Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimally Training a Cascade Classifier

Cascade classifiers are widely used in real-time object detection. Different from conventional classifiers that are designed for a low overall classification error rate, a classifier in each node of the cascade is required to achieve an extremely high detection rate and moderate false positive rate. Although there are a few reported methods addressing this requirement in the context of object detection, there is no a principled feature selection method that explicitly takes into account this asymmetric node learning objective. We provide such an algorithm here. We show a special case of the biased minimax probability machine has the same formulation as the linear asymmetric classifier (LAC) of \cite{wu2005linear}. We then design a new boosting algorithm that directly optimizes the cost function of LAC. The resulting totally-corrective boosting algorithm is implemented by the column generation technique in convex optimization. Experimental results on object detection verify the effectiveness of the proposed boosting algorithm as a node classifier in cascade object detection, and show performance better than that of the current state-of-the-art.
Natural Scene Categories Revealed in Distributed Patterns of Activity in the Human Brain

Human subjects are extremely efficient at categorizing natural scenes, despite the fact that different classes of natural scenes often share similar image statistics. Thus far, however, it is unknown where and how complex natural scene categories are encoded and discriminated in the brain. We used functional magnetic resonance imaging (fMRI) and distributed pattern analysis to ask what regions of the brain can differentiate natural scene categories (such as forests vs mountains vs beaches). Using completely different exemplars of six natural scene categories for training and testing ensured that the classification algorithm was learning patterns associated with the category in general and not specific exemplars. We found that area V1, the parahippocampal place area (PPA), retrosplenial cortex (RSC), and lateral occipital complex (LOC) all contain information that distinguishes among natural scene categories. More importantly, correlations with human behavioral experiments suggest that the information present in the PPA, RSC, and LOC is likely to contribute to natural scene categorization by humans. Specifically, error patterns of predictions based on fMRI signals in these areas were significantly correlated with the behavioral errors of the subjects. Furthermore, both behavioral categorization performance and predictions from PPA exhibited a significant decrease in accuracy when scenes were presented up-down inverted. Together these results suggest that a network of regions, including the PPA, RSC, and LOC, contribute to the human ability to categorize natural scenes.
The Quarterly Review of Economics and Finance 53.2 (2013): 140-151 Capital structure, product market competition and firm performance: Evidence from South Africa

This paper investigates the relationship between capital structure and firm performance, paying particular attention to the degree of industry competition. The paper applies a novel measure of competition, the Boone indicator, to the leverageperformance relationship. Using panel data consisting of 257 South African firms over the period 1998 to 2009, this paper examines the effect of capital structure on firm performance and investigates the extent to which the relationship depends on the level of product market competition. The results suggest that financial leverage has a positive and significant effect on firm performance. It is also found that product market competition enhances the performance effect of leverage. The results are robust to alternative measures of competition and leverage. JEL classification: G32; L11; L25
High Re-Operation Rates Using Conserve Metal-On-Metal Total Hip Articulations

Introduction: Metal-on-metal hip articulations have been intensely debated after reports of adverse reactions and high failure rates. The aim of this study was to retrospectively evaluate the implant of a metal-on.metal total hip articulation (MOM THA) from a single manufacture in a two-center study. Materials and Methods: 108 CONSERVE® MOM THA were implanted in 92 patients between November 2005 and December 2010. Patients had at time of retrospective evaluation their journals reviewed for re-operations and adverse reactions. Results: 20 hips were re-operated (18.4%) at a mean follow up of 53 months. 4 pseudotumors were diagnosed at time of follow up but no substantiated link was made between adverse reactions and re-operations. Conclusion: The high re-operation rates found in this study raised concern about the usage of the MOM THA and subsequently lead to the termination of implantation of this MOM THA at the two orthopaedic departments.
Probing the effect of promoters on noise in gene expression using thousands of designed sequences

Genetically identical cells exhibit large variability (noise) in gene expression, with important consequences for cellular function. Although the amount of noise decreases with and is thus partly determined by the mean expression level, the extent to which different promoter sequences can deviate away from this trend is not fully known. Here, we present a high-throughput method for measuring promoter-driven noise for thousands of designed synthetic promoters in parallel. We use it to investigate how promoters encode different noise levels and find that the noise levels of promoters with similar mean expression levels can vary more than one order of magnitude, with nucleosome-disfavoring sequences resulting in lower noise and more transcription factor binding sites resulting in higher noise. We propose a kinetic model of gene expression that takes into account the nonspecific DNA binding and one-dimensional sliding along the DNA, which occurs when transcription factors search for their target sites. We show that this assumption can improve the prediction of the mean-independent component of expression noise for our designed promoter sequences, suggesting that a transcription factor target search may affect gene expression noise. Consistent with our findings in designed promoters, we find that binding-site multiplicity in native promoters is associated with higher expression noise. Overall, our results demonstrate that small changes in promoter DNA sequence can tune noise levels in a manner that is predictable and partly decoupled from effects on the mean expression levels. These insights may assist in designing promoters with desired noise levels.
Generation of Human Female Reproductive Tract Epithelium from Human Embryonic Stem Cells

Background Recent studies have identified stem/progenitor cells in human and mouse uterine epithelium, which are postulated to be responsible for tissue regeneration and proliferative disorders of human endometrium. These progenitor cells are thought to be derived from Müllerian duct (MD), the primordial female reproductive tract (FRT). Methodology/Principal Findings We have developed a model of human reproductive tract development in which inductive neonatal mouse uterine mesenchyme (nMUM) is recombined with green fluorescent protein (GFP)-tagged human embryonic stem cells (hESCs); GFP-hESC (ENVY). We demonstrate for the first time that hESCs can be differentiated into cells with a human FRT epithelial cell phenotype. hESC derived FRT epithelial cells emerged from cultures containing MIXL1+ mesendodermal precursors, paralleling events occurring during normal organogenesis. Following transplantation, nMUM treated embryoid bodies (EBs) generated epithelial structures with a typical MD phenotype that expressed the MD markers PAX2, HOXA10. Functionally, the hESCs derived FRT epithelium responded to exogenous estrogen by proliferating and secreting uterine-specific glycodelin A (GdA). Conclusions/Significance These data show nMUM can induce differentiation of hESC to form the FRT epithelium. This may provide a model to study early developmental events of the human FRT.
Token-based Code Clone Detection Technique in a Student's Programming Exercise

The acts to submit the copied programs of other person make problems in the subject of the programming exercise in university curriculum. Teachers could not make accurate scores and evaluate the reached learning level of students. The code clone detection technique is to automatically detect the copied programs. Researches of the code clone detection technique have been proposed. The object of these researches, however, focused on the source code of industrial field. There are some problems to detect illicit copied codes of reports made by students. In this research, we developed the code clone detection algorithm focusing on the detection of illicit copied codes of submitted reports of students in a programming exercise. Our proposed algorithm is based on the comparison of tokens and can declare the illicit copied codes invalid. The features of illicit copied codes such as swapping the functions and program lines, renaming variable names, changing digits, comments and string constants and changing source codes using formatting tools are detected. We implemented the proposed algorithm and experimented to evaluate our system for the submitted subjects of 119 students. Compared to the human detection for small size of source codes of students in a programming exercise, our system found 32 codes as the illicit copy in 36 illicit copied codes among 14,042 combination detective rules with the threshold which are realized the recall=0.8. The miss detection finding as the copied code was 72 codes with precision=0.302.
Strength of Intentional Effort Enhances the Sense of Agency

Sense of agency (SoA) refers to the feeling of controlling one’s own actions, and the experience of controlling external events with one’s actions. The present study examined the effect of strength of intentional effort on SoA. We manipulated the strength of intentional effort using three types of buttons that differed in the amount of force required to depress them. We used a self-attribution task as an explicit measure of SoA. The results indicate that strength of intentional effort enhanced self-attribution when action-effect congruency was unreliable. We concluded that intentional effort importantly affects the integration of multiple cues affecting explicit judgments of agency when the causal relationship action and effect was unreliable.
Proteomics Reveals Plastid- and Periplastid-Targeted Proteins in the Chlorarachniophyte Alga Bigelowiella natans

Chlorarachniophytes are unicellular marine algae with plastids (chloroplasts) of secondary endosymbiotic origin. Chlorarachniophyte cells retain the remnant nucleus (nucleomorph) and cytoplasm (periplastidial compartment, PPC) of the green algal endosymbiont from which their plastid was derived. To characterize the diversity of nucleus-encoded proteins targeted to the chlorarachniophyte plastid, nucleomorph, and PPC, we isolated plastid–nucleomorph complexes from the model chlorarachniophyte Bigelowiella natans and subjected them to high-pressure liquid chromatography-tandem mass spectrometry. Our proteomic analysis, the first of its kind for a nucleomorph-bearing alga, resulted in the identification of 324 proteins with 95% confidence. Approximately 50% of these proteins have predicted bipartite leader sequences at their amino termini. Nucleus-encoded proteins make up >90% of the proteins identified. With respect to biological function, plastid-localized light-harvesting proteins were well represented, as were proteins involved in chlorophyll biosynthesis. Phylogenetic analyses revealed that many, but by no means all, of the proteins identified in our proteomic screen are of apparent green algal ancestry, consistent with the inferred evolutionary origin of the plastid and nucleomorph in chlorarachniophytes.
The Contribution of Genetic and Epigenetic Changes in Granulosa Cell Tumors of Ovarian Origin

Purpose: Granulosa cell tumors (GCTs) are relatively rare and are subtypes of the sex-cord stromal neoplasms. A better understanding of the molecular genetics underlying various steps in malignant transformation is critical to success in the battle against this disease. Changes in the status of methylation, known as epigenetic alterations, are one of the most common molecular alterations in human cancers, including GCTs. Chromosomal instability and microsatellite instability (MSI) are common in these GCTs. We tested the hypothesis that C→T transition polymorphism in the promoter region of cytosine DNA-methyltransferase-3B (DNMT3B) and its altered expression are also associated with hypermethylation of the genes. We also attempted to determine the relationship between MSI of ovarian carcinoma and hMLH1 hypermethylation in these tumors. Experimental Design: We studied chromosome instability in 25 GCTs by detecting gross chromosome rearrangements in cultured peripheral blood lymphocytes. MSI was assessed using six microsatellite markers (BAT25, BAT26, D2S123, D5S346, D11S1318, and D17S250). Using sensitive methylation-specific PCR, we searched for aberrant promoter hypermethylation in a panel of genes including p16, BRCA1, RASSF1A, ER-α, TMS1, TIMP3, Twist, GSTP1, AR, and hMLH1. Polymorphism in the DNMT3B gene was assessed by the PCR-RFLP method, and DNMT3B expression was studied by reverse transcription-PCR assay. Results: Chromosome instability was indicated by significantly higher frequencies of chromosome aberrations (6.24%; P < 0.001) compared with controls (2.12%). The most frequently observed changes include trisomy 14 and monosomy 22. MSI has been found in 19 of 25 tumors, and loss of heterozygosity has been found in 9 of 25 tumors. Frequencies of methylation in GCTs were 40% for p16 and ER-α; 36% for BRCA1 and RASSF1A; 28% for hMLH1; 24% for TIMP3, Twist, and GSTP1; and 20% in TMS1 and AR. TT genotype was found only in two cases; the remainder were either CC or CT type. There was no significant alteration in the expression of DNMT3B in these patients. Conclusions: Coexistence of chromosome instability, MSI, and hypermethylation suggests that both genetic and epigenetic mechanisms may act in concert to inactivate the above-mentioned genes in these GCTs. These mechanisms can be an early event in the pathogenesis of these tumors, and it can be a critical step in the tumorigenic process. All these events might play an important role in early clinical diagnosis and in chemotherapeutic management and treatment of the disease. Larger studies may lend further understanding to the etiology and clinical behavior of these tumors.
The Effect of Ginseng (The Genus Panax) on Glycemic Control: A Systematic Review and Meta-Analysis of Randomized Controlled Clinical Trials

Importance Despite the widespread use of ginseng in the management of diabetes, supporting evidence of its anti-hyperglycemic efficacy is limited, necessitating the need for evidence-based recommendations for the potential inclusion of ginseng in diabetes management. Objective To elucidate the effect of ginseng on glycemic control in a systematic review and meta-analysis of randomized controlled trials in people with and without diabetes. Data sources MEDLINE, EMBASE, CINAHL and the Cochrane Library (through July 3, 2013). Study selection Randomized controlled trials ≥30 days assessing the glycemic effects of ginseng in people with and without diabetes. Data extraction Relevant data were extracted by 2 independent reviewers. Discrepancies were resolved by consensus. The Heyland Methodological Quality Score and the Cochrane risk of bias tool were used to assess study quality and risk of bias respectively. Data synthesis Sixteen trials were included, in which 16 fasting blood glucose (n = 770), 10 fasting plasma insulin (n = 349), 9 glycated hemoglobin (n = 264), and 7 homeostasis model assessment of insulin resistance (n = 305) comparisons were reported. Ginseng significantly reduced fasting blood glucose compared to control (MD = −0.31 mmol/L [95% CI: −0.59 to −0.03], P = 0.03). Although there was no significant effect on fasting plasma insulin, glycated hemoglobin, or homeostasis model assessment of insulin resistance, a priori subgroup analyses did show significant reductions in glycated hemoglobin in parallel compared to crossover trials (MD = 0.22% [95%CI: 0.06 to 0.37], P = 0.01). Limitations Most trials were of short duration (67% trials<12wks), and included participants with a relatively good glycemic control (median HbA1c non-diabetes = 5.4% [2 trials]; median HbA1c diabetes = 7.1% [7 trials]). Conclusions Ginseng modestly yet significantly improved fasting blood glucose in people with and without diabetes. In order to address the uncertainty in our effect estimates and provide better assessments of ginseng's anti-diabetic efficacy, larger and longer randomized controlled trials using standardized ginseng preparations are warranted. Trial Registration ClinicalTrials.gov NCT01841229
Hip Joint Pathology: Clinical Presentation and Correlation Between Magnetic Resonance Arthrography, Ultrasound, and Arthroscopic Findings in 25 Consecutive Cases

BackgroundThe hip joint is becoming increasingly recognized as a source of groin pain and, in the authors' experience, buttock and low back pain. ObjectivesTo determine the range of pathologic diagnoses, clinical presentation, and the correlation between magnetic resonance arthrographic, ultrasonographic, and arthroscopic findings in the hip joint. MethodsWe prospectively studied 25 consecutive hip arthroscopies to determine the range of pathologic diagnoses, clinical presentation, and the correlation between magnetic resonance arthrographic, ultrasonographic, and arthroscopic findings. ResultsAll of the hips arthroscoped had pathology. Back pain and hip pain were the 2 most common presentations. The only consistently positive clinical test result was a restricted and painful hip quadrant compared with the contralateral hip. Of the 17 patients whose flexion, abduction, external rotation (FABER) test results were reported at the time of examination, 15 (88%) were positive, and 2 (12%) negative. Plain radiographs were normal in all patients. All but 1 patient underwent magnetic resonance arthrography. Although specificity of 100% was achieved in our study, the sensitivity was significantly lower, with a relatively high number of false negatives. Hip arthroscopy proved the definitive diagnostic procedure for intraarticular pathology. ConclusionsHip pathology, particularly labral pathology, may be more common than has been previously recognized. In those patients with chronic groin and low back pain, a high index of suspicion should be maintained. Clinical signs of a painful, restricted hip quadrant and a positive FABER test result should suggest magnetic resonance arthrography in the first instance, but a negative magnetic resonance image should not preclude hip arthroscopy if there is high clinical suspicion of hip joint pathology.
Temporo-parietal and fronto-parietal lobe contributions to theory of mind and executive control: an fMRI study of verbal jokes

‘Getting a joke’ always requires resolving an apparent incongruity, but the particular cognitive operations called upon vary depending on the nature of the joke itself. Previous research has identified the primary neural correlates of the cognitive and affective processes called upon to respond to humor generally, but little work has been done on the substrates underlying the distinct cognitive operations required to comprehend particular joke types. This study explored the neural correlates of the cognitive processes required to successfully comprehend three joke types: bridging-inference jokes (BJs), exaggeration jokes (EJs), and ambiguity jokes (AJs). For all joke types, the left dlPFC appeared to support common cognitive mechanisms, such as script-shifting, while the vACC was associated with affective appreciation. The temporo-parietal lobe (TPJ and MTG) was associated with BJs, suggesting involvement of these regions with ‘theory of mind’ processing. The fronto-parietal lobe (IPL and IFG) was associated with both EJs and AJs, suggesting that it supports executive control processes such as retrieval from episodic memory, self-awareness, and language-based decoding. The social-affective appreciation of verbal jokes was associated with activity in the orbitofrontal cortex, amygdala, and parahippocampal gyrus. These results allow a more precise account of the neural processes required to support the particular cognitive operations required for the understanding of different types of humor.
The Cysteine Rich Necrotrophic Effector SnTox1 Produced by Stagonospora nodorum Triggers Susceptibility of Wheat Lines Harboring Snn1

The wheat pathogen Stagonospora nodorum produces multiple necrotrophic effectors (also called host-selective toxins) that promote disease by interacting with corresponding host sensitivity gene products. SnTox1 was the first necrotrophic effector identified in S. nodorum, and was shown to induce necrosis on wheat lines carrying Snn1. Here, we report the molecular cloning and validation of SnTox1 as well as the preliminary characterization of the mechanism underlying the SnTox1-Snn1 interaction which leads to susceptibility. SnTox1 was identified using bioinformatics tools and verified by heterologous expression in Pichia pastoris. SnTox1 encodes a 117 amino acid protein with the first 17 amino acids predicted as a signal peptide, and strikingly, the mature protein contains 16 cysteine residues, a common feature for some avirulence effectors. The transformation of SnTox1 into an avirulent S. nodorum isolate was sufficient to make the strain pathogenic. Additionally, the deletion of SnTox1 in virulent isolates rendered the SnTox1 mutated strains avirulent on the Snn1 differential wheat line. SnTox1 was present in 85% of a global collection of S. nodorum isolates. We identified a total of 11 protein isoforms and found evidence for strong diversifying selection operating on SnTox1. The SnTox1-Snn1 interaction results in an oxidative burst, DNA laddering, and pathogenesis related (PR) gene expression, all hallmarks of a defense response. In the absence of light, the development of SnTox1-induced necrosis and disease symptoms were completely blocked. By comparing the infection processes of a GFP-tagged avirulent isolate and the same isolate transformed with SnTox1, we conclude that SnTox1 may play a critical role during fungal penetration. This research further demonstrates that necrotrophic fungal pathogens utilize small effector proteins to exploit plant resistance pathways for their colonization, which provides important insights into the molecular basis of the wheat-S. nodorum interaction, an emerging model for necrotrophic pathosystems.