Miracle-dz/UniFAR-FTUs huggingface dataset:
Parameterized Algorithms for Partial Cover Problems

Covering problems are fundamental classical problems in optimization, computer science and complexity theory. Typically an input to these problems is a family of sets over a finite universe and the goal is to cover the elements of the universe with as few sets of the family as possible. The variations of covering problems include well known problems like Set Cover, Vertex Cover, Dominating Set and Facility Location to name a few. Recently there has been a lot of study on partial covering problems, a natural generalization of covering problems. Here, the goal is not to cover all the elements but to cover the specified number of elements with the minimum number of sets. In this paper we study partial covering problems in graphs in the realm of parameterized complexity. Classical (non-partial) version of all these problems have been intensively studied in planar graphs and in graphs excluding a fixed graph $H$ as a minor. However, the techniques developed for parameterized version of non-partial covering problems cannot be applied directly to their partial counterparts. The approach we use, to show that various partial covering problems are fixed parameter tractable on planar graphs, graphs of bounded local treewidth and graph excluding some graph as a minor, is quite different from previously known techniques. The main idea behind our approach is the concept of implicit branching. We find implicit branching technique to be interesting on its own and believe that it can be used for some other problems.
Assessment of Functional Impairment in Spanish Children

Le pressent travaux verifie l’applicabilite et la validite du CAFAS, un instrument pour evaluer l’incapacite fonctionnel dans une population espagnole. L’echantillon est forme par 441 malades ambulatoires psychiatriques d’entre 8 et 17 annees et leurs parents, et aussi par un echantillon de 74 malades ambulatoires pediatriques. On a applique differents instruments pour evaluer l’incapacite fonctionnel, la psychopathologie, et autres variables psychologiques. La fiabilite intra observateur varie entre moderee et bonne. L’accord entre les ponctuations obtenues avec l’information des parents et des infants varie entre faible et moderee. Les correlations avec autres mesures d’incapacite et du fonctionnement sont significatives mais moderee. Les ponctuations CAFAS differencient significativement les enfants avec et sans psychopathologie. Les resultats obtenus avalisent l’utilisation du CAFAS pour les etudes en psychopathologie, en incapacite fonctionnel et pour planifier interventions et services de sante mental. The present work tests the applicability and validity of the CAFAS, an instrument for assessing functional impairment, in the Spanish population. The sample included 441 psychiatric outpatients from 8 to 17 years old and their parents, and a pediatric group of 74 outpatients. Different instruments for assessing functional impairment, psychopathology, and other related variables were used. Interrater reliability ranged from moderate to very good. Weak-to-moderate agreement between CAFAS scores based on information from parents and children was obtained. Correlations with other measures of impairment and functioning were moderate. CAFAS scores differentiated significantly between children with and without psychopathology. These results permit the use of the instrument for studies on psychopathology and functional impairment, and for planning intervention and mental health services.
Mining probabilistically frequent sequential patterns in uncertain databases

Data uncertainty is inherent in many real-world applications such as environmental surveillance and mobile tracking. As a result, mining sequential patterns from inaccurate data, such as sensor readings and GPS trajectories, is important for discovering hidden knowledge in such applications. Previous work uses expected support as the measurement of pattern frequentness, which has inherent weaknesses with respect to the underlying probability model, and is therefore ineffective for mining high-quality sequential patterns from uncertain sequence databases. In this paper, we propose to measure pattern frequentness based on the possible world semantics. We establish two uncertain sequence data models abstracted from many real-life applications involving uncertain sequence data, and formulate the problem of mining probabilistically frequent sequential patterns (or p-FSPs) from data that conform to our models. Based on the prefix-projection strategy of the famous PrefixSpan algorithm, we develop two new algorithms, collectively called U-PrefixSpan, for p-FSP mining. U-PrefixSpan effectively avoids the problem of "possible world explosion", and when combined with our three pruning techniques and one validating technique, achieves good performance. The efficiency and effectiveness of U-PrefixSpan are verified through extensive experiments on both real and synthetic datasets.
Differences in the Growth of Paired Ugandan Isolates of Mycobacterium tuberculosis within Human Mononuclear Phagocytes Correlate with Epidemiological Evidence of Strain Virulence

ABSTRACT Previous studies have suggested that isolates of Mycobacterium tuberculosis responsible for tuberculosis outbreaks grow more rapidly within human mononuclear phagocytes than do other isolates. Clinical scenarios suggesting virulence of specific M. tuberculosis isolates are readily identified. Determination of appropriate “control” isolates for these studies is more problematic, but equally important for validating these assays and, ultimately, for identifying biologic differences between M. tuberculosis strains that contribute to virulence. We utilized the database from a study of Ugandan tuberculosis patients and their household (HH) contacts to identify M. tuberculosis isolates transmitted within HH and nontransmitted control isolates. Isolate pairs were evaluated from matched HH in each of three clinical scenarios: (i) coprevalent disease and no disease, (ii) incident disease and no disease, and (iii) M. tuberculosis infection (purified protein derivative [PPD] positive) and no infection (PPD negative). Intracellular growth of paired organisms was determined in a blinded fashion using two models of intracellular infection in which we have previously demonstrated correlation between intracellular growth and strain virulence, primary human monocytes (MN) and THP-1 human macrophage-like cells. In both models, transmitted isolates from coprevalent disease HH displayed more rapid growth than nontransmitted control isolates. In the THP-1 model, this was also true of transmitted isolates from HH with incident disease and their controls. Differences in production of tumor necrosis factor alpha and interleukin-10 by matched isolates showed correlation with growth patterns in the THP-1 cells but not in MN. Paired isolates characterized in this manner may be of particular interest for further investigations of the virulence of M. tuberculosis.
Quantitative comparison between single-photon emission computed tomography and positron emission tomography imaging of lung ventilation with 99mTc-technegas and 68Ga-gallgas in patients with chronic obstructive pulmonary disease: A pilot study

The aim of this study was quantitative comparison between 68Ga-Gallgas positron emission tomography (PET) and 99mTc-Technegas single photon emission computed tomography (SPECT) for lung ventilation function assessment in patients with moderate-to-severe obstructive pulmonary disease and to identify image-derived texture features correlating to the physiologic parameters. Five patients with moderate-to-severe chronic obstructive pulmonary disease with PET and SPECT lung ventilation scans were selected for this study. Threshold-based segmentations were used to compare ventilated regions between both imaging techniques. Histograms of both scans were compared to reveal main differences in distributions of radiotracers. Volumes of segmentation as well as 50 textural features measured in the pulmonary region were correlated to the forced expiratory volume in 1 s (FEV1) as the relevant physiological variable. A better peripheral distribution of the radiotracer was observed in PET scans for three out of five patients. A segmentation threshold of 27% and 31% for normalized scans, for PET and SPECT respectively, was found optimal for volume correlation with FEV1. A high correlation (Pearson correlation coefficient >0.9) was found between 16 texture features measured from SPECT and 7 features measured from PET and FEV1. Quantitative measurements revealed different tracer distribution in both techniques. These results suggest that tracer distribution patterns may depend on the cause of the pulmonary obstruction. We found several texture features measured from SPECT to correlate to FEV1.
Population dynamics of human activated natural killer cells in culture

The growth kinetics and population dynamics of recombinent interleukin‐2 (rlL‐2) stimulated human natural killer (NK) cell–enriched populations were studied in vitro. The NK‐enriched populations was obtained from normal peripheral blood mononuclear cells (PBMNC) by immunomagnetic bead depletion of CD3+ and CD5+ T cells. The growth kinetics of NK cells, T cells, monocytes, and total cells are shown. In the absence of PBMNC accessory cells, the NK‐enriched population showed limited expansion. In the presence of PBMNC accessory cells, the NK‐enriched population expanded threefold more than in the absence of accessory cells due to increased NK cell growth rate and increased duration of exponential growth. Using a Transwell system, which separates two cell population by a polycarbonate membrane, the accessory cells were shown to act on the NK‐enriched population via a diffusible factor. Accessory cell conditioned media was able to replace the accessory cell population to stimulate NK cell expansion. A monocyte‐enriched population prepared by sheep red blood cell rosetting of T cells was extensively phenotyped and compared with the NK‐enriched populations. Although the final cultured cells were phenotypically homogeneous for CD56+/CD3− NK cells, the initial NK precusor populations appear to be different. Namely, the NK cell precursors in the monocyte‐enriched population were predominantly CD56+/CD2−. Kinetic equations were formulated for this culture system and the effects of major culture variables are investigated.
Measuring Audience Responses of Video Advertisements using Physiological Sensors

The selection of the audio track, the best timing to overlay the logo, and the overall duration, all these issues affect the effectiveness of immersive media. Since traditional methods to evaluate the user experience of potential consumers (e.g., surveys or eye tracking) have severe limitations, we used data gathered from physiological sensor to measure the viewers' watching experiences. In this paper we report how we used our own Galvanic Skin Response (GSR) sensors to measure audience experience for the two different audio tracks of a commercial. Our results show that our GSR technology can play an important role for the advertisement community. In contrast with surveys, using GSR data relevant results can be obtained even with small number of participants, and the viewers' experiences are more vividly visualized. This enables advertisers to, for example, be able to decide the proper length of a commercial.
Statistical modelling of craniofacial shape

With prior knowledge and experience, people can easily observe rich shape and texture variation for a certain type of objects, such as human faces, cats or chairs, in both 2D and 3D images. This ability helps us recognise the same person, distinguish different kinds of creatures and sketch unseen samples of the same object class. The process of capturing this prior knowledge is mathematically interpreted as statistical modelling. The outcome is a morphable model, a vector space representation of objects, that captures the variation of shape and texture. This thesis presents research aimed at constructing 3DMMs of craniofacial shape and texture using new algorithms and processing pipelines to offer enhanced modelling abilities over existing techniques. In particular, we present several fully automatic modelling approaches and apply them to a large dataset of 3D images of the human head, the Headspace dataset, thus generating the first public shape-and- texture 3D Morphable Model (3DMM) of the full human head. We call this the Liverpool-York Head Model, reflecting the data collection and statistical modelling respectively. We also explore the craniofacial symmetry and asymmetry in template morphing and statistical modelling. We propose a Symmetry-aware Coherent Point Drift (SA-CPD) algorithm, which mitigates the tangential sliding problem seen in competing morphing algorithms. Based on the symmetry-constrained correspondence output of SA-CPD, we present a symmetry-factored statistical modelling method for craniofacial shape. Also, we propose an iterative process of refinement for a 3DMM of the human ear that employs data augmentation. Then we merge the proposed 3DMMs of the ear with the full head model. As craniofacial clinicians like to look at head profiles, we propose a new pipeline to build a 2D morphable model of the craniofacial sagittal profile and augment it with profile models from frontal and top-down views. Our models and data are made publicly available online for research purposes.
Genetic Characterization of the Bile Salt Response in Lactobacillus plantarum and Analysis of Responsive Promoters In Vitro and In Situ in the Gastrointestinal Tract

ABSTRACT In this paper we describe the growth, morphological, and genetic responses of Lactobacillus plantarum WCFS1 to bile. Growth experiments revealed that a stepwise increase in the porcine bile concentration led to a gradual decrease in the maximal growth rate. Moreover, the final density reached by an L. plantarum culture growing in MRS containing 0.1% bile was approximately threefold lower than that in MRS lacking bile. The morphology of the cells grown in MRS containing 0.1% bile was investigated by scanning electron microscopy, which revealed that cells clumped together and had rough surfaces and that some of the cells had a shrunken and empty appearance, which clearly contrasted with the characteristic rod-shaped, smooth-surface morphology of L. plantarum cells grown in MRS without bile. An alr complementation-based genome-wide promoter screening analysis was performed with L. plantarum, which led to identification of 31 genes whose expression was potentially induced by 0.1% porcine bile. Remarkably, 11 membrane- and cell wall-associated functions appeared to be induced by bile, as were five functions involved in redox reactions and five regulatory factors. Moreover, the lp_0237 and lp_0775 genes, identified here as genes that are inducible by bile in vitro, were previously identified in our laboratory as important for L. plantarum in vivo during passage in the mouse gastrointestinal tract (P. A. Bron, C. Grangette, A. Mercenier, W. M. de Vos, and M. Kleerebezem, J. Bacteriol. 186:5721-5729, 2004). A quantitative reverse transcription-PCR approach focusing on these two genes confirmed that the expression level of lp_0237 and lp_0775 was significantly higher in cells grown in the presence of bile and cells isolated from the mouse duodenum than in cells grown on laboratory medium without bile.
Nanoindentation Behaviour and Microstructural Evolution of Annealed Single-Crystal Silicon

— The nanoindentation behaviour and transformation of annealed single-crystal silicon wafers are examined. The silicon specimens are annealed at temperatures of 250, 350 and 450ºC, respectively, for 15 minutes and are then indented to maximum loads of 30, 50 and 70 mN. The phase changes induced in the indented specimens are observed using transmission electron microscopy (TEM) and micro-Raman scattering spectroscopy (RSS). For all annealing temperatures, an elbow feature is observed in the unloading curve following indentation to a maximum load of 30 mN. Under higher loads of 50 mN and 70 mN, respectively, the elbow feature is replaced by a pop-out event. The elbow feature reveals a complete amorphous phase transformation within the indented zone, whereas the pop-out event indicates the formation of Si XII and Si III phases. The experimental results show that the formation of these crystalline silicon phases increases with an increasing annealing temperature and indentation load. The hardness and Young’s modulus both decrease as the annealing temperature and indentation load are increased.
Shrinkage-to-Tapering Estimation of Large Covariance Matrices

In this paper, we introduce a shrinkage-to-tapering approach for estimating large covariance matrices when the number of samples is substantially fewer than the number of variables (i.e., n,p→∞ and p/n→∞). The proposed estimator improves upon both shrinkage and tapering estimators by shrinking the sample covariance matrix to its tapered version. We first show that, under both normalized Frobenius and spectral risks, the minimum mean-squared error (MMSE) shrinkage-to-identity estimator is inconsistent and outperformed by a minimax tapering estimator for a class of high-dimensional and diagonally dominant covariance matrices. Motivated by this observation, we propose a shrinkage-to-tapering oracle (STO) estimator for efficient estimation of general, large covariance matrices. A closed-form formula of the optimal coefficient ρ of the proposed STO estimator is derived under the minimum Frobenius risk. Since the true covariance matrix is to be estimated, we further propose a STO approximating (STOA) algorithm with a data-driven bandwidth selection procedure to iteratively estimate the coefficient ρ and the covariance matrix. We study the finite sample performances of different estimators and our simulation results clearly show the improved performances of the proposed STO estimators. Finally, the proposed STOA method is applied to a real breast cancer gene expression data set.
Partitioned External-Memory Value Iteration

Dynamic programming methods (including value iteration, LAO*, RTDP, and derivatives) are popular algorithms for solving Markov decision processes (MDPs). Unfortunately, however, these techniques store the MDP model extensionally in a table and thus are limited by the amount of main memory available. Since the required space is exponential in the number of domain features, these dynamic programming methods are ineffective for large problems. To address this problem, Edelcamp et al. devised the external memory value iteration (EMVI) algorithm, which uses a clever sorting scheme to efficiently move parts of the model between disk and main memory. While EMVI can handle larger problems than previously addressed, the need to repeatedly perform external sorts still limits scalability. This paper proposes a new approach. We partition an MDP into smaller pieces (blocks), keeping just the relevant blocks in memory and performing Bellman backups block by block. Experiments show that our algorithm is able to solve large MDPs an order of magnitude faster than EMVI.
Metabolic host responses to infection by intracellular bacterial pathogens

The interaction of bacterial pathogens with mammalian hosts leads to a variety of physiological responses of the interacting partners aimed at an adaptation to the new situation. These responses include multiple metabolic changes in the affected host cells which are most obvious when the pathogen replicates within host cells as in case of intracellular bacterial pathogens. While the pathogen tries to deprive nutrients from the host cell, the host cell in return takes various metabolic countermeasures against the nutrient theft. During this conflicting interaction, the pathogen triggers metabolic host cell responses by means of common cell envelope components and specific virulence-associated factors. These host reactions generally promote replication of the pathogen. There is growing evidence that pathogen-specific factors may interfere in different ways with the complex regulatory network that controls the carbon and nitrogen metabolism of mammalian cells. The host cell defense answers include general metabolic reactions, like the generation of oxygen- and/or nitrogen-reactive species, and more specific measures aimed to prevent access to essential nutrients for the respective pathogen. Accurate results on metabolic host cell responses are often hampered by the use of cancer cell lines that already exhibit various de-regulated reactions in the primary carbon metabolism. Hence, there is an urgent need for cellular models that more closely reflect the in vivo infection conditions. The exact knowledge of the metabolic host cell responses may provide new interesting concepts for antibacterial therapies.
Activin A and Equine Chorionic Gonadotropin Recover Reproductive Dysfunction Induced by Neonatal Exposure to an Estrogenic Endocrine Disruptor in Adult Male Mice1

Abstract We aimed to elucidate the mechanism of action of estrogenic endocrine disruptors and the rescue of reproductive function, particularly the responsiveness of testes to eCG and/or activin A (ACT) after establishing reproductive disorders. Newborn male mice (n = 29) were randomly divided into an untreated group and three treatment groups that received diethylstilbestrol (DES; 100 μg per animal) subcutaneously on Postnatal Day 3 to establish reproductive disorders and daily treatment with PBS (controls: DES + PBS), eCG (eCG group: DES + eCG), or eCG + ACT (eCG + ACT group: DES + eCG + ACT) at 6–8 wk of age prior to mating. After treatment, the controls showed diminished Leydig cells in the testes and thin germ cell layers containing pyknotic germ cells and multinucleated cells. In the eCG and eCG + ACT groups, spermatids and Leydig cells increased markedly. The immunoexpression of androgen receptors in the eCG group and steroidogenic acute regulatory (STAR) protein in the eCG and eCG + ACT groups recovered to approximately the levels in the untreated group; plasma LH and testosterone levels also increased relative to those in the controls. In addition, the cell proliferation index, which is estimated from 5-bromo-2′-deoxyuridine immunoexpression in spermatogonia, increased significantly under eCG treatment, and even more with eCG + ACT. However, the numbers of germ and Leydig cells decreased at 12 wk of age. Thus, ACT and eCG help the testes to recover from the dysfunction induced by neonatal DES administration. Furthermore, the permanent male reproductive disorder induced by neonatal exposure to estrogenic agents may be more likely to result from dysfunction of the hypothalamic-pituitary axis than from dysfunction of the lower reproductive organs.