Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptativity of Stochastic Gradient Descent

We consider the random-design least-squares regression problem within the reproducing kernel Hilbert space (RKHS) framework. Given a stream of independent and identically distributed input/output data, we aim to learn a regression function within an RKHS H, even if the optimal predictor (i.e., the conditional expectation) is not in H. In a stochastic approximation framework where the estimator is updated after each observation, we show that the averaged unregularized least-mean-square algorithm (a form of stochastic gradient descent), given a sufficient large step-size, attains optimal rates of convergence for a variety of regimes for the smoothnesses of the optimal prediction function and the functions in H. Our results apply as well in the usual finite-dimensional setting of parametric least-squares regression, showing adaptivity of our estimator to the spectral decay of the covariance matrix of the covariates.
Adaptive Control of Nonlinear Systems Using Bacterial Foraging Algorithm

 Abstract—In this paper bacterial foraging algorithm (BFA) have been implemented for indirect adaptive control of two nonlinear systems. The nonlinear systems considered in present analysis are liquid level control of surge tank and armature controlled DC motor speed control system. Simulation has been carried out in MATLAB. Using bacterial foraging algorithm plant nonlinearities component alpha and beta have been estimated and compared with actual plant nonlinearities for both the nonlinear systems. Liquid level estimated by BFA adaptive controller and actual liquid level has been compared in the liquid level nonlinear control system. Angular speed estimated by BFA adaptive controller and actual trajectory has been compared for DC motor speed control system. Fitness for the best member in the population of bacteria has been observed for both the nonlinear systems. In DC motor speed tracking obtained using indirect BFA adaptive control have been obtained and compared with reference one. Also liquid level set by indirect BFA adaptive controller have been obtained and compared with reference trajectory of level. Error plots show that error between desired and actual trajectory reduces after ten seconds of system operation in both nonlinear systems. Simulations studies have been also carried out through genetic algorithm (GA) for both nonlinear systems. A comparison of BFA results with GA shows that BFA based indirect adaptive controller are more effective in tracking the desired trajectory in both the nonlinear systems.
Guidelines for Conducting Bridging Studies in Alzheimer Disease

Summary:This report provides guidelines for conducting bridging studies in patients with Alzheimer disease (AD). Bridging studies are late phase I safety/tolerance studies that determine the maximum tolerated dose (MTD) in patients before phase II efficacy studies are initiated, facilitating the transition from phase I to phase II development. Determining the MTD in patients maximizes the potential to detect efficacy by permitting the use of the highest tolerated doses in phaseII while providing a good understanding of potential adverse events. Bridging studies should be double-blind, placebocontrolled, inpatient studies conducted in acute-care facilities by clinical personnel who are equipped to handle unexpected contingencies under the oversight of a competent, multidisciplinary review board. Patients should be in good physical health (excluding AD), and a comprehensive informed consent procedure must be instituted. We recommend initially using a fixed-dose panel design with a dose schedule based on the MTD in normal volunteers and later establishing the dose titration MTD.
The regulatory network of ThbZIP1 in response to abscisic acid treatment

Previously, a bZIP transcription factor from Tamarix hispida, ThbZIP1, was characterized: plants overexpressing ThbZIP1 displayed improved salt stress tolerance but were sensitive to abscisic acid (ABA). In the current study, we further characterized the regulatory network of ThbZIP1 and the mechanism of ABA sensitivity mediated by ThbZIP1. An ABF transcription factor from T. hispida, ThABF1, directly regulates the expression of ThbZIP1. Microarray analysis identified 1662 and 1609 genes that were respectively significantly upregulated or downregulated by ThbZIP1 when exposed to ABA. Gene ontology (GO) analysis showed that the processes including “response to stimulus,” “catalytic activity,” “binding function,” and “metabolic process” were highly altered in ThbZIP1 expressing plants exposed to ABA. The gene expression in ThbZIP1 transformed plants were compared between exposed to ABA and salt on the genome scale. Genes differentially regulated by both salt and ABA treatment only accounted for 9.75% of total differentially regulated genes. GO analysis showed that structural molecule activity, organelle part, membrane-enclosed lumen, reproduction, and reproductive process are enhanced by ABA but inhibited by salt stress. Conversely, immune system and multi-organism process were improved by salt but inhibited by ABA. Transcription regulator activity, enzyme regulator activity, and developmental process were significantly altered by ABA but were not affected by salt stress. Our study provides insights into how ThbZIP1 mediates ABA and salt stress response at the molecular level.
Design and Analysis of High-Throughput Lossless Image Compression Engine Using VLSI-Oriented FELICS Algorithm

In this paper, the VLSI-oriented fast, efficient, lossless image compression system (FELICS) algorithm, which consists of simplified adjusted binary code and Golomb-Rice code with storage-less k parameter selection, is proposed to provide the lossless compression method for high-throughput applications. The simplified adjusted binary code reduces the number of arithmetic operation and improves processing speed. According to theoretical analysis, the storage-less k parameter selection applies a fixed k value in Golomb-Rice code to remove data dependency and extra storage for cumulation table. Besides, the color difference preprocessing is also proposed to improve coding efficiency with simple arithmetic operation. Based on VLSI-oriented FELICS algorithm, the proposed hardware architecture features compactly regular data flow, and two-level parallelism with four-stage pipelining is adopted as the framework of the proposed architecture. The chip is fabricated in TSMC 0.13-¿m 1P8M CMOS technology with Artisan cell library. Experiment results reveal that the proposed architecture presents superior performance in parallelism-efficiency and power-efficiency compared with other existing works, which characterize high-speed lossless compression. The maximum throughput can achieve 4.36 Gb/s. Regarding high definition (HD) display applications, our encoding capability can achieve a high-quality specification of full-HD 1080p at 60 Hz with complete red, green, blue color components. Furthermore, with the configuration as the multilevel parallelism, the proposed architecture can be applied to the advanced HD display specifications, which demand huge requirement of throughput.
Optimal High Dimensional Multiple Testing Under Linear Models ∗

High dimensional multiple testing has many important applications. Motivated by genome-wide association studies (GWAS), we consider the problem of mulitiple testing under high dimensional sparse linear model in order to identify the genetic markers associated with the trait of interest. The model is an extension of the normal mixture model under arbitrary dependence. We propose a multiple testing procedure, which ranks and thresholds the adjusted z-surrogate. It is shown that the procedure can control mfdr level and minimize mfnr level asymptotically among all the methods based on the original data. Numerical results show that our method performs well under linear models with correlated predictors. The procedure is further illustrated through an analysis of a genome-wide association study in hypertension. At mfdr level equal to 0.05, it identifies 11 genetic markers assciated with systolic blood pressure and 11 associated with diastolic blood pressure. Many of the markers are located in the regions associated with human blood pressure based on the Rat Genome Database.
THE IMPACT OF ANGLE PARAMETERISATION ON TERRESTRIAL LASER SCANNER SELF-CALIBRATION

The angular fields of view in which a terrestrial laser scanner captures data differ according to instrument construction. Both the socalled panoramic and hybrid instruments scan through a full horizontal field of view but their vertical fields of view can differ considerably in terms of range and mode of data acquisition. The differences in operational mode govern the allowable range for each of the two angular observables, namely the horizontal direction and the elevation angle, and, ultimately, their parameterisation as observation equations. The impact of the angle parameterisation on the quality of terrestrial laser scanning instrument selfcalibration has been studied. Specifically, the correlation between the scanner orientation angles and the collimation axis error coefficient, whose estimation in terrestrial laser scanner self-calibration has been reported to be unreliable as a result of this mechanism, was examined. It is been demonstrated with both simulated and real data that the angle parameterisation used for hybrid-type scanners is not only the cause of unreliable collimation axis error estimation but is also the reason for the reported ineffectiveness of certain self-calibration network design measures, notably the capture of scans having orthogonal orientations from the same nominal location
Developing Use Cases from Organizational Modeling

The object oriented development paradigm has attracted many supporters in the Software Engineering community. One of the most important advances was the Unified Language Modeling (UML), a standard for visual modeling. Use Cases Diagrams have been used for capturing system functional requirements. However, the system development occurs in a context where organization processes are well established. Therefore, we need to capture organizational requirements to define how the system fulfils the organization goals, why it is necessary, what are the possible alternatives, what are the implications to the involved parts, etc. Unfortunately, UML and other scenario-based techniques are ill equipped for modeling organizational requirements. We need other techniques, such as i*, to represent these aspects. Nevertheless, organizational requirements must be related to functional requirements represented as Use Cases. In this paper we present some guidelines to assist requirement engineers in the development of use cases from the organizational models represented by i* technique.
The Stroop Color-Word Test: Genetic and environmental influences; reading, mental ability ability, and personality correlates.

Using a relatively large adult sample (271 participants in the Minnesota Study of Twins Reared Apart, including 50 pairs of monozygotic and 37 pairs of dizygotic twins), the authors evaluated prior findings of reading, mental ability, and personality correlates of Stroop Color-Word Test (SCWT; J. R. Stroop, 1935) scores. The twin sample allowed the authors to estimate genetic and environmental influences associated with the SCWT scores. No meaningful personality correlates were detected. Genetic influences ranged from 35% for the Interference effect to 53% for the Word score. In spite of significant correlations between the SCWT scores and selected measures of mental ability, genetic influence on SCWT scores was relatively unaffected when the influences of correlated ability measures were removed. (PsycINFO Database Record (c) 2016 APA, all rights reserved)
The mediating role of mind wandering in the relationship between working memory capacity and reading comprehension.

The primary goal of this study was to investigate the mediating role of mind wandering in the relationship between working memory capacity (WMC) and reading comprehension as predicted by the executive-attention theory of WMC (e.g., Kane & Engle, 2003). I used a latent-variable, structural-equation-model approach with three WMC span tasks, seven reading comprehension tasks, and three attention-restraint tasks. Mind wandering was assessed using experimenter-scheduled thought probes during four different tasks. The results support the executive-attention theory of WMC. Mind wandering is a significant mediator in the relationship between WMC and reading comprehension, suggesting that the relationship is driven, in part, by attention control over intruding thoughts. I discuss implications for theories of WMC, attention control, and reading comprehension.
Malignant lymphoma with primary manifestation in the gonad a clinicopathologic study of 38 patients

This study is based on 38 patients, each of whom had a malignant lymphoma in which the gonad was the site of the main tumor mass at the time of diagnosis. Histiocytic lymphoma was the predominant type in the 27 male patients; in the 11 female patients, poorly differentiated lymphocytic lymphoma was the most frequent type (36%). All of the neoplasms in the males were diffuse, whereas two of the females had neoplasms that were nodular and diffuse. A striking feature was the high frequency of vascular invasion (41%) in the testicular lymphomas, which was reflected in a high incidence (86%) of noncontiguous lung involvement at autopsy, suggesting hematogenous spread. Clinically occult disease is probably responsible for the short interval between the discovery of a gonadal mass and the appearance of generalized disease. A poor prognosis may be expected if there is evidence of generalized disease within one year after diagnosis. Only 2 patients had disseminated disease after a year, whereas all those who died of disseminated disease manifested it within six months after diagnosis. Disease‐free survival times in excess of 60 months in 3 patients who were treated only by orchiectomy or oophorectomy indicate that the gonads may be the primary site of a malignant lymphoma.
Performance of Multi-Channel MAC Incorporating Opportunistic Cooperative Diversity

This paper proposes a medium access control (MAC) protocol, termed as CD-MMAC, for wireless networks that utilizes multiple channels and incorporates opportunistic cooperative diversity dynamically to improve its performance. The IEEE 802.11b standard protocol allows the use of multiple channels available at the physical layer but its MAC protocol is designed only for a single channel. The proposed protocol utilizes multiple channels by using single interface and incorporates opportunistic cooperative diversity by using a cross-layer MAC. The new protocol leverages the multi-rate capability of IEEE 802.11b and allows wireless nodes far away from destination node to transmit at a higher rate by using intermediate nodes as a relays. The protocol incorporates opportunistic cooperative diversity by the design of a cross-layer MAC. The protocol improves network throughput and packet delivery ratio significantly and reduces packet delay. The performance improvement is further evaluated by simulation and analysis.
Rickettsia felis in Ctenocephalides spp. Fleas, Brazil

In June 2000, suspected cases of Brazilian spotted fever (BSF) occurred in Coronel Fabriciano Municipality, Minas Gerais State, Brazil. Pooled fleas collected near two fatal cases contained rickettsial DNA. The nucleotide sequence alignment of the 391-bp segment of the 17-kDa protein gene showed that the products were identical to each other and to the R. felis 17-kDa gene, confirming circulation of R. felis in Brazil.
Extending a method of devising software contracts

Classes in object-oriented programs can be specified using assertions, specifically, preconditions and postconditions on individual methods and invariants on whole classes. Such assertions can be seen as forming a contract between a class and its client classes and, by extension, between the developers of class and the developers of client classes. In some programming environments, the contracts can be checked at runtime. A published method of devising contracts is applied to a small framework based on the observer pattern, raising a number of problems of writing contracts for a set of collaborating classes, rather than for individual classes such as those formed in data structure libraries. As well as providing an example of tackling such problems, the paper identifies desirable extensions to the method of devising contracts, to address aspects of performance (keeping the run-time cost of evaluating preconditions low); privacy (ensuring that one client of a class cannot discover the identities of other clients); extensibility (allowing subclasses to weaken preconditions without invalidating existing postconditions, and allowing subclasses to adopt different frame rules); and kinds of constraints (distinguishing physical and logical constraints).
Evolving generalized Voronoi diagrams for accurate cellular image segmentation

Analyzing cellular morphologies on a cell‐by‐cell basis is vital for drug discovery, cell biology, and many other biological studies. Interactions between cells in their culture environments cause cells to touch each other in acquired microscopy images. Because of this phenomenon, cell segmentation is a challenging task, especially when the cells are of similar brightness and of highly variable shapes. The concept of topological dependence and the maximum common boundary (MCB) algorithm are presented in our previous work (Yu et al., Cytometry Part A 2009;75A:289–297). However, the MCB algorithm suffers a few shortcomings, such as low computational efficiency and difficulties in generalizing to higher dimensions. To overcome these limitations, we present the evolving generalized Voronoi diagram (EGVD) algorithm. Utilizing image intensity and geometric information, EGVD preserves topological dependence easily in both 2D and 3D images, such that touching cells can be segmented satisfactorily. A systematic comparison with other methods demonstrates that EGVD is accurate and much more efficient. © 2010 International Society for Advancement of Cytometry
Which Crashes Should I Fix First?: Predicting Top Crashes at an Early Stage to Prioritize Debugging Efforts

Many popular software systems automatically report failures back to the vendors, allowing developers to focus on the most pressing problems. However, it takes a certain period of time to assess which failures occur most frequently. In an empirical investigation of the Firefox and Thunderbird crash report databases, we found that only 10 to 20 crashes account for the large majority of crash reports; predicting these “top crashes” thus could dramatically increase software quality. By training a machine learner on the features of top crashes of past releases, we can effectively predict the top crashes well before a new release. This allows for quick resolution of the most important crashes, leading to improved user experience and better allocation of maintenance efforts.
Second Language Identities

Introduction 1. Identity in the social sciences today 2. Waking the dead: Identity in early second language learning research 3. Identity in adult migrant contexts 4. Identity in foreign language contexts 5. Identity in study abroad contexts 6. Second language identities: the state of play and future directions.
Cytotoxicity and characterization of an active metabolite of benzamide riboside, a novel inhibitor of IMP dehydrogenase

Benzamide riboside exhibits significant cytotoxicity against a variety of human tumor cells in culture. On the basis of metabolic studies, the primary target of this drug's action appears to be IMP dehydrogenase (IMPDH). Incubation of human myelogenous leukemia K562 cells with an IC50 concentration of benzamide riboside resulted in an expansion of IMP poofs (5.9‐fold), with a parallel reduction in the concentration of GMP (90%), GDP (63%), GTP (55%) and dGTP (40%). On kinetic grounds, it was deduced that benzamide riboside (whose Ki versus IMPDH is 6.4 mM, while that of its 5′‐monophosphate is 3.9 mM) or its 5′‐monophosphate were unlikely to be responsible for inhibition of this target enzyme, IMPDH, since only micromolar concentrations of benzamide riboside were needed to exert potent inhibition of tumor‐cell growth. Studies on the metabolism of this C‐nucleoside have revealed the presence of a new peak eluting in the nucleoside diphosphate area on HPLC. Treatment of this peak with venom phosphodiesterase degraded it and concurrently nullified its inhibitory activity versus IMPDH; alkaline phosphatase, on the other hand, totally failed to digest the anabolite. These results suggest that the metabolite in question is the phosphodiester, benzamide adenine dinucleotide (BAD). Evidence that the inhibitor was an analog of NAD, wherein the nicotinamide moiety has been replaced by benzamide, was provided by both NMR and mass spectrometric analysis and confirmed by enzymatic synthesis. Further insight into the nature of the active principle was obtained from kinetic studies, which established that BAD competitively inhibited NAD utilization by partially purified IMPDH from K562 cells with a Ki of O.118 μM. In concert, these studies establish that benzamide riboside exhibits potent antiproliferative activity by inhibiting IMPDH through BAD.
GLAD package : Gain and Loss Analysis of DNA

This document presents an overview of the GLAD package (Gain and Loss Analysis of DNA). This package is devoted to the analysis of Array Comparative Genomic Hybridization (array CGH) (Pinkel et al., 1998; Snijders et al., 2001; Solinas-Toldo et al., 1997; Ishkanian et al., 2004) . The methodology for detecting the breakpoints delimiting altered regions in genomic patterns and assigning a status (normal, gained or lost) to each chromosomal region described in the paper Hupé et al. (2004) is implemented in this package. Some graphical functions are provided as well.
Volume animation using the skeleton tree

We describe a technique to animate volumes using a volumetric skeleton. The skeleton is computed from the actual volume, based on a reversible thinning procedure using the distance transform. Polygons are never computed, and the entire process remains in the volume domain. The skeletal points are connected and arranged in a "skeleton tree", which can be used for articulation in an animation program. The full volume object is regrown from the transformed skeletal points. Since the skeleton is an intuitive mechanism for animation, the animator deforms the skeleton and causes corresponding deformations in the volume object. The volumetric skeleton can also be used for volume morphing, automatic path navigation, volume smoothing and compression/decimation.