptotic cancer therapy via understanding its relevant molecular signaling and key proteins.
Meta -analysis of mathematics instruction with young children

by Elena V. Malofeeva A meta-analytic methodology was used to synthesize 29 intervention studies in the area of mathematics conducted from 1977 to 2003 with preschool or kindergarten children. A total of 1845 students were identified as participants in these 29 studies. On average, the mean weighted effect size for the difference between the experimental and control groups was . 467. A combination of direct and guided instruction was the most beneficial instructional approach followed by guided instruction. In addition, interventions including controlling task difficulty, additional explanations provided about taught concepts, sequencing activities, and small group games showed larger effect sizes than interventions not including these techniques. The magnitude of mean weighted effect size was lower for skill-specific than for
Asking questions: information needs in a surgical intensive care unit

Even in the information-rich environment of hospitals, health-care providers face challenges in addressing their various information needs. Through a study of a patient-care team in a tertiary care Surgical Intensive Care Unit (SICU), we expanded our understanding of health-care providers' information needs in two important ways. First, the study focused on a patient-care team instead of individual health-care providers. Second, information needs were examined in a particular organizational setting, the SICU, which had not been previously studied. We found that organizational information was extremely important to SICU team members. Furthermore, the first resource that team members utilized was not electronic or paper but rather human: another team member.
The Impact of Structured Writing and Developing Awareness of Learning Preferences on the Performance and Attitudes of Engineering Teams

This paper discusses efforts to develop metacognition in teams of engineering students by: first, exploring personal learning patterns, and second, ongoing biweekly journaling exercises. Thirtythree junior and senior engineering students (30 chemical engineer, one each from mechanical, civil and electrical) working on semester-long projects in the Rowan Engineering Clinics were broken into four groups. Members of the first determined their learning patterns by taking the Learning Connections Inventory (LCI) then met with faculty advisors to discuss their patterns and those of their teammates. The second group performed structured writing assignments focusing on team dynamics and logistical barriers to success. The third received both LCI instruction and the writing assignments, while the fourth received neither. Students who received instruction on their own learning patterns as well as those of their teammates performed better on semesterlong team projects and reported a significant improvement in their attitude towards teaming skills. Structured writing assignments focusing on team dynamics also seemed to benefit performance, but were less popular with the students.
The Implementation, Deployment and Evaluation of a Mobile Personal Learning Environment

The application of ICT to learning, the Web 2.0 trends and the widespread use of technologies such as mobile devices make it necessary to provide new solutions to satisfy the needs of learners. Such solutions should treat the students as the centre of the learning process. The students should be able to decide which tools they will use to learn, and the learning institution must consider the behaviour of students in such personal learning activities independently of the location where learning activities are carried out. In addition, learners can choose the type of devices they will use with special attention to mobile technologies. The work described in this paper proposes a service-based approach to defining mobile personal learning environments that facilitates communication with institutional learning platforms. Such an approach is implemented as a proof-of-concept and evaluated via a pilot study to demonstrate that such types of mobile learning platforms are feasible and can increase students' motivation to help them learn.