Miracle-dz/UniFAR-FTUs huggingface dataset:
Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search

: Genome annotation relies to a large extent on the recognition of homologs to already known genes. The starting point for such protocols is a collection of known sequences from one or more species, from which a model is constructed – either automatically or manually – that encodes the deﬁning features of a single gene or a gene family. The quality of these models eventually determines the success rate of the homology search. We propose here a novel approach to model construction that not only captures the characteristic motifs of a gene, but are also adjusts the search pattern by including phylogenetic information. Computational tests demonstrate that this can lead to a substantial improvement of homology search models.
UniqueProt: creating representative protein sequence sets

UniqueProt is a practical and easy to use web service designed to create representative, unbiased data sets of protein sequences. The largest possible representative sets are found through a simple greedy algorithm using the HSSP-value to establish sequence similarity. UniqueProt is not a real clustering program in the sense that the 'representatives' are not at the centres of well-defined clusters since the definition of such clusters is problem-specific. Overall, UniqueProt is a reasonable fast solution for bias in data sets. The service is accessible at http://cubic.bioc. columbia.edu/services/uniqueprot; a command-line version for Linux is downloadable from this web site.
Visualising the temporal aspects of collaborative inquiry-based learning processes in technology-enhanced physics learning

ABSTRACT This study presents new ways of visualising technology-enhanced collaborative inquiry-based learning (CIBL) processes in an undergraduate physics course. The data included screen-capture videos from a technology-enhanced learning environment and audio recordings of discussions between students. We performed a thematic analysis based on the phases of inquiry-based learning (IBL). The thematic analysis was complemented by a content analysis, in which we analysed whether the utilisation of technological tools was on a deep-level, surface-level, or non-existent basis. Student participation was measured in terms of frequency of contributions as well as in terms of impact. We visualised the sequence of the face-to-face interactions of two groups of five students by focussing on the temporal aspects of IBL, technology enhancement and collaborative learning. First, instead of the amount of time the groups spent on a specific IBL phase, the between-group differences in the most frequent transitions between the IBL phases determined their differential progress in the CIBL process. Second, we found that the transitions were triggered by the groups’ ways of utilising technological tools either at the deep level or at the surface level. Finally, we found that the level of participation inequity remained stable throughout the CIBL process. As a result, only some of the members of the groups played a role in the most frequent transitions. Furthermore, this study reveals the need for scaffolds focussing on inquiry, technological and collaborative skills at the beginning of the learning process.
Multichannel detection of Gaussian signals with uncalibrated receivers

We consider the detection of unknown Gaussian signals received by an array of uncalibrated nonidentical sensors, which is a problem that appears in radio astronomy. The problem is formulated as a test on the covariance structure. The generalized likelihood ratio test (GLRT) for this problem is stated and related to a simpler ad-hoc detector. We compare the method to the conventional multichannel subspace detector and show its robustness to nonidentical channels on data collected with the Westerbork radio telescope.
Configuring buffer pools in DB2 UDB

Database Management Systems (DBMSs) use a main memory area as a buffer to reduce the number of disk accesses performed by a transaction. DB2 Universal Database divides the buffer area into a number of independent buffer pools and each database object (table or index) is assigned to a specific buffer pool. The tasks of configuring the buffer pools, which defines the mapping of database objects to buffer pools and setting a size for each of the buffer pools, is crucial for achieving optimal performance.Mapping database objects to buffer pools, which we refer to as the "buffer pool configuration problem", is the focus of this paper. Mapping database objects to buffer pools can be viewed as a partitioning problem, that is, we partition the database objects into groups where each group is assigned a separate buffer pool. The partitioning of objects is based on how the objects are used and on the inherent properties of objects. We present an approach to the configuration problem based on analyzing the access behaviour of a given database workload to the set of database objects. The approach is demonstrated with a typical OLTP workload.
Quantification of the impact in mid-latitudes of chemical ozone depletion in the 1999/2000 Arctic polar vortex prior to the vortex breakup

Abstract. For the winter 1999/2000 transport of air masses out of the vortex to mid-latitudes and ozone destruction inside and outside the northern polar vortex is studied to quantify the impact of earlier winter (before March) polar ozone destruction on mid-latitude ozone. Nearly 112 000 trajectories are started on 1 December 1999 on 6 different potential temperature levels between 500–600 K and for a subset of these trajectories photo-chemical box-model calculations are performed. We linked a decline of −0.9% of mid-latitude ozone in this layer occurring in January and February 2000 to ozone destruction inside the vortex and successive transport of these air masses to mid-latitudes. Further, the impact of denitrification, PSC-occurrence and anthropogenic chlorine loading on future stratospheric ozone is determined by applying various scenarios. Lower stratospheric temperatures and denitrification were found to play the most important role in the future evolution of polar ozone depletion.
Investigating students’ situation-specific emotional state and motivational goals during a learning project within one primary school classroom

ABSTRACT This study explores fluctuation in students’ emotional state and motivational goals during a learning project that requires self-regulation. The research asks the following questions: (1) How do students’ emotional state and motivational goal fluctuate between the gStudy learning sessions during a two-month project? (2) How do students with different situational motivation describe their use of motivation regulation strategies? and (3) How is students’ situational motivation associated with their learning outcomes? The students (N = 20) in one classroom evaluated their emotional state and motivational goals repeatedly with an emotion awareness tool during a two-month-long science project. At the end of the project, they completed a learning test and were interviewed about their regulation strategies. The results show that the students’ situational motivation fluctuated in the course of the learning project. The students with a trend of a low situational motivation reported particularly the use of performance and mastery self-talk strategies, the students with moderate situational motivation emphasised environmental structuring and self-consequating, while the students with high situational motivation reported the use of self-consequating and interest enhancement strategies. The students typically reporting high or moderate situational motivation gained significantly more inquiry learning skills compared to their peers with low situational motivation.
A Novel Approach to Creating Disambiguated Multilingual Dictionaries

Multilingual lexicons are needed in various applications, such as cross-lingual information retrieval, machine translation, and some others. Often, these applications suffer from the ambiguity of dictionary items, especially when an intermediate natural language is involved in the process of the dictionary construction, since this language adds its ambiguity to the ambiguity of working languages. This paper aims to propose a new method for producing multilingual dictionaries without the risk of introducing additional ambiguity. As a disambiguated intermediate language we use the so-called Universal Words. A set of more than 200,000 unambiguous Universal Words have been constructed automatically on the basis of the well-known English lexical database WordNet. This approach is being used for the construction of a five language-dictionary in the field of cultural heritage within the framework of the PATRILEX project sponsored by the Spanish Research Council.
Extended Capabilities for a Privacy-Enhanced Participatory Sensing Infrastructure (PEPSI)

Participatory sensing is emerging as an innovative computing paradigm that targets the ubiquity of always-connected mobile phones and their sensing capabilities. In this paper, a multitude of pioneering applications increasingly carry out pervasive collection and dissemination of information and environmental data, such as traffic conditions, pollution, temperature, and so on. Participants collect and report measurements from their mobile devices and entrust them to the cloud to be made available to applications and users. Naturally, due to the personal information associated to the reports (e.g., location, movements, etc.), a number of privacy concerns need to be considered prior to a large-scale deployment of these applications. Motivated by the need for privacy protection in participatory sensing, this paper presents a privacy-enhanced participatory sensing infrastructure. We explore realistic architectural assumptions and a minimal set of formal requirements aiming at protecting privacy of both data producers and consumers. We propose two instantiations that attain privacy guarantees with provable security at very low additional computational cost and almost no extra communication overhead.
Spatial search strategies of job seekers and the role of unemployment insurance

Job search is a spatially oriented activity. Searching farther is costly, and working far away from home entails high costs, affecting job acceptance decisions. We build a simple theoretical framework where job seekers choose how much to search, how far to search, and what lowest wage they accept for a given commute distance. In this setup, unemployment insurance discourages broader job search through reducing the net gain from getting a job. Opposite forces encourage broader search, either through the re-entitlement effect or, under liquidity constraints, to finance costly spatial job search. We use a unique dataset on all workers entering unemployment in Austria between 1995 to 2004 to investigate these forces. We find that newly unemployed workers initially find relatively more frequently jobs in the same workplace as they used to be employed. As the unemployment spell gets longer, they both accept lower wages and progressively enlarge their radius of search, ending up with a job farther away from their previous workplace (but not necessarily farther away from their residence). Unemployment insurance reduces reservation wages at a given accepted commute distance, and encourages search outside the municipality of the previous job. Reducing potential benefit duration affects wages and commuting distance more strongly than changes in the benefit level.
On Spectral Methods and the Structuring of Home Videos

Accessing and organizing home videos present technical challenges due to their unrestricted content and lack of storyline. In this paper, we propose a spectral method to group video shots into scenes based on their visual similarity and temporal relations. Spectral methods exploit the eigenvector decomposition of a pair-wise similarity matrix and can be effective in capturing perceptual organization features. In particular, we investigate the automatic selection of the number of clusters, which is currently an open research issue for spectral methods. We first analyze the behaviour of the algorithm with respect to variations in the number of clusters, and then propose measures to assess the validity of a grouping result. The methodology is used to group scenes from a six-hour home video database, and is assessed with respect to a ground-truth generated by multiple humans. The results indicate the validity of the proposed approach, both compared to existing techniques as well as the human ground-truth.
A Pragmalinguistics Analysis of Anger Expressions in the Crime Movies

This study focuses on (1) the pragmalinguistics forms of anger expressions used by the characters in the crime movies, and (2) the intentions of expressing anger by the characters in the crime movies. This study is a qualitative research which describes the data systematically. The data of this study were the entire conversations which contained anger expressions in the crime movies. In collecting the data the researcher used observation and documentation methods. The data were analyzed by using Madow’s theory of pragmalinguistics form of anger expressions, Searle’s theory of speech act, and Leech’s theory of speech situation. The result of the study revealed that there are three pragmalinguistics forms of anger expressions used by the characters. Those forms of anger expressions are direct form (53%), thinly veiled form (45%), and indirect form (2%). Direct anger form is the most dominant anger form appeared in those movies. The result of the study also showed that there are thirteen intentions of expressing anger. They are questioning (23%), asserting (21%), swearing (11%), commanding (11%), criticizing (10%), mocking (4%), disbelieving (4%), ordering (4%), suggesting (4%), disagreeing (2%), warning (2%), refusing (2%), and declaring (2%). Questioning is the most dominant intention used by the characters in those movies.
Minimizing the Reprojection Error in Surface Reconstruction from Images

This paper addresses the problem of image-based surface reconstruction. The main contribution is the computation of the exact derivative of the reprojection error functional. This allows its rigorous minimization via gradient descent surface evolution. The main difficulty has been to correctly take into account the visibility changes that occur when the surface moves. A geometric and analytical study of these changes is presented and used for the computation of derivative. Our analysis shows the strong influence that the movement of the contour generators has on the reprojection error. As a consequence, during the proper minimization of the reprojection error, the contour generators of the surface are automatically moved to their correct location in the images. Therefore, current methods adding additional silhouettes or apparent contour constraints to ensure this alignment can now be understood and justified by a single criterion: the reprojection error.
Transform-based image enhancement algorithms with performance measure

This paper presents a new class of the "frequency domain"-based signal/image enhancement algorithms including magnitude reduction, log-magnitude reduction, iterative magnitude and a log-reduction zonal magnitude technique. These algorithms are described and applied for detection and visualization of objects within an image. The new technique is based on the so-called sequency ordered orthogonal transforms, which include the well-known Fourier, Hartley, cosine, and Hadamard transforms, as well as new enhancement parametric operators. A wide range of image characteristics can be obtained from a single transform, by varying the parameters of the operators. We also introduce a quantifying method to measure signal/image enhancement called EME. This helps choose the best parameters and transform for each enhancement. A number of experimental results are presented to illustrate the performance of the proposed algorithms.
Truck Platooning Based on Lead Vehicle Speed Profile Optimization and Artificial Physics

Several approaches to truck platooning over varying road topographies are introduced, evaluated, and compared. A simple, stochastic optimization procedure was applied to the lead vehicle speed profiles (covering sections of 10 km), resulting in average lead vehicle fuel savings of around 15.4% relative to standard cruise control. Moreover, several models involving artificial physics were evaluated for the actual platooning, i.e. for the motion of the vehicles following the lead vehicle, with the aim of minimizing the total fuel consumption of the entire platoon. One such model, based on modified artificial gravity, was found to slightly outperform a more standard approach involving adaptive cruise control, while maintaining safety and coherence of the platoon.
A Numerical Study of the Performance of a Quantum Adiabatic Evolution Algorithm for Satisfiability

Quantum computation by adiabatic evolution, as described in quant-ph/0001106, will solve satisfiability problems if the running time is long enough. In certain special cases (that are classically easy) we know that the quantum algorithm requires a running time that grows as a polynomial in the number of bits. In this paper we present numerical results on randomly generated instances of an NP-complete problem and of a problem that can be solved classically in polynomial time. We simulate a quantum computer (of up to 16 qubits) by integrating the Schrodinger equation on a conventional computer. For both problems considered, for the set of instances studied, the required running time appears to grow slowly as a function of the number of bits.
Vision-Based Method for Forward Vehicle Detection and Tracking

Vehicle detection and tracking is the basis of advanced driver assistance system. This paper focused on improving the performance of vehicle detection system with single camera and proposed a vision-based method for forward vehicle detection and tracking. The shadow underneath vehicle was segmented accurately by using histogram analysis method and utilized to detect vehicle at daytime. The initial candidates were generated by combining horizontal and vertical edge feature of shadow, and these initial candidates were further verified by using a vehicle classifier based on the histogram of gradient and support vector machine. Kalman filters were used for tracking of the detected vehicles to improve system performance. The results show that the proposed method could be adapt to different illumination circumstances robustly and has a detection rate of 95.78 percent and a false rate of 1.97 percent in normal light condition.
MR-Based PET Motion Correction Procedure for Simultaneous MR-PET Neuroimaging of Human Brain

Positron Emission Tomography (PET) images are prone to motion artefacts due to the long acquisition time of PET measurements. Recently, simultaneous magnetic resonance imaging (MRI) and PET have become available in the first generation of Hybrid MR-PET scanners. In this work, the elimination of artefacts due to head motion in PET neuroimages is achieved by a new approach utilising MR-based motion tracking in combination with PET list mode data motion correction for simultaneous MR-PET acquisitions. The method comprises accurate MR-based motion measurements, an intra-frame motion minimising and reconstruction time reducing temporal framing algorithm, and a list mode based PET reconstruction which utilises the Ordinary Poisson Algorithm and avoids axial and transaxial compression. Compared to images uncorrected for motion, an increased image quality is shown in phantom as well as in vivo images. In vivo motion corrected images show an evident increase of contrast at the basal ganglia and a good visibility of uptake in tiny structures such as superior colliculi.
Sexting as 'Sexual Behavior' under Rape Shield Laws

As part of the proliferation of online communications, there has been a global increase in sexually explicit social media messages and consensual sexting among teenagers and adults of all ages. As a result, these kinds of electronic communications have begun to be used as evidence in a wide variety of court cases, including sexual harassment and discrimination cases. However, courts have only begun to consider whether such communications, particularly sexting communications, should be usable to impeach a sexual assault complainant, or whether these kinds of communications should be protected under rape shield laws as sexual “conduct” or “behavior. ” This article traces the history of rape shield laws in four common law countries: the United States, Canada, the United Kingdom, and Australia, and, using the history and purpose of these laws, argues that sexting should be protected under rape shield laws to protect sexual assault victims from unnecessary questioning about evidence that is likely to be embarrassing, prejudicial, and irrelevant to the case. ________________________________________________________________________
Global Optimization for Semi-supervised K-means

So far most of the K-means algorithms use the number of the labeled data as the K value, but sometimes it doesn’t work well. In this paper, we propose a semi-supervised K-means algorithm based on the global optimization. It can select an appropriate number of clusters as the K value directly and plan a great amount of supervision data by using only a small amount of the labeled data. Combining the distribution characteristics of data sets and monitoring information in each cluster after clustering, we use the voting rule to guide the cluster labeling in the data sets. The experiments indicated that the global optimization algorithm for semi-supervised K-means is quite helpful to improve the K-means algorithm, it can effectively find the best data sets for K values and clustering center and enhancing the performance of clustering.
IDL: sharing intermediate representations

IDL (Interface Description Language) is a practical and useful tool for controlling the exchange of structured data between different components of a large system. IDL is a notation for describing collections of programs and the data structures through which they communicate. Using IDL, a designer gives abstract descriptions of data structures, together with representation specifications that specialize the abstract structures for particular programs. A tool, the IDL translator, generates readers and writers that map between concrete internal representations and abstract exchange representations.
Vitamin D in Early Childhood and the Effect on Immunity to Mycobacterium tuberculosis

A potential role for vitamin D as a therapeutic immunomodulator in tuberculosis (TB) has been recognised for over 150 years, but has only recently returned to the centre of the research arena due to the increasing awareness of the global vitamin D deficiency epidemic. As early as birth a child is often deficient in vitamin D, which may not only affect their bone metabolism but also modulate their immune function, contributing to the increased susceptibility to many infections seen early in life. Recent studies have begun to explain the mechanisms by which vitamin D affects immunity. Antimicrobial peptides are induced in conjunction with stimulation of innate pattern recognition receptors enhancing immunity to particular infections. In contrast the role of vitamin D within the adaptive immune response appears to be more regulatory in function, perhaps as a mechanism to reduce unwanted inflammation. In this paper we focus on the effect of vitamin D on immunity to TB. Where much of the attention has been paid by past reviews to the role of vitamin D in adult TB patients, this paper, where possible, focuses on research in paediatric populations.