Miracle-dz/UniFAR-FTUs huggingface dataset:
Mario. A system for iterative and interactive processing of biological data

This thesis address challenges in metagenomic data processing on clusters of computers; in particular the need for interactive response times during development, debugging and tuning of data processing pipelines. Typical metagenomics pipelines batch process data, and have execution times ranging from hours to months, making configuration and tuning time consuming and impractical. We have analyzed the data usage of metagenomic pipelines, including a visualization frontend, to develop an approach that use an online, data-parallel processing model, where changes in the pipeline configuration are quickly reflected in updated pipeline output available to the user. We describe the design and implementation of the Mario system that realizes the approach. Mario is a distributed system built on top of the HBase storage system, that provide data processing using commonly used bioinformatics applications, interactive tuning, automatic parallelization and data provenance support. We evaluate Mario and its underlying storage system, HBase, using a benchmark developed to simulate I/O loads that are representative for biological data processing. The results show that Mario adds less than 100 milliseconds to the end-to-end latency of processing one item of data. This low latency, combined with Mario’s storage of all intermediate data generated by the processing, enables easy parameter tuning. In addition to improved interactivity, Mario also offer integrated data provenance, by storing detailed pipeline configurations associated with the data. The evaluation of Mario demonstrate that it can be used to achieve more interactivity in the configuration of pipelines for processing biological data. We believe that biology researchers can take advantage of this interactivity to perform better parameter tuning, which may lead to more accurate analyses,
Advances with support vector machines for novel drug discovery

ABSTRACT Introduction: Novel drug discovery remains an enormous challenge, with various computer-aided drug design (CADD) approaches having been widely employed for this purpose. CADD, specifically the commonly used support vector machines (SVMs), can employ machine learning techniques. SVMs and their variations offer numerous drug discovery applications, which range from the classification of substances (as active or inactive) to the construction of regression models and the ranking/virtual screening of databased compounds. Areas covered: Herein, the authors consider some of the applications of SVMs in medicinal chemistry, illustrating their main advantages and disadvantages, as well as trends in their utilization, via the available published literature. The aim of this review is to provide an up-to-date review of the recent applications of SVMs in drug discovery as described by the literature, thereby highlighting their strengths, weaknesses, and future challenges. Expert opinion: Techniques based on SVMs are considered as powerful approaches in early drug discovery. The ability of SVMs to classify active or inactive compounds has enabled the prioritization of substances for virtual screening. Indeed, one of the main advantages of SVMs is related to their potential in the analysis of nonlinear problems. However, despite successes in employing SVMs, the challenges of improving accuracy remain.
Evaluating GQM+ Strategies Framework for Planning Measurement System

Context. Most organizations are aware of the significance of software measurement programs to help organizations assess and improve the ways they develop software. Measurement plays a vital role in improving software process and products. However, the number of failing measurement programs is high and the reasons are vary. A recent approach for planning measurement programs is GQM+Strategies, which makes an important extension to existing approaches, it links measurements and improvement activities to strategic goals and ways to achieve this goals. However, concrete guides of how to collect the information needed to use GQM+strategies is not provided in the literature yet. Objectives. The contribution of this research is to propose and assess an elicitation approach (The Goal Strategy Elicitation (GSE) approach) for the information needed to apply GQM+strategies in an organization, which also leads to a partial evaluation of GQM+strategies as such. In this thesis, the initial focus is placed on eliciting the goals and strategies in the most efficient way. Methods. The primary research approach used is action research, which allows to flexibly assess a new method or technique in an iterative manner, where the feedback of one iteration is taken into the next iteration, thus improving on the method or technique proposed. Complementary to that, we used literature review with the primary focus to position the work, explore GQM+strategies, and to determine which elicitation approach for the support of measurement programs have been proposed. Results. The Goal Strategy Elicitation (GSE) approach as a tool for eliciting goals and strategies within the software organization to contribute in planning a measurement program has been developed. The iterations showed that the approach of elicitation may not be too structured (e.g. template/notation based), but rather shall support the stakeholders to express their thoughts relatively freely. Hence, the end-result was an interview guide, not based on notations (as in the first iteration), and asking questions in a way that the interviewees are able to express themselves easily without having to e.g. distinguish definitions for goals and strategies. Conclusions. We conclude that the GSE approach is a strong tool for the software organization to be able to elicit the goals and strategies to support GQM+Strategies. GSE approach evolved in each iteration and the latest iteration together with the guideline is still used within the studied company for eliciting goals and strategies, and the organization acknowledged that they will continue to do so. Moreover, we conclude that there is a need for further empirical validation of the GSE approach in further full-scale industry trials.
Course Modularization Applied: The Interface System and Its Implications For Sequence Control and Data Analysis.

The Interface System is a comprehensive method for developing and managing computer-assisted instructional courses or computer-managed instructional courses composed of sets of instructional modules. Each module is defined by one or more behavioral objectives and by a list of prerequisite modules that must be completed successfully before the specific module can be attempted. The system's key components are: 1) a standari general structure for all modules; 2) a consistent methcd of labeling logic and text elements; and 3) computer programs (presently written in COURSEWRITER with Assembly Language functions) to regulate inter-module student traffic and to execute system-controlled and student-controlled instructional decisions. (PB) Professional Paper 10-73 HumRRO-PP-10.73 iffumFIFICS Course Modularization Applied: The Interface System and Its Implications For Sequence Control and Data Analysis
Heart Failure: A Review on Pathogenesis and Treatments

Heart failure(HF)has been considered as a life threatening disease that may occurdue to improper blood supply to the body from the heart in order to maintain the normal physiological function or may be due to increase demand of oxygen and nutrient in the body. However, HF can beclassifie d mainly as acute and chronic heart failure ,but certain other classification sincludingside of the heart involved, on the basis of insufficient contraction, pressure overload and cardiac output hasalso been documented.Numbers of causative factor sthatlead toHF include ischemic heart disease, cigarette smoking, hypertension, obesity, diabetes and vulvular heart disease . Further, varioussignaling mechanismareinvolved in the pathogenesisofHF including insulin growth like factor I (IGF-I),renin-angiotensin system (RAS), mitogen activated prokinase (MAPK), C -jun-N-terminal kinase (JNK), fibroblast growth factor (FBF) and t umornecroticfactor-alpha (TNF-�± ). Moreover, numeroustreatment st rategies forHF involve angiotensinconvertingenzyme (ACE) inhibitors,beta(�≤) blockersand aldosterone receptor a ntagonist (ARA). The presentreview on HF illustrate s various signaling mechanism sleading toHF alongwith treatment strategies.
Second language writing classification system based on word-alignment distribution

The present paper introduces an automatic classification system for assisting second language(L2) writing evaluation. This system, which classifies sentences written by L2 learners as eithernative speaker-like or learner-like sentences, is constructed by machine learning algorithmsusing word-alignment distributions as classification features for detecting word-bywordtranslated expressions. The experimental results demonstrated that our classificationsystem provided adequate classification results with respect to (i) high classification accuracy,(ii) classification results reflecting the properties of L2 learner sentences, and (iii) identificationof learner-like expressions. These results suggest that our classification system can beused to evaluate L2 learner sentences.
PySpline: A Modern, Cross‐Platform Program for the Processing of Raw Averaged XAS Edge and EXAFS Data

PySpline is a modern computer program for processing raw averaged XAS and EXAFS data using an intuitive approach which allows the user to see the immediate effect of various processing parameters on the resulting k‐ and R‐space data. The Python scripting language and Qt and Qwt widget libraries were chosen to meet the design requirement that it be cross‐platform (i.e. versions for Windows, Mac OS X, and Linux). PySpline supports polynomial pre‐ and post‐edge background subtraction, splining of the EXAFS region with a multi‐segment polynomial spline, and Fast Fourier Transform (FFT) of the resulting k3‐weighted EXAFS data.
Separation and Recognition Method for Off-line Handwritten Manchu Character Strokes

Correct strokes separation has great influence on the recognition result.This paper elaborates on the method separating and recognizing off-line handwritten Manchu character strokes.Based on the structure and characteristic of Manchu,the character is pre-processed.Then the mid-axis of Manchu character is defined and stroke growth algorithm is created to separate the strokes.The separated stroke is recognized by comparing its characteristic with the standard stroke characteristic.Simulation results show that the method is effective in separating and recognizing restricted off-line handwritten Manchu characters.
CRIKEY - a temporal planner looking at the integration of scheduling and planning

For many temporal planning domains, the planning and scheduling problems are not tightly coupled and so can be solved separately. However, in some cases, where the problems do interact, this approach will fail. A domain is presented where this is the case. CRIKEY, a planner that separates out the logical and temporal reasoning, is introduced. It detects where they interact and the paper explains both how it detects them and also how, in these cases, CRIKEY solves the problems simultaneously. It will also look at CRIKEY as an architecture that uses a series of relaxations to find a plan. Preliminary results show its potential.
Delaunay mesh simplification with differential evolution

Delaunay meshes (DM) are a special type of manifold triangle meshes --- where the local Delaunay condition holds everywhere --- and find important applications in digital geometry processing. This paper addresses the general DM simplification problem: given an arbitrary manifold triangle mesh M with n vertices and the user-specified resolution m (< n), compute a Delaunay mesh M* with m vertices that has the least Hausdorffdistance to M. To solve the problem, we abstract the simplification process using a 2D Cartesian grid model, in which each grid point corresponds to triangle meshes with a certain number of vertices and a simplification process is a monotonic path on the grid. We develop a novel differential-evolution-based method to compute a low-cost path, which leads to a high quality Delaunay mesh. Extensive evaluation shows that our method consistently outperforms the existing methods in terms of approximation error. In particular, our method is highly effective for small-scale CAD models and man-made objects with sharp features but less details. Moreover, our method is fully automatic and can preserve sharp features well and deal with models with multiple components, whereas the existing methods often fail.
Processing of SAR data exploiting spatial, polarimetric and topological information

The Markov random field (MRF) approach is very useful in synthetic aperture radar (SAR) image classification and segmentation. Unfortunately, it exhibits the drawback that fine structures tend to disappear during the segmentation process due to the morphology of the cliques used for the region label model. In this paper, a new method is described that tailors the shape of the cliques to topological information. The validity of the approach is shown by the results obtained by applying the method to multi-polarimetric SAR images.
Dairy farming in Kenya : resources and nitrogen flows

Introduction The central highlands of Kenya are characterised by a large variation of agricultural activities including cultivation of cash crops, vegetables and staple food, as well as milk production. Small farmers keeping 1-3 cows produce most of the milk, demand for which is expected to increase, due to growing population and rising incomes (Omore et al., 1999). Hence, Market-Oriented Small-holder Dairy Research is a main thrust of national institutions (Ministry of Agriculture; Kenya Agricultural Research Institute, KARI) as well as the International Livestock Research Institute (ILRI). Livestock are part of an integrated crop-livestock system and are used to achieve multiple objectives. Smallholder farmers face many problems, including shortage of land. Many farmers grow Napier; other feeds are road side grass, weeds, maize (thinnings and stover), and concentrates. Shortage of feed and under-nutrition of animals are common. This contributes to low milk yields and long calving intervals. This study was conducted to examine the balance of feed supply and animal production in Kiambu district, one of the main milk suppliers for Nairobi city. Also the effect of manure on the estimated profitability of the system and the effect of livestock on N flows was examined.
Electromechanical Motion Devices

PREFACE xi 1 MAGNETIC AND MAGNETICALLY COUPLED CIRCUITS 1 2 ELECTROMECHANICAL ENERGY CONVERSION 49 3 DIRECT-CURRENT MACHINES 97 4 WINDINGS AND ROTATING MAGNETOMOTIVE FORCE 145 5 INTRODUCTION TO REFERENCE-FRAME THEORY 185 6 SYMMETRICAL INDUCTION MACHINES 213 7 SYNCHRONOUS MACHINES 287 8 PERMANENT-MAGNET ac MACHINE 345 9 STEPPER MOTORS 415 10 UNBALANCED OPERATION AND SINGLE-PHASE INDUCTION MOTORS 451 APPENDIX A ABBREVIATIONS, CONSTANTS, CONVERSIONS, AND IDENTITIES 477 APPENDIX B MATRIX ALGEBRA 481 APPENDIX C THREE-PHASE SYSTEMS 489 INDEX 493
Comparação dos Índices de Placa e Sangramento à sondagem em pacientes com periodontite crônica e agressiva/Comparison of plaque and bleeding on probing indexes of chronic and aggressive periodontitis patients

O objetivo do presente estudo foi comparar os indices de placa e sangramento a sondagem de pacientes com periodontite cronica e agressiva. Cinquenta pacientes foram divididos em dois grupos, segundo o tipo de doenca: Grupo A) periodontite cronica (n=25), idade superior a 35 anos de idade e presenca de no minimo 8 sitios com profundidade de sondagem (PS) ≥ 5 mm e sangramento a sondagem; Grupo B) periodontite agressiva (n=25): menos de 35 anos, presenca de no minimo 8 sitios com PS ≥ 5 mm e sangramento a sondagem, incluindo incisivos centrais e primeiros molares. Todos os pacientes foram avaliados quanto aos Indices de Placa (Ainamo e Bay, 1975) e Sangramento a sondagem (Muhleman e Son, 1971) na sessao inicial por um unico examinador calibrado. As medias foram comparadas por meio do teste t de Student nao pareado, com nivel de significância de 5%. A idade media (±dp) dos pacientes do grupo A foi de 45,52±8,15 anos, com diferenca estatistica em relacao ao grupo B (24,5±4,6 anos). A media do IP dos pacientes portadores de periodontite cronica foi de 50,23±16,35% e dos pacientes com Periodontite Agressiva 55,70±17,60%, sem diferenca estatistica (p>0,05). Os Indices de Sangramento a sondagem foram 30,77±16,23% e 26,37±15,60% para pacientes com doenca cronica e agressiva respectivamente, tambem sem diferenca estatistica (p>0,05). Pode-se concluir que os indices de placa e sangramento gengival observados em pacientes portadores de periodontite cronica e periodontite agressiva sao semelhantes e nao podem ser utilizados como diferencial diagnostico entre as doencas.
Semantic Modeling for the Acquisition of Topographic Information from Images and Maps: Smati 97

From the Publisher: Acquiring spatial data for Geoinformationsystems still is mainly done by human operators who analyse images using classical photogrammetric equipment or digitise maps, possibly assisted by some low level image processing. Automation of these tasks is difficult due to the complexity of the object, the topography, and the deficiency of current pattern recognition and image analysis tools for achieving a reliable transition from the data to the high level description of topographic objects. It appears that progress in automation only can be achieved by incorporating domain specific semantic models into the analysis procedures. This volume collects papers which were presented at the Workshop "SMATI 97". The workshop focused on the "Semantic Modeling for the Acquisition of Topographic Information from Images and Maps".
Extending Inquiry: Collaborative Learning with Immersive, Interactive Projection

: We report two studies that highlight how immersive, interactive projection technology supported collaborative STEM inquiry learning. The immersive experience was brief (15 minutes) but inquiry extended well beyond. In study 1, this extension was provoked by a student noticing a pattern and leading the class to derive a formula. In study 2, students graphed data from the dome, provoking questions about superficially-understood phenomena. We found pairing immersive, interactive projection with problem-based lessons provoked generative learning
Clustering based Segmentation Approach to Detect Brain Tumor from MRI Scan

To detect the tumor in the brain is very important task but the major problem occurred is that its very time consuming. We provide an approach towards the automation of this process in this paper. We take magnetic resonance images of the brain as a input and attempt to calculated the position and the size of the tumor. Each pixel in each slice will be processed to detect the tumor. All the process used is automatic and independent from users capability demonstration of the experiment that methods can successfully achieve segmentation for MRI to help pathologist distinguish exactly size and region. Keywordsk-means algorithm, magnetic resonance images, nervous system, spinal cord, skull.
Rule based system for interpretation of evoked potential waveforms

Results obtained with a prototype expert decision-support system for interpretation of sensory evoked-potential waveforms are described. An analytic module calculates several parameters from the waveform, and the parameters are converted into scores to be used by a rule-based module. The scores are treated as linguistic variables to determine whether a response is present with low, medium, or high confidence. Results obtained with the system are presented. The parameters can also be summarized by fuzzy descriptors. The advantages and disadvantages of the two approaches are discussed. <<ETX>>
Factor once

A common operation in geometry processing is solving symmetric and positive semi-definite systems on a subset of a mesh, with conditions for the vertices at the boundary of the region. This is commonly done by setting up the linear system for the sub-mesh, factorizing the system (potentially applying preordering to improve sparseness of the factors), and then solving by back-substitution. This approach suffers from a comparably high setup cost for each local operation. We propose to reuse factorizations defined on the full mesh to solve linear problems on sub-meshes. We show how an update on sparse matrices can be performed in a particularly efficient way to obtain the factorization of the operator on a sun-mesh significantly outperforming general factor updates and complete refactorization. We analyze the resulting speedup for a variety of situations and demonstrate that our method outperforms factorization of a new matrix by a factor of up to 10 while never being slower in our experiments.
Sosyal Bilgiler ve Türkçe Öğretmeni Adaylarının Okuma Durumları: (İlgi, Alışkanlık ve Okuma Stratejilerini Kullanım Düzeyleri)

Okuma, yasam boyu ogrenmenin geceklestirilmesi icin gerekli olan bir edinimdir. Bireyler okuma becerilerini kullanabildikleri ve okuduklarini anlayip elestirebildikleri oranda demokratik toplumsal sistem icerisinde yer edinebilirler. Model niteligindeki ogretmen adaylarinin, boylesine onemli bir kazanima ne oranda sahip olduklari, ogretmen adaylari tarafindan okuma stratejilerinin ne oranda kullanildigi cevaplanmasi gereken onemli sorulardir. Bu calisma, bu sorulara cevap bulmak amaciyla Ahi Evran Universitesi Egitim Fakultesinde gerceklestirilmistir. Arastirmada Turkce ve Sosyal Bilgiler Ogretmenligi Bolumlerinden 577 ogrenciye anket uygulanmistir. Arastirmanin bulgularina gore Turkce ogretmeni adaylarinin okuma sikliklari sosyal bilgiler ogretmeni adaylarina gore yuksek ciksa da genelde ogretmen adaylarinin okuma sikliklari dusuk oranda gerceklesmistir. Gun icerisinde kitle iletisim araclarina ayrilan surenin okumaya ayrilan sureyi olumsuz yonde etkiledigi belirlenmistir. Kutuphane kullanma aliskanliginin zayif oldugu, kutuphanelerin ders calismak, gazete-dergi okumak icin kullanildigi belirlenmistir. Ayrica kiz ogrencilerin okuma sikliklari ve okuma stratejilerinin kullanimi bakimindan erkeklere oranla daha ust duzeyde olduklari da calismanin bulgulari arasindadir. Arastirmada okuma sikliklari ile okuma stratejilerinin kullanimi arasinda olumlu yonde bir iliski bulunmustur.