Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Deregulated microRNAs in Breast Cancer Progression Using FFPE Tissue

MicroRNAs (miRNAs) contribute to cancer initiation and progression by silencing the expression of their target genes, causing either mRNA molecule degradation or translational inhibition. Intraductal epithelial proliferations of the breast are histologically and clinically classified into normal, atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). To better understand the progression of ductal breast cancer development, we attempt to identify deregulated miRNAs in this process using Formalin-Fixed, Paraffin-Embedded (FFPE) tissues from breast cancer patients. Following tissue microdissection, we obtained 8 normal, 4 ADH, 6 DCIS and 7 IDC samples, which were subject to RNA isolation and miRNA expression profiling analysis. We found that miR-21, miR-200b/c, miR-141, and miR-183 were consistently up-regulated in ADH, DCIS and IDC compared to normal, while miR-557 was uniquely down-regulated in DCIS. Interestingly, the most significant miRNA deregulations occurred during the transition from normal to ADH. However, the data did not reveal a step-wise miRNA alteration among discrete steps along tumor progression, which is in accordance with previous reports of mRNA profiling of different stages of breast cancer. Furthermore, the expression of MSH2 and SMAD7, two important molecules involving TGF-β pathway, was restored following miR-21 knockdown in both MCF-7 and Hs578T breast cancer cells. In this study, we have not only identified a number of potential candidate miRNAs for breast cancer, but also found that deregulation of miRNA expression during breast tumorigenesis might be an early event since it occurred significantly during normal to ADH transition. Consequently, we have demonstrated the feasibility of miRNA expression profiling analysis using archived FFPE tissues, typically with rich clinical information, as a means of miRNA biomarker discovery.
ENDPOINT REGULARITY OF 2

We prove an ε-regularity theorem at the endpoint of connected arcs for 2-dimensional Mumford-Shah minimizers. In particular we show that, if in a given ball Br(x) the jump set of a given MumfordShah minimizer is sufficiently close, in the Hausdorff distance, to a radius of Br(x), then in a smaller ball the jump set is a connected arc which terminates at some interior point y0 and it is C 1,α up to y0.
Using OWL Design Patterns for Modeling and Reasoning with Organizational Policies

Organizations use policies to manage business cases effectively and efficiently. However, when they start defining their policies, they are often incomplete. In order to enact the incomplete set of policies they define a default policy that is used for cases that do not match the initial policy set. Since matching a business case to a set of policies is a classification problem, we suggest that the Web Ontology Language (OWL), a conceptual modeling language founded on ontological foundations, could be used to represent and reason with policies. However, default policies require closed-world reasoning, which is not easily supported in OWL. As a modeling approach, we defined a set of ontology design patterns (ODPs) that we created to support closed-world reasoning in OWL for policy-related classification problems. We distinguish among three sub-classes of this classification problem. To validate the ODPs, we represent the real-world examples using our ODPs and reason with them.
Comparing the Readability of Graph Layouts using Eyetracking and Task-oriented Analysis

In this paper we present the results of a user study comparing the readability of force-directed, orthogonal, and hierarchical graph layouts. To this end we identified prototypical tasks which are solved using visual representations of graphs. Based on the correctness of answers and the related response time we evaluated for each task which layout is better suited. In addition, we found possible explanations for these results by analyzing the eye-tracking data. Finally, we discuss some implications of our findings for algorithm designers and application developers.
Routing Patterns for Self-Management

This paper contributes towards engineering self-managing systems, starting from known routing schemes. Routing schemes are self-managing, because they create and maintain a set of distributed states in a dynamic environment, enabling service delivery under various constraints. Using the approach of separating the update propagation from the routing table computation in routing protocols, we construct a navigation pattern, which underlies DUAL and OSPF, two known Internet routing protocols. This pattern, called progressive wave, defines a generic information distribution mechanism. We instrument it and show how to collect global statistics about any mechanism using this pattern, and apply these statistics to performance monitoring or troubleshooting. In particular, we demonstrate how the propagation of waves carrying routing updates can be monitored and analyzed. We argue that the progressive wave pattern can be used in self-organizing systems that locate resources under constraints – on the network level, as well as on the service level.
Gas-phase exposure history derived from material-phase concentration profiles

Non-reactive gas-phase pollutants such as benzene diffuse into indoor furnishings and leave behind a unique materialphase concentration profile that serves as a record of the past gas-phase indoor concentrations. The inverse problem to be solved is the diffusion equation in a slab such as vinyl flooring. Using knowledge of the present material-phase concentration profile in the slab, we seek to determine the historical material-phase concentration at the surface exposed to indoor air, and hence the historical gas-phase concentration, which can be used directly to determine exposure. The problem as posed has a unique solution that may be solved using a variety of approaches. We use a trained artificial neural network (ANN) to derive solutions for hypothetical exposure scenarios. The ANN results show that it is possible to estimate the intensity and timing of past exposures from the material-phase concentration profile in a building material. The overall method is limited by (1) the resolution of techniques for measuring spatial material-phase concentration profiles, (2) how far back in time we seek to determine exposure and (3) the representational power of the ANN solution. For example, we estimate that this technique can estimate exposure to phenol up to 0.5 y in the past from analyses of vinyl flooring. r 2006 Published by Elsevier Ltd.
Neural Representation of Amplified Speech Sounds

Objective: To determine if (1) evoked potentials elicited by amplified speech sounds (/si/ and /∫i/) can be recorded reliably in individuals, (2) amplification alters neural response patterns, and (3) different amplified speech sounds evoke different neural patterns. Design: Cortical evoked potentials were recorded in sound field from seven normal-hearing young adults in response to naturally produced speech tokens /si/ and /∫i/ from the Nonsense Syllable Test. With the use of a repeated-measures design, subjects were tested and then retested within an 8-day period in both aided and unaided conditions. Results: (1) Speech-evoked cortical potentials can be recorded reliably in individuals in both aided and unaided conditions. (2) Hearing aids that provide a mild high-frequency gain only subtly enhance peak amplitudes relative to unaided cortical recordings. (3) If the consonant-vowel boundary is preserved by the hearing aid, it can also be detected neurally, resulting in different neural response patterns for /si/ and /∫i/. Conclusions: Speech-evoked cortical potentials can be recorded reliably in individuals during hearing aid use. A better understanding of how amplification (and device settings) affects neural response patterns is still needed.
Effect of Self-etch Primer-adhesive and Conventional Adhesive Systems on the Shear Bond Strength and Bond Failure of Orthodontic Brackets: A Comparative Study.

BACKGROUND Prompt-L-Pop is a sixth generation bonding system contains methacrylated phosphoric acid esters that combine an acidic component for etching the enamel and a primer, is an all-in-one adhesive. This study was undertaken to compare the bonding strength of brackets to enamel with traditional bonding technique and the new Prompt-L-Pop system using the same composite resin. MATERIALS AND METHODS In this in vitro experimental study, 60 human premolar teeth extracted for orthodontic treatment were collected. The samples were randomly divided into three groups comprising of 20 teeth in each group. Shear bond strength and ARI scores for the specimens were measured. Comparison was done using one way ANOVA and Chi-square test. RESULTS Fourth generation bonding adhesive system depicted similar bond strength to fifth generation bonding adhesive system. Both fourth and fifth generation exhibited higher shear bond strength as compared to sixth generation bonding adhesive system. CONCLUSION Fourth and fifth generation exhibited higher shear bond strength as compared to sixth generation bonding adhesive system but the sixth generation has clinically acceptable shear bond strength. Also, it was found that sixth generation leaves less residual adhesive on the tooth after bracket removal.
Functional Diversity of Genes for the Biosynthesis of Paeoniflorin and Its Derivatives in Paeonia

The Paeonia root, with or without bark, are considered vital traditional Chinese medicine materials; the examples are those of Bai Shao, Chi Shao, and Dan Pi. In this study, we examine 24 genes and their expressions involved in the biosynthesis of paeoniflorin and its derivatives, which are active compounds of the Paeonia root, in Paeonia lactiflora and P. suffruticosa, as well as other related plants, Punica granatum, Rhus radicans, and Coriaria nepalensis. Our phylogenetic analyses suggest that these genes have functional diversity, and analysis of the transcriptional level shows paeoniflorin and gallic acid biosynthesis-related genes exhibit different transcription profiles in flowers, carpels, bark-free roots, and bark of P. lactiflora. The correlation analysis of gene expression and active compound contents support the idea that hydroxymethylglutaryl-CoA synthase and phosphomevalonate kinase in the mevalonate pathway and 3-dehydroquinate dehydratase/shikimate dehydrogenase in shikimate biosynthesis are potentially closely related to the accumulation of paeoniflorin and benzoylpaeoniflorin. Coupling gene diversity with chemical analysis, we show that paeoniflorin and its derived aromatic amino acids are predominant in bark.
Assessing Risks to Sea Otters and the Exxon Valdez Oil Spill: New Scenarios, Attributable Risk, and Recovery

ABSTRACT The Exxon Valdez oil spill occurred more than two decades ago, and the Prince William Sound ecosystem has essentially recovered. Nevertheless, discussion continues on whether or not localized effects persist on sea otters (Enhydra lutris) at northern Knight Island (NKI) and, if so, what are the associated attributable risks. A recent study estimated new rates of sea otter encounters with subsurface oil residues (SSOR) from the oil spill. We previously demonstrated that a potential pathway existed for exposures to polycyclic aromatic hydrocarbons (PAHs) and conducted a quantitative ecological risk assessment using an individual-based model that simulated this and other plausible exposure pathways. Here we quantitatively update the potential for this exposure pathway to constitute an ongoing risk to sea otters using the new estimates of SSOR encounters. Our conservative model predicted that the assimilated doses of PAHs to the 1-in-1000th most-exposed sea otters would remain 1–2 orders of magnitude below the chronic effects thresholds. We re-examine the baseline estimates, post-spill surveys, recovery status, and attributable risks for this subpopulation. We conclude that the new estimated frequencies of encountering SSOR do not constitute a plausible risk for sea otters at NKI and these sea otters have fully recovered from the oil spill.
DEVELOPMENT OF A UNIVERSITY-BASED HIGH PERFORMANCE COMPUTING SYSTEM OF PC CLUSTERS

The rapid increase in performance of mass-market commodity microprocessors and significant disparity in pricing between PCs and scientific workstations, has provided an opportunity for substantial gains in performance to cost by harnessing PC technology in parallel ensembles to provide high-end capability for scientific and engineering applications. AHPCG is an Ateneo de Manila University initiative that aims to explore and develop a Beowulf-class Supercomputing Cluster. The project aims to build a 8-node cluster that will serve as a starting point for further research in the field of parallel computing. The cluster aims to pinpoint and remedy hardware, software and support related weaknesses found in many previous cluster designs and implementations, while building on their strengths. This gives us the ability to attain supercomputing power with off-the-shelf hardware and free software. It also eliminates the need for acquiring expensive supercomputers and at the same time addresses the question-”What do we do with our unwanted hardware? ” This affordable, buildable and maintainable computing capability will be a boon to Philippine scientific, research and educational efforts. 1. Problem Statement In the Philippines today, there is a dearth of high-performance computer systems (HPCS) available to researchers. Although workstations have become quite common, computing power in the gigaflops or even tens of gigaflops level is not generally available for use in research and development. Consequently, there are research and development activities that cannot be done in this country because there are not enough gigaflops to make them practicable.
Innovations in Practice: Avatar-based virtual reality in CAMHS talking therapy: two exploratory case studies.

BACKGROUND Avatar-based virtual reality therapy is an emerging digital technology that can be used to assist the treatment of common mental health problems. This may be particularly appealing to young people who are highly familiar with digital technologies and may provide a medium to facilitate communication within face-to-face therapy. METHOD We present two case summaries of young people who used ProReal, who had difficulties engaging in talking therapies. ProReal is a software package providing avatar-based virtual reality therapy, used as part of talking psychological therapies provided within a CAMHS outpatient clinic. Young people completed pre and postuse routine outcome measures and took part in qualitative interviews assessing their experience of ProReal. RESULTS Outcome measures showed a reduction over time. The two young people felt ProReal was highly accessible, with both young people positively describing how ProReal helped them externalize their inner worlds to help them to reappraise their thoughts, feelings and experiences. They also reported ProReal being a helpful tool to facilitate communication with the clinician. CONCLUSION These case summaries demonstrate how ProReal can be readily integrated into clinical practice and how it can facilitate communication and therapy with young people who find it difficult to express themselves.
Effect of candesartan on microalbuminuria and albumin excretion rate in diabetes: three randomized trials.

BACKGROUND Microalbuminuria in diabetes is strongly predictive of nephropathy, end-stage renal disease, and premature cardiovascular morbidity and mortality. Effective preventive therapies are therefore a clinical priority. OBJECTIVE To determine whether the angiotensin-receptor blocker candesartan compared with placebo affects microalbuminuria incidence or rate of change in albuminuria in type 1 and type 2 diabetes. DESIGN 3 randomized trials of the DIRECT (Diabetic Retinopathy Candesartan Trials) Program. SETTING 309 secondary care centers. PATIENTS 3326 and 1905 patients with type 1 and type 2 diabetes, respectively. Most were normotensive, and all had normoalbuminuria (median urinary albumin excretion rate, 5.0 microg/min). INTERVENTION Candesartan, 16 mg/d increasing to 32 mg/d, versus placebo. Assignment was done centrally using an interactive voice-response system. Patients, caregivers, and researchers were blinded to treatment assignment. During a median follow-up of 4.7 years, 793 patients discontinued therapy and 63 were lost to follow-up. MEASUREMENTS Urinary albumin excretion rate, assessed annually by 2 overnight collections; if it was 20 microg/min or greater, then 2 further collections were done. The primary end point was new microalbuminuria (3 or 4 collections of urinary albumin excretion rate >or=20 microg/min). The secondary end point was rate of change in albuminuria. RESULTS Individual and pooled results of the 3 trials showed that candesartan had little effect on risk for microalbuminuria (pooled hazard ratio, 0.95 [95% CI, 0.78 to 1.16]; P = 0.60). Pooled results showed that the annual rate of change in albuminuria was 5.53% lower (CI, 0.73% to 10.14%; P = 0.024) with candesartan than with placebo. LIMITATIONS Investigators recruited mainly normotensive patients or patients with well-controlled hypertension who were at low overall vascular risk, which resulted in a low rate of microalbuminuria. Studies were powered for retinal and not renal end points. CONCLUSION Candesartan, 32 mg/d, for 4.7 years did not prevent microalbuminuria in mainly normotensive patients with type 1 or type 2 diabetes.
Hybrid Particle Swarm Optimizers with a General Fitness Evaluation Strategy

The particle swarm optimization (PSO) is a stochastic population-based optimization technique, which is gaining popularity but may cause premature convergence, especially for multimodal and high-dimensional function optimization. The general fitness evaluation strategy (GFES) is a novel strategy proposed most recently, by which a particle is evaluated in multiple subspaces so as to take diverse paces toward the destination position. This paper hybridizes GFES with several PSO's variants. Experiments are conducted on some benchmark optimization problems. The results show that these hybrid PSOs are effective for coping with multimodal problems.
8 Features Based on Auditory Physiology and Perception

It is well known that human speech processing capabilities far surpass the capabilities of current automatic speech recognition and related technologies, despite very intensive research in automated speech technologies in recent decades. Indeed, since the early 1980’s, this observation has motivated the development of speech recognition feature extraction approaches that are inspired by auditory processing and perception, but it is only relatively recently that these approaches have become effective in their application to computer speech processing. The goal of this chapter is to review some of the major ways in which feature extraction schemes based on auditory processing have facilitated greater speech recognition accuracy in recent years, as well as to provide some insight into the nature of current trends and future directions in this area. We begin this chapter with a brief review of some of the major physiological and perceptual phenomena that have motivated feature extraction algorithms based on auditory processing. We continue with a review and discussion of three seminal ‘classical’ auditory models of the 1980s that have had a major impact on the approaches taken by more recent contributors to this field. Finally, we turn our attention to selected more recent topics of interest in auditory feature analysis, along with some of the feature extraction approaches that have been based on them. We conclude with a discussion of the attributes of auditory models that appear to be most effective in improving speech recognition accuracy in difficult acoustic environments.
EFFICIENT PEEC MODELING OF MULTI-LAYER BOARDS AND MULTI-CHIP MODULES

Multi-Chip Modules (MCM) for high speed digital applications use meshed planes between the signal layers for shielding and power supply. Both wave impedances of the signal lines and coupling behavior between different signal layers are influenced by the properties of these meshed planes. Together with the quick increase of operating frequency of high-speed integrated circuits (IC), this may cause problems such as dispersion, crosstalk, and packaging effects which must be investigated by means of simulations. The Partial Elements Equivalent Circuit (PEEC) method has proven to be suitable to deal with such systems, particularly to investigate ground bounce effects. For analysis of large interconnect and packaging structures, however, the computing time increases very rapidly with the system’s complexity. To reduce the costs of calculation, especially for inductance and capacitance calculation, a method is introduced that leads to both accurate and fast results. The validity of the modeling is verified with Sparameter calculations of blocking measures in a multilayer board and shall be used for investigations of multichip modules.
Dynamic-vector execution on a general purpose EDGE chip multiprocessor

This paper proposes a cost-effective technique that morphs the available cores of a low power chip multiprocessor (CMP) into an accelerator for data parallel (DLP) workloads. Instead of adding a special-purpose vector architecture as an accelerator, our technique leverages the resources of each CMP core to mimic the functionality of a vector processor. The morphing provides dynamic vector execution (DVX) on a general purpose CMP, by adding minimal hardware for vector control. DVX enhances the vector execution by dynamically configuring the allocation of compute and memory resources to match particular workload requirements. As an energy efficient substrate, we utilize modest dual issue cores based on an Explicit Data Graph Execution (EDGE) architecture. The results show that a DVX enabled 4-core EDGE CMP improves the energy-delay product over 14x, at the cost of only 1.1% of additional area. We compare DVX against a CMP that adds a dedicated DLP accelerator based on a conventional high performance vector design. The vector accelerator increases the area footprint over 74%, which greatly affects the cost of the modest processor. DVX avoids the additional costs and yet gains over 86% of the speedup obtained with the dedicated accelerator.
A Normalized Cuts Based Image Segmentation Method

A new image segmentation method is proposed in the framework of Normalized Cuts to solve the perceptual grouping problem by means of graph partitioning, and the multiscale graph decomposition to obtain image features. Texture features is modeled with orientation histograms defined on the different scale level. The global optimal segmentation can be efficiently computed via graph cuts. The segmentation is implemented by partitioning a graph representing an image at the finest scale level to obtain accurate segmentation, while the weights of the graph are calculated from all the scales. Due to the reduced dimensionality based on texton, the speed of Normalized Cuts is increased. Efficiency and accuracy of the method is demonstrated on the nature images and remote sensing images segmentation.