Miracle-dz/UniFAR-FTUs huggingface dataset:
Digital Photo Annotation in Ubiquitous Computing Environment

This paper proposes a method that can be utilized for automatically annotating digital photos anytime, anywhere. A digital camera or an annotation server connected to the digital camera through a ubiquitous computing network can automatically annotate captured photos using the proposed method. Annotating digital images is not a new research problem. We have developed a novel method of classifying seven nature objects from digital images. Thus, this paper describes the method and shows that it is superior to previous methods of classifying nature objects.
A Prospective Study of Trans Fatty Acids in Erythrocytes and Risk of Coronary Heart Disease

Background— High consumption of trans fat has been linked to the risk of coronary heart disease (CHD). We assessed the hypothesis that higher trans fatty acid contents in erythrocytes were associated with an elevated risk of CHD in a nested case-control study among US women. Methods and Results— Blood samples were collected from 32 826 participants of the Nurses' Health Study from 1989 to 1990. During 6 years of follow-up, 166 incident cases of CHD were ascertained and matched with 327 controls. Total trans fatty acid content in erythrocytes was significantly correlated with dietary intake of trans fat (correlation coefficient=0.44, P<0.01) and was associated with increased plasma low-density lipoprotein cholesterol (P for trend =0.06), decreased plasma high-density lipoprotein cholesterol concentrations (P for trend <0.01), and increased plasma low-density lipoprotein to high-density lipoprotein ratio (P for trend <0.01). After adjustment for age, smoking status, and other dietary and lifestyle cardiovascular risk factors, higher total trans fatty acid content in erythrocytes was associated with an elevated risk of CHD. The multivariable relative risks (95% confidence intervals) of CHD from the lowest to highest quartiles of total trans fatty acid content in erythrocytes were 1.0 (reference), 1.6 (0.7 to 3.6), 1.6 (0.7 to 3.4), and 3.3 (1.5 to 7.2) (P for trend <0.01). The corresponding relative risks were 1.0, 1.1, 1.3, and 3.1 (P for trend <0.01) for a total of 18:1 trans isomers and 1.0, 1.5, 2.5, and 2.8 (P for trend <0.01) for a total of 18:2 trans isomers. Conclusions— These biomarker data provide further evidence that high trans fat consumption remains a significant risk factor for CHD after adjustment for covariates.
The role of the third β strand in gp120 conformation and neutralization sensitivity of the HIV-1 primary isolate DH012

Neutralization of HIV-1 primary isolates has been a tremendous challenge for AIDS vaccine development. Here, we identify a single amino acid change (T198P) in gp120 that alters the neutralization sensitivity of the primary isolate DH012 to antibodies against multiple neutralization epitopes that include the V3, CD4-induced, and CD4 binding sites in gp120. This mutation is located in the V1/V2 stem region that forms the third β strand (β3) of the bridging sheet of gp120. The conformation of variable loops, especially V1/V2 and V3, was proposed to regulate the accessibility of these neutralization epitopes. The results of this study indicate a direct association between the V1/V2 and V3 loops of DH012 gp120. The single amino acid mutation T198P in the β3 severely compromises the interaction between the V1/V2 and V3 loops. These results suggest that interaction of V1/V2 and V3 can mask the neutralization epitopes and that the β3 plays a critical role in determining the neutralization sensitivity by modulating the interaction. This study provides an insight into why primary isolates are relatively resistant to antibody neutralization and might facilitate the development of anti-HIV strategies against HIV-1 infection.
Estimating treatment effect heterogeneity in randomized program evaluation

When evaluating the efficacy of social programs and medical treatments using randomized experiments, the estimated overall average causal effect alone is often of limited value and the researchers must investigate when the treatments do and do not work. Indeed, the estimation of treatment effect heterogeneity plays an essential role in (1) selecting the most effective treatment from a large number of available treatments, (2) ascertaining subpopulations for which a treatment is effective or harmful, (3) designing individualized optimal treatment regimes, (4) testing for the existence or lack of heterogeneous treatment effects, and (5) generalizing causal effect estimates obtained from an experimental sample to a target population. In this paper, we formulate the estimation of heterogeneous treatment effects as a variable selection problem. We propose a method that adapts the Support Vector Machine classifier by placing separate sparsity constraints over the pre-treatment parameters and causal heterogeneity parameters of interest. The proposed method is motivated by and applied to two well-known randomized evaluation studies in the social sciences. Our method selects the most effective voter mobilization strategies from a large number of alternative strategies, and it also identifies the characteristics of workers who greatly benefit from (or are negatively affected by) a job training program. In our simulation studies, we find that the proposed method often outperforms some commonly used alternatives.
An effective damage identification approach in thick steel beams based on guided ultrasonic waves for structural health monitoring applications

An inverse analysis using artificial intelligence based on the guided ultrasonic waves is proposed for effective identification of damage in thick steel beams for the purpose of structural health monitoring applications. Parameterized modeling for finite element analysis is applied to constitute the damage parameter database cost-effectively. For signal processing and feature extraction, wavelet transform is employed. A novel feature extraction technique, damage characteristic points, is applied to constitute the database for pattern recognition procedures. Using the extracted metrics, a multilayer feedforward artificial neural network under supervision of an error-backpropagation algorithm is developed and trained. The generalization performance of the artificial neural network has been examined experimentally. Results illustrate that the proposed metrics together with artificial neural network technique are powerful tools for effective identification of damage in the case of thick structures.
Inorganic write-once disc with quadruple recording layers for Blu-ray Disc system

The optical disc with larger capacity and higher speed data recording rate will be required in coming broadband network society. We have developed the inorganic write-once disc with quadruple recording layers for the blu-ray system. We obtained the reflectivity of more than 5% and a jitter value of less than 10% for each recording layer. As a result, we proved the possibility of 100 GB user capacity of 120 mm diameter size.
Coordinate descent with arbitrary sampling I: algorithms and complexity†

We study the problem of minimizing the sum of a smooth convex function and a convex block-separable regularizer and propose a new randomized coordinate descent method, which we call ALPHA. Our method at every iteration updates a random subset of coordinates, following an arbitrary distribution. No coordinate descent methods capable to handle an arbitrary sampling have been studied in the literature before for this problem. ALPHA is a very flexible algorithm: in special cases, it reduces to deterministic and randomized methods such as gradient descent, coordinate descent, parallel coordinate descent and distributed coordinate descent—both in nonaccelerated and accelerated variants. The variants with arbitrary (or importance) sampling are new. We provide a complexity analysis of ALPHA, from which we deduce as a direct corollary complexity bounds for its many variants, all matching or improving best known bounds.
Joint Video Coding and Statistical Multiplexing for Broadcasting Over DVB-H Channels

A novel joint video encoding and statistical multiplexing (StatMux) method for broadcasting over digital video broadcasting for handhelds (DVB-H) channels is proposed to improve the quality of encoded video and to decrease the end-to-end delay in a broadcast system. The main parts of end-to-end delay in a DVB-H system result from a time-sliced transmission scheme that is used in DVB-H and from the bit rate variations of service bit streams. The time-sliced transmission scheme is utilized in DVB-H to reduce the power consumption of DVB-H receivers. Variable bit rate (VBR) video bit streams are used in DVB-H to improve the video quality and compression performance. The time-sliced transmission scheme has increased the channel switching delay, i.e., switching to a new audio-visual service, in DVB-H. The used VBR bit streams increase the required buffering delays in the whole system. The different parts of end-to-end delay in a DVB-H system can be affected by the used video encoding and multiplexing methods. Different scenarios for encoding and StatMux of video sources for DVB-H application are studied in this paper. Moreover, a new method for jointly encoding and StatMux of video sources is proposed that not only decreases the end-to-end delay but also improves the average quality of compressed video by dynamically distributing available bandwidth between the video sources according to their relative complexity. Performance of the proposed method is validated by simulation results.
Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing

A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly those from fungi, are a central part of this process, and many have been isolated and characterised. However, relatively little is known of how fungi respond to lignocellulose and produce the enzymes necessary for dis-assembly of plant biomass. We studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA sequencing we showed that, 24 hours after exposure to straw, gene expression of known and presumptive plant cell wall-degrading enzymes represents a huge investment for the cells (about 20% of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal arsenal of enzymes for the degradation of plant biomass. Using transcription factor deletion mutants (xlnR and creA) to study the response to both lignocellulosic substrates and low carbon source concentrations, we showed that a subset of genes coding for degradative enzymes is induced by starvation. Our data support a model whereby this subset of enzymes plays a scouting role under starvation conditions, testing for available complex polysaccharides and liberating inducing sugars, that triggers the subsequent induction of the majority of hydrolases. We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions.
A unique pathway of double-strand break repair operates in tandemly repeated genes

The RAD52 gene product of the yeast Saccharomyces cerevisiae is required for most spontaneous recombination and almost all double-strand break (DSB) repair. In contrast to recombination elsewhere in the genome, recombination in the ribosomal DNA (rDNA) array is RAD52 independent. To determine the fate of a DSB in the rDNA gene array, a cut site for the HO endonuclease was inserted into the rDNA in a strain containing an inducible HO gene. DSBs were efficiently repaired at this site, even in the absence of the RAD52 gene product. Efficient RAD52-independent DSB repair was also observed at another tandem gene array, CUP1, consisting of 18 repeat units. However, in a smaller CUP1 array, consisting of only three units, most DSBs (ca. 80%) were not repaired and resulted in cell death. All RAD52-independent DSB repair events examined resulted in the loss of one or more repeat units. We propose a model for DSB repair in repeated sequences involving the generation of single-stranded tails followed by reannealing.
GDP-to-GTP exchange on the microtubule end can contribute to the frequency of catastrophe

Microtubules are dynamic polymers of αβ-tubulin that have essential roles in chromosome segregation and organizing the cytoplasm. Catastrophe – the switch from growing to shrinking – occurs when a microtubule loses its stabilizing GTP cap. Recent evidence indicates that the nucleotide on the microtubule end controls how tightly an incoming subunit will be bound (trans-acting GTP), but most current models do not incorporate this information. We implemented transacting GTP into a computational model for microtubule dynamics. In simulations, growing microtubules often exposed terminal GDP-bound subunits without undergoing catastrophe. Transient GDP exposure on the growing plus end slowed elongation by reducing the number of favorable binding sites on the microtubule end. Slower elongation led to erosion of the GTP cap and an increase in the frequency of catastrophe. Allowing GDP to GTP exchange on terminal subunits in simulations mitigated these effects. Using mutant αβ-tubulin or modified GTP, we showed experimentally that a more readily exchangeable nucleotide led to less frequent catastrophe. Current models for microtubule dynamics do not account for GDP to GTP exchange on the growing microtubule end, so our findings provide a new way of thinking about the molecular events that initiate catastrophe.
Regeneration niche of the Canarian juniper: the role of adults, shrubs and environmental conditions

Abstract• Canarian Juniper woodlands, now very scarce, are rich in endemic and endangered plants. However, many aspects of juniper regeneration are almost unknown. • This paper relates occurrence and abundance of recruits of Juniperus turbinata ssp. canariensis to (1) small-scale soil characteristics; (2) vegetation cover; and (3) distance to conspecific adults in two contrasting juniper stands in the eastern mountains of Tenerife. We used non-parametric classification trees and generalised linear models (GLM) to evaluate the effect and importance of each explanatory variable on the occurrence of juniper saplings. • Sapling density, vitality and growth rate, as well as fruit production by adult trees, but neither cone density on the ground nor sapling size, varied significantly with respect to slope orientation, representing environmental stress. Within each stand, distance to nearest adult tree was the most important variable explaining the spatial distribution of juniper saplings and availability of seeds in cones. Additionally, saplings were positively associated with shrub cover at the microsite-level, but not with spiny shrub cover. Soil depth and rock cover had a weak negative effect on sapling establishment, but only at the south-facing site and in the open space microhabitat. • Results suggest that recruitment of Canarian juniper is facilitated by microhabitats offered by adults and shrubs. The key factors affecting recruitment are thought to be (1) favourable micro-environmental conditions and (2) high ambient seed availability. Browsing intensity in recent decades was very low. The presence of spiny shrubs did not favour juniper establishment. Facilitation therefore appears to result from amelioration of abiotic conditions rather than from protection against herbivory.
Reperfusion of pulmonary arteriovenous malformations after embolotherapy.

PURPOSE To describe the mechanisms and risk factors associated with reperfusion of successfully treated pulmonary arteriovenous malformations (PAVMs) after embolotherapy. MATERIALS AND METHODS Among 112 consecutive patients with PAVMs treated by embolotherapy, 19 patients were identified who had 33 angiographically confirmed reperfused PAVMs. A retrospective analysis of computed tomography (CT) and angiography was performed in patients with documented reperfused PAVMs in which reperfused PAVMs were compared with nonreperfused PAVMs. CT images were examined for persistence of the aneurysm and/or draining vein after initial embolotherapy and correlated with angiography to determine the mechanism of reperfusion. PAVM and embolic agent characteristics (eg, feeding artery size and number; PAVM location; coil size, number, and location) were evaluated for association with reperfusion. The outcomes of repeat embolotherapy for reperfused PAVMs were evaluated. RESULTS The PAVM aneurysm and/or draining vein persisted on CT after initial embolotherapy in all reperfused PAVMs and resolved in all nonreperfused PAVMs (in patients with nondiffuse PAVMs). Recanalization was the mechanism of reperfusion in 88%. Reperfusion was associated with the use of a single coil (P < .0001), oversized coils (P < .0001), coil placement more than 1 cm from the aneurysm (P < .0001), and increased feeding artery size (P < .001). Repeat embolotherapy for reperfused PAVMs was technically successful in 94% of cases. In the remaining 6% of cases, insufficient feeding artery length prevented safe repeat treatment. After a mean follow-up of 41 months, 42% of reperfused PAVMs in our series have been successfully treated again and occluded. CONCLUSIONS Recanalization is the most common mechanism of PAVM reperfusion. Increased feeding artery diameter, low number of coils, use of oversized coils, and proximal coil placement within the feeding artery are associated with reperfusion. Distal coil placement facilitates repeat embolization if reperfusion occurs.
Coaching: a new model for academic and career achievement

Background Individualized education is emerging as an innovative model for physician training. This requires faculty coaching to guide learners’ achievements in academic performance, competency development, and career progression. In addition, coaching can foster self-reflection and self-monitoring using a data-guided approach to support lifelong learning. Context Coaching differs from mentoring or advising, and its application in medical education is novel. Because of this, definitions of the concept and the constructs of coaching as applied to medical education are needed to accurately assess the coaching relationship and coaching processes. These can then be linked to learner outcomes to inform how coaching serves as a modifier of academic and competency achievement and career satisfaction. Innovation We developed definitions and constructs for academic coaching in medical education based on review of existing education and non-education coaching literature. These constructs focus on 1) establishing relationship principles, 2) conducting learner assessments, 3) developing and implementing an action plan, and 4) assessing results and revising plans accordingly. Implication Coaching is emerging as an important construct in the context of medical education. This article lays the vital groundwork needed for evaluation of coaching programs aimed at producing outstanding physicians.
Clonal Relatedness of Enterotoxigenic Escherichia coli Strains Isolated from a Cohort of Young Children in Guinea-Bissau

ABSTRACT In a cohort study of 200 young children in Guinea-Bissau, it was previously found that some enterotoxigenic Escherichia coli (ETEC) strains were more pathogenic than others, depending on the type of toxin that they could produce, and that natural ETEC infections induced substantial protection against new infections with ETEC strains that had the same combination of toxins and colonization factors (CFs). We wanted to describe the clonal relatedness of the ETEC strains isolated during this study and to investigate whether the protective antigens and the virulence factors that were responsible for the pathogenic traits were common to strains that were clonally closely related or whether they were more likely to be encoded by the ETEC virulence plasmids that normally encode the toxins and the CFs. By performing repetitive sequence-based PCR analysis of strains representing 452 infections, we found that strains that had the same toxin-CF profile were usually closely related, although a few were unrelated. Strains that did not have the same toxin-CF profiles but that were positive for a given toxin or for a given CF were not consistently more closely related to each other than to strains that were negative for the same toxin or CF. Our results indicate that the pathogenic traits of ETEC were mainly attributed to genes carried on the ETEC virulence plasmids. Because most strains that had the same toxin-CF profile were closely related, it seems likely that the toxin-CF-specific protection was clonal and was not targeting antigens encoded by the virulence plasmids. These results are of relevance to the ETEC vaccine development effort.
Generalization of ERM in Stochastic Convex Optimization: The Dimension Strikes Back

In stochastic convex optimization the goal is to minimize a convex function $F(x) \doteq {\mathbf E}_{{\mathbf f}\sim D}[{\mathbf f}(x)]$ over a convex set $\cal K \subset {\mathbb R}^d$ where $D$ is some unknown distribution and each $f(\cdot)$ in the support of $D$ is convex over $\cal K$. The optimization is commonly based on i.i. d. ~samples $f^1,f^2,\ldots,f^n$ from $D$. A standard approach to such problems is empirical risk minimization (ERM) that optimizes $F_S(x) \doteq \frac{1}{n}\sum_{i\leq n} f^i(x)$. Here we consider the question of how many samples are necessary for ERM to succeed and the closely related question of uniform convergence of $F_S$ to $F$ over $\cal K$. We demonstrate that in the standard $\ell_p/\ell_q$ setting of Lipschitz-bounded functions over a $\cal K$ of bounded radius, ERM requires sample size that scales linearly with the dimension $d$. This nearly matches standard upper bounds and improves on $\Omega(\log d)$ dependence proved for $\ell_2/\ell_2$ setting by Shalev-Shwartz et al. (2009). In stark contrast, these problems can be solved using dimension-independent number of samples for $\ell_2/\ell_2$ setting and $\log d$ dependence for $\ell_1/\ell_\infty$ setting using other approaches. We further show that our lower bound applies even if the functions in the support of $D$ are smooth and efficiently computable and even if an $\ell_1$ regularization term is added. Finally, we demonstrate that for a more general class of bounded-range (but not Lipschitz-bounded) stochastic convex programs an infinite gap appears already in dimension 2.
Liquor Bilirubin Levels and False Prediction of Severity in Rhesus Haemolytic Disease

Liquor bilirubin levels gave a false prediction of outcome for the fetus in 80 out of 716 rhesus-sensitized women referred for treatment during 1965-9. Trauma caused by amniocentesis seemed to be responsible for an increase in the severity of immunization in a significant proportion of cases. In addition, contamination of liquor samples by plasma, particularly fetal plasma, completely invalidated liquor bilirubin estimations. Errors in estimation of gestational length were also found to be associated with misleading results and a poor fetal prognosis.