Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia

Most children with acute lymphoblastic leukemia (ALL) can be cured, but the prognosis is dismal for the minority of patients who relapse after treatment. To explore the genetic basis of relapse, we performed genome-wide DNA copy number analyses on matched diagnosis and relapse samples from 61 pediatric patients with ALL. The diagnosis and relapse samples typically showed different patterns of genomic copy number abnormalities (CNAs), with the CNAs acquired at relapse preferentially affecting genes implicated in cell cycle regulation and B cell development. Most relapse samples lacked some of the CNAs present at diagnosis, which suggests that the cells responsible for relapse are ancestral to the primary leukemia cells. Backtracking studies revealed that cells corresponding to the relapse clone were often present as minor subpopulations at diagnosis. These data suggest that genomic abnormalities contributing to ALL relapse are selected for during treatment, and they point to new targets for therapeutic intervention.
Denoising of Magnetic Resonance Images using Wavelet Domain Transform based methods

The field of image processing developed from electrical engineering as an extension to the signal processing branch. When the images are created, transmitted and decoded they are distorted by different type of noises. Thus further processing these images does not lead to good results. Hence it is necessary that data should be kept close to originality. In this paper the undecimated discrete wavelet transform (UDWT) is used for denoising of Magnetic Resonance Images (MRI). The Undecimated discrete wavelet transform is based on the idea of no decimation. It omits the down sampling at the decomposition step and up sampling at the synthesis step, thus it produces more precise information. A quantitative measure of comparison is provided by the Peak signal to noise ratio (PSNR) of the image and by the Mean structural similarity index metrics (MSSIM) of the image. KeywordsMagnetic Resonance Images (MRI), Mean structural similarity index metrics (MSSIM), Peak signal to noise ratio (PSNR), Undecimated discrete wavelet transform (UDWT)
Bilingual N-gram Statistical Machine Translation

This paper describes a statistical machine translation system that uses a translation model which is based on bilingual n-grams. When this translation model is log-linearly combined with four specific feature functions, state of the art translations are achieved for Spanish-to-English and English-to-Spanish translation tasks. Some specific results obtained for the EPPS (European Parliament Plenary Sessions) data are presented and discussed. Finally, future research issues are depicted.
Blood lead levels and dietary calcium intake in 1- to 11-year-old children: the Second National Health and Nutrition Examination Survey, 1976 to 1980.

Whether, and to what degree, dietary calcium is inversely associated with blood lead levels was examined in 2,926 black and white children, 1 to 11 years of age, from the Second National Health and Nutrition Examination Survey (NHANES II). Blood lead levels were significantly higher in black than in white children, whereas white children had significantly higher dietary calcium intake (P less than .0001). Using covariance analysis and multiple regression analysis, determinants of blood lead levels were assessed as follows. The dependent variable was log10 lead, with independent variables age, sex, race, height, Quetelet index, dietary intake of calcium, phosphorous, fat, carbohydrate, and calories, community size index, poverty index ratio, geographic region, urbanization index, and all two-way interactions of the preceding. In the multiple regression analysis, the following independent variables were significant, P less than . 05. Race (black) and sex (male) were positively associated with blood lead level (P less than .0001 for both). The lower the family income and the more urban the family residence, the higher were the blood lead levels (P less than .0001, less than .008, respectively). A significant independent inverse association of blood lead levels with year of examination was noted, reflecting a downward secular trend in blood lead levels. Height was inversely associated with blood lead level (P less than .0001). Dietary calcium intake was also inversely associated with blood lead level (P = .028). Dietary intake of phosphorous, fat, carbohydrate, and total calories were not significantly associated with blood lead levels. The most direct strategy for prevention of childhood lead poisoning involves primary prevention to reduce exposure. (ABSTRACT TRUNCATED AT 250 WORDS)
Hybrid mobility model with pheromones for UAV detection task

Over the last years, the activities related to unmanned aerial vehicle have seen an exponential growth in several application domains. In that context, a great interest has been devoted to search and tracking scenarios, which require the development of novel UAV mobility management solutions. Recent works on mobility models have shown that bio-inspired algorithms such as ant colonies, have a real potential to tackle complex scenarios. Nevertheless, most of these algorithms are either modified path planning algorithms or dynamical algorithms with no a priori knowledge. This paper proposes H3MP, a hybrid model based on Markov chains and pheromones to take advantage of both static and dynamic methods. Markov chains are evolved to generate a global behavior guiding UAVs to promising areas while pheromones allow local and dynamical mobility management thanks to information sharing between UAVs via stigmergy. Experimental results demonstrate the ability of H3MP to rapidly detect and keep watch on targets compared to random and pheromone based models.
Dopamine Transporter (DAT) Inhibitors Alleviate Specific Parkinsonian Deficits in Monkeys: Association with DAT Occupancy in Vivo

Viable dopamine neurons in Parkinson's disease express the dopamine transporter (DAT) and release dopamine (DA). We postulated that potent DAT inhibitors, with low affinity for the serotonin transporter (SERT), may elevate endogenously released extracellular dopamine levels to provide therapeutic benefit. The therapeutic potential of eight DAT inhibitors was investigated in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-treated cynomolgus monkeys (Macaca fascicularis), with efficacy correlated with DAT occupancy as determined by positron emission tomography imaging in striatum. Four potent DAT inhibitors, with relatively high norepinephrine transporter, but low SERT affinities, that occupied the DAT improved activity in parkinsonian monkeys, whereas three high-affinity DAT inhibitors with low DAT occupancy did not. 2β-Carbomethoxy-3α-(3,4-dichlorophenyl)-7β-hydroxy-8-methyl-8-azabicyclo[3.2. 1. ]octane (O-1163) occupied the DAT but had short-lived pharmacological effects. The benztropine analog difluoropine increased general activity, improved posture, reduced body freeze, and produced sleep disturbances at high doses. (1R)-2β-(1-Propanoyl)-3α-(4-fluorophenyl)tropane (O-1369) alleviated parkinsonian signs in advanced parkinsonian monkeys, by increasing general activity, improving posture, reducing body freeze, and sedation, but not significantly reducing bradykinesia or increasing locomotor activity. In comparison with the D2-D3 DA receptor agonist quinelorane, O-1369 elicited oral/facial dyskinesias, whereas quinelorane did not improve posture or reduce balance and promoted stereotypy. In conclusion, DAT inhibitors with therapeutic potential combine high DAT affinity in vitro and high DAT occupancy of brain striatum in vivo with enduring day-time effects that do not extend into the nighttime. Advanced parkinsonian monkeys (80% DAT loss) respond more effectively to DAT inhibitors than mild parkinsonian monkeys (46% DAT loss). The therapeutic potential of dopamine transport inhibitors for Parkinson's disease warrants preclinical investigation.
Neurophysiological Measures and Developmental Dyslexia: Auditory Segregation Analysis

Les recentes etudes dans le domaine de la dyslexie soulignent les difficultes des enfants dyslexiques dans le traitement rapide de stimuli auditifs complexes. Nous etudions ici la segregation des sons co-occurrents chez des enfants dyslexiques et non dyslexiques au moyen de donnees comportementales et electro-physiologiques (les potentiels evoques). Vingt deux enfants âges de 8 a 12 ans, ont ete etudies ; la moitie presente une dyslexie phonologique. Cinq sons complexes dont la troisieme harmonique peut etre plus ou moins discordante par sa frequence sont presentes, les enfants doivent indiquer s’ils entendent un ou deux sons en utilisant des boutons reponses. Les composantes refletant les differents stades de traitement auditif precoce (N1a, b, c, P1a) ainsi que l’onde negative relative au traitement de l’objet (object-related negativity ORN) ont ete mesurees.Les performances des enfants dyslexiques sont legerement moins bonnes et leurs temps de reaction plus longs que les enfants non-dyslexiques. Les stimuli discordants evoquent des reponses plus larges ainsi que des latences retardees entre 150 et 200ms. Les dyslexiques presentent des composantes plus larges (N1a, ORN) et des composantes plus precoces (P1a, N1c) que les controles. Ainsi, les effets sont specifiques de la composante mesuree ce qui suggere que toutes les etapes du traitement precoce des frequences auditives ne sont pas affectees dans la dyslexie.
Corrected transposition of the great arteries without associated defects in adult patients: clinical profile and follow up.

OBJECTIVE--To assess the clinical course of adult patients with corrected transposition of the great arteries without associated anomalies. DESIGN--All patients with corrected transposition of the great arteries without associated anomalies were reviewed with complete clinical and echocardiographic assessment. The complications were evaluated in each decade. SETTING--Tertiary centre with a specific unit dealing with "grown-up" adolescent and adult congenital heart disease, designated as a quaternary centre and a general hospital with a referral centre for "grown-up" congenital heart disease. PATIENTS--18 patients (nine male and nine female) aged 16-61 years followed for 1-30 years (mean 10 years). RESULTS--There were no deaths. Six patients had a worsening ability index during follow up. Complications were: (a) complete heart block in seven, three of whom required pacemaker insertion; (b) significant left atrioventricular valve regurgitation in 50%, appearing only in the third decade (12%), with increasing frequency thereafter. Infective endocarditis was responsible for increasing left atrioventricular valve regurgitation in only one patient; (c) supraventricular arrhythmia appeared in the fifth decade, and occurred in all patients over the age of 60 years. One patient aged 61 had recurrent sustained ventricular tachycardia; and (d) congestive heart failure developed only after 50 years in 66%. One patient had severe left atrioventricular valve regurgitation; the function of the systemic ventricle was only moderately reduced in the other three. Three of the nine women had seven uneventful pregnancies. CONCLUSIONS--Patients with corrected transposition of the great arteries without associated defects may remain undiagnosed until adult life. Symptoms occur rarely before the fourth and fifth decades, when rhythm disturbance, left atrioventricular valve regurgitation, and moderately impaired systemic ventricular function cause congestive cardiac failure. The role of pacemaker insertion or surgery for left atrioventricular valve regurgitation needs further assessment.
Fucoidan from Seaweed Fucus vesiculosus Inhibits Migration and Invasion of Human Lung Cancer Cell via PI3K-Akt-mTOR Pathways

Background Recently there has been an increased interest in the pharmacologically active natural products associated with remedies of various kinds of diseases, including cancer. Fucoidan is a polysaccharide derived from brown seaweeds and has long been used as an ingredient in some dietary supplement products. Although fucoidan has been known to have anti-cancer activity, the anti-metastatic effects and its detailed mechanism of actions have been poorly understood. Therefore, the aims of this study were to demonstrate the anti-metastatic functions of fucoidan and its mechanism of action using A549, a highly metastatic human lung cancer cell line. Methods and Principal Findings Fucoidan inhibits the growth of A549 cells at the concentration of 400 µg/ml. Fucoidan treatment of non-toxic dose (0–200 µg/ml) exhibits a concentration-dependent inhibitory effect on the invasion and migration of the cancer cell via decreasing its MMP-2 activity. To know the mechanism of these inhibitory effects, Western blotting was performed. Fucoidan treatment down-regulates extracellular signal-related kinase 1 and 2 (ERK1/2) and phosphoinositide 3-kinase (PI3K)–Akt–mammalian target of rapamycin (PI3K-Akt-mTOR) pathways. Furthermore, fucoidan decreases the cytosolic and nuclear levels of Nuclear Factor-kappa B (p65). Conclusions/Significance The present study suggests that fucoidan exhibits anti-metastatic effect on A549 lung cancer cells via the down-regulation of ERK1/2 and Akt-mTOR as well as NF-kB signaling pathways. Hence, fucoidan can be considered as a potential therapeutic reagent against the metastasis of invasive human lung cancer cells.
Development of sensory systems in mammals

THE VISUAL SYSTEM: Prenatal Development of Visual System Structures Behavioral Analysis of Visual Development The Role of Experience in Visual Development THE AUDITORY SYSTEM: Development of Auditory System Structures Experiential Factors in Auditory System Development THE VESTIBULAR SYSTEM: Development of the Vestibular System THE SOMATOSENSORY SYSTEM: Peripheral Alteration and Somatosensory Development THE CHEMICAL SENSES: Olfactory Development Taste Development DEVELOPMENT OF SENSORY SYSTEMS IN OVERVIEW: Summary of Epigenic and Experiential Contributions Underlying Formation of Sensory Systems in Mammals Conclusions.
Measuring Acute Poverty in the Developing World: Robustness and Scope of the Multidimensional Poverty Index

This paper presents the Multidimensional Poverty Index (MPI), a measure of acute poverty, understood as a person’s inability to meet simultaneously minimum international standards in indicators related to the Millennium Development Goals and to core functionings. It constitutes the first implementation of the direct method to measure poverty for over 100 developing countries. After presenting the MPI, we analyse its scope and robustness, with a focus on the data challenges and methodological issues involved in constructing and estimating it. A range of robustness tests indicate that the MPI offers a reliable framework that can complement global income poverty estimates.
ExactU(Nc)→U(N1)×U(N2)factorization of Seiberg-Witten curves andN=1vacua

$\mathcal{N}=2$ gauge theories broken down to $\mathcal{N}=1$ by a tree level superpotential are necessarily at the points in the moduli space where the Seiberg-Witten curve factorizes. We find an exact solution to the factorization problem of Seiberg-Witten curves associated with the breaking of the ${U(N}_{c})$ gauge group down to two factors ${U(N}_{1})\ifmmode\times\else\texttimes\fi{}{U(N}_{2}). $ The result is a function of three discrete parameters and two continuous ones. We find discrete identifications between various sets of parameters and comment on their relation to the global structure of $\mathcal{N}=1$ vacua and their various possible dual descriptions. In an appendix we show directly that the integrality of the periods leads to factorization.
The Shaping of Inter-Organisational Information Systems: Main Design Considerations of an International Comparative Research Project

Based on a critical analysis of the literature on the development and adoption of interorganisational information systems (IOIS) we propose a new unit of analysis for IOIS studies, define levels of analysis based on this unit in order to organize a large set of variables pertinent to the study of IOIS, and show how this design will be implemented within an international collaborative research project. The main goal of our research is to shed light on the interaction between characteristics of IOIS and their development trajectories on the one hand and characteristics of industries and countries on the other hand. We expect that both, industry characteristics and characteristics of national environments have a significant influence on the type and development of IOIS but submit that understanding of these relationships is in its infancy and that significant new insights can be gained by carefully specifying the network level of analysis. Better understanding of the way IOIS are shaped can greatly assist in evaluating the extent to which adoption experiences in one industry or country can be validly used to inform policy choices in another industry or country.
Exploiting Procedural Domain Control Knowledge in State-of-the-Art Planners

Domain control knowledge (DCK) has proven effective in improving the efficiency of plan generation by reducing the search space for a plan. Procedural DCK is a compelling type of DCK that supports a natural specification of the skeleton of a plan. Unfortunately, most state-of-the-art planners do not have the machinery necessary to exploit procedural DCK. To resolve this deficiency, we propose to compile procedural DCK directly into PDDL2.1, thus enabling any PDDL2.1-compatible planner to exploit it. The contribution of this paper is threefold. First, we propose a PDDL-based semantics for an Algol-like, procedural language that can be used to specify DCK in planning. Second, we provide a polynomial algorithm that translates an ADL planning instance and a DCK program, into an equivalent, program-free PDDL2.1 instance whose plans are only those that adhere to the program. Third, we argue that the resulting planning instance is well-suited to being solved by domain-independent heuristic planners. To this end, we propose three approaches to computing domain-independent heuristics for our translated instances, sometimes leveraging properties of our translation to guide search. In our experiments on familiar PDDL planning benchmarks we show that the proposed compilation of procedural DCK can significantly speed up the performance of a heuristic search planner. Our translators are implemented and available on the web.
An ACT-R Model of the Evolution of Strategy Use and Problem Difficulty

Research has shown the importance of strategies in guiding problem solving behavior. The experiment and model presented here provide further specification of how more optimal strategies come to be adopted with experience. Isomorphs of the Tower of Hanoi were used to allow participants to develop a degree of expertise with a novel task. In the solutions, evidence for at least two strategies is apparent. The results suggest that when strategies are not successful in achieving the goal, other strategies may emerge and eventually come to dominate performance in a task. The ACT-R model of this task captures participant performance by using the same strategies to solve the problems and by gradually switching to more effective ones as simple strategies fail in solving the problems.
Supervisory control of DES using the positive invariance property

This document presents a method for the supervisory control of the discrete event systems modeled by Petri nets based on positive invariance property, largely used in the field of control and analysis of continuous systems. Contrary to the structural approach, this method gives necessary and sufficient conditions of inhibition/authorization of firing transitions ensuring the invariance of the polyhedron of constraints, with the assumption that the transitions of the given net are all controllable. This method gives for each transition, in which side (of space) it must be authorized in order to satisfy polyhedron constraints and the enabling condition of the considered transition.
A deterministic model for the occurrence and dynamics of multiple mutations in hierarchically organized tissues

Cancers are rarely caused by single mutations, but often develop as a result of the combined effects of multiple mutations. For most cells, the number of possible cell divisions is limited because of various biological constraints, such as progressive telomere shortening, cell senescence cascades or a hierarchically organized tissue structure. Thus, the risk of accumulating cells carrying multiple mutations is low. Nonetheless, many diseases are based on the accumulation of such multiple mutations. We model a general, hierarchically organized tissue by a multi-compartment approach, allowing any number of mutations within a cell. We derive closed solutions for the deterministic clonal dynamics and the reproductive capacity of single clones. Our results hold for the average dynamics in a hierarchical tissue characterized by an arbitrary combination of proliferation parameters. We show that hierarchically organized tissues strongly suppress cells carrying multiple mutations and derive closed solutions for the expected size and diversity of clonal populations founded by a single mutant within the hierarchy. We discuss the example of childhood acute lymphoblastic leukaemia in detail and find good agreement between our predicted results and recently observed clonal diversities in patients. This result can contribute to the explanation of very diverse mutation profiles observed by whole genome sequencing of many different cancers.
A genome-wide linkage scan for bone mineral density in an extended sample: evidence for linkage on 11q23 and Xq27

Background: Osteoporosis is a major public health problem, mainly quantified by low bone mineral density (BMD). The majority of BMD variation is determined by genetic effects. A pilot whole genome linkage scan (WGS) was previously reported in 53 white pedigrees with 630 subjects. Several genomic regions were suggested to be linked to BMD variation. Objective: To substantiate these previous findings and detect new genomic regions. Methods: A WGS was conducted on an extended sample where the size was almost tripled (1816 subjects from 79 pedigrees). All the subjects were genotyped with 451 microsatellite markers spaced ∼8.1 cM apart across the human genome. Two point and multipoint linkage analyses were carried out using the variance component method. Results: The strongest linkage signal was obtained on Xq27 with two point LOD scores of 4.30 for wrist BMD, and 2.57 for hip BMD, respectively. Another important region was 11q23, which achieved a maximum LOD score of 3.13 for spine BMD in multipoint analyses, confirming the results on this region in two earlier independent studies. Suggestive linkage evidence was also found on 7p14 and 20p12. Conclusions: Together with the findings from other studies, the current study has further delineated the genetic basis of bone mass and highlights the importance of increasing sample size to confirm linkage findings and to identify new regions of linkage.