Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyclin D1 downregulation is important for permanent cell cycle exit and initiation of differentiation induced by anchorage‐deprivation in human keratinocytes

To understand the relationship between permanent cell cycle exit and differentiation the immortalized keratinocyte cell line, SIK and the squamous cell carcinoma, SCC9 were compared during differentiation induced by anchorage‐deprivation. The SIK cells when placed in suspension culture promptly lost almost all ability to reinitiate growth by 2 days concomitantly expressing the differentiation specific proteins, transglutaminase (TGK) and involucrin. These cells rapidly underwent G1 cell cycle arrest with complete disappearance of phosphorylated RB. In contrast SCC9 cells neither showed TGK expression nor increase in involucrin. They decreased their colony‐forming ability much more slowly, which coordinated well with a gradual decrease in phosphorylated RB, demonstrating the significant resistance to loss of colony‐forming ability and cell cycle exit. In accordance, cyclin D1, a positive regulator of cyclin‐dependent kinase (CDK) 4/6 which phosphorylates RB decreased drastically in anchorage deprived SIK but not in SCC9 cells. Endogenous cyclin D1 knockdown in SCC9 cells by siRNA enhanced loss of the colony‐forming ability during anchorage‐deprivation. Conversely enforced expression of cyclin D1 in SIK cells and in another immortalized keratinocyte cell line, HaCaT, partly prevented loss of their colony‐forming abilities. Cyclin D1 overexpression antagonized Keratin 10 expression in suspended HaCaT cells. The result demonstrates the importance of cyclin D1 down regulation for proper initiation of keratinocyte differentiation. J. Cell. Biochem. 106: 63–72, 2009. © 2008 Wiley‐Liss, Inc.
A Probabilistic Joint Sparse Regression Model for Semisupervised Hyperspectral Unmixing

Semisupervised hyperspectral unmixing finds the ratio of spectral library members in the mixture of hyperspectral pixels to find the proportion of pure materials in a natural scene. The two main challenges are noise in observed spectral vectors and high mutual coherence of spectral libraries. To tackle these challenges, we propose a probabilistic sparse regression method for linear hyperspectral unmixing, which utilizes the implicit relations of neighboring pixels. We partition the hyperspectral image into rectangular patches. The sparse coefficients of pixels in each patch are assumed to be generated from a Laplacian scale mixture model with the same latent variables. These latent variables specify the probability of existence of endmembers in the mixture of each pixel. Experiments on synthetic and real hyperspectral images illustrate the superior performance of the proposed method over alternatives.
Does Auditor Industry Specialization Improve Audit Quality ? Evidence from Comparable Clients

The objective of this study is to examine the relation between auditor industry specialization and audit quality using an alternative research design to mitigate the influence of client characteristics. After matching clients of specialist and non-specialist auditors according to industry, size and performance, I find no significant differences in audit quality between these two groups of auditors. My findings are robust to using alternative matching approaches, to using various proxies for auditor industry specialization and audit quality, and to controlling for the effect of imperfectly matched characteristics. In addition, I perform two analyses that do not rely primarily on matched samples. First, in examining a sample of Arthur Andersen clients that switched auditors in 2002, I find no evidence of industry-specialization effects following the auditor change. Second, I observe that the industry-specialization effects are simulated by randomly assigning clients to auditors. Overall, these findings do not imply that industry knowledge is not important for auditors, but that the extant methodology may not fully parse out the effects of auditor industry expertise from client characteristics. * This paper is based on the first chapter of my dissertation at the University of Toronto, Rotman School of Management. I gratefully acknowledge the guidance provided by my co-chairs Gordon Richardson and Ping Zhang, as well as the other members of my dissertation committee, Jeffrey Callen and Gus De Franco. I thank Yiwei Dou, Stephanie Larocque, Alastair Lawrence, Yanju Liu, Matthew Lyle, Ole-Kristian Hope, Yu Hou, Dushantkumar Vyas, and seminar participants at the University of Toronto, and the 2010 CAAA PhD Consortium, for helpful comments and suggestions. I also acknowledge the financial support of the Canadian Public Accountability Board. All errors are my own.
Generation and Analysis of Expressed Sequence Tags from Chimonanthus praecox (Wintersweet) Flowers for Discovering Stress-Responsive and Floral Development-Related Genes

A complementary DNA library was constructed from the flowers of Chimonanthus praecox, an ornamental perennial shrub blossoming in winter in China. Eight hundred sixty-seven high-quality expressed sequence tag sequences with an average read length of 673.8 bp were acquired. A nonredundant set of 479 unigenes, including 94 contigs and 385 singletons, was identified after the expressed sequence tags were clustered and assembled. BLAST analysis against the nonredundant protein database and nonredundant nucleotide database revealed that 405 unigenes shared significant homology with known genes. The homologous unigenes were categorized according to Gene Ontology hierarchies (biological, cellular, and molecular). By BLAST analysis and Gene Ontology annotation, 95 unigenes involved in stress and defense and 19 unigenes related to floral development were identified based on existing knowledge. Twelve genes, of which 9 were annotated as “cold response,” were examined by real-time RT-PCR to understand the changes in expression patterns under cold stress and to validate the findings. Fourteen genes, including 11 genes related to floral development, were also detected by real-time RT-PCR to validate the expression patterns in the blooming process and in different tissues. This study provides a useful basis for the genomic analysis of C. praecox.
An evaluation of methods for the stratified analysis of clustered binary data in community intervention trials

A simulation study is conducted in a community intervention setting. Several methods of stratified analysis of clustered binary data are compared in terms of empirical significance and empirical power levels. They are the Mantel–Haenszel test statistic (χ2MH), the adjusted Mantel–Haenszel test statistic of Donald–Donner (χ2DD), Rao–Scott (χ2RSN and χ2RSP), and Zhang–Boos (χ2ZBN and χ2ZBP), Wald (χ2W), robust Wald (χ2RW), score (χ2S), robust score (χ2RS), and the test statistic based on generalized linear mixed model (GLMM) (χ2GLMM). When ρ ≠ 0, χ2MH has inflated type I error, and it should not be used when observations are correlated. The results also warn of the use of χ2RSN and χ2RW due to their poor performance in terms of empirical significance level. χ2ZBP and χ2GLMM have better empirical significance levels as compared to other statistics; however, χ2ZBP tends to have lower empirical powers than other statistics when the number of clusters (N) is less than 24. χ2RSP provides the highest empirical powers when ρ ≥ 0.1 and N ≤ 12. When ρ ≤ 0.01, we recommend the use of χ2RS and χ2GLMM since they have better overall performance in terms of empirical significance levels and empirical power levels. Copyright © 2003 John Wiley & Sons, Ltd.
Higher Volume at Time of Breast Conserving Surgery Reduces Re-Excision in DCIS

Purpose. The purpose of this study was to compare the surgical and pathological variables which impact rate of re-excision following breast conserving therapy (BCS) with or without concurrent additional margin excision (AM). Methods. The pathology database was queried for all patients with DCIS from January 2004 to September 2008. Pathologic assessment included volume of excision, subtype, size, distance from margin, grade, necrosis, multifocality, calcifications, and ER/PR status. Results. 405 cases were identified and 201 underwent BCS, 151-BCS-AM, and 53-mastectomy. Among the 201 BCS patients, 190 underwent re-excision for close or involved margins. 129 of these were treated with BCS and 61 with BCS-AM (P < .0001). The incidence of residual DCIS in the re-excision specimens was 32% (n = 65) for BCS and 22% (n = 33) for BCS-AM (P < .05). For both the BCS and the BCS-AM cohorts, volume of tissue excised is inversely correlated to the rate of re-excision (P = .0284). Multifocality (P = .0002) and ER status (P = .0382) were also significant predictors for rate of re-excision and variation in surgical technique was insignificant. Conclusions. The rate of positive margins, re-excision, and residual disease was significantly higher in patients with lower volume of excision. The performance of concurrent additional margin excision increases the efficacy of BCS for DCIS.
Outdoor Scene Labeling Using ALE and LSC Superpixels

Scene labeling has been an important and popular area of computer vision and image processing for the past few years. It is the process of assigning pixels to specific predefined categories in an image. A number of techniques have been proposed for scene labeling but all have some limitations regarding accuracy and computational time. Some methods only incorporate the local context of images and ignore the global information of objects in an image. Therefore, accuracy of scene labeling is low for these methods. There is a need to address these issues of scene labeling to improve labeling accuracy. In this paper, we perform outdoor scene labeling using Automatic labeling Environment (ALE). We enhance this framework by incorporating bilateral filter based preprocessing, LSC superpixels and large co-occurrence weight. Experiments on a publicly available MSRC v1 dataset showed promising results with 89.44% pixel-wise accuracy and 78.02% class-wise accuracy.
International capital crunches: the time-varying role of informational asymmetries

We examine the determinants of capital flows to four developing countries during the 1990s using an explicitly disequilibrium econometric framework in which the supply and demand for capital are not necessarily equal and the actual amount of the flow is determined by the ‘short side’ of the market. We are thus able to detect instances of ‘international capital crunch’ – where capital flows are curtailed because of supply-side rationing – and to relate these instances to movements in the underlying fundamentals. The analysis highlights the role of asymmetric information – as distinct from the traditional concern with default risk – in conditioning capital flows.
Inattentive and Socially Desirable Responding

Researchers consistently have demonstrated the distorting effects that inattentive (responding without regard for survey content) and socially desirable (presenting one’s self in an overly positive way) responding can have on quantitative data. These threats to validity usually go undetected in counseling research, which is concerning given that counseling research often considers implications for practice and that research-based practice is in demand. In this article, the authors review practical approaches for detecting and addressing inattentive and socially desirable response tendencies in counseling research, thereby optimizing the validity of conclusions inferred from data.
Implicit Relational Assessment Procedure and Body-Weight Bias: Influence of Gender of Participants and Targets

The Implicit Relational Assessment Procedure (IRAP) and explicit measures were used with 21 college students to determine if body weight of target stimuli (photographic images of slim and overweight individuals) influenced perceptions of intelligence. The explicit measure was a computerized adaptation of the Anti-Fat Attitudes Questionnaire designed to reduce participant error. A Covert Perception Task was developed as an additional explicit measure in which participants rated the likelihood of success of slim and overweight job applicants. Correlational analyses were used to determine if disparity between current and idealized body mass index (BMI) influenced responding. Statistical analyses were applied to data to determine influence exerted by the gender of participants and/or by the gender of the portrayed target stimuli. Findings are discussed in relation to pro-slim versus anti-fat bias and gender differences in body-weight bias related to participants and targets.
INFECTION OF C57BL/6 MICE BY TRYPANOSOMA MUSCULI MODULATES HOST IMMUNE RESPONSES DURING BRUCELLA ABORTUS COCOLONIZATION

Abstract Brucellosis, which results in fetal abortions in domestic and wildlife animal populations, is of major concern in the US and throughout much of the world. The disease, caused by Brucella abortus, poses an economic threat to agriculture-based communities. A moderately efficacious live attenuated vaccine (B. abortus strain RB51) exists. However, even with vaccine use, outbreaks occur. Evidence suggests that elk (Cervus canadensis), a wild host reservoir, are the source of recent outbreaks in domestic cattle herds in Wyoming, USA. Brucella abortus establishes a chronic, persistent infection in elk. The molecular mechanisms allowing the establishment of this persistent infective state are currently unknown. A potential mechanism could be that concurrent pathogen burdens contribute to persistence. In Wyoming, elk are chronically infected with Trypanosoma cervi, which may modulate host responses in a similar manner to that documented for other trypanosomes. To identify any synergistic relationship between the two pathogens, we simulated coinfection in the well-established murine brucellosis model using Trypanosoma musculi and B. abortus S19. Groups of C57BL/6 mice (Mus musculus) were infected with either B. abortus strain 19 (S19) or T. musculi or both. Sera were collected weekly; spleens from euthanized mice were tested to determine bacterial load near the end of normal brucellosis infection. Although changes in bacterial load were observed during the later stages of brucellosis in those mice coinfected with T. musculi, the most significant finding was the suppression of gamma interferon early during the infection along with an increase in interleukin-10 secretion compared with mice infected with either pathogen alone. These results suggest that immune modulatory events occur in the mouse during coinfection and that further experiments are warranted to determine if T. cervi impacts Brucella infection in elk.
Risk of fracture in urolithiasis: a population-based cohort study using the health improvement network.

BACKGROUND AND OBJECTIVES Studies have shown decreased bone mineral density in individuals with urolithiasis, but their burden of fracture remains unclear. This study sought to determine whether urolithiasis is associated with increased fracture risk across the lifespan and to delineate sex effects. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS A population-based retrospective cohort study using The Health Improvement Network was performed. The median calendar year for the start of the observation period was 2004 (1994-2012). This study identified 51,785 participants with ≥1 of 87 diagnostic codes for urolithiasis and 517,267 randomly selected age-, sex-, and practice-matched participants. Cox regression was used to estimate the hazard ratio (HR) for first fracture. Fractures identified using diagnostic codes were classified by anatomic site. RESULTS Median age was 53 years, and 67% of participants were men, confirming their greater urolithiasis burden. Median time from urolithiasis diagnosis to fracture was 10 years. The HR for fracture associated with urolithiasis differed by sex and age (P for interactions, P≤0.003). In men, the adjusted HR was greatest in adolescence (1.55; 95% confidence interval [95% CI], 1.07 to 2.25) with an overall HR of 1.10 (95% CI, 1.05 to 1.16). Urolithiasis was associated with higher fracture risk in women aged 30-79 years (HR, 1.17-1.52), and was highest in women aged 30-39 years (HR, 1.52; 95% CI, 1.23 to 1.87). Peak background fracture rates were highest in boys aged 10-19 years and in women aged 70-79 years. The incidence per 10,000 person-years in participants with versus without urolithiasis was 392 versus 258 in male participants aged 10-19 years, and 263 versus 218 in women aged 70-79 years. Distribution of fracture site within sex did not differ between participants with versus without urolithiasis. CONCLUSIONS Urolithiasis was associated with higher incident fracture risk. The significantly higher risk at times of peak background fracture incidence in adolescent boys and elderly women has profound public health implications.
Risky driving among UK regular armed forces personnel: changes over time

Objectives To compare the prevalence of self-reported risky driving in a sample of UK military personnel at 2 different time points (2004 and 2009), and to identify the incidence of new onset risky driving and possible determinants of becoming a new risky driver. Methods Data were used from 2 phases of a military cohort study investigating the health and well-being of UK military personnel between 2004 and 2009. Participants were included if they were undertaking regular (rather than reserve) engagements, had completed both surveys and reported being a driver at both surveys. Univariable and multivariable logistic regression analyses were performed to examine the relationship between risky driving status and sociodemographic and military characteristics. Data analysis was conducted in 2011. Results The prevalence of risky driving reduced from 18% to 14%, over an average of 3.3 years. The incidence of new onset risky driving was 7%. Predictors for becoming a new risky driver were: younger age, not being in a relationship at phase 2 and harmful alcohol use. Those deployed after 2007 were less likely to become risky drivers following deployment, compared with those deployed before 2007 (adjusted OR 0.62 (95% CI 0.40 to 0.95)). Conclusions The prevalence of becoming a risky driver appears to have reduced over time. This paper suggests a number of explanations for this reduction, including changes in the way that the UK military have dealt with road safety with the introduction of the road safety campaign (in 2007).
The Effect of Oculomotor Adjustments on Apparent Size

An object of fixed angular size looks smaller when the eyes are adjusted for near vision than when they are adjusted for far vision. This fact was reported first by Wheatstone, the inventor of the stereoscope.1 Wheatstone's qualitative observations were confirmed by several later investigators,2 and quantitative studies of the phenomenon have been made by Adams, Frank, Hermans, and Swenson.3 The research lXeported below deals mainly with two questions to which the previous investigators have not given clear answers. The first is whether the changes in apparent size are related to changes in apparent distance in the manner postulated by several current theories of 'size-constancy. '4 The second is which of the oculomotor adjustments, or possibly which combination of adjustments, controls the changes in apparent size. The principal oculomotor adjustments that are made in response to a change in viewing distance are (1) changes in the angle of convergence of the visual axes, (2) changes in the power of the lens (accommodation), and (3) changes in the diameter of the pupil. Convergence and accommodation are so linked that a change in one produces a change in the other, and a change in either is usually accompanied by a change in the diameter of the pupil.
Stent Retriever-Based Thrombectomy in Octogenarians

Background and Aims: Stent retriever-based thrombectomy (SRT) may be beneficial in patients with large hemispheric stroke. Previous studies concluded that favorable outcomes are far less frequent after endovascular therapy in older patients but have not explored outcomes in the era of newer-generation stent retrievers. Materials and Methods: Consecutive patients with large hemispheric stroke treated with SRT were included. We compared neurological and functional outcomes between patients younger and older than 80. Results: We included 16 patients older than 80 (22.5%, mean age 84.1 ± 4.4, 56% females) and compared them to 55 patients that were younger than 80 (77.5%, mean age 63.1 ± 12.5, 51% females). Risk factor profile, admission neurological severity, stroke etiology and procedure-related variables including excellent target vessel recanalization did not differ between the groups. Favorable outcome at 90 days (modified Rankin score ≤2) was more common in younger patients (77 vs. 23%; p = 0.031). In contrast, mortality rates were higher in octogenarians (40 vs. 7%; p = 0.01). Logistic regression analysis adjusting for neurological severity and collateral state identified age over 80 (odds ratio, OR 0.15, 95% CI 0.03-0.75; p = 0.02) and reperfusion state (OR 7.4, 95% CI 1.1-49.9; p = 0.04) as significant modifiers of favorable outcome. Similarly, age over 80 was identified as a positive predictor of mortality (OR 8.1, 95% CI 1.8-36.7; p = 0.007). Conclusions: Octogenarians have higher chances of mortality and lower probability of achieving functional independence even after SRT. Nevertheless, because some elderly patients do achieve favorable outcomes, the cost-effectiveness of SRT in this population needs to be further studied.
Self-Control in Daily Life

In this daily diary study, we investigated the flexibility-enhancing effects of positive affect on the self-reported success of self-control strategies followed in daily life; 297 participants completed a 13-day daily diary that included measures of positive affect, desire, and habit strength as well as three self-control strategies (i.e., monitoring, distraction, and stimulus control). We found specific effects of positive affect on self-control strategies: Individuals with higher positive affect were most successful when following a strategy of distraction (e.g., thinking about something else), particularly when faced with strong tempting desires. These results reinforce the idea that positive affect is associated with both cognitive flexibility and distractibility, which may help people distract them from tempting desires.
Information Is Bliss

If school choice programs are to provide any degree of equitable access to educational opportunities, then useful information about academic quality needs to be available to all participants, not just those who hob knob with the school board members or chat with the superintendent over the backyard fence. This study draws upon a unique data set to identify two information sources (parent websites and school choice enrollment guides) associated with low-income and minority families’ selection of higher quality schools in Denver. The study also highlights two types of information lacked by low-income and minority families who ended up selecting lower quality schools.
Productivity or Endowments? Sectoral Evidence for Hong Kong's Aggregate Growth

The author provides sectoral evidence that sheds new light on the current debate regarding the sources of growth of the East Asian miracle. The author tests both the productivity-driven and endowment-driven hypotheses using Hong Kong's sectoral data. The results show that most of the growth in the services sector is driven by the rapidly accumulating capital endowments, and not by productivity growth. In addition, productivity growth in the manufacturing sector is also unimpressive. The manufacturing sector is more labor intensive and its growth is hindered by the reallocation of resources into the services sector as a result of the growth of capital endowments and imports. Overall, sectoral evidence supports the endowment-driven hypothesis for Hong Kong's aggregate growth.