Miracle-dz/UniFAR-FTUs huggingface dataset:
Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers

To catalog protein-altering mutations that may drive the development of prostate cancers and their progression to metastatic disease systematically, we performed whole-exome sequencing of 23 prostate cancers derived from 16 different lethal metastatic tumors and three high-grade primary carcinomas. All tumors were propagated in mice as xenografts, designated the LuCaP series, to model phenotypic variation, such as responses to cancer-directed therapeutics. Although corresponding normal tissue was not available for most tumors, we were able to take advantage of increasingly deep catalogs of human genetic variation to remove most germline variants. On average, each tumor genome contained ∼200 novel nonsynonymous variants, of which the vast majority was specific to individual carcinomas. A subset of genes was recurrently altered across tumors derived from different individuals, including TP53, DLK2, GPC6, and SDF4. Unexpectedly, three prostate cancer genomes exhibited substantially higher mutation frequencies, with 2,000–4,000 novel coding variants per exome. A comparison of castration-resistant and castration-sensitive pairs of tumor lines derived from the same prostate cancer highlights mutations in the Wnt pathway as potentially contributing to the development of castration resistance. Collectively, our results indicate that point mutations arising in coding regions of advanced prostate cancers are common but, with notable exceptions, very few genes are mutated in a substantial fraction of tumors. We also report a previously undescribed subtype of prostate cancers exhibiting “hypermutated” genomes, with potential implications for resistance to cancer therapeutics. Our results also suggest that increasingly deep catalogs of human germline variation may challenge the necessity of sequencing matched tumor-normal pairs.
Estrildinae Finches (Aves, Passeriformes) from Africa, South Asia and Australia: a Molecular Phylogeographic Study

Estrildid finches are distributed throughout Africa, South Asia, Australia and neighbouring islands in the Indian and Pacific Oceans. Some specific phylogenetic and systematic debated questions have been clarified in the present study by mitochondrial cytochrome b DNA sequencing of 61 species of Estrildids and subsequent analyses of results by both Bayesian Inference and Maximum Likelihood methodologies. Our results support that Estrildids are a monophyletic group with polytomies that may have started evolving by Middle Miocene Epoch (about 16, 5 million years ago). This proposed timing is coincidental with the Fringillinae finches' radiation starting time and also with the biggest Hymalayan and Ti- betan Plateau uplift, triggered by the Indian tectonic plate strongest collision; this established present day southern Asia monsoon regime and other drastic climatic changes, like a dryer weather in Tibetan Plateau and China deserts. The Estrildid finches form a monophyletic group which includes several polytomies and comprises African, Asian and Austra- lian birds. The most ancient evolutive group comprises African (African silverbill), Asian (Indian silverbill) and Austra- lian (diamond firetail); this suggests that the whole Estrildids radiation might have originated around India.More Estrildid species will be studied in order to further establish this group phylogeography. In addition, monophyletic radiations in- clude species from different Continents. Finally, Ploceinae Genus Quelea finches is a group separate and basal from Estrildini and Viduini species in our dendrograms.
Fuzzy Interpolation and Extrapolation: A Practical Approach

Fuzzy interpolation does not only help to reduce the complexity of fuzzy models, but also makes inference in sparse rule-based systems possible. It has been successfully applied to systems control, but limited work exists for its applications to tasks like prediction and classification. Almost all fuzzy interpolation techniques in the literature make strong assumptions that there are two closest adjacent rules available to the observation, and that such rules must flank the observation for each attribute. Also, some interpolation approaches cannot handle fuzzy sets whose membership functions involve vertical slopes. To avoid such limitations and develop a more practical approach, this paper extends the work of Huang and Shen. The result enables both interpolation and extrapolation which involve multiple fuzzy rules, with each rule consisting of multiple antecedents. Two realistic applications, namely truck backer-upper control and computer activity prediction, are provided in this paper to demonstrate the utility of the extended approach. Experiment-based comparisons to the most commonly used Mamdani fuzzy reasoning mechanism, and to other existing fuzzy interpolation techniques are given to show the significance and potential of this research.
Early Childhood Teachers Coping with Educational Change

THIS PAPER DESCRIBES a study of early childhood teachers' (educators of children aged four – eight years in school settings) perceptions of key factors which impact on their ability to cope with the implementation of mandated educational change in the workplace. Using qualitative methodology including surveys, focus groups and in-depth interviews, this study revealed that early childhood teachers' attitudes and approaches to change impacted on their active engagement and continuance in their profession, as did the support they received from work colleagues and line managers. In addition, access to information and professional development sessions, as well as involvement in and ownership of the change process, further contributed to how they coped during implementation of educational change.
Ice core precipitation record in central Tibetan plateau since AD 1600

Lack of reliable long-term precipitation record from northern Tibetan Plateau has constrained the understanding of precipitation variation in this region. An ice core drilled from the Puruogangri Ice Field on central Tibetan Plateau in the year 2000 helped reveal the precipitation variations since AD 1600. Analysis of the annual accumulation data presented precipitation changes from AD 1600, indicative of wet and dry periods in the past 400 year in the central Tibetan Plateau. Accordingly, the 18th and 20th centuries experienced high precipitation period, whilst the 19th century experienced low precipitation period. Such a feature was consistent with precipitation recorded in ice cores from Dunde and Guliya Glaciers, northern Tibetan Plateau. Besides, the results also pointed to consistency in precipitation-temperature correlation on the northern Tibetan Plateau, in a way that temperature and precipitation were positively correlated. But this feature was contrary to the relationship revealed from Dasuopu ice cores, southern Tibetan Plateau, where temperature and precipitation were negatively correlated. The north-south contrast in precipitation amount and its relationship with temperature may shed light on the reconstruction of Asian monsoon since AD 1600.
EMF1, A Novel Protein Involved in the Control of Shoot Architecture and Flowering in Arabidopsis

Shoot architecture and flowering time in angiosperms depend on the balanced expression of a large number of flowering time and flower meristem identity genes. Loss-of-function mutations in the Arabidopsis EMBRYONIC FLOWER (EMF) genes cause Arabidopsis to eliminate rosette shoot growth and transform the apical meristem from indeterminate to determinate growth by producing a single terminal flower on all nodes. We have identified the EMF1 gene by positional cloning. The deduced polypeptide has no homology with any protein of known function except a putative protein in the rice genome with which EMF1 shares common motifs that include nuclear localization signals, P-loop, and LXXLL elements. Alteration of EMF1 expression in transgenic plants caused progressive changes in flowering time, shoot determinacy, and inflorescence architecture. EMF1 and its related sequence may belong to a new class of proteins that function as transcriptional regulators of phase transition during shoot development.
Differential expression and function of survivin during the progress of pterygium.

PURPOSE To investigate the expression pattern and function of survivin in the development of pterygium. METHODS Primary pterygia at quiescent or advanced clinical stage and normal human conjunctival tissues were used in this study. Pterygium epithelial cells (PECs) were cultured in keratinocyte serum-free defined medium and harvested at different growth stages. Tissue sections and cultured cells were detected with survivin, phosphorylated survivin (Thr43), p63, p57, and p21 on protein, and/or mRNA level. Cell Counting Kit (CCK)-8 assay was performed to measure proliferation status of primary cultured PECs. Small interfering (si) RNA specific for survivin was transfected on PECs at subconfluence stage. RESULTS Survivin was highly expressed in all pterygium tissues, but not in normal human conjunctiva, at mRNA and protein levels. It was mainly present in the epithelial cytoplasm of pterygium at quiescent stage, while present in the nucleus of pterygium at advanced stage. Phosphorylated survivin was upregulated in pterygium at advanced stage. Pterygium epithelial cells cultured under subconfluence stage showed higher expression of survivin and p63, but lower expression of p57 and p21, compared with PECs reached confluence. Both total and phosphorylated survivin was mainly expressed in the nuclei of PECs under subconfluence, and there was cytoplasmic translocation of survivin when PECs reached confluence. The knockdown of survivin by siRNA inhibited proliferation of PECs, accompanied by downregulation of p63, and upregulation of p57 and p21. CONCLUSIONS Higher subcellular expression and phosphorylation of survivin may play roles in the development of pterygium. Survivin could be targeted for the treatment of pterygium.
Autonomous Sustain and Resupply, Phase 1 Report

Abstract : This report presents our progress to date on the DRDC Autonomous Sustain and Resupply project. We are using the ASR problem as the key motivating problem for the AI and autonomy research in our lab. The document is structured as follows. First we state our general approach, which is unchanged from the proposal. Then we summarize our progress to date, referencing detailed descriptions of our work provided as chapters of this report. Next we provide the research plan, which is slightly revised from the version in our proposal. Next is the literature review, followed by our formal model of the problem, and then a design for a planning-based solution. The remainder is a series of chapters describing our progress during Phase 1 on various aspects of the ASR problem.
ERP as an organizational innovation: key users and cross-boundary knowledge management

Purpose The purpose of this study is to provide more insight in the ways key users act as knowledge managers and boundary spanners during the enterprise resource planning (ERP) system usage phase. Despite the recognized importance of key users during the implementation phase of an ERP system, little is known about their role in the ERP usage phase. Design/methodology/approach To provide rich insight in the boundary-spanning mechanisms utilized by key users to share knowledge, a qualitative approach was applied. In this study, “abductive” theme coding for 58 interviews with key users, end-users and managers has been used. This paper found six mechanisms and characterized them as “crossing” structural, social or cognitive boundaries. Findings Six boundary-spanning mechanisms have been distinguished which have been applied by key users to overcome several knowledge management issues. Subsequently, these mechanisms lead to a model which describes three different roles that key users may fulfill to efficiently share and transfer knowledge during the ERP usage phase. Research limitations/implications Knowledge barriers during an ERP implementation and their accompanying six boundary-crossing mechanisms have been distinguished. Practical implications The recognition of the essential role that key users can fulfill during the usage phase of an ERP system is an important implication. Management has to take into account that tasks and responsibilities of key users have to be clear from the start and they may cautiously select employees who are suited to become key users. Originality/value The main contribution is the importance of the impact of key users on the effectivity of knowledge management during the ERP usage phase.
Do You Trust to Get Trust? A Study of Trust Reciprocity Behaviors and Reciprocal Trust Prediction

Trust reciprocity, a special form of link reciprocity, exists in many networks of trust among users. In this paper, we seek to determine the extent to which reciprocity exists in a trust network and develop quantitative models for measuring reciprocity and reciprocity related behaviors. We identify several reciprocity behaviors and their respective measures. These behavior measures can be employed for predicting if a trustee will return trust to her trustor given that the latter initiates a trust link earlier. We develop for this reciprocal trust prediction task a number of ranking method and classification methods, and evaluated them on an Epinions trust network data. Our results show that reciprocity related behaviors provide good features for both ranking and classification based methods under different
Analytic regularization for landmark-based image registration

Landmark-based registration using radial basis functions (RBF) is an efficient and mathematically transparent method for the registration of medical images. To ensure invertibility and diffeomorphism of the RBF-based vector field, various regularization schemes have been suggested. Here, we report a novel analytic method of RBF regularization and demonstrate its power for Gaussian RBF. Our analytic formula can be used to obtain a regularized vector field from the solution of a system of linear equations, exactly as in traditional RBF, and can be generalized to any RBF with infinite support. We statistically validate the method on global registration of synthetic and pulmonary images. Furthermore, we present several clinical examples of multistage intensity/landmark-based registrations, where regularized Gaussian RBF are successful in correcting locally misregistered areas resulting from automatic B-spline registration. The intended ultimate application of our method is rapid, interactive local correction of deformable registration with a small number of mouse clicks.
Predicting loss in magnetic steels under arbitrary induction waveform and with minor hysteresis loops

We have studied ways of predicting power losses in soft magnetic laminations for generic time dependence of the periodic magnetic polarization J(t). We found that, whatever the frequency and the induction waveform, the loss behavior can be quantitatively assessed within the theoretical framework of the statistical loss model. The prediction requires a limited set of preemptive experimental data, depending on whether or not the arbitrary J(t) waveform is endowed with local slope inversions (i.e., minor hysteresis loops) in its periodic time behavior. In the absence of minor loops, such data reduce, for any peak polarization value J/sub p/, to the loss figures obtained under sinusoidal J(t) at two different frequency values. In the presence of minor loops of semiamplitude J/sub m/, the two-frequency loss experiment should be carried out for both peak polarization values J/sub p/ and J/sub m/. Additional knowledge of the quasi-static major loop, to be used for modeling hysteresis loss, does improve the accuracy of the prediction method. A more general approach to loss in soft magnetic laminations is obtained in this way, the only limitation apparently being the onset of skin effect at high frequencies.
GROUP REACTIONS TO RISKY PROSPECTIVE MEMBERS

Most research on the consequences of rejection focuses on intrapersonal issues, such as an increased need to belong, negative affect, and decreased self-esteem. Rejected individuals often seek to cope with these problems by establishing new social bonds. However, there is no research on whether these efforts are successful. A prospective member rejected by one group may seem risky and thus unattractive to other groups he or she seeks to join. My research extended Sitkin and Pablo's (1992) model of risky decision-making from individuals to groups, so that group responses to such persons could be examined. A field experiment was carried out on small classroom groups (N = 57) that worked together on group activities throughout a semester. Students' course grades were partially determined by the performance of their groups. Five group characteristics were measured and correlated with risk propensity (the tendency for groups to take risks). Groups that were more cohesive, potent, ambitious, successful, and perceived that outside help was available and valuable, had lower risk propensities. Risk propensity was unrelated to how risky prospective members seemed, or how willing groups were to admit them. Rejected individuals were perceived as riskier than non-rejected individuals, and groups were less willing to admit rejected than non-rejected individuals. A 2 (Reason for rejection: task vs. social) x 2 (Expectancy: high vs. low) repeated measures design examined how the characteristics of rejected individuals affected how risky they seemed to groups, and how willing groups were to admit them. Groups perceived individuals who were rejected for reasons likely to occur again (high expectancy) as riskier, and they were less willing to admit these individuals. Groups also perceived more risk among prospective members who were rejected for reasons relevant to their group's orientation (task or social). Rejection apparently makes it difficult for individuals to enter new groups, which could exacerbate the negative intrapersonal effects of rejection.
A new look at dynamo cycle amplitudes

We explore the dependence of the amplitude of stellar dynamo cycle variability (as seen in the Mount Wilson Ca II HK timeseries data) on other stellar parameters.We find that the fractional cycle amplitude Acyc (i.e. the ratio of the peak-to-peak variation to the average) decreases somewhat with mean activity, increases with decreasing effective temperature, but is not correlated with inverse Rossby number Ro–1. We find that Acyc increases with the ratio of cycle and rotational frequencies ωcyc/Ω along two, nearly parallel branches.
Expertness framework in multi-agent systems and its application in credit assignment problem

One of the challenging problems in artificial intelligence is credit assignment which simply means distributing the credit among a group, such as a group of agents. We made an attempt to meet this problem with the aid of the reinforcement learning paradigm. In this paper, expertness framework is defined and applied to the multi-agent credit assignment problem. In the expertness framework, the critic agent, who is responsible for distributing credit among agents, is equipped with learning capability, and the proposed credit assignment solution is based on the critic to learn to assign a proportion of the credit to each agent, and the used proportion should be learned by reinforcement learning. The paper also reports the degree of expertness framework robustness and the amount of performance decline in noisy environments. Experimental results show the superiority of the method over the common methods of credit assignment used in lots of different domains and also show that performance reduction with respect to the quantity of the noise is tolerable and the system ultimately converges to the stable and correct behavior, therefore the agents are still capable of efficiently performing in the noisy environments.
Model Selection using Response Measurements: Bayesian Probabilistic Approach

A Bayesian probabilistic approach is presented for selecting the most plausible class of models for a structural or mechanical system within some specified set of model classes, based on system response data. The crux of the approach is to rank the classes of models based on their probabilities conditional on the response data which can be calculated based on Bayes’ theorem and an asymptotic expansion for the evidence for each model class. The approach provides a quantitative expression of a principle of model parsimony or of Ockham’s razor which in this context can be stated as “simpler models are to be preferred over unnecessarily complicated ones. ” Examples are presented to illustrate the method using a single-degree-of-freedom bilinear hysteretic system, a linear two-story frame, and a ten-story shear building, all of which are subjected to seismic excitation.
The Impact of WebQuest and Gender on Writing Achievement in Professional Business English

This article reports the results of an experimental study that examined the relative effectiveness of the WebQuest (WQ) technological model in improving the English for Occupational Purposes (EOP) writing proficiency of a cohort of English as a foreign language (EFL) learners who were enrolled in a certified university professional business program in Lebanon. The study looked into the question of whether WebQuest is perceived as a significant and efficacious teaching tool. The study is based on the assumptions that language instructors can use the WQ as a useful source of authentic materials that enrich the content and exercises of the regular English for Specific Purposes (ESP) textbooks. The study employed an experimental pretest-posttest control group design. Descriptive statistics were calculated on performance scores of learners in the control and experimental groups, and by gender, following which a Multivariate Analysis of Covariance (MANCOVA) test was conducted in order to address the questions raised in the study regarding the effect of the treatment conditions, gender, and the interaction between treatment and gender. The results of the study showed no WQI significant treatment effects, and no significant interaction effects of treatment and gender on writing achievement. It was also found that females outperformed males.