Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial mass, a new metabolic biomarker for stem-like cancer cells: Understanding WNT/FGF-driven anabolic signaling

Here, we developed an isogenic cell model of “stemness” to facilitate protein biomarker discovery in breast cancer. For this purpose, we used knowledge gained previously from the study of the mouse mammary tumor virus (MMTV). MMTV initiates mammary tumorigenesis in mice by promoter insertion adjacent to two main integration sites, namely Int-1 (Wnt1) and Int-2 (Fgf3), which ultimately activates Wnt/β-catenin signaling, driving the propagation of mammary cancer stem cells (CSCs). Thus, to develop a humanized model of MMTV signaling, we over-expressed WNT1 and FGF3 in MCF7 cells, an ER(+) human breast cancer cell line. We then validated that MCF7 cells over-expressing both WNT1 and FGF3 show a 3.5-fold increase in mammosphere formation, and that conditioned media from these cells is also sufficient to promote stem cell activity in untransfected parental MCF7 and T47D cells, as WNT1 and FGF3 are secreted factors. Proteomic analysis of this model system revealed the induction of i) EMT markers, ii) mitochondrial proteins, iii) glycolytic enzymes and iv) protein synthesis machinery, consistent with an anabolic CSC phenotype. MitoTracker staining validated the expected WNT1/FGF3-induced increase in mitochondrial mass and activity, which presumably reflects increased mitochondrial biogenesis. Importantly, many of the proteins that were up-regulated by WNT/FGF-signaling in MCF7 cells, were also transcriptionally over-expressed in human breast cancer cells in vivo, based on the bioinformatic analysis of public gene expression datasets of laser-captured patient samples. As such, this isogenic cell model should accelerate the discovery of new biomarkers to predict clinical outcome in breast cancer, facilitating the development of personalized medicine. Finally, we used mitochondrial mass as a surrogate marker for increased mitochondrial biogenesis in untransfected MCF7 cells. As predicted, metabolic fractionation of parental MCF7 cells, via MitoTracker staining, indicated that high mitochondrial mass is a new metabolic biomarker for the enrichment of anabolic CSCs, as functionally assessed by mammosphere-forming activity. This observation has broad implications for understanding the role of mitochondrial biogenesis in the propagation of stem-like cancer cells. Technically, this general metabolic approach could be applied to any cancer type, to identify and target the mitochondrial-rich CSC population. The implications of our work for understanding the role of mitochondrial metabolism in viral oncogenesis driven by random promoter insertions are also discussed, in the context of MMTV and ALV infections.
An efficient algorithm for rank-1 sparse PCA

Sparse principal component analysis (PCA) imposes extra co nstraints or penalty terms to the original PCA to achieve sparsity. In this paper, we introduce an efficient algorithm to find a single sparse principal compone nt with a specified cardinality. The algorithm consists of two stages. In the fir st stage, it identifies an active index set with desired cardinality corresponding to the nonzero entries of the principal component. In the second one, it finds the best d irection with respect to the active index set, using the power iteration method. Ex periments on both randomly generated data and real-world data sets show that o ur lgorithm is very fast, especially on large and sparse data sets, while the num rical quality of the solution is comparable to other methods.
Sentiment and social mitosis: Implications of Heider's Balance Theory

Two Monte Carlo simulations were developed to investigate the social consequences of balancing sentiment relations among triads of members of a larger group, when balancing one triad can imbalance others. Using assumptions of Balance Theory (Heider, 1958), random starting combinations of liking, disliking and no relations among 9 or16 people were iteratively adjusted to determine if the relations ever settled to a steady state and what subgroups might emerge. Results show that, regardless of the starting configuration of sentiments, all imbalances in a group are eventually balanced in a steady state containing no more than two subgroups. Two subgroups are the rule; their relative size depends on the starting number of positive, negative and null relations. Members within each subgroup are linked by positive relations (liking), and show only negative relations (disliking) towards members of the other subgroup, a form of social mitosis. A second simulation demonstrates that a starting configuration containing only positive and negative relations (no null relations) will completely determine who will eventually belong to which of the two groups. As null relations become more plentiful in the starting configuration, the order or historical trajectory of restoring balance among triads also contributes to subgroup membership.
Surprisal Analysis of Transcripts Expression Levels in the Presence of Noise: A Reliable Determination of the Onset of a Tumor Phenotype

Towards a reliable identification of the onset in time of a cancer phenotype, changes in transcription levels in cell models were tested. Surprisal analysis, an information-theoretic approach grounded in thermodynamics, was used to characterize the expression level of mRNAs as time changed. Surprisal Analysis provides a very compact representation for the measured expression levels of many thousands of mRNAs in terms of very few - three, four - transcription patterns. The patterns, that are a collection of transcripts that respond together, can be assigned definite biological phenotypic role. We identify a transcription pattern that is a clear marker of eventual malignancy. The weight of each transcription pattern is determined by surprisal analysis. The weight of this pattern changes with time; it is never strictly zero but it is very low at early times and then rises rather suddenly. We suggest that the low weights at early time points are primarily due to experimental noise. We develop the necessary formalism to determine at what point in time the value of that pattern becomes reliable. Beyond the point in time when a pattern is deemed reliable the data shows that the pattern remain reliable. We suggest that this allows a determination of the presence of a cancer forewarning. We apply the same formalism to the weight of the transcription patterns that account for healthy cell pathways, such as apoptosis, that need to be switched off in cancer cells. We show that their weight eventually falls below the threshold. Lastly we discuss patient heterogeneity as an additional source of fluctuation and show how to incorporate it within the developed formalism.
Total Generalized Variation in Diffusion Tensor Imaging

We study the extension of total variation (TV), total deformation (TD), and (second-order) total generalized variation ($\TGV^2$) to symmetric tensor fields. We show that for a suitable choice of finite-dimensional norm, these variational seminorms are rotation-invariant in a sense natural and well suited for application to diffusion tensor imaging (DTI). Combined with a positive definiteness constraint, we employ these novel seminorms as regularizers in Rudin--Osher--Fatemi (ROF) type denoising of medical in vivo brain images. For the numerical realization, we employ the Chambolle--Pock algorithm, for which we develop a novel duality-based stopping criterion which guarantees error bounds with respect to the functional values. Our findings indicate that TD and $\TGV^2$, both of which employ the symmetrized differential, provide improved results compared to other evaluated approaches.
NIST 2008 speaker recognition evaluation: performance across telephone and room microphone channels

We describe the 2008 NIST Speaker Recognition Evaluation, including the speech data used, the test conditions included, the participants, and some of the performance results obtained. This evaluation was distinguished by including as part of the required test condition interview type speech as well as conversational telephone speech, and speech recorded over microphone channels as well as speech recorded over telephone lines. Notable was the relative consistency of best system performance obtained over the different speech types, including those involving different types in training and test. Some comparison with performance in prior evaluations is also discussed.
Territorial Stigmatization in the Age of Advanced Marginality

The comparative sociology of the structure, dynamics, and experience of urban relegation in the United States and the European Union during the past three decades reveals the emergence of a new regime of marginality. This regime generates forms of poverty that are neither residual, nor cyclical or transitional, but inscribed in the future of contemporary societies insofar as they are fed by the ongoing fragmentation of the wage labour relationship, the functional disconnection of dispossessed neighbourhoods from the national and global economies, and the reconfiguration of the welfare state in the polarizing city. Based on a methodical comparison between the black American ghetto and the French working-class banlieue at century's turn, this article spotlights three distinctive spatial properties of `advanced marginality' — territorial fixation and stigmatization, spatial alienation and the dissolution of `place', and the loss of a hinterland — and draws out their implications for the formation of the `precariat' in postindustrial societies.
BPAG1n4 is essential for retrograde axonal transport in sensory neurons

Disruption of the BPAG1 (bullous pemphigoid antigen 1) gene results in progressive deterioration in motor function and devastating sensory neurodegeneration in the null mice. We have previously demonstrated that BPAG1n1 and BPAG1n3 play important roles in organizing cytoskeletal networks in vivo. Here, we characterize functions of a novel BPAG1 neuronal isoform, BPAG1n4. Results obtained from yeast two-hybrid screening, blot overlay binding assays, and coimmunoprecipitations demonstrate that BPAG1n4 interacts directly with dynactin p150Glued through its unique ezrin/radixin/moesin domain. Studies using double immunofluorescent microscopy and ultrastructural analysis reveal physiological colocalization of BPAG1n4 with dynactin/dynein. Disruption of the interaction between BPAG1n4 and dynactin results in severe defects in retrograde axonal transport. We conclude that BPAG1n4 plays an essential role in retrograde axonal transport in sensory neurons. These findings might advance our understanding of pathogenesis of axonal degeneration and neuronal death.
Group Premarital Counseling Using a Premarital Assessment Questionnaire: Evaluation from Group Leaders

No research to date addresses premarital assessment questionnaire (PAQ) use within group settings. The current study evaluated the benefits and drawbacks of group use of one PAQ (the RELATE Inventory). Results were obtained via semi-structured interviews of group leaders and indicate overall leader agreement on the perceived desirability, benefits, and drawbacks of using PAQs in group premarital efforts. Recommended principles/guidelines for effective group PAQ use are organized into four categories: PAQ Considerations, Group Leader Considerations, Couple Considerations, and Group Content/Process Considerations.
University of Dundee GEN 1 from a thermophilic fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes

Processing of Holliday junctions is essential in recombination. We have identified the gene for the junctionresolving enzyme GEN1 from the thermophilic fungus Chaetomium thermophilum and expressed the N-terminal 487-amino-acid section. The protein is a nuclease that is highly selective for four-way DNA junctions, cleaving 1 nt 3′ to the point of strand exchange on two strands symmetrically disposed about a diagonal axis. CtGEN1 binds to DNA junctions as a discrete homodimer with nanomolar affinity. Analysis of the kinetics of cruciform cleavage shows that cleavage of the second strand occurs an order of magnitude faster than the first cleavage so as to generate a productive resolution event. All these properties are closely similar to those described for bacterial, phage and mitochondrial junction-resolving enzymes. CtGEN1 is also similar in properties to the human enzyme but lacks the problems with aggregation that currently prevent detailed analysis of the latter protein. CtGEN1 is thus an excellent enzyme with which to engage in biophysical and structural analysis of eukaryotic GEN1. © 2014 MRC Laboratory of Molecular Biology. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).
Combining Geometric, Textual and Visual Features for Predicting Prepositions in Image Descriptions

We investigate the role that geometric, textual and visual features play in the task of predicting a preposition that links two visual entities depicted in an image. The task is an important part of the subsequent process of generating image descriptions. We explore the prediction of prepositions for a pair of entities, both in the case when the labels of such entities are known and unknown. In all situations we found clear evidence that all three features contribute to the prediction task.
CPU Power Management in Video Transcoding Servers

To support the diverse requirements of mobile clients and fluctuating network bandwidth, video content for wireless streaming is usually transcoded into several versions. However, transcoding requires a lot of computation, resulting in high power consumption by the server. We examine the characteristics of transcoding workloads and characterize them in terms of deadline and computation time. We then propose a new dynamic voltage and frequency scaling (DVFS) scheme that allocates a frequency and a workload to each CPU with the aim of minimizing power consumption while meeting all transcoding deadlines. Experimental results show that our scheme can reduce system-wide energy consumption by 10% to 16% compared with the Linux On-demand governor while ensuring all the transcoding tasks meet their deadlines.
EARs in the wild: large-scale analysis of execution after redirect vulnerabilities

Execution After Redirect vulnerabilities---logic flaws in web applications where unintended code is executed after a redirect---have received little attention from the research community. In fact, we found a research paper that incorrectly modeled the redirect semantics, causing their static analysis to miss EAR vulnerabilities. To understand the breadth and scope of EARs in the real world, we performed a large-scale analysis to determine the prevalence of EARs on the Internet. We crawled 8,097,283 URLs from 255,957 domains. We employ a black-box approach that finds EARs which manifest themselves by information leakage in the HTTP redirect response. For this type of EAR, we developed a classification system that discovered 2,173 security-critical EARs among 416 domains. This result shows that EARs are a serious and prevalent problem on the Internet today and deserve future research attention.
Capturing age-related changes in functional contrast sensitivity with decreasing light levels in monocular and binocular vision.

PURPOSE It is challenging to separate the effects of normal aging of the retina and visual pathways independently from optical factors, decreased retinal illuminance, and early stage disease. This study determined limits to describe the effect of light level on normal, age-related changes in monocular and binocular functional contrast sensitivity. METHODS We recruited 95 participants aged 20 to 85 years. Contrast thresholds for correct orientation discrimination of the gap in a Landolt C optotype were measured using a 4-alternative, forced-choice (4AFC) procedure at screen luminances from 34 to 0.12 cd/m(2) at the fovea and parafovea (0° and ±4°). Pupil size was measured continuously. The Health of the Retina index (HRindex) was computed to capture the loss of contrast sensitivity with decreasing light level. Participants were excluded if they exhibited performance outside the normal limits of interocular differences or HRindex values, or signs of ocular disease. RESULTS Parafoveal contrast thresholds showed a steeper decline and higher correlation with age at the parafovea than the fovea. Of participants with clinical signs of ocular disease, 83% had HRindex values outside the normal limits. Binocular summation of contrast signals declined with age, independent of interocular differences. CONCLUSIONS The HRindex worsens more rapidly with age at the parafovea, consistent with histologic findings of rod loss and its link to age-related degenerative disease of the retina. The HRindex and interocular differences could be used to screen for and separate the earliest stages of subclinical disease from changes caused by normal aging.
Institutional Repositories: Benefits and incentives

The Information Age is characterized by new ways of information generation, managing, and dissemination because of the use of information and communication technology (ICT) (Moahi, 2003; Paul, 2007). Institutional Repositories (IRs) play a fundamental role in centralizing, preserving, and making accessible institution's intellectual capital and, at the same time, they form part of a global system of distributed and interoperable repositories that provide the foundation for a new disaggregated model of scholarly publishing (Johnson, 2002; Nagahban, 2010). A study of nine libraries in the National Capital Region of India was conducted to: identify benefits of IRs, learn the satisfaction level of users with respect to IR facilities, identify the incentives for publication in IRs, and identify the appropriate policies to be adopted by institutions for implementing IRs. The results of the responses from the 496 respondents indicate that: 1) Most Faculty members and Research scholars in this study indicated that they do not publish their research in IRs. 2) Opinions about benefits of IRs are user-specific. For instance, a substantially large percentage of those Faculty members and Research scholars in the study who do use IRs are Most satisfied with potential benefits of IR while a relatively higher percentage of Students fall in the Satisfied category. 3) The benefits of IRs ranked most highly, although this varied by the different user groups was wider readership. Students ranked this and "quality aspect" – the opportunity to improve the quality of one's work through the provision of feedback from other researchers. 4) A serious concern about publishing in IRs is the potential for plagiarism and overall lower control over one's work. A second concern is the potential loss of content in IRs, which are often not archived as well as scholarly journals are. The findings suggest that institutions need to give due attention to policies related to two aspects of publication, especially those related to quality and copyright issues and to the academic value of research output. Other policy-related topics include citation in other publication with due acknowledgement, inclusion in indexing systems for retrieval, interoperability with other IRs, and Permanent storage.
Promoting Organ Donation Through an Entertainment— Education TV Program in Korea

The purpose of this study is to investigate the effects of the characteristics of the program, Open Your Eyes, an entertainment—education TV program in Korea, on parasocial interaction and behavioral intention for organ donation. The results indicated that affective evaluation positively affected parasocial interaction with the program but cognitive evaluation negatively affected involvement with beneficiaries in the program. Also, it was found that cognitive evaluation of Open Your Eyes had a significant positive effect on behavioral intention. In addition, a significant positive effect of program engagement on the behavioral intention was found. Thus, the results indicate that individuals who feel program engagement of Open Your Eyes will be more likely to proceed with organ donation. However, no direct effect of involvement with the beneficiary and program hosts was found.
A SITUATIONAL JUDGMENT TEST OF PERSONAL INITIATIVE AND ITS RELATIONSHIP TO PERFORMANCE

Although situational judgment tests have been found to be valid predictors of performance, they have rarely been used to measure particular constructs. In this study, we apply the situational judgment test method to the measurement of personal initiative, a construct defined as situated action. We used respondents' situated preferences in mental simulations of work scenarios as formative indicators of their overall level of personal initiative at work. Results from a validation study showed that the situational judgment test of personal initiative (SJT-PI) had adequate validity and complemented a Likert-type self-report measure of personal initiative in predicting behavioral criteria. Situated preferences for personal initiative were hypothesized to be proximal predictors of actual behavior and were accordingly found to mediate the relationship between generalized self-efficacy, felt responsibility, and actual behavior. Furthermore, situated preferences for personal initiative could be differentiated empirically from organizational citizenship behavior. We conclude that situational judgment tests are a promising method for measuring personal initiative and may be a general means of improving the validity of measurement in organizations.
Using Rhetorical Structure Theory (RST) to describe the development of coherence in interpreting trainees

Making global sense has long been seen as one of the most important criteria for judging the success of a given interpretation. For consecutive in particular, special emphasis is placed on the coherence and structure of the rendition. This study addresses the question of how to investigate coherence in interpreting and observe its development in trainees. We propose Rhetorical Structure Theory (RST), as a framework for exploring how coherence is realised in interpretations produced by professional as well as trainee interpreters. A corpus of 66 consecutive interpretations, by eight novice and three professional interpreters, of three Chinese and three English speeches, was transcribed, segmented into functional units, and mapped into a tree-like RST description. The analyses and results reveal that novices tend to focus on local cohesion while professionals tend to emphasise the global structure of the discourse. This difference can usefully be addressed in training.
How Demography, Life History, and Kinship Shape the Evolution of Genomic Imprinting

How phenomena like helping, dispersal, or the sex ratio evolve depends critically on demographic and life‐history factors. One phenotype that is of particular interest to biologists is genomic imprinting, which results in parent‐of‐origin‐specific gene expression and thus deviates from the predictions of Mendel’s rules. The most prominent explanation for the evolution of genomic imprinting, the kinship theory, originally specified that multiple paternity can cause the evolution of imprinting when offspring affect maternal resource provisioning. Most models of the kinship theory do not detail how population subdivision, demography, and life history affect the evolution of imprinting. In this work, we embed the classic kinship theory within an island model of population structure and allow for diverse demographic and life‐history features to affect the direction of selection on imprinting. We find that population structure does not change how multiple paternity affects the evolution of imprinting under the classic kinship theory. However, if the degree of multiple paternity is not too large, we find that sex‐specific migration and survival and generation overlap are the primary factors determining which allele is silenced. This indicates that imprinting can evolve purely as a result of sex‐related asymmetries in the demographic structure or life history of a species.