Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting Splicing Variants in Idiopathic Pulmonary Fibrosis from Non-Differentially Expressed Genes

Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease of unknown cause that lacks a proven therapy for altering its high mortality rate. Microarrays have been employed to investigate the pathogenesis of IPF, but are presented mostly at the gene-expression level due to technologic limitations. In as much as, alternative RNA splicing isoforms are increasingly identified as potential regulators of human diseases, including IPF, we propose a new approach with the capacity to detect splicing variants using RNA-seq data. We conducted a joint analysis of differential expression and differential splicing on annotated human genes and isoforms, and identified 122 non-differentially expressed genes with a high degree of “switch” between major and minor isoforms. Three cases with variant mechanisms for alternative splicing were validated using qRT-PCR, among the group of genes in which expression was not significantly changed at the gene level. We also identified 35 novel transcripts that were unique to the fibrotic lungs using exon-exon junction evidence, and selected a representative for qRT-PCR validation. The results of our study are likely to provide new insight into the pathogenesis of pulmonary fibrosis and may eventuate in new treatment targets.
Experiments in simple one-dimensional lossy image compression schemes

The paper examines some one-dimensional lossy image compression schemes. To perform one-dimensional compression, an image is scanned into a one-dimensional array which is then compressed. Three types of scanning are considered: raster scan, Hilbert scan, and binary scan. Hilbert and binary scan are found to outperform raster scan. The methods considered for compression are integer wavelet transforms, a piecewise approximation with triggers (PAT) procedure introduced by Walach and Karnin (1986), and a modified PAT algorithm (MPAT). Wavelets outperform MPAT in compression, and MPAT in turn outperforms PAT; however, MPAT and PAT are computationally far simpler than wavelet transforms.
University of Wolverhampton at the TREC 2011 Microblog Track

In this report we discuss the experiments we conducted at the University of Wolverhampton for the Microblog Track at TREC-2011. As this was the first time we participated in TREC and the particular task presents some unique challenges we initially focused on properly analyzing and indexing the new Tweets2011 Corpus. We experimented with the effects that some standard IR techniques, such as query expansion and proximity models have in this setting. Initial results indicated that both techniques provide small increases in precision, but more experiments are needed for final conclusions to be reached. Lastly, we experimented with using the page that a tweet links to as part of the tweet. The results were particularly low, indicating a potential error in the indexing process or a natural outcome, due to the increased length of the combined documents. More research into answering the issue is underway.
Validation of a simple activity participation measure for rheumatoid arthritis clinical trials.

OBJECTIVE To examine the validity, reliability and sensitivity to change of the Activity Participation Questionnaire (APaQ), a simple measure of activity participation for patients with RA. METHODS The questionnaire contained two items: (i) number of days in the past month of being unable to perform one's usual activities because of RA; and (ii) a score measuring how often one's usual activities could be completed. The APaQ was administered to 1043 RA patients in two clinical trials of abatacept. Construct validity was evaluated by examining changes from baseline in activity scores by clinical response measured by the European League Against Rheumatism (EULAR) and ACR criteria and minimal disease activity (MDA) state and by correlations with patient-reported outcome measures of physical function, disease activity, pain and fatigue at study end-point. Internal consistency, test-retest reliability and sensitivity to change were assessed. RESULTS Both activity participation items were significantly associated with levels of EULAR and ACR response and the achievement of MDA state (P < 0.0005 for all comparisons). Moderate correlations with patient-reported outcomes were consistently found (correlations 0.5-0.6). Cronbach's alpha was 0.7 indicating good internal consistency, the intraclass correlation coefficient of 0.6 suggesting acceptable test-retest reliability. Sensitivity to change was demonstrated by the treatment differences and the standardized response mean (0.39 and 0.30) for the two activity items. CONCLUSION The APaQ is a simple, reliable and valid measure of patient activity, which is sensitive to change, suggesting its suitability for use in clinical trials.
Transfer learning based maximum entropy clustering

The classical maximum entropy clustering (MEC) algorithm can only work on a single dataset, which might result in poor effectiveness in the condition that the capacity of the dataset is insufficient. To resolve this problem, using the strategy of transfer learning, this paper proposed the novel transfer learning based maximum entropy clustering (TL_MEC) algorithm. TL_MEC employs the historical cluster centers and membership of the past data as the references to guide the clustering on the current data, which promotes its performance distinctly from three aspects: clustering effectiveness, anti-noise, as well as privacy protection. Thus TL_MEC can work well on those small dataset if enough historical data are available. The experimental studies verified and demonstrated the contributions of this study.
A Multi-Camera Pose Tracker for Assisting the Visually Impaired

6DOF Pose tracking is useful in many contexts, e.g., in augmented reality (AR) applications. In particular, we seek to assist visually impaired persons by providing them with an auditory interface to their environment through soni.cation. For this purpose, accurate head tracking in mixed indoor/outdoor settings is the key enabling technology. Most of the work to date has concentrated on single-camera systems with a relatively small . eld of view, but this presents a fundamental limit on the accuracy of such systems. We present a multi-camera pose tracker that handles an arbitrary con.guration of cameras rigidly . xed to the object of interest. By using multiple cameras, we increase both the robustness and the accuracy by which a 6-DOF pose is tracked. However, in a multi-camera rig setting, earlier methods for determining the unknown pose from three world-tocamera correspondences are no longer applicable, as they all assume a common center of projection. In this paper, we present a RANSAC-based method that copes with this limitation and handles multi-camera rigs. In addition, we present quantitative results to serve as a design guide for full system deployments based on multicamera rigs. Our formulation is completely general, in that it handles an arbitrary, heterogeneous collection of cameras in any arbitrary con.guration.
Towards a low cost open architecture wearable sensor network for health care applications

Wireless sensor networks present a growing interest in health care applications since they can replace wired devices for detecting signals of physiological origin and continuously monitoring health parameters, offering a reliable and inexpensive solution. In this paper a low cost open architecture wearable sensor network for health care applications is presented. Through this study, an experimental wireless sensor network (WSN) architecture has been built from scratch in order to investigate and present the development procedure and the corresponding capabilities and limitations of such a system. Moreover, technological aspects regarding implementation are also presented.
Bayesian Personalized Ranking for Non-Uniformly Sampled Items

In this paper, we describe our approach to track 2 of the KDD Cup 2011. The task was to predict which 3 out of 6 candidate songs were positively rated { instead of not rated at all { by a user. The candidate items were not sampled uniformly, but according to their general popularity. We develop an adapted version of the Bayesian Personalized Ranking (BPR) optimization criterion [9] that takes the non-uniform sampling of negative test items into account. Furthermore, we present a modied version of the generic BPR learning algorithm that maximizes the new criterion. We use it to train ranking matrix factorization models as components of an ensemble. Additionally, we combine the ranking predictions with rating prediction models to also take into account rating data. With an ensemble of such combined models, we ranked 8th (out of more than 300 teams) in track 2 of the KDD Cup 2011, without using the additional taxonomic information oered by the competition organizers.
Mobile Sign Translator for the Thai Language

--In this paper, I describe a simple smartphonebased system that translates signs written in Thai to English. The system captures an image of a sign written in Thai from the phone's camera and detects the text boundaries using an algorithm based on K-means clustering. Then, it extracts the text using Tesseract 1 Optical Character Recognition (OCR) engine and translates it to English using Google Translate 2. The text detection algorithm implemented works well for single-line signs written in Thai that have a strong color distinction between letters and background within the text's bounding box. The algorithm assumes that the user placed the text at the center of the viewfinder with a horizontal orientation. By testing the system using a set of sign images, I found that the performance of the overall system was limited by the performance of the Thai OCR. Tesseract, with the Thai language file available, gave inaccurate results, especially classifying vowels that occurred above or below the line of text. By limiting the number of characters that Tesseract could recognize, the presented system was able to successfully translate Thai signs from a subset of the sign images considered.
outputs Anticipating discussion activity on community forums Conference Item

Attention economics is a vital component of the Social Web, where the sheer magnitude and rate at which social data is published forces web users to decide on what content to focus their attention on. By predicting popular posts on the Social Web, that contain lengthy discussions and debates, analysts can focus their attention more effectively on content that is deemed more influential. In this paper we present a two-step approach to anticipate discussions in community forums by a) identifying seed posts i.e., posts that generate discussions, and b) predicting the length of these discussions. We explore the effectiveness of a range of features in anticipating discussions such as user and content features, and present focus features that capture the topical concentration of a user. For identifying seed posts we show that content features are better predictors than user features, while achieving an F1 value of 0.792 when using all features. For predicting discussion activity we find a positive correlation between the focus of the user and discussion volumes, and achieve an nDCG@1 value of 0.89 when predicting using user features.
Emergence, self-organization and network efficiency in gigantic termite-nest-networks build using simple rules

Termites, like many social insects, build nests of complex architecture. These constructions have been proposed to optimize different structural features. Here we describe the nest network of the termite Nasutitermes ephratae, which is among the largest nest-network reported for termites and show that it optimizes diverse parameters defining the network architecture. The network structure avoids multiple crossing of galleries and minimizes the overlap of foraging territories. Thus, these termites are able to minimize the number of galleries they build, while maximizing the foraging area available at the nest mounds. We present a simple computer algorithm that reproduces the basics characteristics of this termite nest network, showing that simple rules can produce complex architectural designs efficiently.
Understanding the lived experience of bullying in Australian workplaces: An interpretative phenomenological analysis

ABSTRACT The purpose of this article is to develop a deeper understanding of a negative behavior at work through a study of the lived experience of bullying in Australian workplaces. Although there is considerable research available on workplace bullying, extant research largely provides empirical examinations of the prevalence, causes, and consequences of the phenomenon. By contrast, the research herein reported offers an in-depth account of bullying from the frame of reference of those who have experienced it and demonstrates the difficulties faced by them when coping with it. The study’s data source is drawn from reports submitted to the Australian Parliamentary Inquiry on workplace bullying. The reports were analyzed by using the principles of interpretative phenomenological analysis. The study highlights the impact of bullying at work on individuals’ lives and the coping mechanisms used for dealing with the impact. This article also reveals that bullying destroys organizations’ succession planning efforts as competent and talented individuals leave jobs as a way of coping with bullying. The study further shows that some individuals eventually choose to end their lives as a way of coping with bullying. The article thus adds evidence to anecdotal suggestions of the link between bullying and suicide in Australia.
Maximum discriminant margin transform of discriminant functions

Many current multiclass classification approaches can be described by a set of discriminant functions, where the label of the class with the largest discriminant function is chosen as the best prediction. We develop an affine transform called maximum discriminant margin (MDM), which can use independently estimated discriminant functions to solve multiclass classification problems.
‘It definitely felt very white’: race, gender, and the performative politics of assembly at the Women’s March in Victoria, British Columbia

Abstract This article reflects upon the challenges of building solidarity across the racial divide in the struggle for women’s rights as displayed at the Women’s March on Washington and the ‘sister’ marches in cities across the United States and beyond. In particular, we highlight the concerns that women of color raised regarding the ‘whiteness’ of the marches and the lack of reciprocity that they often experience when participating in interracial coalitions with white ‘allies. ’ Drawing upon Judith Butler’s recent work on the performative politics of assembly and Chantal Mouffe’s conception of radical democracy, we argue that concerted bodily action and the enactment of collective political subjectivities are contested processes in which ‘bodies-in-alliance’ may march together but do not necessarily act in conformity. It is therefore crucial to cultivate agonistic spaces within solidarity movements in which adversarial conflicts among ‘allies’ can emerge if such movements are to remain committed to radical democratic politics. We explore these issues further by discussing our own conflicting experiences at the rally to support the Women’s March in Victoria, British Columbia.
Impact of socioeconomic status on coronary mortality in people with symptoms, electrocardiographic abnormalities, both or neither: the original Whitehall study 25 year follow up

OBJECTIVES To determine the impact of socioeconomic status (SES) on coronary heart disease (CHD) mortality in people with and without prevalent CHD at baseline. DESIGN Cohort study with 25 year follow up; prevalent CHD was defined by Q, ST or T wave electrocardiographic (ECG) abnormalities or symptoms (defined by the Rose chest pain questionnaire and self reported doctor diagnosis) or both. SES was defined by four civil service employment grades. SETTING London. PARTICIPANTS 17 907 male civil servants aged 40–69 years. MAIN OUTCOME MEASURES CHD mortality (n=2695 deaths). RESULTS The lowest versus highest employment grade was associated with increased CHD mortality (age adjusted hazard ratio 1.56 (95% CI 1.2, 2.1)), prevalence of symptoms and, among symptomatic participants only, the prevalence of Q, ST or T abnormalities. Thirty one per cent of CHD deaths occurred in participants with prevalent CHD at baseline. Among participants without Q, ST or T abnormality employment grade was associated with CHD mortality; the hazard ratios (lowestv highest grade) adjusted for age, systolic and diastolic blood pressure were 1.72 (95% CI 1.4, 2.1) for asymptomatic and 1.52 (95% CI 1.1, 2.1) for symptomatic participants; among participants with Q, ST or T abnormality the corresponding hazard ratios were 1.46 (95% CI 0.7, 2.9) and 1.14 (95% CI 0.6, 2.0) respectively. CONCLUSIONS SES was inversely associated with CHD mortality in civil servants with and without prevalent CHD at baseline. Further distinguishing the relative contribution of SES to the initiation and progression of CHD requires repeated measures studies of pre-clinical and clinical measures of CHD.
How Fast Can a BDI Agent Respond?

It is very important to know how fast a BDI agent can react to and process incoming event sequences if we want to apply such autonomous agents into time-sensitive applications like the Close-In weapon system in air-carriers. In [15], we proposed an analysis method for traditional sequential agents. In this paper we extend the theoretical analysis method to parallel BDI agents. Our method can estimate the average response time using the average attributes of a sequence of events based on probability and queueing theory. The simulation experiments show that our theoretical analysis method is effective. We also show by an experiment that an agent that dynamically allocates its computational time resources perform better than one that does not. Thus, the theoretical method suggests a way to quickly estimate the performance of an agent if the average attributes of the incoming event sequence are known in advance. Such an analysis of average response time can definitely benefit constructing more efficient BDI agents that situate in time-sensitive environments.
Diastolic Heart Failure: Evidence of Increased Myocardial Collagen Turnover Linked to Diastolic Dysfunction

Background— The pathophysiology of diastolic heart failure (DHF) is poorly understood. One potential explanation is an active fibrotic process that produces increased ventricular stiffness, which compromises filling. The present study investigates collagen metabolism in hypertensive patients in different phases of diastolic function with and without proven DHF. Methods and Results— We studied 86 hypertensive patients divided into groups according to the presence of DHF (32 with, 54 without) and phase of diastolic function (20 with normal function, 38 with impaired relaxation, 10 with pseudonormalization, and 16 with restrictive-like filling). Serum carboxy-terminal, amino-terminal, and carboxy-terminal telopeptide of procollagen type I, amino-terminal propeptide of procollagen type III, matrix metalloproteinases (MMPs; total MMP-1, active MMP-2, and MMP-9), and tissue inhibitor of MMPs levels were assayed by radioimmunoassay and ELISA. Doppler-echocardiographic assessment of diastolic filling was made with measurements of E/A ratio, E-wave deceleration time, and isovolumic relaxation time. Serum carboxy-terminal telopeptide of procollagen type I, carboxy-terminal telopeptide of procollagen type I, amino-terminal propeptide of procollagen type III, MMP-2, and MMP-9 levels (P<0.001 for all, controlled for age and gender) were greater in patients with DHF than in those without. When we controlled for age and gender, levels of serum carboxy-terminal telopeptide of procollagen type I, tissue inhibitor of MMP-1, amino-terminal propeptide of procollagen type III (all P<0.001), carboxy-terminal telopeptide of procollagen type I(P=0.008), and MMP-2 (P=0.03) were greater in more severe phases of diastolic dysfunction. Within phases of diastolic dysfunction, serum carboxy-terminal telopeptide of procollagen type I, amino-terminal propeptide of procollagen type III, MMP-2, and MMP-9 were elevated in those with DHF compared with those without DHF (all P<0.001). Conclusions— These data demonstrate serological evidence of an active fibrotic process in DHF, which is more marked in more severe diastolic dysfunction. This observation may help explain the pathophysiology of DHF and may suggest new avenues for diagnostic and therapeutic intervention.
Summary of muscle parameters for Hill-based muscle modeling in the human lower limb

A summary is presented of five mechanical parameters from human lower limb skeletal muscles critical for Hill-based muscle modeling: the optimal fiber length, the fiber pennation angle, the physiological cross-sectional area (PCSA), the unloaded tendon length, and the fast-twitch fiber fraction. The data presented are drawn from a total of 29 publications including human cadaver studies, in vivo imaging studies of live humans, musculoskeletal modeling studies, and combinations of these methods. Where possible, parameter values were adjusted from the referenced data to present them with consistent definitions (normalization of measured fiber lengths to optimal sarcomere length, and calculation of PCSA as the ratio of fiber volume to fiber length). It is seen that within a specific muscle, optimal fiber lengths are fairly consistent between studies, pennation angles and PCSAs vary widely between studies, and data for unloaded tendon length are comparatively sparse. Few studies have reported fiber type fractions for a large number of muscles. Guidelines for implementing these parameter values in muscle modeling and musculoskeletal modeling are suggested. Update History December 2, 2016: original submission December 3, 2016: discussion on maximum isometric force and specific tension added December 6, 2016: minor edits for typos, clarity, and missing references December 7, 2016: Tirrell et al. (2012) study added
Tools for monitoring, visualizing, and refining collections of noisy documents

Developing better systems for document image analysis requires understanding errors, their sources, and their effects. The interactions between various processing steps are complex, with details that can be obscured by the statistical methods that are employed in many cases. In this paper, we describe tools we are building to help the user view and understand the results of common document analysis procedures. Unlike existing platforms for ground-truthing page images, our system also allows users to visualize the results of automated error analyses. Recognition errors can be corrected interactively, with the effort to do so recorded as a measure that is useful in performance evaluation. Beyond this functionality for exploring error behavior, we consider how such tools could be designed to improve the quality of collections of badly recognized documents incrementally as users interact with them on a regular basis. We conclude by discussing topics for future research.
Optimum routing and scheduling for estimation in wireless sensor networks

In this paper, the distributed estimation in wireless sensor network using optimal task scheduling is considered. The main goal is to maximize network lifetime where it consists of a fusion center and a set of sensor nodes. Lifetime defined as the number of rounds accomplished before network becomes nonfunctional. In order to prolong network lifetime, we determine the optimal number of active sensor nodes and the number of samples provided by each of them using linear optimization problem. Sensor observations are quantized into messages and then forwarded to a fusion center where a final estimation is performed based on degree of certainty. Simulation results show that our optimal proposed algorithm has achieved significant efficiency when compared with other heuristic methods.