Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence from the Genetics of Landbirds for a Forested Pleistocene Glacial Refugium in the Haida Gwaii Area

Abstract. Pleistocene refugia likely contributed to the modern biodiversity of northern areas. Using the mitochondrial DNA cytochrome-b gene, we compared 11 forest-dwelling bird species from Haida Gwaii (formerly the Queen Charlotte Islands) with populations from Alaska, Washington, and other locations in the United States. If Haida Gwaii was an unglaciated refugium, its modern populations should feature a high number of endemic lineages and divergence times that predate the end of the last glacial maximum, ca. 13,000–19,000 years before present (ybp). Furthermore, the genetic diversity of these populations should be higher than that in areas colonized after the glacial retreat. Four of the species examined from Haida Gwaii showed old divergences and a high percentage of endemic lineages: the Northern Saw-whet Owl (Aegolius acadicus), Hairy Woodpecker (Picoides villosus), Steller's Jay (Cyanocitta stelleri), and Pine Grosbeak (Pinícola enucleator); all four have endemic subspecies on these islands. The Pacific Wren (Troglodytes pacificus) and Song Sparrow (Melospiza melodia) showed genetic trends associated with populations in refugia, including high genetic diversity on Haida Gwaii. Estimated divergence dates of these six species were fairly uniform (∼20,000–30,000 ybp), being greatest for the Hairy Woodpecker (>70,000 ybp) and Pine Grosbeak (>120,000 ybp). There was an association between apparent occurrence in a refugium and a sedentary lifehistory strategy and a trend for endemic subspecies (4 of 6) also to show this association. Our findings suggest that the Haida Gwaii area hosted a forested refugium during the cycles of climatic change in the late Pleistocene.
Integrated Multimodal Copy-Paste Checking

Although the use of advanced computing and communications technology has made learning a significantly richer experience for learners, it also introduces greater ease in committing academic cheating. There is a growing increase of internet usage in educational communities. Powerful search engines and media gateways gives an ease of access to wide spreading and different types of information sources, this in turn reduces the need for learners to perform diligent research or study. A learner can easily copy information, found on the internet, relevant to the task at hand. E-learning systems would then need to incorporate extended functionalities to enable multimodal copy-paste checking. Besides the mere detection of text copy-paste activities, there is a need to determine deeper similarity relations in text and various other media formats. Furthermore, the introduction of a facility to monitor and check the student's ways of searching, reading and writing can improve the learning process. Our previous paper [1] describes the architecture and design of an integrated Copy- Paste system aimed to provide a platform addressing these concerns. This paper extends the work and shows our pioneering explorations in extending student modeling capability of e-learning systems. We discuss the use of layered similarity assessment techniques to add value to conventional copy-paste detection systems.
Mothers' and fathers' perceptions of the family context and children's adjustment : coparenting young twins

Mothers’ and fathers’ perceptions of the quality of coparenting – the way in which they work together in their role as parents – forms the focus of three papers that comprise this thesis. Using a novel sample of ‘intact’ families with young twins, this research extends the existing coparenting literature beyond its typical focus on first-born children, to include more complex families. Participants were families who were part of the Twins, Family and Behaviour (TFaB) Study, a longitudinal, multimethod study of UK families with twins born in 2009/10 conducted by myself and my colleague over a two-year period. Paper 1 examines bidirectional associations between coparenting and the marital relationship during the transition-to-school period. Controlling for cross-sectional associations and temporal stability, parents’ perceptions of higher quality coparenting were associated with their subsequent report of a higher quality marital relationship. Reciprocal associations between the marital relationship and subsequent coparenting, however, were not evidenced. These findings highlight the salience of coparenting for the marital relationship, and suggest that interventions seeking to improve the couples’ marital relationship should pay close attention to their coparenting. Paper 2 focuses on parenting sense of competence (PSOC), examining the role of children’s disruptive behaviour, coparenting, and their interaction. For both mothers and fathers there was a significant interaction between their perceptions of coparenting and children’s disruptive behaviour such that high quality coparenting may protect the PSOC of parents dealing with high levels of children’s disruptive behaviour. These findings imply that practitioners and interventions concerned with promoting PSOC should pay due attention to the quality of coparenting as an important family context. Paper 3 examines family-wide and child-specific effects of coparenting and coercive parenting on the development of children’s disruptive behaviour. Mothers’ perceptions of coparenting interacted with maternal overall coercive parenting such that high quality coparenting intensified the toxicity of maternal coercive parenting for children’s disruptive behaviour. This novel – and unexpected – finding indicates that the influence of high quality coparenting is not necessarily always positive. Coparenting interventions aiming to improve child outcomes would therefore be well-advised to also consider parenting strategies. Further research is encouraged to explore these research questions within samples of socioeconomic diversity and across family types, as well as studies designed to examine twin and non-twin family differences.
Hedging Predictions in Machine Learning: The Second Computer Journal Lecture

Recent advances in machine learning make it possible to design efficient prediction algorithms for data sets with huge numbers of parameters. This article describes a new technique for 'hedging' the predictions output by many such algorithms, including support vector machines, kernel ridge regression, kernel nearest neighbours and by many other state-of-the-art methods. The hedged predictions for the labels of new objects include quantitative measures of their own accuracy and reliability. These measures are provably valid under the assumption of randomness, traditional in machine learning: the objects and their labels are assumed to be generated independently from the same probability distribution. In particular, it becomes possible to control (up to statistical fluctuations) the number of erroneous predictions by selecting a suitable confidence level. Validity being achieved automatically, the remaining goal of hedged prediction is efficiency: taking full account of the new objects' features and other available information to produce as accurate predictions as possible. This can be done successfully using the powerful machinery of modern machine learning.
A Model of Corticostriatal Plasticity for Learning Oculomotor Associations and Sequences

Abstract We present models that learn context-dependent oculomotor behavior in (1) conditional visual discrimination and (2) sequence reproduction tasks, based on the following three principles: (1) Visual input and efferent copies of motor output produce patterns of activity in cortex. (2) Cortex influences the saccade system in part via corticostriatal projections. (3) A reinforcement learning mechanism modifies corticostriatal synapses to link patterns of cortical activity to the correct saccade responses during trial-and-error learning. Our conditional visual discrimination model learns to associate visual cues with the corresponding saccades to one of two left-right targets. A visual cue produces patterns of neuronal activity in inferotemporal cortex (IT) that projects to the oculomotor region of the striatum. Initially random saccadic "guesses," when directed to the correct target for the current cue, result in increased synaptic strength between the cue-related IT cells and the striatal cells that participate in the correct saccade, increasing the probability that this cue will later elicit the correct saccade. We show that the model generates "inhibitory gradients" on the striatum as the substrate for spatial generalization. Our sequence reproduction model learns, when presented with temporal sequences of spatial targets, to reproduce the corresponding sequence of saccades. At any point in the execution of a saccade sequence, the current pattern of activity in pre-frontal cortex (PFC), combined with visual input and the motor efferent copy of the previous saccade, produces a new pattern of activity in PFC to be associated with the next saccade. Like IT, PFC also projects to the oculomotor region of the striatum. Correct guesses for the subsequent saccade in the sequence results in strengthening of corticostriatal synapses between active PFC cells and striatal cells involved in the correct saccade. The sequence is thus reproduced as a concatenation of associations. We compare the results of this model with data previously obtained in the monkey and discuss the nature of cortical representations of spatiotemporal information.
Suppression of Her2/Neu mammary tumor development in mda-7/IL-24 transgenic mice

Melanoma differentiation associated gene-7/interleukin-24 (mda-7/IL-24) encodes a tumor suppressor gene implicated in the growth of various tumor types including breast cancer. We previously demonstrated that recombinant adenovirus-mediated mda-7/IL-24 expression in the mammary glands of carcinogen-treated (methylnitrosourea, MNU) rats suppressed mammary tumor development. Since most MNU-induced tumors in rats contain activating mutations in Ha-ras, which arenot frequently detected in humans, we presently examined the effect of MDA-7/IL-24 on Her2/Neu-induced mammary tumors, in which the RAS pathway is induced. We generated tet-inducible MDA-7/IL-24 transgenic mice and crossed them with Her2/Neu transgenic mice. Triple compound transgenic mice treated with doxycycline exhibited a strong inhibition of tumor development, demonstrating tumor suppressor activity by MDA-7/IL-24 in immune-competent mice. MDA-7/IL-24 induction also inhibited growth of tumors generated following injection of Her2/Neu tumor cells isolated from triple compound transgenic mice that had not been treated with doxycycline, into the mammary fat pads of isogenic FVB mice. Despite initial growth suppression, tumors in triple compound transgenic mice lost mda-7/IL-24 expression and grew, albeit after longer latency, indicating that continuous presence of this cytokine within tumor microenvironment is crucial to sustain tumor inhibitory activity. Mechanistically, MDA-7/IL-24 exerted its tumor suppression effect on HER2+ breast cancer cells, at least in part, through PERP, a member of PMP-22 family with growth arrest and apoptosis-inducing capacity. Overall, our results establish mda-7/IL-24 as a suppressor of mammary tumor development and provide a rationale for using this cytokine in the prevention/treatment of human breast cancer.
DOA Estimation Based on RBFNN for Minimum Redundancy Linear Array (MRLA)

The mutual coupling matrix (MCM) of uniform linear array (ULA) can be modeled as a banded symmetric Toeplitz matrix. However, the MCM of MRLA is a symmetric but not a Toeplitz matrix. Many conventional calibration algorithms based on the banded symmetric Toeplitz matrix for ULA can’t be applied to MRLA. Based on RBF neural network, a DOA estimation algorithm in the presence of mutual coupling for MRLA is proposed in this paper. Since the array correlation matrix is symmetry and there is no DOA information on its diagonal, the upper triangular half of the matrix is extracted as the input vectors. This method not only reduces the dimension of the input vectors but also present a modified preprocessing scheme to handle the problem at the endfire angles of the array. Simulation results demonstrate the proposed algorithm is efficient and valid.
Gene expression pattern A Xenopus homolog of a human p 53-activated gene , PA 26 , is speci ® cally expressed in the notochord

The LIM class homeodomain protein Xlim-1 is speci®cally expressed in the organizer and later in the notochord in Xenopus. By seeking genes which are activated by Xlim-1 in animal caps, we isolated a gene which encodes a protein highly homologous to human PA26-T2, a p53-inducible nuclear factor, which we refer to as XPA26. Northern blot analysis showed that maternal transcripts of XPA26 are detected at cleavage stages and reduced during gastrulation. Whole-mount in situ hybridization showed that zygotic transcripts of XPA26 were initially detected in the anterior portion of developing notochord at neurula stages, and later in the entire notochord except its posterior region at tailbud stages. Thus the zygotic expression of XPA26 was detected exclusively in the notochord. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
Error Estimates for Finite Element Discretizations of Elliptic Problems with Oscillatory Coefficients

In this paper we will consider elliptic boundary value problems with oscillatory diffusion coefficient, say A. We will derive regularity estimates in Sobolev norms which are weighted by certain derivatives of A. The constants in the regularity estimates then turn out to be independent of the variations in A. These regularity results will be employed for the derivation of error estimates for hp-finite element discretizations which are explicit with respect to the local variations of the diffusion coefficient.
Partially supervised learning for radical opinion identification in hate group web forums

Web forums are frequently used as platforms for the exchange of information and opinions, as well as propaganda dissemination. But online content can be misused when the information being distributed, such as radical opinions, is unsolicited or inappropriate. However, radical opinion is highly hidden and distributed in Web forums, while non-radical content is unspecific and topically more diverse. It is costly and time consuming to label a large amount of radical content (positive examples) and non-radical content (negative examples) for training classification systems. Nevertheless, it is easy to obtain large volumes of unlabeled content in Web forums. In this paper, we propose and develop a topic-sensitive partially supervised learning approach to address the difficulties in radical opinion identification in hate group Web forums. Specifically, we design a labeling heuristic to extract high quality positive examples and negative examples from unlabeled datasets. The empirical evaluation results from two large hate group Web forums suggest that our proposed approach generally outperforms the benchmark techniques and exhibits more stable performance than its counterparts.
Self-organizing trees for visualizing protein dataset

Clustering and visualizing multidimensional or structured data are important tasks for data analysis, especially in bioinformatics. Self-organizing models are often used to address both of these issues. In this paper we introduce a hierarchical and topological visualization technique called Self-organizing Trees (SoT) which is able to represent data in hierarchical and topological structure. The experiment is conducted on a real-world protein data set.
Clustering toward detecting cyber attacks

Several anomaly methods have been proposed to cope with the recent booming of HTTP-related vulnerabilities which renders the security breaches of lots of vital HTTP-based services on the internet. This paper proposes a novel bottom-up agglomerative clustering method which not only spares the nuisance of a learning process that involves a big amount of manual sample taggings, but also presents a much stronger adaptiveness in being able to coping with variant situations and in detecting new samples.
Theory of latency-insensitive design

The theory of latency-insensitive design is presented as the foundation of a new correct-by-construction methodology to design complex systems by assembling intellectual property components. Latency-insensitive designs are synchronous distributed systems and are realized by composing functional modules that exchange data on communication channels according to an appropriate protocol. The protocol works on the assumption that the modules are stallable, a weak condition to ask them to obey. The goal of the protocol is to guarantee that latency-insensitive designs composed of functionally correct modules behave correctly independently of the channel latencies. This allows us to increase the robustness of a design implementation because any delay variations of a channel can be "recovered" by changing the channel latency while the overall system functionality remains unaffected. As a consequence, an important application of the proposed theory is represented by the latency-insensitive methodology to design large digital integrated circuits by using deep submicrometer technologies.
Manual ability classification system for children with cerebral palsy in a school setting and its relationship to home self-care activities.

OBJECTIVE Our aim in this study was to investigate the relationship between (a) the manual abilities of children with cerebral palsy (CP), assessed with the Manual Ability Classification System (MACS) in a school rehabilitation setting, and (b) the children's performance of self-care activities at home, assessed with the Pediatric Evaluation of Disability Inventory (PEDI). In addition, we assessed the interobserver reliability of the MACS. METHOD Sixty-one children with CP were included (mean age = 10.3 yr, range = 5-14). The MACS was classified by 2 independent raters. The PEDI was scored in a structured interview. RESULTS The Spearman correlation coefficient between the MACS and the self-care domain of the PEDI Caregiver Assistance Scale was high and statistically significant (r = .72). The interobserver reliability of the MACS was good (weighted kappa = .86). CONCLUSION The MACS is a reliable instrument in a school environment and is related to the performance of daily life self-care activities at home.
Differential effects of dairy snacks on appetite, but not overall energy intake

Dietary regulation of appetite may contribute to the prevention and management of excess body weight. The present study examined the effect of consumption of individual dairy products as snacks on appetite and subsequent ad libitum lunch energy intake. In a randomised cross-over trial, forty overweight men (age 32 (sd 9) years; BMI 27 (sd 2) kg/m2) attended four sessions 1 week apart and received three isoenergetic (841 kJ) and isovolumetric (410 ml) servings of dairy snacks or water (control) 120 min after breakfast. Appetite profile was determined throughout the morning and ad libitum energy intake was assessed 90 min after the intake of snacks. Concentrations of amino acids, glucose, insulin, ghrelin and peptide tyrosine tyrosine were measured at baseline (0 min) and 80 min after the intake of snacks. Although the results showed that yogurt had the greatest suppressive effect on appetite, this could be confounded by the poor sensory ratings of yogurt. Hunger rating was 8, 10 and 24 % (P < 0·001) lower after the intake of yogurt than cheese, milk and water, respectively. Energy intake was 11, 9 and 12 % (P < 0·02) lower after the intake of yogurt, cheese and milk, respectively, compared with water (4312 (se 226) kJ). Although there was no difference in the postprandial responses of hormones, alanine and isoleucine concentrations were higher after the intake of yogurt than cheese and milk (P < 0·05). In conclusion, all dairy snacks reduced appetite and lunch intake compared with water. Yogurt had the greatest effect on suppressing subjective appetite ratings, but did not affect subsequent food intake compared with milk or cheese.
Using goals to identify aspects in business process models

Modularization of business process models using aspects is a new line of research. Aspectual languages in this context have been proposed and are still under development. However, most of the guidelines for aspects identification in this domain is still dependent on the idea of process model elements repetition. In this paper, we explore a new way of identifying aspects, based on the ideas of the GPM (Generic Process Model) and process goals. We present a procedure for aspect identification and provide an example to illustrate its application
Modelling web navigation with the user in mind

In this research we introduce the ABBA framework for the generation of advanced screen readers. Current solutions do not enable blind users to participate in the Web in a satisfactory way because they are not time-efficient, cumbersome to use, and do not provide enough overview and orientation within a document. Also, they hide away important layout information from the user. Our approach overcomes these limitations by unifying different semantic views of a document into one multi-axial model and making them accessible to the user in an intuitive interface. The benefit to the user is a higher level of control in different navigation scenarios.
Fast approximate calculation of multiply scattered lidar returns.

An efficient method is described for the approximate calculation of the intensity of multiply scattered lidar returns. It divides the outgoing photons into three populations, representing those that have experienced zero, one, and more than one forward-scattering event. Each population is parameterized at each range gate by its total energy, its spatial variance, the variance of photon direction, and the covariance of photon direction and position. The result is that for an N-point profile the calculation is O(N2) efficient and implicitly includes up to N-order scattering, making it ideal for use in iterative retrieval algorithms for which speed is crucial. In contrast, models that explicitly consider each scattering order separately are at best O(Nm/m! ) efficient for m-order scattering and often cannot be performed to more than the third or fourth order in retrieval algorithms. For typical cloud profiles and a wide range of lidar fields of view, the new algorithm is as accurate as an explicit calculation truncated at the fifth or sixth order but faster by several orders of magnitude.
The effect of the repeated subcultures of Helicobacter pylori on adhesion, motility, cytotoxicity, and gastric inflammation.

In vitro subcultures of bacteria can lead to genetic and phenotypic changes. This study aimed at investigating the effect of repeated subcultures on the adhesion, motility, cytotoxicity, and gastric inflammation caused by Helicobacter pylori. H.pylori SS1 strain was subcultured 64 times on agar plates containing Brucella broth and 5% bovine calf serum. The adhesion, motility, cytotoxicity, and gastric inflammation produced in Mongolian gerbils were compared between the first and 64th subcultured strain. The adhesion rates, following 3 hr exposure of AGS cells to either the first strain or the 64th-transferred strain, were 21% and 12%, respectively. The motility of the 64th-transferred strain decreased significantly when compared to the 1st strain (9.1 mm vs. 15.1 mm). The cytotoxicity index tended to be higher in the first strain than in the 64th-transferred strain (73.7% vs. 69.2%). The initial infection rate on the gerbils showed no difference between the two strains. However, chronic gastric inflammation of the first strain-infected gerbils was somewhat more severe than that of the 64th-transferred strain-infected gerbils. Therefore, the use of repeatedly subcultured strains of H. pylori in virulence experiments can lead to different results from those of the original strain.