Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Methods for the Modelling of Label-Free Shotgun Proteomic Data in Cell Line Biomarker Discovery

In this work it has been developed and implemented a data analysis pipeline for the discovery of biomarkers by high throughput shotgun proteomics. Specifically the solution has been optimized for the analysis of secretomes of tumor cell lines by label-free LC-MS/MS, with proteins quantified by peptide spectral counts. Along the development it has been shown the incidence and relevance of batch effects in the comparative analysis of label-free proteomics by LC-MS/MS. Also the features providing reproducibility to potential biomarkers have been identified. The model has been developed on empirical data obtained from a series of spiked experiments, and with the help of simulations to evaluate its performance. The pipeline comprises an exploratory data analysis (EDA) R/Bioconductor package, msmsEDA, based on multidimensional analysis tools and a R/Bioconductor inference package, msmsTests, based on generalized linear models (GLM) with Poisson or negative binomial distributions, or the quasi-likelihood GLM extension. Two graphical interfaces have also been produced to ease the use of the provided solution in a MS lab by non experts, and are freely available at GitHub. The designed model is devised to discover differentially expressed proteins in tumor cell line secretomes, using the cell as the unit of interest. The model allows blocking factors as a mean for batch effects correction. The normalization to cell units is embedded in the model through the use of offsets, and no previous data treatment is required. The two packages developed, msmsEDA and msmsTests, allow for: • Dataset quality assessment. • The identification of outliers • The identification of confounding factors or batch effects. • The discovery of potential biomarkers by using the distribution best fitting the available data. • The improvement of reproducibility by a post test filter based of effect size and signal levels. Different papers have been published in peer-reviewed proteomics journals develo-ping each data treatment step, and demonstrating its use and value in biological experiments carried out in the Tumor Biomarker lab at VHIO.
Pengaruh ekstrak goldenfish pada umpan bubu dasar terhadap hasil tangkapan ikan-ikan karang

Bubu dasar merupakan salah satu alat tangkap yang umum digunakan oleh masyarakat nelayan untuk menangkap ikan-ikan karang, karena konstruksinya sederhana, relatif murah dan mudah dioperasikan dengan kapal atau perahu ukuran kecil. Keberhasilan alat tangkap berumpan sangat ditentukan oleh aktivitas hidup ikan dalam hal mencari dan menangkap makanan. Pemberian ekstrak goldenfish pada umpan, diduga dapat meningkatkan kemampuan tangkap dari bubu dasar. Namun informasi ilmiah seperti ini belum banyak tersedia. Oleh karena itu, penelitian ini bertujuan untuk mempelajari pengaruh pemberian ekstrak goldenfish pada umpan bubu terhadap hasil tangkapan ikan-ikan karang; dan mengidentifikasi jenis-jenis ikan yang tertangkap. Penelitian ini dikerjakan di perairan pantai Kampung Bira, Kecamatan Tabukan Tengah, Kapupaten Kepulauan Sangihe; didasarkan pada metode eksperimental. Enam unit bubu bambu dioperasikan selama sembilan trip untuk mengumpulkan data; dimana tiga unit menggunakan umpan malalugis yang disuntikan dengan ekstrak goldenfish; dan tiga unit lainnya menggunakan umpan malalugis tanpa ekstrak goldenfish; dan data tangkapan dinalisis dengan uji t. Hasil tangkapan bubu selama penelitian berjumlah 176 ekor, sebanyak124 ekor tertangkap dengan umpan berekstrak dan 52 ekor tertangkap dengan umpan bubu tanpa ekstrak. Analisis uji t menunjukkan bahwa bahwa penggunaan umpan berekstrak pada bubu memberikan hasil tangkapan yang nyata lebih baik dibandingkan dengan umpan tanpa ekstrak pada bubu. Kata-kata kunci: bubu dasar, ekstrak goldenfish, umpan, ikan karang
Studies on System Analysis and Synthesis by Markov Renewal Processes

System analysis and synthesis by Markov renewal processes (which include renewal processes and discrete • time Markov chains as special cases) are discussed in this thesis. ' tt ReliabUity analysis of redundant systems of repairabLe units are considered and the Lapaiace-Stieltjes ' transforms of the time distributions to first syStem down are obtained. Signai f'lo.w graph rnethod of obtaining the Lapaice--Stieltjes trabsforms by usi,ng Masbn's gain formuia is aiso presented. A standby redundant repairable system with preventive maintenance is also ' presented. ' Markovian decision processeMs" and Markov renewal ' pnograrns are diseussed as system sYnthesis. In MarkQvian decision processes the )dliey iteration 'and iinear Pnogrammi.ng a.lgorithms for the discounted and , the nondis6ounted modeis ave discussed and the relationship betueen the two qlgorithms is also diseussed. ''X' A new a.lgorithm is proposed fi? om the relationship. ' Numerical e'xampies and'comparison tiiith the three algorithms just mentioned above are presented for Markovian deeision proeesses. The similar diseussions are made for Markov renewai pnograms. '
Effects of Dependents and Own Sex on Planning for and Thinking about One's Death

We investigated whether an extended sense of self based on having dependents or being socialized into an emotional caretaker (woman's) role would lead to planning for and thinking about one's dying and death more frequently and with less denial. 169 young adult men and women anonymously answered the denial questionnaire of Westman, Canter, and Boitos, reported whether they had dependents, wills, arranged for disposition of their bodies, and indicated how frequently they thought about their own death and what led them to think or not think about it. As hypothesized, young adults with dependents and women regardless of whether they had dependents were more likely to have wills and have arranged for disposition of their bodies. However, contrary to expectation, they were not less likely to deny their own dying. Having dependents or being female correlated for young adults with concrete behaviors concerning, but not with a corresponding change in attitude toward, their own dying or death. The more frequent reasons for their thinking or not thinking about death also are reported.
An exploration of novice compilation behaviour in BlueJ

Our research explores the process by which beginning programmers go about writing programs. We have focused our explorations on what we call compilation behaviour: the programming behaviour a student engages in while repeatedly editing and compiling their programs in an attempt to make them syntactically, if not semantically, correct. The students whose behaviour we have observed were engaged in learning to program in an objects-first style using BlueJ, an environment designed for supporting novice programmers just starting out with the Java programming language. The significant results of our work are two-fold. First, we have developed tools for visualising the process by which students write their programs. Using these tools, we can quickly obtain valuable information about their process, and use that information to inform further research regarding their behaviour, or apply it immediately in a classroom context to better support the struggling learner. Second, we have proposed a quantification of novice compilation behavior which we call the error quotient. Using this metric, we can determine how well (or poorly) a student fares with syntax errors while learning to program. This quantity, like our tools for visualisation, provides a powerful indicator for how much or little a student is struggling with the language while programming, and correlates significantly with traditional indicators for academic progress.
Management Aspects of Software Clone Detection and Analysis

Copying a code fragment and reusing it by pasting with or without minor modifications is a common practice in software development for improved productivity. As a result, software systems often have similar segments of code, called software clones or code clones. Due to many reasons, unintentional clones may also appear in the source code without awareness of the developer. Studies report that significant fractions (5% to 50%) of the code in typical software systems are cloned. Although code cloning may increase initial productivity, it may cause fault propagation, inflate the code base and increase maintenance overhead. Thus, it is believed that code clones should be identified and carefully managed. This Ph.D. thesis contributes in clone management with techniques realized into tools and large-scale in-depth analyses of clones to inform clone management in devising effective techniques and strategies. To support proactive clone management, we have developed a clone detector as a plug-in to the Eclipse IDE. For clone detection, we used a hybrid approach that combines the strength of both parser-based and text-based techniques. To capture clones that are similar but not exact duplicates, we adopted a novel approach that applies a suffix-tree-based k-difference hybrid algorithm, borrowed from the area of computational biology. Instead of targeting all clones from the entire code base, our tool aids clone-aware development by allowing focused search for clones of any code fragment of the developer’s interest. A good understanding on the code cloning phenomenon is a prerequisite to devise efficient clone management strategies. The second phase of the thesis includes large-scale empirical studies on the characteristics (e.g., proportion, types of similarity, change patterns) of code clones in evolving software systems. Applying statistical techniques, we also made fairly accurate forecast on the proportion of code clones in the future versions of software projects. The outcome of these studies expose useful insights into the characteristics of evolving clones and their management implications. Upon identification of the code clones, their management often necessitates careful refactoring, which is dealt with at the third phase of the thesis. Given a large number of clones, it is difficult to optimally decide what to refactor and what not, especially when there are dependencies among clones and the objective remains the minimization of refactoring efforts and risks while maximizing benefits. In this regard, we developed a novel clone refactoring scheduler that applies a constraint programming approach. We also introduced a novel effort model for the estimation of efforts needed to refactor clones in source code. We evaluated our clone detector, scheduler and effort model through comparative empirical studies and user studies. Finally, based on our experience and in-depth analysis of the present state of the art, we expose avenues for further research and development towards a versatile clone management system that we envision.
SPSS Programming And Data Management: A Guide For SPSS And SAS Users

Data Analytics Tool Comparison: Excel, SPSS and SAS tools we discuss, SAS is more programming-oriented while Excel and SPSS are based on interactive. To start the download or read Spss Programming And Data Management: A Guide for Spss And Sas Users you must register. Start your FREE month! SPSS Programming and Data Management, 3rd Edition A Guide for SPSS and SAS® Users Raynald Levesque and SPSS Inc. Read Online Download.
Puisi Syauqi dalam pendidikan beriman dan bernegara

Buku ini berjudul “Puisi Syauqi Dalam Pendidikan Beriman Dan Bernegara”. Ditulis penulis karena memperhitungkan berbagai tuntutan mahasiswa dan masyarakat peminat sastra. Sastra mempunyai berbagai bentuk; misalnya prosa, puisi, drama, pidato, hikmah, kata mutiara, dll. Penulis memilih puisi yang muatannya sarat dengan pesan dan kesan. Puisi Syauqi saat ini dipilih yang berkaitan dengan iman & patriotism bernegara, mengingat hubungan erat hubungan akhir akhir ni agak pudar untuk itu perlu dipelajari ulang, Karena arah globalisasi & modernisasi, yang kadang membingungkan. Inilah puisi Syauqi dianalisis sebagai pedoman bagi pejuang, patriotism sejati dalam menuju sukses mencapai cita-cita beriman & bernegara. Semoga buku ini berguna bagi setiap peminatnya. Dan saran/kritik diharapkan sebagai tulisan selanjutnya, terimakasih.
SMP and embedded real-time

With the advent of multithreaded/multicore CPUs, even embedded real-time applications are starting to run on SMP systems -for example, both the Xbox 360 and PS/3 are multithreaded, and there even have been SMP ARM processors! As this trend continues, there will be an increasing need for real-time response from SMP systems. Because not all embedded systems vendors will be willing or able to create or purchase SMP real-time operating systems, we can expect that a number of them will make use of Linux. Because of this change, a number of real-time tenets have now become myths. This article exposes these myths and then discusses some of the challenges that Linux is surmounting in order to meet the needs of this new SMP-real-time-embedded world.
XML Path Language (XPath) Version 1.0

XPath is a language for addressing parts of an XML document, designed to be used by both XSLT and XPointer. Status of this document This document has been reviewed by W3C Members and other interested parties and has been endorsed by the Director as a W3C Recommendation. It is a stable document and may be used as reference material or cited as a normative reference from other documents. W3C's role in making the Recommendation is to draw attention to the specification and to promote its widespread deployment. This enhances the functionality and interoperability of the Web. XML Path Language (XPath) http://www.w3.org/TR/1999/REC-xpath-19991116 (1 of 30) [7/19/2001 5:31:03 PM] The list of known errors in this specification is available at http://www.w3.org/1999/11/REC-xpath-19991116-errata. Comments on this specification may be sent to www-xpath-comments@w3.org; archives of the comments are available. The English version of this specification is the only normative version. However, for translations of this document, see http://www.w3.org/Style/XSL/translations.html. A list of current W3C Recommendations and other technical documents can be found at http://www.w3.org/TR. This specification is joint work of the XSL Working Group and the XML Linking Working Group and so is part of the W3C Style activity and of the W3C XML activity.
Simulation of load balancing algorithms for discrete event simulations

Efficiently simulating discrete-event models in a parallel and distributed manner is a challenging endeavour. On one hand, various factors, such as hardware infrastructure or model characteristics, have to be considered. On the other hand, there is a wide variety of algorithms which address subproblems of parallel and distributed simulation and whose performance depends on the application at hand. This work illustrates the resulting difficulties with respect to the development of parallel and distributed simulation systems for general purposes. It is reasoned to what extent a prior analysis could facilitate this task. Approaches to predict the performance of parallel and distributed simulation systems are discussed. It is argued that the simulation of such a simulation system is a feasible approach. This claim is underpinned by implementing SimSim, a sequential simulator to simulate parallel and distributed simulation systems. Then, SimSim is used to develop a load balancing algorithm for the simulation of PDEVS models. The algorithm’s performance is analysed using SimSim. Finally, the predicted performance is compared to the real performance of the algorithm when running in the simulation system James II.
On the Preliminary Adaptive Random Testing of Aspect-Oriented Programs

Adaptive random testing (ART) is a new family of random-based test data generation and selection strategies that enhances the effectiveness of tests over the classical random testing (RT). ART has been widely investigated and studied in numerous research papers over the recent years. These studies have included proposing various techniques for implementing and improving the intuition behind ART (evenly spread of test cases over the input domain, measured by some distance measures) generally for procedural programs with numerical input domain and most recently object-oriented programs. However, there is currently no work available in the literature that discusses the applicability of ART to aspect-oriented programming (AOP), as it is gaining popularity in software development. Inspired by this, this paper aims to investigate the possible ways that ART can be applied to AOP. This investigation focuses on a multi-perspective analysis of the current ART-based techniques. In this respect, we identified three related perspectives based on the current state of art in the area of ART. Each perspective was analyzed in terms of its applicability and possibility for aspect-oriented programs, particularly its constituent distance measure. As a result, our study gives rise to some interesting points and outlines a number of potential research directions in applying ART to AOP. This can pave the way for efficient development on applying of ART to AOP and finally AOP success.
A Study of the Use of Conjunctions across Grades and Ethnic Groups. Technical Report No. 158.

This study examines children's use of conjunctions. Three major issues are addressed: linguistic complexity, developmental differences, and ethnic differences. The participants in the study third, sixth, and ninth graders were of Anglo, Black, and Hispanic ethnicity. They completed sentence fragments ending in the conjunctions and, but, because, and even though. These conjunctions can be paired, and-but and because-even though, where the second member of each pair is basically the negative of the first. Scores based on the authors' judgments of the appropriateness of the sentence completions indicate that the positive member of each pair was easier than the negative one; the complete order of difficulty for the four conjunctions was because < and < but < even though. The order of difficulty was constant across grades and ethnic groups. For all ethnic groups there was improvement in the use of conjunctions between third and ninth grade. However, the grade by which effective mastery of each conjunction was reached differed for the three ethnic groups, being in general earliest for Anglos and latest for Hispanics. For all groups correct use of conjunctions was correlated with reading comprehension. One of the most important educational issues in the U.S. today centers around the poor literacy skills of non-mainstream children. In an attempt to discover the source of the problem, many researchers have employed contrastive analysis, comparing the child's first dialect or language with Standard English, noting points of difference, and then attempting to demonstrate the effects of interference from the home dialect or language on developing literacy in Standard English. These endeavors have met with mixed success. Although in some instances contrastive analyses have been able to account for points of difficulty for the child (e.g., Labov, 1970; Hall & Turner, 1972; Barrera, 1978), in many other cases no interference has been found (e.g., Schaaf, 1971; Nolen, 1972; Hockman, 1973; Flores, 1982). Consequently, it appears improbable that differences between home and school language per se are a major source of difficulty. The work of Hess and Shipman (1965) and Bernstein (1962, 1970) among others suggests that The research reported herein was supported in part by the National Institute of Education under Contract No. US-NIE-C-400-76-0116. Research in the Teaching of English, Vol. 19, No. 3, October 1985
Usage of the MELDEX Digital Music Library

Online Digital Music Libraries are becoming increasing common and more sophisticated; however, availability of information on how users access and navigate these resources is limited. This type of information is crucial for improving user interface design and for providing users with better supported services. Here we present an analysis of the logs for our digital music library, Meldex, for a 1 year period to discover patterns of usage.
Towards an Operational Semantics of Verilog

The mission of UNU/IIST is to assist developing countries in the application and development of software technology. UNU/IIST contributes through its programmatic activities: 1. advanced development projects in which software techniques supported by tools are applied, 2. research projects in which new techniques for software development are investigated, 3. curriculum development projects in which courses of software technology for universities in developing countries are developed, 4. courses which typically teach advanced software development techniques, 5. events in which conferences and workshops are organised or supported by UNU/IIST, and 6. dissemination, in which UNU/IIST regularly distributes to developing countries information on international progress of software technology. Fellows, who are young scientists and engineers from developing countries, are invited to actively participate in all these projects. By doing the projects they are trained. At present, the technical focus of UNU/IIST is on formal methods for software development. UNU/IIST is an internationally recognised center in the area of formal methods. However, no software technique is universally applicable. We are prepared to choose complementary techniques for our projects, if necessary. UNU/IIST produces a report series. Reports are either Research R , Technical T , Compendia C or Administrative A. They are records of UNU/IIST activities and research and development achievements. Many of the reports are also published in conference proceedings and journals. Abstract We give an operational semantics of simple version of Verilog hardware description language.
The Basics of MRI

A system for controlling ambient temperature having a valve that adjusts the amount of fluid flow is disclosed. The valve includes a chamber containing thermal-expansive material and a piston which moves outwardly from the chamber to retard fluid flow when the thermal-expansive material is heated. The valve further includes a heater for heating the thermal-expansive material and a thermistor disposed in close thermal-relationship with the heater. Because of this close thermal-relationship, the resistance of the thermistor quickly changes in response to temperature changes in the heater. Since the thermistor is part of an electrical circuit for energizing or de-energizing the heater, ambient temperature is controlled. The system also includes a safety switch for de-energizing the heater in the event an open-circuit appears across the thermistor and is further adapted to control ambient temperature whether the fluid flow consists of hot or cold water.
Neuronal Processing of Affective Environmental Sounds : a 128 Channel EEG-Study

2 There can be no knowledge without emotion. We may be aware of a truth, yet until we have felt its force, it is not ours. To the cognition of the brain must be added the experience of the soul.DANK First I want to thank Mrs. Margaret Bradley and Mrs. Brigitte Rockstroh for giving their experts opinion to my work, I am also grateful for the knowledge they gave me during their lectures. I was glad to have some helping hands and brains around me during the study, there always was advice, helpful comments, interesting ideas and a very nice working atmosphere provided by