Miracle-dz/UniFAR-FTUs huggingface dataset:
Accumulation of segmental alterations determines progression in neuroblastoma.

PURPOSE Neuroblastoma is characterized by two distinct types of genetic profiles, consisting of either numerical or segmental chromosome alterations. The latter are associated with a higher risk of relapse, even when occurring together with numerical alterations. We explored the role of segmental alterations in tumor progression and the possibility of evolution from indolent to aggressive genomic types. PATIENTS AND METHODS Array-based comparative genomic hybridization data of 394 neuroblastoma samples were analyzed and linked to clinical data. RESULTS Integration of ploidy and genomic data indicated that pseudotriploid tumors with mixed numerical and segmental profiles may be derived from pseudotriploid tumors with numerical alterations only. This was confirmed by the analysis of paired samples, at diagnosis and at relapse, as in tumors with a purely numerical profile at diagnosis additional segmental alterations at relapse were frequently observed. New segmental alterations at relapse were also seen in patients with segmental alterations at diagnosis. This was not linked to secondary effects of cytotoxic treatments since it occurred even in patients treated with surgery alone. A higher number of chromosome breakpoints were correlated with advanced age at diagnosis, advanced stage of disease, with a higher risk of relapse, and a poorer outcome. CONCLUSION These data provide further evidence of the role of segmental alterations, suggesting that tumor progression is linked to the accumulation of segmental alterations in neuroblastoma. This possibility of genomic evolution should be taken into account in treatment strategies of low- and intermediate-risk neuroblastoma and should warrant biologic reinvestigation at the time of relapse.
Error‐correction Mechanism Tests for Cointegration in a Single‐equation Framework

A new test is proposed for cointegration in a single‐equation framework where the regressors are weakly exogenous for the parameters of interest. The test is denoted as an error‐correction mechanism (ECM) test and is based upon the ordinary least squares coefficient of the lagged dependent variable in an autoregressive distributed lag model augmented with leads of the regressors. The limit distributions of the standardized coeffi cient and t‐ratio versions of the ECM tests are obtained and critical values are provided. These limit distributions do not depend upon nuisance parameters but they depend on the number of regressors. Finally, we compare their power properties with those of other cointegration tests available in the literature and find the circumstances under which the ECM tests have a better performance.
Cycle and phase accurate DSP modeling and integration for HW/SW co-verification

We present our practical experience in the modeling and integration of cycle/phase-accurate instruction set architecture (ISA) models of digital signal processors (DSPs) with other hardware and software components. A common approach to the modeling of processors for HW/SW co-verification relies on instruction-accurate ISA models combined (i.e. wrapped) with the bus interface model (BIM) that generate the clock/phase-accurate timing at the component's interface pins. However, for DSPs and new microprocessors with complex architectural features this approach is from our perspective not acceptable. The additional extensive modeling of the pipeline and other architectural details in the BIM would force us to develop two detailed processor models with a complex BIM API between them. We therefore propose an alternative approach in which the processor ISAs themselves are modeled in a full cycle/phase-accurate fashion. The bus interface model is then reduced to just modeling the connection to the pins. Our models have been integrated into a number of cycle-based and event-driven system simulation environments. We present one such experience in incorporating these models into a VHDL environment. The accuracy has been verified cycle-by-cycle against the gate/RTL level models. Multiprocessor debugging and observability into the precise cycle-accurate processor state is provided. The use of co-verification models in place of the RTL resulted in system speedups up to 10 times, with the cycle-accurate ISA models themselves reaching performances of up to 123 K cycles/s.
Seismic reflector imaging using internal multiples with Marchenko-type equations

We present an imaging method that creates a map of reflection coefficients in correct one-way time with no contamination from internal multiples using purely a filtering approach. The filter is computed from the measured reflection response and does not require a background model. We demonstrate that the filter is a focusing wavefield that focuses inside a layered medium and removes all internal multiples between the surface and the focus depth. The reflection response and the focusing wavefield can then be used for retrieving virtual vertical seismic profile data, thereby redatuming the source to the focus depth. Deconvolving the upgoing by the downgoing vertical seismic profile data redatums the receiver to the focus depth and gives the desired image. We then show that, for oblique angles of incidence in horizontally layered media, the image of the same quality as for 1D waves can be constructed. This step can be followed by a linear operation to determine velocity and density as a function of depth. Numerical simulations show the method can handle finite frequency bandwidth data and the effect of tunneling through thin layers.
Sweepers in the CNS: Microglial Migration and Phagocytosis in the Alzheimer Disease Pathogenesis

Microglia are multifunctional immune cells in the central nervous system (CNS). In the neurodegenerative diseases such as Alzheimer's disease (AD), accumulation of glial cells, gliosis, occurs in the lesions. The role of accumulated microglia in the pathophysiology of AD is still controversial. When neuronal damage occurs, microglia exert diversified functions, including migration, phagocytosis, and production of various cytokines and chemokines. Among these, microglial phagocytosis of unwanted neuronal debris is critical to maintain the healthy neuronal networks. Microglia express many surface receptors implicated in phagocytosis. It has been suggested that the lack of microglial phagocytosis worsens pathology of AD and induces memory impairment. The present paper summarizes recent evidences on implication of microglial chemotaxis and phagocytosis in AD pathology and discusses the mechanisms related to chemotaxis toward injured neurons and phagocytosis of unnecessary debris.
Hidden Topic Markov Models

Algorithms such as Latent Dirichlet Allocation (LDA) have achieved significant progress in modeling word document relationships. These algorithms assume each word in the document was generated by a hidden topic and explicitly model the word distribution of each topic as well as the prior distribution over topics in the document. Given these parameters, the topics of all words in the same document are assumed to be independent. In this paper, we propose modeling the topics of words in the document as a Markov chain. Specifically, we assume that all words in the same sentence have the same topic, and successive sentences are more likely to have the same topics. Since the topics are hidden, this leads to using the well-known tools of Hidden Markov Models for learning and inference. We show that incorporating this dependency allows us to learn better topics and to disambiguate words that can belong to different topics. Quantitatively, we show that we obtain better perplexity in modeling documents with only a modest increase in learning and inference complexity.
Quality of Life in Brazilian Breast Cancer Survivors Age 45–65 Years: Associated Factors

Abstract: The objectives of this study were to evaluate quality of life (QOL) and identify its associated factors in climacteric women with a history of breast cancer. A cross‐sectional study was performed including 75 breast cancer survivors age 45–65 years who had undergone complete oncologic treatment and nonusers of hormone therapy or tamoxifen in the last 6 months. Sociodemographic and clinical characteristics in addition to the prevalence of climacteric symptoms were evaluated. QOL was evaluated by the Medical Outcomes Study 36‐item Short‐Form Health Survey (SF‐36) questionnaire, including eight components that can be condensed into two summaries: a physical component summary (physical functioning, role‐physical, body pain, general health) and a mental component summary (vitality, social functioning, role‐emotional, and mental health). Generalized linear models were used to analyze the data, allowing the identification of factors affecting QOL, adjusting for confounding variables. The mean age of the participants was 53.1 ± 5.9 years. Breast cancer survivors reported good QOL. The most prevalent symptoms were nervousness (69%) and hot flashes (56%). Factors associated with poorer QOL were dizziness, postmenopausal status, and breast‐conserving therapy (physical component), as well as insomnia and being married (mental component). In conclusion, participants demonstrated good QOL. We identified factors that may influence QOL in women with breast cancer, highlighting being married, climacteric symptoms, postmenopausal status, and breast‐conserving therapy. Given the impact of these factors, health professionals and patients must discuss choices for alleviating climacteric symptoms and explanations for the potential repercussions of breast cancer treatment.
Kleptocracy and Divide-and-Rule: A Model of Personal Rule

Many developing countries have suffered under the personal rule of kleptocrats, who implement highly inefficient economic policies, expropriate the wealth of their citizens, and use the proceeds for their own glorification or consumption. We argue that the success of kleptocrats rests, in part, on their ability to use a divide-and-rule strategy, made possible by the weakness of institutions in these societies. Members of society need to cooperate in order to depose a kleptocrat, yet such cooperation may be defused by imposing punitive rates of taxation on any citizen who proposes such a move, and redistributing the benefits to those who need to agree to it. Thus the collective action problem can be intensified by threats which remain off the equilibrium path. In equilibrium, all are exploited and no one challenges the kleptocrat. Kleptocratic policies are more likely when foreign aid and rents from natural resources provide rulers with substantial resources to buy off opponents; when opposition groups are shortsighted; when the average productivity in the economy is low; and when there is greater inequality between producer groups (because more productive groups are more difficult to buy off). (JEL: O12, H00) Copyright (c) 2004 The European Economic Association.
Conversion of Procedural Morphologies to Finite-State Morphologies: A Case Study of Arabic

In this paper we describe a conversion of the Buckwalter Morphological Analyzer for Arabic, originally written as a Perl-script, into a pure finite-state morphological analyzer. Representing a morphological analyzer as a finite-state transducer (FST) confers many advantages over running a procedural affix-matching algorithm. Apart from application speed, an FST representation immediately offers various possibilities to flexibly modify a grammar. In the case of Arabic, this is illustrated through the addition of the ability to correctly parse partially vocalized forms without overgeneration, something not possible in the original analyzer, as well as to serve both as an analyzer and a generator.
Stress responsivity and socioeconomic status: a mechanism for increased cardiovascular disease risk?

AIMS Low socioeconomic status is associated with increased cardiovascular disease risk. We hypothesized that psychobiological pathways, specifically slow recovery in blood pressure and heart rate variability following mental stress, partly mediate social inequalities in risk. METHODS AND RESULTS Participants were 123 men and 105 women in good health aged 47-58 years drawn from the Whitehall II cohort of British civil servants. Grade of employment was the indicator of socioeconomic status. Cardiovascular measures were monitored during performance of two behavioural tasks, and for 45 min following stress. Post-stress return of blood pressure and heart rate variability to resting levels was less complete after 45 min in the medium and low than in the high grade of employment groups. The odds of failure to return to baseline by 45 min in the low relative to the high grade of employment groups were 2.60 (95% CI 1.20-5.65) and 3.85 (1.48-10.0) for systolic and diastolic pressure, respectively, and 5.19 (1.88-18.6) for heart rate variability, adjusted for sex, age, baseline levels and reactions to tasks. Subjective ratings of task difficulty, involvement and stress did not differ by socioeconomic status. CONCLUSIONS Lower socioeconomic status is associated with delayed recovery in cardiovascular function after mental stress. Impaired recovery may reflect heightened allostatic load, and constitute a mechanism through which low socioeconomic status enhances cardiovascular disease risk.
Refining the treatment of membrane proteins by coarse‐grained models

Obtaining a quantitative description of the membrane proteins stability is crucial for understanding many biological processes. However the advance in this direction has remained a major challenge for both experimental studies and molecular modeling. One of the possible directions is the use of coarse‐grained models but such models must be carefully calibrated and validated. Here we use a recent progress in benchmark studies on the energetics of amino acid residue and peptide membrane insertion and membrane protein stability in refining our previously developed coarse‐grained model (Vicatos et al., Proteins 2014;82:1168). Our refined model parameters were fitted and/or tested to reproduce water/membrane partitioning energetics of amino acid side chains and a couple of model peptides. This new model provides a reasonable agreement with experiment for absolute folding free energies of several β‐barrel membrane proteins as well as effects of point mutations on a relative stability for one of those proteins, OmpLA. The consideration and ranking of different rotameric states for a mutated residue was found to be essential to achieve satisfactory agreement with the reference data. Proteins 2016; 84:92–117. © 2015 Wiley Periodicals, Inc.
The Dynamics of Entrepreneurship: Evidence from Global Entrepreneurship Monitor Data

Learning about entrepreneurship has major implications for the way we understand economic change and progress. At a time when governments all over the world look to entrepreneurship as a way to increase the wealth and well-being of their countries, The Dynamics of Entrepreneurship examines the causes of differences in entrepreneurial propensity between individuals, the factors that explain variations in the type and quantity of entrepreneurship at the aggregate level, and the macroeconomic implications of entrepreneurship. Using Global Entrepreneurship Monitor (GEM) data, the book brings together contributions from leading scholars to provide a comprehensive overview of current scholarship on entrepreneurial activity. Discussed topics include entrepreneurial motivation, gender and migration, entrepreneurial financing, urban entrepreneurship, growth-oriented entrepreneurship, economic growth, and regional entrepreneurship policies. The book concludes by summarizing its contribution to existing literature, with particular attention paid to the policy implications and the ongoing debate on entrepreneurship. Contributors to this volume - Maria Minniti (Southern Methodist University) Philipp Koellinger (Erasmus University) Christian Schade (Humboldt University) Elaine Allen (Babson College) Nan Langowitz (Babson College) Jonathan Levie (University of Strathclyde) Mark Hart (University of Aston). William Bygrave (Babson College) Niels Bosma (Utrecht University) Ramona Heck (CUNY - Baruch College) Edward Rogoff (CUNY - Baruch College) Zoltan Acs (George Mason University) Rolf Sternberg (Leibniz Universitat Hannover) Roy Thurik (Erasmus University) Chantal Hartog (EIM Business and Policy Research) Erik Stam (Cambridge University) Andre van Stel (University of Amsterdam) Ernesto Amoros (Universidad del Desarrollo) Oscar Cristi (Universidad del Desarrollo) Saul Estrin (London School of Economics) Tomasz Mickiewicz (University College of London) Kent Jones (Babson College) Megan Way (Babson College) David Audretsch (Indiana University)
Column Generation for Bi-Objective Vehicle Routing Problems with a Min-Max Objective

Column generation has been very useful in solving single objective vehicle routing problems (VRPs). Its role in a branch-and-price algorithm is to compute a lower bound which is then used in a branch-and-bound framework to guide the search for integer solutions. In spite of the success of the method, only a few papers treat its application to multi-objective problems and this paper seeks to contribute in this respect. We study how good lower bounds for bi-objective VRPs in which one objective is a min-max function can be computed by column generation. A way to model these problems as well as a strategy to effectively search for columns are presented. We apply the ideas to two VRPs and our results show that strong lower bounds for this class of problems can be obtained in "reasonable" times if columns are intelligently managed. Moreover, the quality of the bounds obtained from the proposed model are significantly better than those obtained from the corresponding "standard" approach.
WREATH PRODUCTS IN MODULAR GROUP ALGEBRAS OF SOME FINITE 2-GROUPS

Let K be field of characteristic 2 and let G be a finite non- abelian 2-group with the cyclic derived subgroup G 0 , and there exists a central element z of order 2 in Z(G)\G 0 . We prove that the unit group of the group algebra KG possesses a section isomorphic to the wreath product of a group of order 2 with the derived subgroup of the group G, giving for such groups a positive answer to the question of A. Shalev.
LINKAGE BETWEEN OUTPUT OF ELECTRIC ENERGY BY POLAR TISSUES AND CELL OXIDATION.

Evidence is presented in this report which it is believed establishes the following facts: (a) A quantitative relation exists between cell oxidation and the continuously maintained E.M. F. 's in the root of the onion, Allium cepa. (b) Equal change in oxygen concentration around different regions of the root tip produces an unequal change in E.M. F. ; in this way the characteristic distribution of'E.M. F. 's per unit length of root and therefore the pattern of the correlation currents in the root are modified in a characteristic manner by change in oxygen tension. (c) The velocity of oxygen consumption per unit volume of tissue is greatest in the region of active cell division, and the velocity of oxidation in this region is also changed to a greater degree by the same change in oxygen tension than in other regions of the root tip. This fact, which appears to have an important bearing upon the nature of bioelectric currents, was previously discovered in the Obelia stem (17). The experiments supply the connecting link in the evidence for the validity of the theory that the continuously maintained E.M. F. in a polar cell is that of a redox system maintained in state of flux equilibrium as defined elsewhere by one of us (17). There is a correspondence of morphological, functional, and electrical polarity along the root axis of A. cepa. In the unstimulated uninjured condition, the region of active cell division is invariably electropositive in the external circuit to more basal regions; and the distribution of potentials is in general characteristic but in detail specific for each root. For illustrations of the exact distribution of these potentials the reader is referred to the curves in the paper by LUND and KENYON (13). Under constant external conditions, spontaneous fluctuations in electric polarity occur and the distribution of E.M. F. per unit length varies from time to time (20). The first evidence that cell respiration and electric potentials on the root are linked phenomena was furnished by LUND and KENYON (13). They found that the greatest reduction of methylene blue per unit length occurs in the region of high positive potential, where active cell division takes place, and the same region also produces more CO2 per unit length. A corresponding distribution of the concentration of sulphydryl groups per unit length has been demonstrated; the region of active cell division exhibits the most intense color when the nitroprusside test is applied (17). 27
DNA Topoisomerase I from Mycobacterium smegmatis

A type I topoisomerase has been purified to homogeneity from Mycobacterium smegmatis. It is the largest single subunit enzyme of this class having molecular mass of 110 kDa. The enzyme is Mg2+ dependent and can relax negatively supercoiled DNA, catenate, and knot single-stranded DNA, thus having typical properties of type I topoisomerases. Furthermore, the enzyme makes single-stranded nicks and the 5′-phosphoryl end of the nicked DNA gets covalently linked with a tyrosine residue of the enzyme. However,M. smegmatis enzyme shows some distinctive features from the prototype Escherichia coli topoisomerase I. The enzyme is relatively stable at higher temperatures and not inhibited by spermidine. It apparently does not contain any bound Zn2+and on modification of cysteine residues retains the activity, suggesting the absence of the zinc-finger motif in DNA binding. Partially purified Mycobacterium tuberculosis topoisomerase I exhibits very similar properties with respect to size, stability, and reaction characteristics. Sequence comparison of topoisomerase I fromE. coli and M. tuberculosis shows the absence of zinc-finger motifs in mycobacterial enzyme. Using a two-substrate assay system, we demonstrate that the enzyme acts processively at low ionic strength and switches over to distributive mode at high Mg2+ concentration. Significantly, the enzyme activity is stimulated by single strand DNA-binding protein. There is a potential to exploit the characteristics of the enzyme to develop it as a molecular target against mycobacterial infections.
Training a parametric-based logF0 model with the minimum generation error criterion

This paper describes an approach for improving a statistical parametric-based logF0 model using minimum-generationerror (MGE) training. Compared with the previous scheme based on decision tree clustering, MGE allows the minimisation of the error in the generated logF0 to take into account not only each cluster by itself, but also the way in which the clusters interact with each other in the generation of the F0 over the whole sentence. Moreover, the “weights” of each component of the model, which previously were adjusted manually, are optimized automatically by the MGE training during the re-estimation of the model covariances. Objective evaluation indicated that, although the logF0 contours generated by the models trained with MGE have approximately the same root mean square error and correlation factor as those generated with the baseline models, they present a higher dynamic range. The subjective evaluation shows a small but significant preference for the system trained with MGE.