Miracle-dz/UniFAR-FTUs huggingface dataset:
Choosing among Partition Models in Bayesian Phylogenetics

Bayesian phylogenetic analyses often depend on Bayes factors (BFs) to determine the optimal way to partition the data. The marginal likelihoods used to compute BFs, in turn, are most commonly estimated using the harmonic mean (HM) method, which has been shown to be inaccurate. We describe a new more accurate method for estimating the marginal likelihood of a model and compare it with the HM method on both simulated and empirical data. The new method generalizes our previously described stepping-stone (SS) approach by making use of a reference distribution parameterized using samples from the posterior distribution. This avoids one challenging aspect of the original SS method, namely the need to sample from distributions that are close (in the Kullback–Leibler sense) to the prior. We specifically address the choice of partition models and find that using the HM method can lead to a strong preference for an overpartitioned model. In contrast to the HM method and the original SS method, we show using simulated data that the generalized SS method is strikingly more precise (repeatable BF values of the same data and partition model) and yields BF values that are much more reasonable than those produced by the HM method. Comparisons of HM and generalized SS methods on an empirical data set demonstrate that the generalized SS method tends to choose simpler partition schemes that are more in line with expectation based on inferred patterns of molecular evolution. The generalized SS method shares with thermodynamic integration the need to sample from a series of distributions in addition to the posterior. Such dedicated path-based Markov chain Monte Carlo analyses appear to be a cost of estimating marginal likelihoods accurately.
Key skills for science learning: the importance of text cohesion and reading ability

To explore the importance of text cohesion, we conducted two experiments. We measured online (reading times) and offline (comprehension accuracy) processes for texts that were high and low cohesion. In study one (n = 60), we manipulated referential cohesion using noun repetition (high cohesion) and synonymy (low cohesion). Students showed enhanced comprehension accuracy and faster comprehension responses for text that were high in referential cohesion. In study two (n = 52), we examined connective text designs (‘because’, ‘and’ and ‘no connective’). Students demonstrated enhanced reading times for text using a ‘because’ connective. Additionally, we examined the individual differences (reading ability, science self-concept and self-esteem) as predictors of achievement with science comprehension tasks. Across both experiments reading ability predicted comprehension with both high (noun-repetition text and ‘and’ text) and low cohesion text (synonym text and ‘no connective’ text). These findings highlight the importance of good reading abilities and text cohesion for promoting science comprehension and learning.
A wireless-based home rehabilitation system for monitoring 3D movements

This paper deals with a home rehabilitation system, based on wireless motion sensors, for assisting therapists in assessing recovery of patients with motor dysfunctions. Measurements in home rehabilitation may complement the subjective perception of therapist with objective observations that lead to quantitative evaluation. The goal of this work is to discuss design and implementation of a complete system capable of bringing a real-time 3D reconstruction of human posture to therapist's desk, starting from exercises performed at patient's house. Attention has been paid to reducing costs and clutter of home-side equipments as much as possible.
HCI engineering integrated with capability and maturity models

It is well known that despite the large advancement of Human-Computer Interaction (HCI) engineering as regards the definition of methods, techniques and standards, the majority of enterprises do not use them in practice. Contrary to this scenario, software engineering has been widely applied in industry through the implementation of Software Process Capability and Maturity (SPCM) models. We argue that the definition of a workbench of approaches from HCI that could really support SPCM models can promote a largely use of HCI engineering in industry. Based on this belief we conducted an exploratory study to identify what SPCM models refer in terms of HCI Engineering. We identified explicit and implicit citations that could be interpreted in benefit of HCI engineering. Based on this analysis, we identified a set of methods, techniques and standards that should be used for the definition of guidelines to apply HCI engineering in the implementation of SPCM models.
Using Bloom's taxonomy to enhance interactive concentric circles representation

Concentric circles representation has been developed for visualizing the periodic character of temporal data set. It is particularly useful for visually interpreting periodic time-oriented patterns extracted by data mining techniques. However, this requires a cognitive study to support the transformation into the closest mental representation to reality. In this paper, the proposed information visualization tool is enhanced taking into account key human factors for temporal patterns perception and cognition. This allows facilitating visual analysis of data space to make the right decision by exerting a minimum of cognitive load. We based our work on the taxonomy proposed by Bloom of cognitive domain to improve the concentric circles technique.
Building global and scalable systems with atomic multicast

The rise of worldwide Internet-scale services demands large distributed systems. Indeed, when handling several millions of users, it is common to operate thousands of servers spread across the globe. Here, replication plays a central role, as it contributes to improve the user experience by hiding failures and by providing acceptable latency. In this work, we claim that atomic multicast, with strong and well-defined properties, is the appropriate abstraction to efficiently design and implement globally scalable distributed systems. We substantiate our claim with the design of two modern online services atop atomic multicast, a strongly consistent key-value store and a distributed log.
Representing and querying multiple ontologies with Contextual Logic Programming

The system presented in this paper uses Contextual Logic Programming as a computational hub for representing and reasoning over knowledge modeled by web ontologies, integrating the approach with similar mechanisms which we already developed. As a result of its Logic Programming heritage, the system may also recursively interrogate other ontologies or data repositories, providing a semantic integration of multiple sources. The components required to behave as a SPARQL query engine are explained and examples of integration of deferent sources are shown - in particular, the case of multiple OWL ontologies is discussed.
Optimizing Channel Access in Wireless Local Area Network Environments with a New Backoff Approach

Over the past few years, several backoff algorithms such as Exponential Increase Exponential Decrease (EIED) and Adaptive Enhanced Distributed Coordination Function (AEDCF)) have been proposed for wireless local area networks to improve channel access. We propose a new backoff technique that monitors the number of backoff counter pauses experienced and modifies the contention window accordingly. We evaluate and compare the performance of our proposed approach with EIED and AEDCF channel access techniques. Our simulations results, obtained under different network conditions, show improved performance for metrics such as the fairness index and end-to-end delay.
More than words: a literature review of language of mathematics research

This paper presents the results of a systematic search of the empirical literature on language of mathematics. Historically, mathematics educators and policy-makers have focused primarily on the importance of vocabulary in helping students move from everyday language to more formal mathematical language in order to promote academic outcomes. Utilizing Gee’s notion of Discourse, which includes many aspects of language as well as notions of identity and power, we synthesize the extant literature to explore the multifaceted ways researchers have extended the traditional focus on vocabulary. Our findings suggest that for students to be successful in mathematics classrooms, educators must become cognizant of the role of language in establishing classroom norms, negotiating identities, and challenging inequitable distributions of power. We also utilize Gee’s seven building blocks of language to identify aspects of language that remain ripe for future research.
The Cost of Caring: Childhood Disability and Poor Families

Children in poor families are at heightened risk for disabilities and chronic health problems, and care for these children can impose substantial costs on families and public programs. Although the prevalence and costs of disabilities among poor children have important policy implications, they have been largely overlooked in research on poverty and welfare and on the costs of childhood disabilities. This article analyzes the prevalence of childhood disabilities and chronic illness among welfare recipient families in California and the probability families caring for these children experience higher out‐of‐pocket costs and material hardship than do other similar families.
Characterization of High-Current Stress-Induced Instability in Amorphous InGaZnO Thin-Film Transistors by Low-Frequency Noise Measurements

The instability of amorphous InGaZnO thin-film transistors is investigated under high drain current stress by applying bias voltages to both gate and drain electrodes. The instability involves positive threshold voltage shift, reduction of the ON-state current and recovery of the transfer characteristic toward the prestressed state when the stressed device is unbiased in dark at room temperature for an extended period. This instability behavior is investigated by low-frequency noise measurements before and after stress in the forward and reverse configurations. The overall results are consistent with the instability mechanism involving electron trapping in the existing donor-like gate oxide trap states near the source side.
Exploiting don't cares to minimize *BMDs

We present for the first time methods to minimize *BMDs exploiting don't care conditions. These minimization methods can be used during the verification of circuits by *BMDs. By changing function values for input vectors, which are in the don't care set, smaller *BMDs can be computed to keep peak memory consumption during *BMD construction as low as possible. Preliminary experimental results prove the methods to be very effective in minimizing *BMD sizes.
Reminiscing About Childhood: The Language Maintenance of an Iranian in the United Kingdom

Many immigrant children might face challenges in maintaining their heritage languages—that is, continuing using their first languages (L1s) or the L1s of their parents. Factors such as pressure from schools and the desire to assimilate into the mainstream society might lead these children to learn a dominant language at the cost of losing their heritage languages. Highlighting the importance of language maintenance, this study aimed to investigate the factors contributing to the language maintenance of an Iranian individual during his 4-year stay in England. Data were collected through an in-depth, semi-structured interview, descriptive and reflective field notes during and after the interview, and the participant's journal writing. Results revealed that the participant's parents, familial attachments, frequent visits to the home country, and the L1 community were the primary reasons why the participant maintained his heritage language.
On Passive One-Way Loss Measurements Using Sampled Flow Statistics

The ability to scalably measure one-way packet loss across different network paths is vital to IP network management. However, the effectiveness of active-measurement techniques de- pends on being able to deploy measurement hosts at appropriate locations, and to inject necessary amounts of probe traffic without impacting the performance of interest. On the other hand, existing passive-measurement methods like (1) require router support and suffer from deployment limitations for the foreseeable future. In this paper, we propose a new estimation technique that does not require any new router features or measurement infrastructure, and only uses the sampled flow level statistics that are routinely collected in operational networks. The technique is designed to handle challenges of sampled flow-level aggregation such as information aggregation and non-alignment of flow records with measurement intervals. We develop three different schemes and derive analytical bounds on the variance of loss estimation from such a flow-based approach. Our analysis shows that link data rates are now becoming sufficiently large to counteract the effects on sampling on estimation accuracy. I. INTRODUCTION
User experience evaluation methods: current state and development needs

The recent shift of emphasis to user experience (UX) has rendered it a central focus of product design and evaluation. A multitude of methods for UX design and evaluation exist, but a clear overview of the current state of the available UX evaluation methods is missing. This is partly due to a lack of agreement on the essential characteristics of UX. In this paper, we present the results of our multi-year effort of collecting UX evaluation methods from academia and industry with different approaches such as literature review, workshops, Special Interest Groups sessions and an online survey. We have collected 96 methods and analyzed them, among other criteria, based on the product development phase and the studied period of experience. Our analysis reveals development needs for UX evaluation methods, such as early-stage methods, methods for social and collaborative UX evaluation, establishing practicability and scientific quality, and a deeper understanding of UX.
Etoposide, methylprednisolone, cytarabine and cisplatin successfully cytoreduces resistant myeloma patients and mobilizes them for transplant without adverse effects

Myeloma remains incurable with a median survival of 4 years, but outcome can be improved by the use of high‐dose therapy. We used the etoposide, methylprednisolone, cytarabine and cisplatin (ESHAP) regimen as second‐line therapy in 42 newly diagnosed myeloma patients who had failed vincristine, adriamycin and dexamethasone (VAD)‐ type therapy (n = 36), responded to first‐line treatment but persisted in having significant residual marrow plasmacytosis (n = 5) or failed prior stem cell harvesting (n = 1), with the dual aim of improving disease response and mobilizing peripheral blood stem cells. Fourteen of 21 (67%) patients with no change or progressive disease after VAD responded to ESHAP; seven of 12 (58%) patients with minor response converted to partial response. Marrow plasmacytosis fell from a median of 52% at diagnosis to 23·5% after primary therapy and to15% after ESHAP. ESHAP chemotherapy was well‐tolerated. There were 11 admissions due to febrile neutropenia (n = 7), nausea and vomiting (n = 2), pneumonia (n = 1) and perforated bowel (n = 1). Renal function deteriorated in 13 of 42 patients after ESHAP, but none required renal support. ESHAP mobilization was performed in 32 patients of whom 87% achieved a CD34+ yield >2 × 106/kg. In all, 38 patients proceeded to high‐dose therapy. The overall survival for all patients was 62% at 4 years following ESHAP. We conclude that ESHAP has acceptable toxicity and efficient stem cell mobilizing capability, effectively cytoreduced this chemoresistant group of patients, and did not appear to adversely affect transplant outcome.
The Management and Mismanagement of Trust

There has been a growing literature on trust over the last decade. It can to some extent be located with concerns over economic productivity, and the fact that societies with cultures of trust tend to be more prosperous than those that do not. However, it can also be traced to concerns over the changing nature of organizations in a post-bureaucratic age, and to more recent widespread educational concerns over the ability of governments to trust professional educators. This article examines a number of meanings of `trust', and argues that different agendas only partially recognize these. Such failure to recognize the complexity of the term, and of the implications of this for educational policy and management, fails to fully realize the impact this has on the morale of teaching professionals, on the acceptable and effective management of schools, and on the ability of educational organizations to cope with the demands of a knowledge-based society. However, despite the obstacles, this article concludes that trust not only is beneficial to the educational enterprise, but may be an inevitable and increasing element of the relationship between governments and educators.
Impact of Measurement Error on Testing Genetic Association with Quantitative Traits

Measurement error of a phenotypic trait reduces the power to detect genetic associations. We examined the impact of sample size, allele frequency and effect size in presence of measurement error for quantitative traits. The statistical power to detect genetic association with phenotype mean and variability was investigated analytically. The non-centrality parameter for a non-central F distribution was derived and verified using computer simulations. We obtained equivalent formulas for the cost of phenotype measurement error. Effects of differences in measurements were examined in a genome-wide association study (GWAS) of two grading scales for cataract and a replication study of genetic variants influencing blood pressure. The mean absolute difference between the analytic power and simulation power for comparison of phenotypic means and variances was less than 0.005, and the absolute difference did not exceed 0.02. To maintain the same power, a one standard deviation (SD) in measurement error of a standard normal distributed trait required a one-fold increase in sample size for comparison of means, and a three-fold increase in sample size for comparison of variances. GWAS results revealed almost no overlap in the significant SNPs (p<10−5) for the two cataract grading scales while replication results in genetic variants of blood pressure displayed no significant differences between averaged blood pressure measurements and single blood pressure measurements. We have developed a framework for researchers to quantify power in the presence of measurement error, which will be applicable to studies of phenotypes in which the measurement is highly variable.
Neuropsychologic function in toddlers exposed to cocaine in utero: A preliminary study

Patterns of neuropsychological performance on A‐not‐B, inhibition, motor, cognitive, language, and behavior tasks were examined in 34 toddlers—17 cocaine‐exposed (CE) and 17 nonexposed (NE) controls. CE toddlers exhibited greater perseveration, less inhibition, poorer emotional regulation, and less task orientation relative to NE toddlers. Overall cognitive and language skills and motor impairment status were comparable among CE and NE toddlers. Differences in perseveration, emotional regulation, and task orientation between CE and NE toddlers remained significant after statistically controlling for overall cognitive skill. Prenatal cocaine exposure may impart selective vulnerability for deficits in executive function, inhibition, and emotional regulation in toddlers, perhaps related to the concurrent rapid frontal lobe maturation and the neurobiology of cocaine. Furthermore, these findings suggest that performance can be broken down into meaningful neuropsychological components in very young children.
Antibody response and leukemia development in mice inoculated neonatally with the Moloney virus.

Mice infected neonatally with homogenates from lymphomas induced by the Moloney virus showed a deficient or delayed antibody response, measured by the indirect fluorescent antibody test against Moloney lymphoma target cells in comparison with mice infected as adults. In neonatally infected mice there was a correlation between the development of antibodies and the length of the preleukemic latency period.
Exact Bayesian regression of piecewise constant functions

We derive an exact and e‐cient Bayesian regression algorithm for piecewise constant functions of unknown segment number, boundary locations, and levels. The derivation works for any noise and segment level prior, e.g. Cauchy which can handle outliers. We derive simple but good estimates for the insegment variance. We also propose a Bayesian regression curve as a better way of smoothing data without blurring boundaries. The Bayesian approach also allows straightforward determination of the evidence, break probabilities and error estimates, useful for model selection and signiflcance and robustness studies. We discuss the performance on synthetic and real-world examples. Many possible extensions are discussed.
Effects of Low-Dose Corticosteroids on the Bone Mineral Density of Patients With Rheumatoid Arthritis

Background The effects of long-term high-dose corticosteroids on bone mineral density (BMD) are clear, but the effects of low-dose corticosteroids in patients with rheumatoid arthritis (RA) remain controversial. The aim of this study was to assess the effects of low-dose corticosteroids on BMD in patients with RA. Methods The authors surveyed randomized controlled studies that examined the effects of low-dose corticosteroids on BMD in patients with RA using MEDLINE and the Cochrane Controlled Trials Register and by performing manual searches. Data were collected on BMD (end-of-period or change-from-baseline) after longest recorded treatment durations. Meta-analysis was performed using a random effects model; outcomes are presented as standardized mean differences (SMDs). Results Seven studies were included in this meta-analysis, which included 7 studies on lumbar BMD meta-analysis and 6 studies on femur BMD meta-analysis. Corticosteroids resulted in a moderate worsening in lumbar BMD compared with controls (SMD = −0.483; 95% confidence interval [CI], −0.815 to −0.151, P = 0.004), whereas the femoral BMD differences were not siginificant (SMD = −0.224; 95% CI, −0.663 to 0.215, P = 0.318). Subgroup analysis of BMD data performed on a change-from-baseline basis showed that corticosteroids had a clear effect on both lumbar and femoral BMDs (SMD = −0.354; 95% CI, −0.620 to −0.088, P = 0.009; SMD = −0.488; 95% CI, −0.911 to −0.065, P = 0.024, respectively). Conclusions This meta-analysis shows BMD loss after low-dose corticosteroid treatment in patients with RA. These findings have practical implications for the long-term management of patients with RA on low-dose corticosteroids.