Miracle-dz/UniFAR-FTUs huggingface dataset:
A Practical Guide for Improving Transparency and Reproducibility in Neuroimaging Research

Recent years have seen an increase in alarming signals regarding the lack of replicability in neuroscience, psychology, and other related fields. To avoid a widespread crisis in neuroimaging research and consequent loss of credibility in the public eye, we need to improve how we do science. This article aims to be a practical guide for researchers at any stage of their careers that will help them make their research more reproducible and transparent while minimizing the additional effort that this might require. The guide covers three major topics in open science (data, code, and publications) and offers practical advice as well as highlighting advantages of adopting more open research practices that go beyond improved transparency and reproducibility.
Incidence of microdeletions in the AZF region of the Y chromosome in Slovak patients with azoospermia.

AIMS The Y chromosome accumulates male-related genes including sex-determining region of Y-chromosome (SRY) and several spermatogenesis-related genes. The long arm contains azoospermia factor (AZF) region (including sub-regions AZFa, AZFb and AZFc). Microdeletions in this region are responsible for azoospermia and oligospermia and result in the male infertility. The aim of this study was to analyze incidence of microdeletions in the AZF region of Y chromosome in patients with azoospermia from Slovakia. PATIENTS AND METHODS Over the period from 2005 to 2009 a total of 239 men (mean age 31.74 years) were analyzed. The diagnosis of azoospermia was established on the basis of semen analysis. All patient samples were analyzed cytogenetically. Chromosomal analysis was performed on all patients on cultured lymphocytes from peripheral blood. For exact diagnosis of microdeletions in AZF region we used a PCR-method using a set of sequence-tagged sites from all AZF sub-regions (according to the recommendation by the European Academy of Andrology and the European Quality Monitoring Network Group). RESULTS Among our 226 patients with azoospermia and with normal karyotype, 8 patients (mean age 30.6 years) had microdeletions in the AZF region of the Y chromosome (3.35%). Considering particular types of deletions we determined deletions in each region AZFa,b,c but also a complete deletion of the entire AZF region. The presence of microdeletion(s) in the AZFc region was the most frequent. In our study we found 12 patients (5%) with 47,XXY karyotype (Klinefelter syndrome), but these patients didn't have microdeletion of Y chromosomes. CONCLUSION The study confirmed that percentage of microdeletions in the AZF region is low in Slovak azoospermic patients, but important from a prognostic view.
Removing color cast of underwater images through non-constant color constancy hypothesis

Color cast is a crucial problem for color image processing. White balance has been widely used to eliminate color cast to improve the image's quality. Most of white balance implementations are based on color constancy hypothesis. A well-known color constancy hypothesis is given in [1], unifying White Patch [2], Grey World [3], Shades of Grey [4], and Grey Edge [1] assumptions in one expression. However, this general hypothesis works on underwater images not as reliable as on common images. In the color constancy hypothesis for common scenes, the ambient light source is spatial constant. But in underwater scenes, the light suffers from serious attenuation, especially in the red part of the visible spectrum. This attenuation causes spatial variance of the ambient light source, which lets classic color constancy hypothesis fail. In this paper, we propose a novel low-level image feature-based color constancy hypothesis for underwater scenes. Based on this hypothesis, we propose an algorithm, using a distance map to estimate multiple gain factors to remove the color cast.
A STATISTICALLY PROVEN AUTOMATIC CURVATURE BASED CLASSIFICATION PROCEDURE OF LASER POINTS

One of the critical aspects of the curvature based classification of spatial objects from laser point clouds is the correct interpretation of the results. This is due to the fact that measurements are characterized by errors and that simplified analytical models are applied to estimate the differential terms used to compute the object surface curvature values. In particular, the differential terms are the first and second order partial derivatives of a Taylor’s expansion used to determine, by the so-called “Weingarten map” matrix, the Gaussian and the mean curvatures. Due to the measurement errors and to the simplified model adopted, a statistical procedure is proposed in this paper. It is based at first on the analysis of variance (ANOVA) carried out to verify the fulfilment of the second order Taylor’s expansion applied to locally compute the curvature differential terms. Successively, the variance covariance propagation law is applied to the estimated differential terms in order to calculate the variance covariance matrix of a two rows vector containing the Gaussian and the mean curvature estimates. An F ratio test is then applied to verify the significance of the Gaussian and of the mean curvature values. By analysing the test acceptance or rejection for K and H, and their sign, a reliable classification of the whole point cloud into its geometrical basic types is carried out. Some numerical experiments on synthetic and real laser data finally emphasize the capabilities of the method proposed.
Flexible Margin Sele tion for Reranking with Full Pairwise Samples

Abstra t. Per eptron like large margin algorithms are introdu ed for the experiments with various margin sele tions. Compared to the previous per eptron reranking algorithms, the new algorithms use full pairwise samples and allow us to sear h for margins in a larger spa e. Our experimental results on the data set of [1℄ show that a per eptron like ordinal regression algorithm with uneven margins an a hieve Re all/Pre ision of 89.5/90.0 on se tion 23 of Penn Treebank. Our result on margin sele - tion an be employed in other large margin ma hine learning algorithms as well as in other NLP tasks.
Detecting rare events using Kullback-Leibler divergence

One main challenge in developing a system for visual surveillance event detection is the annotation of target events in the training data. By making use of the assumption that events with security interest are often rare compared to regular behaviours, this paper presents a novel approach by using Kullback-Leibler (KL) divergence for rare event detection in a weakly supervised learning setting, where only clip-level annotation is available. It will be shown that this approach outperforms state-of-the-art methods on a popular real-world dataset, while preserving real time performance.
An analysis of reference architectures for the internet of things

The Internet of Things (IoT) is a paradigm in which smart objects actively collaborate with other physical and virtual resources available in the Internet. IoT environments are characterized by a high degree of heterogeneity, encompassing devices with different capabilities, functionalities, and network protocols. To address such a heterogeneity, some platforms have been proposed aiming at abstracting away the specificities of such devices and promoting interoperability among them. Nevertheless, the lack of standardization in IoT makes these platforms to often not properly address several important requirements in this context. In this context, reference architectures can de ne an initial set of building blocks for IoT environments and to provide a solid foundation for leveraging its wide adoption. In this paper, we introduce two recent reference architectures for IoT, namely the IoT Architectural Reference Model and the architecture proposed by WSO2. By analyzing the characteristics of these architectures, we intend to shed light on important issues for future research on reference architectures for IoT.
Playing in the Sandbox: Developing games for children with disabilities

Many researchers believe that special games are needed for people with special needs. However, this study highlights some of the issues surrounding computer games and disabled children by conducting interviews to ask them what games they would like to play. Interestingly, they wanted to play the same games that everyone else did. What they do need is a way of interacting with these games, especially those on Xbox and Playstation consoles, which require two very dexterous hands to control. This paper is the start of an ongoing project to investigate input devices for disabled people, to allow them to interact with other players through playing commercial multiplayer games. The study also considers the issues of using computer games to test the abilities of disabled people in an attempt to integrate them into mainstream society.
Ribonuclease-resistant RNA controls (Armored RNA) for reverse transcription-PCR, branched DNA, and genotyping assays for hepatitis C virus.

BACKGROUND Comparison and evaluation of molecular diagnostic assays for the detection and quantification of hepatitis C virus (HCV) RNA have been limited by the lack of RNA controls and calibrators. Armored RNA technology is a means for producing RNA that is completely protected from plasma ribonucleases. This method produces recombinant pseudoviral particles that are noninfectious and contain predefined RNA sequences. METHODS A consensus 412-base sequence from the 5'NCR/Core region of HCV subtype 2b was derived from 34 individually sequenced HCV genotype 2b variants. A DNA fragment encoding the consensus HCV-2b sequence was synthesized de novo, cloned, and expressed as an Armored RNA control. The resulting HCV-2b Armored RNA (AR-HCV-2b) contained the complete HCV-2b consensus RNA sequence encapsidated within a protective protein coat. RESULTS AR-HCV-2b was fully recoverable from human plasma incubated at 4 degrees C for >300 days. The particles were tested in three clinical assay formats: Amplicor HCV Monitor 1.0, Quantiplex HCV RNA 2.0, and INNO-LiPA HCV II. When added into seronegative, nonviremic plasma, AR-HCV-2b showed reproducible signals and linear dilutions in both the Amplicor and Quantiplex assays. AR-HCV-2b was correctly identified as subtype 2b in the INNO-LiPA line probe assay. CONCLUSION The HCV-2b Armored RNA control is a versatile, durable, ribonuclease-resistant viral RNA control that is compatible in three different clinical assay formats.
Intonational variation in the british isles

Models of intonation are typically based on one dialect and one style and do not account for interor intra-speaker variability. Speech data from the IViE corpus, however, demonstrate considerable variation in English intonation that occurs both across and within dialects (IViE = Intonational Variation in English, UK ESRC award R000237145, http://www.phon.ox.ac.k/~esther/ivyweb). In this paper, we introduce the IViE corpus and present a selection of findings. Concentrating on nuclear accents, we provide evidence for (1) variation in the production of nuclear accent types and (2) variation in the phonetic realisation of nuclear accents. We discuss data from seven dialects. The results show that intonational differences between dialects of one language can be greater than intonational differences between dialects of two different languages. They also show that there is considerable intra-dialectal variation.
Shape description using phase-preserving Fourier descriptor

Contour-based Fourier descriptors are established as a simple and effective shape description method for content-based image retrieval. In order to achieve invariance under rotation and starting point change, most Fourier descriptor implementations disregard the phase of the Fourier coefficients. We introduce a novel method for extracting Fourier descriptors, which preserve the phase of Fourier coefficients and have the desired invariance. We propose specific points, called pseudomirror points, to be used as shape orientation reference. Experimental results indicate that the proposed method significantly outperforms other Fourier descriptor based techniques.
Expressive touch: studying tapping force on tabletops

This paper investigates users' ability to perform force-sensitive tapping and explores its potential as an input modality in touch-based systems. We study force-sensitive tapping using Expressive Touch, a tabletop interface that infers tapping force from the sound waves created by the users' finger upon impact. The first part of the paper describes the implementation details of Expressive Touch and shows how existing tabletop interfaces can be augmented to reliably detect tapping force across the entire surface. The second part of the paper reports on the results of three studies of force-sensitive tapping. First, we use a classic psychophysic task to gain insights into participants' perception of tapping force (Study 1). Results show that although participants tap with different absolute tapping forces, they have a similar perception of relative tapping force. Second, we investigate participants' ability to control tapping force (Study 2) and find that users can produce two force levels with 99% accuracy. For six levels of force, accuracy drops to 58%. Third, we investigate the usability of force tapping by studying participants' reactions to seven force-sensitive touch applications (Study 3).
Optimal Stratification of Transactions

The performance of applications is influenced by the way its operations are grouped into global transactions. This in turns influences the performance of business processes which utilize these applications as implementations of process activities/steps. Stratified transactions, as produced by the stratification approach presented in this paper, is a way to manage a global transaction by combining the more elemental transactions coordinated using the two-phase commit protocol and queued transactions. The stratification approach can be applied for optimally fragmenting workflowbased service compositions and support the out- and insourcing scenarios. This paper formally models global transactions and investigates the mechanisms for building an optimally stratified transaction relying on formally defined evaluation criteria. We investigate the applicability of local search algorithms to the optimization of transaction stratification. In particular we consider hill-climbing, simulated annealing, and a novel hybrid method combining both approaches.
Using memory management to detect and extract illegitimate code for malware analysis

Exploits that successfully attack computers are typically based on some form of shellcode, i.e., illegitimate code that is injected by the attacker to take control of the system. Detecting and gathering such code is the first step to its detailed analysis. The amount and sophistication of modern malware calls for automated mechanisms that perform such detection and extraction. In this paper, we present a novel generic and fully automatic approach to detect the execution of illegitimate code and extract such code upon detection. The basic idea is to flag certain memory pages as non-executable and utilize a modified page fault handler to react on the attempt to execute code from them. Our modified page fault handler detects if legitimate code is about to be executed or if the code originates from an untrusted location. In such a case, the corresponding memory content is extracted and execution is continued to retrieve more illegitimate code for analysis. We present an implementation of the approach for the Windows platform called CWXDetector, which involved reverse-engineering the proprietary memory management system of this operating system. Evaluation results using a large corpus of malicious PDF documents show that our system produces no false positives and has a very low false negative rate. To further demonstrate the universality of our approach, we also used it to detect shellcode execution in Flash Player, RealVNC client, and VideoLan Client.
Optimisation of GMM in speaker recognition

Given that the amount of speaker speci(cid:12)c training data is always limited, for a given amount of data a speaker model has an optimum number of components. Here, this is investigated with regard to Gaussian mixture models (GMM) with and without world model adaption. Test results show that maximising the number of components in a speaker model can improve speaker recognition results. Comparisons with vector quantisation (VQ) indicate that sensible use of out-of-class data is essential for optimising a recognition system.
Computational Statistics and Data Analysis a Note on Adaptive Group Lasso

Group lasso is a natural extension of lasso and selects variables in a grouped manner. However, group lasso suffers from estimation inefficiency and selection inconsistency. To remedy these problems, we propose the adaptive group lasso method. We show theoretically that the new method is able to identify the true model consistently, and the resulting estimator can be as efficient as oracle. Numerical studies confirmed our theoretical findings.
Supplementary File for “ Time-mapping Using Space-Time Saliency ”

In this supplementary material, we provide details for the following: (1) multi-scale video segmentation and refinement, (2) STR feature, (3) dynamic programming solution for video re-timing, and (4) computational cost of the proposed system. In addition, we include a video for showing the results on the saliency benchmark dataset and the high-speed video dataset. 1. Multi-scale video segmentation and refinement To capture region of interests in different spatial scales, we construct an l-level pyramid of segmentation by adopting different scale parameters that are used in [5]. Each level of the segmentation pyramid corresponds to the result of executing the algorithm [5] with different scale parameters (i.e., the min parameter in the command gbh stream provided by the LIBSVX1 toolbox). In our work, we set l = 4 and min ∈ {100, 1400, 2700, 4000}. The second column of Fig. 1 illustrates an example of segmenting one video in two scales. The initial segmentation results generated by [5] contained many small and redundant spatio-temporal regions (STRs)2 that affects the smoothness of the computed saliency map. Therefore, we further refine the segmentation by merging adjacent STRs with similar colors. To do that, we compute the χ distance between each pair of adjacent STRs. Any pair with a smaller distance than 0.1 is merged to a single new STR. For instance, the second and the third columns of Fig. 1 compare the segmentation results without and with refinement, respectively. http://www.cse. buffalo.edu/ ̃jcorso/r/ supervoxels/ 2The term “voxel” has been used to represent a segmented spatialtemporal region. Since “voxel” is a fundamental term in graphics that has a different meaning, we do not use it to avoid confusion. 2. STR feature For each STR denoted as rc,t, we compute three feature vectors, one color histogram x c,t , and two flow-based descriptors x c,t and x ori c,t . To compute x c,t ∈ Rcol , we quantize the four color channels (L, A, B and hue) into 8, 16, 16 and 4 bins respectively. The dimension of the color histogram is dcol = 8192, where 8192 = 8 · 16 · 16 · 4. To compute x c,t ∈ Rmag , we uniformly quantize the flow magnitude into dmag = 16 bins. To compute x c,t ∈ Rori , we follow the idea of the HoF descriptor [4] by quantizing the flow orientation into 8 bins and use magnitude for weighting. An additional zero bin is added to account for pixels whose optical flow magnitudes are lower than a threshold. The final dimension of the descriptor is dori = 9. 3. Dynamic programming solution for video re-timing In the paper, we formalize the re-timing problem as minimizing the following sum of least-square errors:
An MS-DOS File System for UNIX Alessandro Forin

We have written DosFs, a new file system for UNIX that uses MS-DOS data structures for permanent storage. DosFs can be used anywhere a traditional UNIX file system can be used, and it can mount disks written by MS-DOS as regular UNIX partitions. DosFs can be used as the root partition, and exported by an NFS server. Our motivation for this work was efficient disk space utilization; DosFs provides from 30% to 80% better disk utilization than the 4.3 BSD Fast File System (FFS). In addition, we found that the disk block allocation algorithm used by DosFs lets us exploit large contiguous disk operations, providing a five-fold improvement over FFS for uncached operations. To the best of our knowledge, this is the first file system implementation that allows the user to specify the logical block size at mount time. A user can mount the same fileystem with a larger block size when file accesses tend to be sequential and a smaller one when they tend to be scattered. The MS-DOS structures were designed for a single-user system and do not support access control. We solved this problem with simple extensions that are backward-compatible with MS-DOS.
Fast Image Registration in Dx9 Graphics Hardware

The analysis of image time series requires a correlation of the information between two images. The gradient flow registration is a method for correlating this information by successively minimizing an appropriate energy along its gradient. A graphics hardware implementation of this approach to image registration is presented. The gradient flow formulation makes use of a robust multi-scale regularization, an efficient multi-grid solver and an effective time-step control. The locality of the involved operations implies a data-flow which is very well suited for an acceleration in the streaming architecture of the DX9 graphics hardware. Therefore, the implementation obtains registration results at very high performance, registering two 2562 in less than 2 seconds, such that it could be used as an interactive tool in medical image analysis.
Program Verification with Flow-Effect Types

This paper develops a flow sensitive type system for higher order programming languages. Flow-effect types are a novel form of type that combine the notion of temporal ordering inherent in type effect systems, with subtype constraint systems which focus on unordered dataflow. The resulting system achieves a high level of precision by cutting very close to the operational behavior of programs. The näıve type closure algorithm completely simulates expression computation, and so is undecidable. The main result of the paper is development of a sound and decidable closure algorithm for flow-effect types.