Miracle-dz/UniFAR-FTUs huggingface dataset:
The Conservation of the Germline Multipotency Program, from Sponges to Vertebrates: A Stepping Stone to Understanding the Somatic and Germline Origins

The germline definition in metazoans was first based on few bilaterian models. As a result, gene function interpretations were often based on phenotypes observed in those models and led to the definition of a set of genes, considered as specific of the germline, named the “germline core”. However, some of these genes were shown to also be involved in somatic stem cells, thus leading to the notion of germline multipotency program (GMP). Because Porifera and Ctenophora are currently the best candidates to be the sister-group to all other animals, the comparative analysis of gene contents and functions between these phyla, Cnidaria and Bilateria is expected to provide clues on early animal evolution and on the links between somatic and germ lineages. Our present bioinformatic analyses at the metazoan scale show that a set of 18 GMP genes was already present in the last common ancestor of metazoans and indicate more precisely the evolution of some of them in the animal lineage. The expression patterns and levels of 11 of these genes in the homoscleromorph sponge Oscarella lobularis show that they are expressed throughout their life cycle, in pluri/multipotent progenitors, during gametogenesis, embryogenesis and during wound healing. This new study in a nonbilaterian species reinforces the hypothesis of an ancestral multipotency program.
The practicum in computer science education: bridging gaps between theoretical knowledge and actual performance

This article focuses on the practicum, one of the more important parts of computer science teacher preparation. During this stage, the prospective teachers practice the teaching of computer science in a high school setting before becoming actual computer science teachers. The practicum is highlighted in this article from three angles: the prospective teacher's perspective, the MTCS course perspective and the university mentor's perspective. For each perspective we illustrate the importance of the practicum by explaining how it bridges a specific gap. These gaps are illustrated by two examples that focus on content and pedagogical aspects of computer science education.
Comparing the effectiveness of testing methods in improving programs: the effect of variations in program quality

We compare the efficacy of different testing methods for improving the reliability of software. Specifically, we use modelling to compare "operational" testing, in which test cases are chosen according to their probability of occurring in actual use of the software, against "debug" testing methods, in which the testers look for test cases which they consider likely to cause failure, or that satisfy some coverage criterion. We base our comparisons on the reliability reached by the program at the end of testing. Differently from previous studies, we consider the probability distribution of the achieved reliability, and thus the probability of satisfying specific requirements, rather than just the average reliability achieved. We take account of two sources of variation. The variation between the actual test histories that are possible for a given program and a given test method: and the fact that different programs start testing with different faults and initial reliability levels. By necessity, we use very simplified models of reality. Yet, we can show some interesting conclusions with important practical consequences. In general, there are stronger arguments in favor of operational testing than previous studies have shown.
cells humanfactors revealed by genome-wide binding studies in multiple Cell-type specific and combinatorial usage of diverse transcription Material Supplemental

Material Supplemental http://genome.cshlp. org/content/suppl/2011/10/21/gr.127597. 111.DC1. html Related Content Genome Res. October , 2011 21: 1757-1767 Lingyun Song, Zhancheng Zhang, Linda L. Grasfeder, et al. that shape cell-type identity Open chromatin defined by DNaseI and FAIRE identifies regulatory elements References http://genome.cshlp. org/content/22/1/9.full. html#related-urls Article cited in: http://genome.cshlp. org/content/22/1/9.full. html#ref-list-1 This article cites 66 articles, 22 of which can be accessed free at:
La détection d’une expression faciale incongrue par rapport à un modèle de situation émotionnel : un défi neurocognitif?

La lecture de phrases evoquant un contexte emotionnel engendre un modele mental de situation emotionnel. Le but de cette these etait d’etudier les consequences electrophysiologiques et comportementales de la detection d’une expression faciale emotionnelle ne correspondant pas a l’attente creee par un modele de situation emotionnel. Nous avons egalement etudie la maniere dont l’empathie autoevaluee (a l’aide du questionnaire EQ ; Baron-Cohen et Wheelwright, 2004) pouvait affecter la maniere dont cette incongruite pragmatique emotionnelle etait traitee. Les resultats comportementaux ont montre, chez 32 participants, que l’incongruite pragmatique emotionnelle est plus difficile a detecter que la congruite pragmatique emotionnelle (plus d’erreurs de reconnaissance et des temps de reponses allonges). L’allongement des temps de reponses en condition incongrue etait d’autant plus grand que les habiletes sociales (mesurees a l’aide du questionnaire EQ) des participants etaient faibles. Les potentiels evoques neuroelectriques affectes par l’incongruite pragmatique emotionnelle etaient la N400, la LPN et, de maniere marginale, la P300. L’activite neuroelectrique evoquee dans la fenetre temporelle de la N400 n’etait pas affectee de la meme maniere par l’incongruite emotionnelle, selon le score a la sous-echelle EQ d’empathie cognitive des participants. Enfin, nous avons teste si les patients schizophrenes pouvaient valider les prerequis necessaires au traitement de l’incongruite pragmatique emotionnelle (effectuer une simulation emotionnelle et categoriser une expression faciale emotionnelle). D’apres nos resultats, ces prerequis peuvent etre remplis, meme s’ils semblent affectes par la pathologie, en particulier en ce qui concerne la categorisation des visages neutres. En conclusion, cette these a permis de mieux comprendre les mecanismes de la detection de l’incongruite emotionnelle et de mettre en valeur son importance sociale.
Dynamic contract layers

Design by Contract (DBC) is a programming technique to separate contract enforcement from application code. DBC provides information about the applicability of methods and helps to narrow down the search space in case of a software failure. However, most DBC implementations suffer from inflexibility: Contract enforcement can only be activated or deactivated at compile-time or start-up, contracts are checked globally and cannot be restricted in their scope such as to the current thread of execution, and contracts cannot be grouped according to the concerns they relate to. In this paper, we present dynamic contract layers (DCL) for fine-grained and flexible contract management. Based on ideas from context-oriented programming, we extend DBC by a grouping mechanism for contracts, thread-local activation and deactivation of such groups, and selective contract enforcement at run-time. PyDCL, our proof-of-concept implementation of DCL, is built onto ContextPy, our COP extension for the Python programming language. We evaluate our approach by applying PyDCL contracts to the Moin-Moin Wiki framework.
An experiment on simplifying conjoint analysis designs for measuring preferences.

In conjoint analysis (CA) studies, choosing between scenarios with multiple health attributes may be demanding for respondents. This study examined whether simplifying the choice task in CA designs, by using a design with more overlap of attribute levels, provides advantages over standard minimal-overlap methods. Two experimental conditions, minimal and increased-overlap discrete choice CA designs, were administered to 353 respondents as part of a larger HIV testing preference survey. In the minimal-overlap survey, all six attribute levels were allowed to vary. In the increased-overlap survey, an average of two attribute levels were the same between each set of scenarios. We hypothesized that the increased-overlap design would reduce cognitive burden, while minimally impacting statistical efficiency. We did not find any significant improvement in consistency, willingness to trade, perceived difficulty, fatigue, or efficiency, although several results were in the expected direction. However, evidence suggested that there were differences in stated preferences. The results increase our understanding of how respondents answer CA questions and how to improve future surveys.
The Methodology of Macroeconomic Thought: A Conceptual Analysis of Schools of Thought in Economics

This revised edition of the author's "Macroeconomic Thought: A Methodological Approach" argues for methodological awareness amongst practising economists as a basis for constructive debate and reasoned argument. The methodological content has been increased to include material on recent developments. After analyzing the historical and methodological development of each of the schools, the author covers the micro-foundations of their macroeconomics and their approaches to key concepts including equilibrium, expectations, money and macroeconomic policy. She seeks to indentify the sources of differences between schools of thought as well as potential and actual commonalities before examining their differences at conceptual level.
Clinicoeconomics and Outcomes Research Dovepress Costs and Health Care Resource Utilization among Chronic Obstructive Pulmonary Disease Patients with Newly Acquired Pneumonia

Background: Patients with chronic obstructive pulmonary disease (COPD) are at increased risk for lung infections and other pathologies (eg, pneumonia); however, few studies have evaluated the impact of pneumonia on health care resource utilization and costs in this population. The purpose of this study was to estimate health care resource utilization and costs among COPD patients with newly acquired pneumonia compared to those without pneumonia. Methods: A retrospective claims analysis using Truven MarketScan ® Commercial and Medicare databases was conducted. COPD patients with and without newly acquired pneumonia diagnosed between January 1, 2004 and September 30, 2011 were identified. Propensity score matching was used to create a 1:1 matched cohort. Patient demographics, comorbidities (measured by Charlson Comorbidity Index), and medication use were evaluated before and after matching. Health care resource utilization (ie, hospitalizations, emergency room [ER] and outpatient visits), and associated health care costs were assessed during the 12-month follow-up. Logistic regression was conducted to evaluate the risk of hospitalization and ER visits, and gamma regression models and two-part models compared health care costs between groups after matching. Results: In the baseline cohort (N=467,578), patients with newly acquired pneumonia were older (mean age: 70 versus [vs] 63 years) and had higher Charlson Comorbidity Index scores (3.3 vs 2.6) than patients without pneumonia. After propensity score matching, the pneumonia cohort was nine times more likely to have a hospitalization (odds ratio; 95% confidence intervals [CI]
On a Liouville type theorem for isotropic homogeneous fully nonlinear elliptic equations in dimension two

In this paper we establish a Liouville type theorem for fully nonlinear elliptic equations related to a conjecture of De Giorgi in R2. We prove that if the level lines of a solution have bounded curvature, then these level lines are straight lines. As a consequence, the solution is one-dimensional. The method also provides a result on free boundary problems of Serrin type.
NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein.

A 130-residue fragment of the Staphylococcus aureus fibronectin-binding protein has been found to exist in a highly unfolded conformation at neutral pH. Measurement of experimental NMR 3JHNalpha coupling constants provides evidence for individual residues having distinct main-chain conformational preferences that are dependent both on the amino acid concerned and on neighbouring residues in the sequence. Analysis shows that these variations in the populations of individual residues can be explained in detail in terms of statistical distributions of conformational states derived from the protein data base. In particular, when the preceding residue has a beta-branched or aromatic side-chain, a significant increase occurs in the population of the less sterically restricted b region of phi,psi space. The results indicate that the local structure of the fibronectin binding protein in solution, under conditions where it displays full activity, approximates very closely to a statistical random coil structure. This may be an important feature in the biological role of this and other polypeptides involved in protein-protein interactions.
COMMD 1 downregulates the epithelial sodium channel through Nedd 4 – 2

Ke Y, Butt AG, Swart M, Liu YF, McDonald FJ. COMMD1 downregulates the epithelial sodium channel through Nedd4–2. Am J Physiol Renal Physiol 298: F1445–F1456, 2010. First published March 17, 2010; doi:10.1152/ajprenal.00257. 2009. —The epithelial sodium channel (ENaC) is important for the long-term control of Na homeostasis and blood pressure. Our previous studies demonstrated that Copper Metabolism Murr1 Domain-containing protein 1 (COMMD1; previously known as Murr1), a protein involved in copper metabolism, inhibited amiloride-sensitive current in Xenopus laevis oocytes expressing ENaC (J Biol Chem 279: 5429, 2004). In this study, we report that COMMD1 inhibits amiloride-sensitive current in mammalian epithelial cells expressing ENaC, that the COMM domain of COMMD1 is sufficient for this effect, and that knockdown of COMMD1 increases amiloride-sensitive current. COMMD1 is coexpressed with ENaC in rat kidney medulla cells. COMMD1 increased ubiquitin modification of ENaC and decreased its cell surface expression. COMMD1 abolished insulin-stimulated amiloride-sensitive current and attenuated the stimulation of current by activated serum and glucocorticoid-regulated kinase (SGK1). COMMD1 was found to interact with both SGK1 and Akt1/protein kinase B, and knockdown of COMMD1 enhanced the stimulatory effect of both SGK1 and Akt1 on amiloride-sensitive current. COMMD1’s effects were reduced in the presence of ENaC proteins containing PY motif mutations, abolished in the presence of a dominant negative form of Nedd4–2, and knockdown of COMMD1 reduced the inhibitory effect of Nedd4–2 on ENaC, but did not enhance current when Nedd4–2 was knocked down. These data suggest that COMMD1 modulates Na transport in epithelial cells through regulation of ENaC cell surface expression and this effect is likely mediated via Nedd4–2.
Rethinking conflict studies : towards a critical realist approach

The study of intra-state conflict has increased exponentially during the post-Cold War period. This has given rise to a variety of competing approaches, which have (i) adopted differing methodological and social theoretical orientations, and (ii) produced contradictory accounts of the causes and nature of violent conflict. This project intervenes in the debates which have resulted from this situation, and develops a critical realist approach to conflict studies. In doing so it rethinks the discipline from the philosophical ground up, by extending the ontological and epistemological insights which are provided by critical realism into more concrete reflections about methodological and social theoretical issues. In addition to engaging in reflection about philosophical, methodological, and social theoretical issues, however, the project also incorporates the insights of two largely neglected literatures into conflict studies. These are, first, the insights of the gender-studies literature, and second, the insights of decolonial/postcolonial forms of thought. It claims that the discipline is strengthened by incorporating the insights of these literatures, and that the critical realist framework provides us with the philosophical basis which is required in order to do so.
Market value and managerial decisions: implications from a decade of feeder cattle teleauctions.

Data from feeder cattle teleauction sales in Georgia from 1977 to 1988 were analyzed using least squares analysis of variance to detect significant (P less than .05) influential factors on price. The sample was divided into two periods, 1977 to 1982 and 1983 to 1988, to test whether the influence of factors had changed over the time periods. The test of equality was rejected (P less than .01) using a Chow test, thus suggesting a change had occurred. Hereford breeds were discounted in the latter period whereas Angus breeds generated a premium in the earlier period. Treatment for specific diseases resulted in premium prices, as did preconditioning, during the 1983 to 1988 period. The effect of seasonality on prices decreased over the two time periods. The optimal lot size increased from 228 to 280 cattle during the time periods.
The Scenario Model Intercomparison Project (ScenarioMIP) for CMIP6

Abstract. Projections of future climate change play a fundamental role in improving understanding of the climate system as well as characterizing societal risks and response options. The Scenario Model Intercomparison Project (ScenarioMIP) is the primary activity within Phase 6 of the Coupled Model Intercomparison Project (CMIP6) that will provide multi-model climate projections based on alternative scenarios of future emissions and land use changes produced with integrated assessment models. In this paper, we describe ScenarioMIP's objectives, experimental design, and its relation to other activities within CMIP6. The ScenarioMIP design is one component of a larger scenario process that aims to facilitate a wide range of integrated studies across the climate science, integrated assessment modeling, and impacts, adaptation, and vulnerability communities, and will form an important part of the evidence base in the forthcoming Intergovernmental Panel on Climate Change (IPCC) assessments. At the same time, it will provide the basis for investigating a number of targeted science and policy questions that are especially relevant to scenario-based analysis, including the role of specific forcings such as land use and aerosols, the effect of a peak and decline in forcing, the consequences of scenarios that limit warming to below 2 °C, the relative contributions to uncertainty from scenarios, climate models, and internal variability, and long-term climate system outcomes beyond the 21st century. To serve this wide range of scientific communities and address these questions, a design has been identified consisting of eight alternative 21st century scenarios plus one large initial condition ensemble and a set of long-term extensions, divided into two tiers defined by relative priority. Some of these scenarios will also provide a basis for variants planned to be run in other CMIP6-Endorsed MIPs to investigate questions related to specific forcings. Harmonized, spatially explicit emissions and land use scenarios generated with integrated assessment models will be provided to participating climate modeling groups by late 2016, with the climate model simulations run within the 2017–2018 time frame, and output from the climate model projections made available and analyses performed over the 2018–2020 period.
On the Discourse of Energy as Material: Future Feedback Technologies and Directions for Experiencing Energy

Engineers are increasingly considering the social dimensions of energy use in the design of energy conservation technologies. This has led to design informed by ethnographic and theoretical inquiry on everyday energy practices and user-technology interactions that will in turn shape future practices and interactions. This paper contributes to the small but growing literature on real-time residential energy feedback displays that more closely examines how users experience such technologies. Survey responses from participants involved in a large-scale residential energy feedback monitoring case study are analyzed and contextualized into a set of positive and negative user “experiences. ” The qualitative data derived from these responses add new insight on the social variables of user interaction with real-time feedback monitors that are of use to both the study of energy feedback monitoring and the design of future smart communities. Finally, an example is given of how these participant “experiences” are being put to the test in the design of a new energy feedback technology with implications for future ways of conceptualizing energy.
Optimal prediction and natural scene statistics in the retina

Almost all neural computations involve making predictions. Whether an organism is trying to catch prey, avoid predators, or simply move through a complex environment, the data it collects through its senses can guide its actions only to the extent that it can extract from these data information about the future state of the world. An essential aspect of the problem in all these forms is that not all features of the past carry predictive power. Since there are costs associated with representing and transmitting information, a natural hypothesis is that sensory systems have developed coding strategies that are optimized to minimize these costs, keeping only a limited number of bits of information about the past and ensuring that these bits are maximally informative about the future. Another important feature of the prediction problem is that the physics of the world is diverse enough to contain a wide range of possible statistical ensembles, yet not all motion is probable. Thus, the brain might not be a generalized predictive machine; it might have evolved to specifically solve the prediction problems most common in the natural environment. This paper reviews recent results on predictive coding and optimal predictive information in the retina and suggests approaches for quantifying prediction in response to natural motion.
How diversification rates and diversity limits combine to create large-scale species–area relationships

Species–area relationships (SARs) have mostly been treated from an ecological perspective, focusing on immigration, local extinction and resource-based limits to species coexistence. However, a full understanding across large regions is impossible without also considering speciation and global extinction. Rates of both speciation and extinction are known to be strongly affected by area and thus should contribute to spatial patterns of diversity. Here, we explore how variation in diversification rates and ecologically mediated diversity limits among regions of different sizes can result in the formation of SARs. We explain how this area-related variation in diversification can be caused by either the direct effects of area or the effects of factors that are highly correlated with area, such as habitat diversity and population size. We also review environmental, clade-specific and historical factors that affect diversification and diversity limits but are not highly correlated with region area, and thus are likely to cause scatter in observed SARs. We present new analyses using data on the distributions, ages and traits of mammalian species to illustrate these mechanisms; in doing so we provide an integrated perspective on the evolutionary processes shaping SARs.