Miracle-dz/UniFAR-FTUs huggingface dataset:
CausalTrail: Testing hypothesis using causal Bayesian networks

Summary Causal Bayesian Networks are a special class of Bayesian networks in which the hierarchy directly encodes the causal relationships between the variables. This allows to compute the effect of interventions, which are external changes to the system, caused by e.g. gene knockouts or an administered drug. Whereas numerous packages for constructing causal Bayesian networks are available, hardly any program targeted at downstream analysis exists. In this paper we present CausalTrail, a tool for performing reasoning on causal Bayesian networks using the do-calculus. CausalTrail's features include multiple data import methods, a flexible query language for formulating hypotheses, as well as an intuitive graphical user interface. The program is able to account for missing data and thus can be readily applied in multi-omics settings where it is common that not all measurements are performed for all samples. Availability and Implementation CausalTrail is implemented in C++ using the Boost and Qt5 libraries. It can be obtained from https://github.com/dstoeckel/causaltrail
Refining thresholds in coupled fire-vegetation models to improve management of encroaching woody plants in grasslands

Summary 1. Restoration priorities are typically established without quantitative information on how to overcome the thresholds that preclude successful restoration of desirable ecosystem properties and services. We seek to demonstrate that quantifying ecological thresholds and incorporating them into management-oriented frameworks provide a more comprehensive perspective on how the threshold concept can be applied to achieve restoration goals. 2. As an example, restoration actions have been largely unsuccessful when based on prevailing ecological knowledge of fire-based thresholds in nonresprouting Juniperus woodland. We build on previous threshold-based research and link well-established models from applied fire physics with a widely applied ecological positive feedback model of woody plant encroachment to introduce a more comprehensive understanding of the mechanism influencing fire intensity and juniper mortality. 3. Our coupling of physical and ecological fire models revealed a critical knowledge gap, a lack of a quantitative estimate on the critical surface fire intensity required to cause mortality of Juniperus ashei trees, which limits the linking of scientific knowledge from these two disciplines. 4. To quantify the relationship between fire intensity and J. ashei mortality, we input data from a previous experiment into Byram’s fireline intensity model. This critical surface fire intensity–mortality threshold was estimated to be Is > 160 kJ m � 1 s � 1 . This value establishes a specific threshold that managers should target when attempting to use restoration to collapse J. ashei woodlands. 5. Synthesis and applications. For scientific information associated with the threshold concept to be useful to practitioners, specific information is needed that demonstrates how to use restoration activities to overcome thresholds and collapse the current, degraded state in favour of a more desired ecological state. With this in mind, we present a broadly applicable decision support model within a state and transition framework that identifies the ecological states where the surface fire intensity–mortality threshold is most likely to meet restoration objectives and provides examples of how fuel properties that drive fire intensity should be targeted in restoration to surpass this threshold.
Novice Teacher Learning and Motivation Across Contexts: Assessment Tools as Boundary Objects

We present a longitudinal study of novice teachers’ appropriation, negotiation, and recontextualization of assessment tools and practices. During the four years of the study, we observed and interviewed beginning mathematics and social studies teachers, along with their colleagues, mentors, and supervisors, from their time in a graduate secondary teacher education program through their second year of professional teaching. Analysis of fieldnotes, interview transcripts, and artifacts suggests that assessment tools function as boundary objects in negotiations within and between the social worlds in which novices learn to teach. Boundary objects serve as reifications or representations of values, goals, and meanings (Bowker & Star, 1999; Star & Griesemer, 1989; Wenger, 1998). Assessment tools and artifacts, as boundary objects, facilitate engagement of teachers, administrators, students, and their families in coordinating activity across social boundaries and are central to the function of educational organizations. Novice teachers’ motivation to learn promoted assessment tools and their affiliated practices changed as they crossed boundaries between university and school and changed positions from student teacher to newcomer to experienced novice. Implications of this analysis for understanding novice teacher learning and motivation, and for assessment policy more broadly, are discussed.
Statistical phase shifting step estimation based on continuous wavelet transform for high resolution interferometry metrology

A statistical phase shifting estimation for temporal phase shifting interferometry (PSI) based on continuous wavelet transform is proposed in this paper. The tests on numerical simulation and Moiré interferometry are performed for the validation. In the temporal PSI, the interferograms are reconstructed upon the assumptions of the accurate estimation of the shifted phase steps. The estimations are usually based on the experimental configuration of the phase shifting mechanism. Due to the calibration error and environmental errors, the phase steps are not constants and vary with time and introduce error in the phase reconstruction. To solve this problem, the researchers proposed different phase step estimation algorithms which explore both temporal (inter-frame) and spatial redundancies (intra-frame) in the data to estimate the shifted phase. Each algorithm imposes different constraints on the structure of the shifted phases. The accuracy of the estimated phase steps varies under different condition and also changes among different interferometers. The proposed methods can serve as a benchmark method for comparing the accuracy of the different phase steps estimation methods statistically.
Dendritic Cells Transduced with an Adenovirus Vector Encoding Epstein-Barr Virus Latent Membrane Protein 2B: a New Modality for Vaccination

ABSTRACT Epstein-Barr virus (EBV) is a herpesvirus commonly associated with several malignancies, particularly in immunocompromised hosts. As a strategy for stimulating immunity against EBV for the treatment of EBV-associated tumors, we have genetically engineered dendritic cells (DC) to express EBV antigens, such as latent membrane protein 2B (LMP2B), using recombinant adenovirus vectors. CD8+ T lymphocytes from HLA-A2.1+, EBV-seropositive healthy donors were cultured with autologous DC infected with recombinant adenovirus vector AdEGFP, encoding an enhanced green fluorescent protein (EGFP), or AdLMP2B at a multiplicity of infection of 250. After 48 h, >95% of the DC were positive for EGFP expression as assessed by fluorescence-activated cell sorting analysis, indicating efficient gene transfer. AdLMP2-transduced DC were used to stimulate CD8+T cells. Responder CD8+ T cells were tested for gamma interferon (IFN-γ) release by enzyme-linked spot (ELISPOT) assay and cytotoxic activity. Prior to in vitro stimulation, the frequencies of T-cells directed against two HLA-A2-presented LMP2 peptides (LMP2 329-337 and LMP2 426-434) were very low as assessed by IFN-γ spot formation (T-cell frequency, <0.003%). IFN-γ ELISPOT assays performed at day 14 showed a significant (2-log) increase of the day 0 frequency of T cells reactive against the LMP2 329-337 peptide, from 0.003 to 0.3 (P < 0.001). Moreover, specific cytolytic activity was observed against the autologous EBV B-lymphoblastoid cell lines after 21 days of stimulation of T-cell responders with AdLMP2-transduced DC (P < 0.01). In summary, autologous mature DC genetically modified with an adenovirus encoding EBV antigens stimulate the generation of EBV-specific CD8+ effector T cells in vitro, supporting the potential application of EBV-based adenovirus vector vaccination for the immunotherapy of the EBV-associated malignancies.
Proceedings of the Gcc Developers' Summit Conference Organizers Proceedings Formatting Team Feedback-directed Optimizations in Gcc with Estimated Edge Profiles from Hardware Event Sampling

Authors retain copyright to all submitted papers, but have granted unlimited redistribution rights to all as a condition of submission. Abstract Traditional feedback-directed optimization (FDO) in GCC uses static instrumentation to collect edge and value profiles. This method has shown good application performance gains, but is not commonly used in practice due to the high runtime overhead of profile collection , the tedious dual-compile usage model, and difficulties in generating representative training data sets. In this paper, we show that edge frequency estimates can be successfully constructed with heuristics using profile data collected by sampling of hardware events, incurring low runtime overhead (e.g., less then 2%), and requiring no instrumentation, yet achieving competitive performance gains. We describe the motivation, design, and implementation of FDO using sample profiles in GCC and also present our initial experimental results with SPEC2000int C benchmarks that show approximately 70% to 90% of the performance gains obtained using traditional FDO with exact edge profiles.
Occupational Inheritance: The Role of Cultural Capital and Gender

It is known that occupational destination is influenced by family cultural resources. Most research on the effects of cultural capital, using nationally representative datasets, has concentrated on paternal occupation and education, finding that higher levels of paternal education are associated with greater educational and occupational attainment. As a result cultural capital has been put forward as a partial explanation for intergenerational class stability. It has been argued that occupational inheritance is more marked for the professional than for the managerial sector of the middle class, due to their greater cultural capital (Savage et al. 1992). This paper explores the effects of father's labour market sector (i.e. managerial or professional) and the educational attainment of both parents, using the National Child Development Study. Evidence was found: 1) that the children of professional fathers are more successful educationally than the children of managers, taking into account measured ability at age 11; and 2) that professional family origins facilitate entry into professional occupations, independently of educational attainments. The effect of gender was also explored. The relative lack of educational attainment on the part of children of managers had a more negative effect on the careers of daughters than of sons.
Site-selective growth of a hormone-responsive human breast carcinoma in athymic mice.

MCF-7 is a human breast cancer line which requires estradiol supplementation for growth in s.c. tissues of athymic mice. In order to evaluate the influence of host site on hormone-dependent tumorigenicity and growth, MCF-7 cells were inoculated into tissues varying in ability to concentrate exogenous estradiol. Tumorigenicity was defined in terms of latency, threshold inoculum size, and tumor growth and progression. We observed that sites such as lung rarely supported MCF-7 tumors. However, moderately estrophilic sites such as mammary fat and adjacent subcutaneum and dermis supported the growth of small MCF-7 tumors from large tumor cell inocula, but only in estrogenized mice. In contrast, the highly estrophilic sites, brain and periuterine tissues, produced rapidly growing tumors from small tumor cell inocula. Only in periuterine tissues did tumors develop in the absence of exogenous estradiol. These studies demonstrate that tumorigenicity and growth rates of estrogen-dependent MCF-7 tumors vary as a function of tissue implantation site.
The Cued Activation of Attachment Relational Schemas

People's interaction expectancies and views of self are shaped by accessible relational schemas, knowledge structures representing regularities in interpersonal experience. Recent research using classical conditioning paradigms has examined the possibility of creating associations between neutral cues and specific relational schemas so that presentation of the cue serves to activate the relational expectancies. In the current study, a lexical decision task was employed to assess the cued activation of acceptance and rejection expectations as a function of chronic attachment orientation. Participants visualized relationships in which they felt noncontingently versus contingently accepted by another person; while doing so they were given repeated computer presentations of distinctive tone sequences. Later, these conditioned tones were played again while participants performed lexical decisions on stimuli that represented if-then contingencies of interpersonal acceptance and rejection. Results indicated that.
Characterization of a Novel Cutaneous Human Papillomavirus Genotype HPV-125

The DNA genome of a novel HPV genotype, HPV-125, isolated from a hand wart of an immuno-competent 19-year old male was fully cloned, sequenced and characterized. The full genome of HPV-125 is 7,809-bp in length with a GC content of 46.4%. By comparing the nucleotide sequence of the complete L1 gene, HPV-125 is phylogenetically placed within cutaneotrophic species 2 of Alphapapillomaviruses, and is most closely related to HPV-3 and HPV-28. HPV-125 has a typical genomic organization of Alphapapillomaviruses and contains genes coding for five early proteins, E6, E7, E1, E2 and E4 and two late capsid proteins, L1 and L2. The genome contains two non-coding regions: the first located between the L1 and E6 genes (nucleotide positions 7,137–7,809, length 673-bp) and the second between genes E2 and L2 (nucleotide positions 3,757–4,216, length 460-bp). The E6 protein of HPV-125 contains two regular zinc-binding domains at amino acid positions 29 and 102, whereas the E7 protein exhibits one such domain at position 50. HPV-125 lacks the regular pRb-binding core sequence within its E7 protein. In order to assess the tissue predilection and clinical significance of HPV-125, a quantitative type-specific real-time PCR was developed. The 95% limit-of-detection of the assay was 2.5 copies per reaction (range 1.7–5.7) and the intra- and inter-assay coefficients of variation were 0.47 and 2.00 for 100 copies per reaction, and 1.15 and 2.15 for 10 copies per reaction, respectively. Testing of a representative collection of HPV-associated mucosal and cutaneous benign and malignant neoplasms and hair follicles (a total of 601 samples) showed that HPV-125 is a relatively rare HPV genotype, with cutaneous tropism etiologically linked with sporadic cases of common warts.
Three Disturbing Questions concerning Lexicostatistics

I have indicated elsewhere that, in my opinion, the techniques of lexicostatistics yield interesting and useful results when handled with care. ' I am seriously disturbed, however, by recent developments originating with the author of the lexicostatistical method, which seem to me to endanger the usefulness of the entire method through drastic reduction of the statistical base, coupled with exaggerated claims as to its validity and precision. The following queries are raised with the hope that they will stimulate careful answers which will in turn both develop the field and prevent the loss of ground already gained. 1. In elaborating the statistical validity of the techniques of lexicostatistics, Lees2 assumed that the test list of 215 items which he used was a small sample of a 'basic-rootmorpheme-inventory' of 'several thousand items. ' This basic inventory was assumed to include 'cultural universals'--i.e. morphemes associated with meanings likely to be found in all cultures, such as body parts, numerals, geographical terms, and simple activities. Swadesh,3 in a recent revision of the test list, reduced the number of items on the list from 200 to 100, and implied that these are almost all of the available items of the basic vocabulary. The list was reduced by eliminating items which had proved to be: not universal (e.g. ice, snow); cultural rather than basic in some instances (e.g.
Automating the performance management of component-based enterprise systems through the use of redundancy

Component technologies are increasingly being used for building enterprise systems, as they can address complex functionality and flexibility problems and reduce development and maintenance costs. Nonetheless, current component technologies provide little support for predicting and controlling the emerging performance of software systems that are assembled from distinct components.This paper presents a framework for automating the performance management of complex, component-based systems. The adopted approach is based on the alternate usage of multiple component variants with equivalent functional characteristics, each one optimized for a different running environment. A fully-automated framework prototype for J2EE is presented, along with results from managing a sample enterprise application on JBoss. A mechanism that uses monitoring data to learn and automatically improve the framework's management behaviour is proposed. The framework imposes no extra requirements on component providers, or on the component technologies.
Parallel Vectors Criteria for Unsteady Flow Vortices

Feature-based flow visualization is naturally dependent on feature extraction. To extract flow features, often higher order properties of the flow data are used such as the Jacobian or curvature properties, implicitly describing the flow features in terms of their inherent flow characteristics (for example, collinear flow and vorticity vectors). In this paper, we present recent research that leads to the (not really surprising) conclusion that feature extraction algorithms need to be extended to a time-dependent analysis framework (in terms of time derivatives) when dealing with unsteady flow data. Accordingly, we present two extensions of the parallel-vectors-based vortex extraction criteria to the time-dependent domain and show the improvements of feature-based flow visualization in comparison to the steady versions of this extraction algorithm both in the context of a high-resolution data set, that is, a simulation specifically designed to evaluate our new approach and for a real-world data set from a concrete application.
When Do Matthew Effects Occur?

What are the boundary conditions of the Matthew Effect? In other words, under what circumstances do initial status differences result in highly skewed reward distributions over the long run, and when, conversely, is the accumulation of status-based advantages constrained? Using a formal model, we investigate the fates of actors in a contest who start off as status-equivalents, produce at different levels of quality, and thus come to occupy distinct locations in a status ordering. We build from a set of equations in which failing to observe cumulative advantage seems implausible and then demonstrate that, despite initial conditions designed to lead inevitably to status monopolization, circumstances still exist that rein in the Matthew Effect. Our results highlight the importance of a single factor governing whether the Matthew Effect operates freely or is circumscribed. This factor is the degree to which status diffuses through social relations. When actors’ status levels are strongly influenced by the status levels of those dispensing recognition to them, then eventually the top-ranked actor is nearly matched in status by the lower-ranked actor she endorses. In contrast, when actors’ status levels are unaffected by the status levels of those giving them recognition, the top-ranked actor amasses virtually all status available in the system. Our primary contribution is the intuition that elites may unwittingly and paradoxically destroy their cumulative advantage beneath the weight of their endorsements of others. Consequently, we find that the Matthew Effect is curtailed by a process that, at least in some social settings, is a property of status itself—its propensity to diffuse through social relations. Implications for future research are discussed.
Genetic Variants of TSLP and Asthma in an Admixed Urban Population

Background Thymic stromal lymphopoietin (TSLP), an IL7-like cytokine produced by bronchial epithelial cells is upregulated in asthma and induces dendritic cell maturation supporting a Th2 response. Environmental pollutants, including tobacco smoke and diesel exhaust particles upregulate TSLP suggesting that TSLP may be an interface between environmental pollution and immune responses in asthma. Since asthma is prevalent in urban communities, variants in the TSLP gene may be important in asthma susceptibility in these populations. Objectives To determine whether genetic variants in TSLP are associated with asthma in an urban admixed population. Methodology and Main Results Ten tag-SNPs in the TSLP gene were analyzed for association with asthma using 387 clinically diagnosed asthmatic cases and 212 healthy controls from an urban admixed population. One SNP (rs1898671) showed nominally significant association with asthma (odds ratio (OR) = 1.50; 95% confidence interval (95% CI): 1.09–2.05, p = 0.01) after adjusting for age, BMI, income, education and population stratification. Association results were consistent using two different approaches to adjust for population stratification. When stratified by smoking status, the same SNP showed a significantly increased risk associated with asthma in ex-smokers (OR = 2.00, 95% CI: 1.04–3.83, p = 0.04) but not significant in never-smokers (OR = 1.34; 95% CI: 0.93–1.94, p = 0.11). Haplotype-specific score test indicated that an elevated risk for asthma was associated with a specific haplotype of TSLP involving SNP rs1898671 (OR = 1.58, 95% CI: 1.10–2.27, p = 0.01). Association of this SNP with asthma was confirmed in an independent large population-based cohort consortium study (OR = 1.15, 95% CI: 1.07–1.23, p = 0.0003) and the results stratified by smoking status were also validated (ex-smokers: OR = 1.21, 95% CI: 1.08–1.34, p = 0.003; never-smokers: OR = 1.06, 95% CI: 0.94–1.17, p = 0.33). Conclusions Genetic variants in TSLP may contribute to asthma susceptibility in admixed urban populations with a gene and environment interaction.
Role of Urease Enzymes in Stability of a 10-Species Oral Biofilm Consortium Cultivated in a Constant-Depth Film Fermenter

ABSTRACT Using a 10-species oral biofilm consortium and defined mutants, we show that high-level capacity to generate ammonia from a common salivary substrate is needed to maintain community diversity. This model appears to be suitable for the study of the effects of individual genetic determinants on the ecology of oral biofilms.
Application of Genetic Algorithms and Ant Colony Optimization for Modelling of E. coli Cultivation Process

Classical biotechnology is the science of production of human-useful processes and products under controlled conditions, applying biological agents – microorganisms, plant or animal cells, their exoand endoproducts, e.g. enzymes, etc. (Viesturs et al., 2004). The conventional agriculture or chemistry cannot perform these processes as efficiently or at all. In fact, conventional biotechnology has been the largest industrial activity on earth for a very long time. Modern biotechnology goes much further with respect to control of the biological processes.