Miracle-dz/UniFAR-FTUs huggingface dataset:
Bounds on the Complexity of the Longest Common Subsequence Problem

The problem of finding a longest common subsequence of two strings is discussed. This problem arises in data processing applications such as comparing two files and in genetic applications such as studying molecular evolution. The difficulty of computing a longest common subsequence of two strings is examined using the decision tree model of computation, in which vertices represent “equal - unequal” comparisons. It is shown that unless a bound on the total number of distinct symbols is assumed, every solution to the problem can consume an amount of time that is proportional to the product of the lengths of the two strings. A general lower bound as a function of the ratio of alphabet size to string length is derived. The case where comparisons between symbols of the same string are forbidden is also considered and it is shown that this problem is of linear complexity for a two-symbol alphabet and quadratic for an alphabet of three or more symbols.
- Based Sequence-to-Sequence Matching

Image-to-image matching methods (e.g., [Faugeras et al. 2001; Hartley and Zisserman 2000; Xu and Zhang 1996; Bergen et al. 1992; Szeliski and Shum 1997; Zhang et al. 1995; Zoghlami et al. 1997]) are inherently restricted to the information contained in individual images, i.e., the spatial variations within image frames (which capture the scene appearance). But there are cases when there is not enough common spatial information within the two images to allow reliable image matching. One such example is illustrated in Fig. 1. The input images 1.a and 1.b contain a single object, but we want to match (or align) the entire frame. Alignment of image 1.a to image 1.b is not uniquely defined (see Fig. 1.c). However, a video sequence contains much more information than any individual frame does. In particular, a video sequence captures information about scene dynamics such as the trajectory of the moving object shown in Fig. 1.d and 1.e, which in this case provides enough information for unique alignment both in space and in time (see Fig. 1.f). The scene dynamics, exemplified here by trajectories of moving objects, is a property that is inherent to the scene, and is thus common to all sequences recording the same scene, even when taken from different video cameras. It therefore forms an additional or alternative powerful cue for matching video sequences. The benefits of exploiting scene dynamics for matching sequences was noted before. Caspi and Irani [Caspi and Irani 2000] described a direct (intensity-based) sequence-to-sequence alignment method. Their method is based on finding the space-time transformation which minimizes the intensity differences (SSD) between the two sequences, and was applied to cases where the spatial relation between the sequences could be modeled by a 2D parametric transformation (a homography). It was shown to be useful for addressing rigid as well as complex non-rigid changes in the scene (e.g., flowing water), and changes in illumination. However, that method does not apply when the two sequences have different appearance properties, such as with sensors of different sensing modalities, nor when the spatial transformation between the two sequences is very large, such as in wide base-line matching, or in large differences in zoom. This paper illustrates a feature-based approach for space-time matching of video sequences. The “features” in our method are space-time trajectories constructed from moving objects. This approach can recover the 3D epipolar geometry between sequences recorded by widely separated video cameras, and can handle significant differences in appearance between the two sequences. The advantage of this approach over using regular feature-based image-to-image matching is illustrated in Fig. 2. This figure shows two sequences recording several small moving objects. Each feature point in the image-frame of Fig. 2.a (denoted by A-E) can in principle be matched to any other feature point in the image-frame
A Parametrizable Dataflow Implementation of Optical Flow

An increasing number of products feature complex functionality through the use of embedded computers. By collecting large amounts of data from multiple sensors and interpreting and responding to complex scenarios in realtime, such devices can become “smart. ” For a control algorithm to make a decision, data from the sensors must be processed before a certain deadline. These constraints may be hardor soft-real-time, and a combination of SRT or HRT applications may be executed on one platform [2]. In streaming applications such as multimedia and signal processing, the dataflow model of computation (MoC) is a good fit because these applications are inherently data-driven [3]. A dataflow program consists of a graph of actors that communicate tokens through channels. An actor can only fire (execute) if all of its input tokens are available, and if there is enough space on its outgoing channels to produce all tokens. Some dataflow flavours such as mode-controlled dataflow (MCDF) and scenario-aware dataflow (SADF) can be used to deal with dynamic behaviour within one application [4, 5]. In this research we consider the processing of image data to obtain direction vectors of moving objects, on the basis of which control algorithms can make decisions. In particular, we use the optical flow algorithm which is commonly used to track features in a sequence of moving images. To execute this algorithm on a contemporary multi-core streaming platform with high performance and while meeting timing constraints, it is useful have a dataflow implementation. Our implementation is based on the algorithm described in [1]. After refactoring in the C language and removal of any dependencies on the external libraries, we ported the algorithm to our CompSOC platform [2]. To distribute the functionality over multiple dataflow actors we recognized three main stages: the loading of frames into local memory, the initial detection of features in a frame, and the optical flow that detects identical features in two consecutive frames. After splitting the algorithm in these three stages it was parallelized and parametrized. The implementation thus obtained allows to exploit the benefits of the aforementioned mode-control and scenario-aware dataflow MoC, as the parameters can be used to set different modes or use-cases. Parallelization is straightforward as frames are split up in blocks and the calculation on each block is completely independent of other blocks. Parameters that can be adjusted are the frame size, the number of cores that will process a fraction of a frame in parallel, and optical flow parameters, namely: threshold, maximum allowed error and window size. The resulting graph for an implementation with two cores is depicted in Figure 1. Actor a is added to determine or receive the parameters, which are stored in its self-edge. These are forwarded to actor c, f and b.
Lifts of Convex Sets and Cone Factorizations

In this paper, we address the basic geometric question of when a given convex set is the image under a linear map of an affine slice of a given closed convex cone. Such a representation or lift of the convex set is especially useful if the cone admits an efficient algorithm for linear optimization over its affine slices. We show that the existence of a lift of a convex set to a cone is equivalent to the existence of a factorization of an operator associated to the set and its polar via elements in the cone and its dual. This generalizes a theorem of Yannakakis that established a connection between polyhedral lifts of a polytope and nonnegative factorizations of its slack matrix. Symmetric lifts of convex sets can also be characterized similarly. When the cones live in a family, our results lead to the definition of the rank of a convex set with respect to this family. We present results about this rank in the context of cones of positive semidefinite matrices. Our methods provide new tools for understanding cone lifts of convex sets.
Les compétences entrepreneuriales et le processus entrepreneurial: une approche dynamique

Depuis une trentaine d’annees, la recherche consacree a l’etude des competences a connu un essor considerable, notamment en sciences de gestion. Cependant, dans le champ de l’entrepreneuriat, la recherche dediee aux processus d’acquisition et de developpement des competences entrepreneuriales a peu evolue ces dernieres annees. Notre etude a pour objectif d’apporter un eclairage touchant a la conceptualisation des competences entrepreneuriales, dans le cadre d’une approche processuelle. Plus particulierement, nous nous focalisons sur l’identification des competences requises par l’entrepreneur tout au long du processus de creation d’entreprise. Pour ce faire, nous souscrivons a la modelisation de C. Bruyat (1993), ainsi qu’a l’approche processuelle de A. Fayolle (2005), selon lesquelles le processus de creation d’entreprise se decline en trois phases : le declenchement du processus, l’engagement de l’entrepreneur et la survie - developpement du projet « entreprise nouvelle ». Nous proposons donc une perspective cognitive permettant de mieux saisir les competences specifiques requises a chaque phase du processus entrepreneurial.
Characterization of Streptomyces albus 18-kilodalton heat shock-responsive protein

In Streptomyces albus during the heat shock response, a small heat shock protein of 18 kDa is dramatically induced. This protein was purified, and internal sequences revealed that S. albus HSP18 showed a marked homology with proteins belonging to the family of small heat shock proteins. The corresponding gene was isolated and sequenced. DNA sequence analysis confirmed that the hsp18 gene product is an analog of the 18-kDa antigen of Mycobacterium leprae. No hsp18 mRNA could be detected at 30 degrees C, but transcription of this gene was strongly induced following heat shock. The transcription initiation site was determined by nuclease S1 protection. A typical streptomycete vegetative promoter sequence was identified upstream from the initiation site. Disruption mutagenesis of hsp18 showed that HSP18 is not essential for growth in the 30 to 42 degrees C temperature range. However, HSP18 is involved in thermotolerance at extreme temperatures.
Crossover and stability of victim type in child molesters

Purpose: This study examined the degree to which child sex offenders demonstrated crossover in victim choice, as defined by age, gender, and relationship to the offender. It also aimed to explore the direction of the shift in victim type with repeated offending within each of the three domains and to identify variables predictive of crossover behaviour. Method: The sample comprised 128 adult male child sexual offenders. All had offended against multiple victims and were attending a community-based assessment and treatment service for sexual offenders at the time of data collection. Variables were gathered, coded, and de-identified from a manual search through clinical casenotes, from client assessment reports as well as from supplementary information consisting of sentencing remarks or other professional reports. Results: More than half of the sample (63.3%, N=81) demonstrated crossover in victim type across at least one domain. Crossover was 48.0% (N=59) in the age domain, 22.0% (N=28) in the gender domain, and 25.8% (N=33) in the relationship to victim domain. Crossover offending was associated with number of victims but unrelated to frequency of offending or to recidivism risk as assessed by a standard risk assessment instrument. Transitional matrices showed general stability in victim type across offences within the gender and relationship domains, but lower stability within the age domain. Conclusions: Crossover offending behaviour was found to be frequent in the age domain, but the high frequency of crossover in this domain may be artifactual. Crossover offending was less frequent in the gender and relationship domains, but should be taken into account in risk assessment. Victim type shows stability across multiple offences in the gender and relationship to victim domains. Analysis of victim type across multiple offences should be replicated under conditions where disclosure of offending is maximized.
Impact of policy and practice on the effectiveness of contact screening for tuberculosis.

BACKGROUND Screening for tuberculosis is conducted because TB is a disease of public health importance that can be prevented if screening is followed by isoniazid prophylaxis for infected individuals. Screening alone is not effective unless that screening is rational and systematic and is followed by prevention where appropriate. Our aim was to consider whether the TB contact screening guidelines are evidence-based and appropriate, how well these guidelines are implemented, and how policy and practice impact on prevention. METHODS A cohort of 1,142 recent contacts screened in 1991 in Victoria, Australia, was studied. We evaluated the appropriateness of the screening guidelines and how well they were implemented and how the combination of these two factors impacted on the efficacy of the screening program. RESULTS The screening guidelines required updating and were not evidence-based. Chest radiograph (CXR) was overused and was the sole screening tool for nearly 40% (449/1,142) of contacts. Eighty percent of repeat CXRs were done following a normal initial study. Skin testing was underused. In nearly 60% (658/1,142) of all contacts, the presence or absence of infection could not be determined because a skin test was not done and the CXR, if done, was clear. Only 22% (38/175) of identified, eligible contacts received isoniazid preventive therapy. CONCLUSIONS Lack of evidence-based guidelines, as well as poor adherence to guidelines, resulted in an inefficient program. This problem may not be unique to the study setting, but cannot be identified without systematic program evaluation, for which we have provided a model.
The role of short messaging service in supporting the delivery of healthcare: An umbrella systematic review

Short messaging service (SMS) messages may present a convenient and cost-effective method to support healthcare interventions. This work assesses the effects of short messaging service on various healthcare interventions found in systematic reviews. The search strategy was based on two key concepts: short messaging service and healthcare delivery. The initial search was conducted in December 2012 and was updated in June 2013. Of the 550 identified references, 13 systematic reviews met the inclusion criteria, of which 8 were published in peer-reviewed journals and 5 were retrieved from the Cochrane library. Data analysis shows that low to moderate research evidence exists on the benefits of short messaging service interventions for appointment reminders, promoting health in developing countries and preventive healthcare. In many interventions, however, there were a few studies that were of high quality, and most of the studies were rated from low to moderate quality or had no rating at all. Healthcare organizations, policy makers, or clinicians using short messaging service messages to support healthcare interventions should (1) implement interventions that have been found to work in healthcare settings, (2) continue evaluating short messaging service interventions that have not been adequately assessed, and (3) improve collaboration between various healthcare entities to develop studies targeted at specific populations to evaluate the long-term impact of short messaging service on healthcare outcomes.
The Size of the Viral Inoculum Contributes to the Outcome of Hepatitis B Virus Infection

ABSTRACT The impact of virus dose on the outcome of infection is poorly understood. In this study we show that, for hepatitis B virus (HBV), the size of the inoculum contributes to the kinetics of viral spread and immunological priming, which then determine the outcome of infection. Adult chimpanzees were infected with a serially diluted monoclonal HBV inoculum. Unexpectedly, despite vastly different viral kinetics, both high-dose inocula (1010 genome equivalents [GE] per animal) and low-dose inocula (10° GE per animal) primed the CD4 T-cell response after logarithmic spread was detectable, allowing infection of 100% of hepatocytes and requiring prolonged immunopathology before clearance occurred. In contrast, intermediate (107 and 104 GE) inocula primed the T-cell response before detectable logarithmic spread and were abruptly terminated with minimal immunopathology before 0.1% of hepatocytes were infected. Surprisingly, a dosage of 101 GE primed the T-cell response after all hepatocytes were infected and caused either prolonged or persistent infection with severe immunopathology. Finally, CD4 T-cell depletion before inoculation of a normally rapidly controlled inoculum precluded T-cell priming and caused persistent infection with minimal immunopathology. These results suggest that the relationship between the kinetics of viral spread and CD4 T-cell priming determines the outcome of HBV infection.
Distribution of Surface Protein Variants among Hyperinvasive Meningococci: Implications for Vaccine Design

ABSTRACT The bacterium Neisseria meningitidis is a major cause of meningitis and septicemia worldwide. Outer membrane proteins (OMPs) are candidates in the search for comprehensive meningococcal vaccines; however, the formulation of OMP vaccines is complicated by antigenic diversity, which is generated by high levels of genetic reassortment and strong positive selection in the meningococcal antigen genes. The genetic and antigenic diversity of three OMPs (FetA, PorA, and PorB) among a global collection of meningococcal isolates representative of the major hyperinvasive clonal complexes was determined. There was evidence for antigenic structuring among the three OMPs that could not be explained purely by descent. These observations violated the predictions of the clonal and epidemic clonal models of population structure but were in concordance with models of strain structure which propose that host immunity selects for nonoverlapping antigen combinations. The patterns of antigenic variant combinations suggested that an OMP-based vaccine with as few as six PorA and five FetA variant sequences could generate homologous immune responses against all 78 isolates examined.
Non-classical receptive-field inhibition and its relation to orientation-contrast pop-out and line and contour salience: A computational approach

These perceptual effects are related to a neural mechanism known as non-classical receptive field (non-CRF) inhibition or surround suppression. Its essence is that the response of an orientation selective neuron (in V1 or V2) to an optimal stimulus in its CRF is modulated, most commonly inhibited, by other stimuli outside the CRF, Fig. 2. For 24% of the cells, surround stimuli of the same orientation as the main stimulus over the CRF have stronger suppression effect than stimuli of other orientations [3]. We refer to this type of modulation as anisotropic inhibition.
Memory phenomena in the law

Memory issues arise in the law in many different ways. At the most fundamental level, assumptions about memory are inherent in both substantive laws and procedural rules that govern the operation of the legal system. For example, the rules and procedures used to govern the conduct of jury trials reflect a great deal of faith in jurors' ability to understand and retain information over long periods of time, often with much intervening information. Memory issues also arise in the context of individual cases. For example, the ability of an attorney to satisfactorily prosecute or defend a case on behalf of a client often relies largely upon the completeness and accuracy of the memory of the client and other witnesses. This paper discusses examples of memory issues in the law and describes how applied research on these issues can be used to inform basic memory theory, particularly with respect to the relationship between emotion and memory.
A Survey on Operational State Complexity

Descriptional complexity is the study of the conciseness of the various models representing formal languages. The state complexity of a regular language is the size, measured by the number of states of the smallest, either deterministic or nondeterministic, finite automaton that recognises it. Operational state complexity is the study of the state complexity of operations over languages. In this survey, we review the state complexities of individual regularity preserving language operations on regular and some subregular languages. Then we revisit the state complexities of the combination of individual operations. We also review methods of estimation and approximation of state complexity of more complex combined operations.
Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

Genetic dissection of complex, polygenic trait variation is a key goal of medical and evolutionary genetics. Attempts to identify genetic variants underlying complex traits have been plagued by low mapping resolution in traditional linkage studies, and an inability to identify variants that cumulatively explain the bulk of standing genetic variation in genome-wide association studies (GWAS). Thus, much of the heritability remains unexplained for most complex traits. Here we describe a novel, freely available resource for the Drosophila community consisting of two sets of recombinant inbred lines (RILs), each derived from an advanced generation cross between a different set of eight highly inbred, completely resequenced founders. The Drosophila Synthetic Population Resource (DSPR) has been designed to combine the high mapping resolution offered by multiple generations of recombination, with the high statistical power afforded by a linkage-based design. Here, we detail the properties of the mapping panel of >1600 genotyped RILs, and provide an empirical demonstration of the utility of the approach by genetically dissecting alcohol dehydrogenase (ADH) enzyme activity. We confirm that a large fraction of the variation in this classic quantitative trait is due to allelic variation at the Adh locus, and additionally identify several previously unknown modest-effect trans-acting QTL (quantitative trait loci). Using a unique property of multiparental linkage mapping designs, for each QTL we highlight a relatively small set of candidate causative variants for follow-up work. The DSPR represents an important step toward the ultimate goal of a complete understanding of the genetics of complex traits in the Drosophila model system.
Modelling and estimation of infectious diseases in a population with heterogeneous dynamic immunity

ABSTRACT The paper presents a model for the evolution of an infectious disease in a population with individual-specific immunity. The immune state of an individual varies with time according to its own dynamics, depending on whether the individual is infected or not. The model involves a system of size-structured (first-order) PDEs that capture both the dynamics of the immune states and the transition between compartments consisting of infected, susceptible, etc. individuals. Due to the unavailability of precise data about the immune states of the individuals, the main focus in the paper is on developing a technique for set-membership estimations of aggregated quantities of interest. The technique involves solving specific optimization problems for the underlying PDE system and is developed up to a numerical method. Results of numerical simulations are presented for a benchmark model of SIS-type, potentially applicable to diseases like influenza and to various sexually transmitted diseases.