Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced multi-protocol analysis via intelligent supervised embedding (EMPrAvISE): detecting prostate cancer on multi-parametric MRI

Currently, there is significant interest in developing methods for quantitative integration of multi-parametric (structural, functional) imaging data with the objective of building automated meta-classifiers to improve disease detection, diagnosis, and prognosis. Such techniques are required to address the differences in dimensionalities and scales of individual protocols, while deriving an integrated multi-parametric data representation which best captures all disease-pertinent information available. In this paper, we present a scheme called Enhanced Multi-Protocol Analysis via Intelligent Supervised Embedding (EMPrAvISE); a powerful, generalizable framework applicable to a variety of domains for multi-parametric data representation and fusion. Our scheme utilizes an ensemble of embeddings (via dimensionality reduction, DR); thereby exploiting the variance amongst multiple uncorrelated embeddings in a manner similar to ensemble classifier schemes (e.g. Bagging, Boosting). We apply this framework to the problem of prostate cancer (CaP) detection on 12 3 Tesla pre-operative in vivo multi-parametric (T2-weighted, Dynamic Contrast Enhanced, and Diffusion-weighted) magnetic resonance imaging (MRI) studies, in turn comprising a total of 39 2D planar MR images. We first align the different imaging protocols via automated image registration, followed by quantification of image attributes from individual protocols. Multiple embeddings are generated from the resultant high-dimensional feature space which are then combined intelligently to yield a single stable solution. Our scheme is employed in conjunction with graph embedding (for DR) and probabilistic boosting trees (PBTs) to detect CaP on multi-parametric MRI. Finally, a probabilistic pairwise Markov Random Field algorithm is used to apply spatial constraints to the result of the PBT classifier, yielding a per-voxel classification of CaP presence. Per-voxel evaluation of detection results against ground truth for CaP extent on MRI (obtained by spatially registering pre-operative MRI with available whole-mount histological specimens) reveals that EMPrAvISE yields a statistically significant improvement (AUC=0.77) over classifiers constructed from individual protocols (AUC=0.62, 0.62, 0.65, for T2w, DCE, DWI respectively) as well as one trained using multi-parametric feature concatenation (AUC=0.67).
Efficient Big Data Transfer Technique for Static Routing Networks

The era of the networks technology encourages sharing scattered information and computing capabilities, limited network bandwidth in communication and memory space needed to store and transfer big data files between client, server and vice versa, which forms a problem that cannot be solved by upgrading the networks' hardware or using current available data transfer protocols. This research suggests and proposes a new novel technique that analyzes parameters related to network technologies and big data files and utilize Huffman Encoding compression algorithm to minimize the files' size and optimize the network performance in the most effective way for static routing networks. The results of this research shows that the time needed to reduce the big data files' size using Huffman Encoding compression algorithm and the time to transfer the compressed files is less than the time calculated to transfer the original big data files in some of the network technologies. Thus, the results of the simulation shows the proposed technique in this research has minimized the transmission time for some technologies and increased the network throughput.
Evaluation of Malaysian's children websites using fuzzy computing with expressions

Children have difficulty in understanding numbers unlike adults. They are easily attracted to displayed images and icons rather than numbers. Therefore, in any evaluation with children, it is better to avoid the use of numerical scaling towards them. For this study is concern on the method used when evaluating with children, this study promotes the use of linguistic expressions as a method in the evaluation process. Linguistic expressions are applicable to children where expressions are much likeable by children than numerical scaling. Evaluation of the linguistic expression is applied during the interviews, questions and answers session with the children. The children websites was chosen in the evaluation because websites technology has becoming more permeable towards children nowadays. Websites are important to children as a medium to provide education learning and entertainment. Despite that, children websites in Malaysia seems to be limited. It is rare enough to find Malaysian based websites for children in the search engine. Hence, this study investigates the current status of Malaysian's children website and their design and content characteristics as well as proposing the method of fuzzy computing with expressions in the evaluation process. In the near future, this study perhaps will initiate Malaysian websites developer to create more children websites in this country.
Blockade of self-reactive IgM significantly reduces injury in a murine model of acute myocardial infarction.

AIMS Coronary artery occlusion resulting in ischaemia/reperfusion (I/R) injury is a major cause of mortality in the western world. Circulating natural IgM has been shown to play a significant role in reperfusion injury, leading to the notion of a pathogenic response against self by the innate immune system. A specific self-antigen (non-muscle myosin heavy chain II) was recently identified as the major target of pathogenic natural IgM. Therefore, we hypothesized that a synthetic peptide mimetope (N2) or monoclonal antibodies directed against the self-antigen would prevent specific IgM binding to the self-antigen and reduce reperfusion injury in the heart. METHODS AND RESULTS We find that treatment with N2 peptide reduces infarct size by 47% and serum cardiac troponin-I levels by 69% following 1 h ischaemia and 24 h reperfusion. N2 peptide or an anti-N2 F(ab')(2) (21G6) is also effective at preventing IgM and complement deposition. Additionally, N2 peptide treatment significantly reduces monocyte and neutrophil infiltration at 24 h and collagen deposition at 5 days. Finally, we show that human IgM (hIgM) also includes specificity for the highly conserved self-antigen and that myocardial injury in antibody-deficient mice reconstituted with hIgM is blocked by treatment with N2 peptide or 21G6 F(ab')(2). CONCLUSION The findings in this study identify potential therapeutics [i.e. N2 peptide or 21G6 F(ab')(2)] that prevent specific IgM binding to ischaemic antigens in the heart, resulting in a significant reduction in cardiac I/R injury.
Title Live Attenuated S . Typhimurium Vaccine with Improved Safety in ImmunoCompromised Mice Permalink

Live attenuated vaccines are of great value for preventing infectious diseases. They represent a delicate compromise between sufficient colonization-mediated adaptive immunity and minimizing the risk for infection by the vaccine strain itself. Immune defects can predispose to vaccine strain infections. It has remained unclear whether vaccine safety could be improved via mutations attenuating a vaccine in immune-deficient individuals without compromising the vaccine’s performance in the normal host. We have addressed this hypothesis using a mouse model for Salmonella diarrhea and a live attenuated Salmonella Typhimurium strain (ssaV). Vaccination with this strain elicited protective immunity in wild type mice, but a fatal systemic infection in immune-deficient cybbnos2 animals lacking NADPH oxidase and inducible NO synthase. In cybbnos2 mice, we analyzed the attenuation of 35 ssaV strains carrying one additional mutation each. One strain, Z234 (ssaV SL1344_3093), was . 1000-fold attenuated in cybbnos2 mice and <100 fold attenuated in tnfr1 animals. However, in wt mice, Z234 was as efficient as ssaV with respect to host colonization and the elicitation of a protective, O-antigen specific mucosal secretory IgA (sIgA) response. These data suggest that it is possible to engineer live attenuated vaccines which are specifically attenuated in immuno-compromised hosts. This might help to improve vaccine safety. Citation: Periaswamy B, Maier L, Vishwakarma V, Slack E, Kremer M, et al. (2012) Live Attenuated S. Typhimurium Vaccine with Improved Safety in ImmunoCompromised Mice. PLoS ONE 7(9): e45433. doi:10.1371/journal.pone. 0045433 Editor: Dipshikha Chakravortty, Indian Institute of Science, India Received June 29, 2012; Accepted August 17, 2012; Published September 24, 2012 Copyright: 2012 Periaswamy et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The support came from the UBS Optimus Foundation (to M.S. and W.D.H.) and National Institutes of Health grant AI075093 (M.M.). A.G. was supported by the BBSRC (BBS/B/02266 to P. Mastroeni and D. Maskell). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: hardt@micro.biol.ethz.ch
TECHNICAL NOTE - Cellular Bucket Brigades

Workers in a bucket brigade production system perform unproductive travel when they walk to get more work from their colleagues. We introduce a new design of bucket brigades to reduce unproductive travel. Under the new design, each worker works on one side of an aisle when he proceeds in one direction and works on the other side when he proceeds in the reverse direction. We propose simple rules for workers to share work under the new design and find a sufficient condition for the system to self-balance. Numerical examples suggest that the improvement in throughput by the new design can be as large as 30%. Even with a 20% reduction in labor, the new design can still increase throughput by 7%.
Processing content-oriented XPath queries

Document-centric XML collections contain text-rich documents, marked up with XML tags that add lightweight semantics to the text. Querying such collections calls for a hybrid query language: the text-rich nature of the documents suggests a content-oriented (IR) approach, while the mark-up allows users to add structural constraints to their IR queries. Hybrid queries tend to be more expressive, which should lead---in principle---to better retrieval performance. In practice, the processing of these hybrid queries within an IR systems turns out to be far from trivial, because a delicate balance between structural and content information needs to be sought. We propose an approach to processing such hybrid content-and-structure queries that decomposes a query into multiple content-only queries whose results are then combined in ways determined by the structural constraints of the original query. We evaluate our methods using the INEX 2003 test-suite, and show (1) that effective ways of processing of content-oriented XPath queries are non-trivial, (2) that there are differences in the effectiveness for different topics types, but (3) that with appropriate processing methods retrieval effectiveness can improve.
Polymorphims in the Interferon-y/Interleukin 26 Gene Region Contribute to Sex Bias in Susceptibility to Rheumatoid Arthritis

Objective. To determine whether polymorphisms in the interferon- (cid:1) (IFN (cid:1) )/interleukin-26 (IL-26; for-merly, AK155) gene cluster contribute to sex-based differential susceptibility to rheumatoid arthritis (RA). Methods. Four microsatellite markers, located in a 118-kb interval that contains both the IFN (cid:1) and IL-26 genes on chromosome 12q15, were typed in 251 patients with RA and 198 unrelated healthy controls (all of whom lived in Northern Ireland) by means of polymerase chain reaction–based fragment analysis. Results. P P 3-marker haplotype, underrepresentation Conclusion.
Assessing Student Performance by Learning Analytics Dashboards

In today’s competitive business environment, multiple diverse applications produce a huge amount of data, which are typically referred to as big data. Business Intelligence and Analytics are increasingly applied in public and private sectors for monitoring complex data using dashboards and effectively support decision making. Business dashboards (BDs), as complete executive information systems, enable business performance to be examined toward defined targets in a visual front-end interface. Institutions in distance learning apply similar methodologies to manage the explosion of educational data by employing data mining and visualization techniques in students' logs. The lack of a daily real-time data analysis and the delay in the immediate presentation of critical information, limit the teachers’ early decisions. With the emergence of Learning Analytics Dashboards (LADs), as a system of collecting, analyzing and simultaneously visualizing vital knowledge in a customizable interface, teachers are provided with information regarding current students’ progress. This study explores specific LADs in the Moodle platform, applied to a seminar offered by the Educational Content Methodology and Technology Laboratory of the Hellenic Open University and visualizes the findings of students’ interactions. The papers’ contribution concerns the enhancement of teacher decision-making and student self-reflection by monitoring their activity and providing accurate feedback on time.
Electrical Stimulation to Conductive Scaffold Promotes Axonal Regeneration and Remyelination in a Rat Model of Large Nerve Defect

Background Electrical stimulation (ES) has been shown to promote nerve regeneration when it was applied to the proximal nerve stump. However, the possible beneficial effect of establishing a local electrical environment between a large nerve defect on nerve regeneration has not been reported in previous studies. The present study attempted to establish a local electrical environment between a large nerve defect, and examined its effect on nerve regeneration and functional recovery. Methodology/Findings In the present study, a conductive scaffold was constructed and used to bridge a 15 mm sciatic nerve defect in rats, and intermittent ES (3 V, 20 Hz) was applied to the conductive scaffold to establish an electrical environment at the site of nerve defect. Nerve regeneration and functional recovery were examined after nerve injury repair and ES. We found that axonal regeneration and remyelination of the regenerated axons were significantly enhanced by ES which was applied to conductive scaffold. In addition, both motor and sensory functional recovery was significantly improved and muscle atrophy was partially reversed by ES localized at the conductive scaffold. Further investigations showed that the expression of S-100, BDNF (brain-derived neurotrophic factor), P0 and Par-3 was significantly up-regulated by ES at the conductive scaffold. Conclusions/Significance Establishing an electrical environment with ES localized at the conductive scaffold is capable of accelerating nerve regeneration and promoting functional recovery in a 15 mm nerve defect in rats. The findings provide new directions for exploring regenerative approaches to achieve better functional recovery in the treatment of large nerve defect.
Relationship between surface resistance and critical current density of HTS thin films in a DC magnetic field

We investigated the relationship between the surface resistance (R/sub s/) and critical current density (J/sub c/) of DyBa/sub 2/Cu/sub 3/O/sub 7-/spl delta// (DyBCO) thin films in a dc magnetic field. The R/sub s/ of DyBCO films at 21.8 GHz was measured using a dielectric resonator method and the J/sub c/ was determined by magnetic measurement and Bean's model. A dc magnetic field of up to 5 T was applied along the c-axis of the films. The relationship between the R/sub s/ and J/sub c/ of DyBCO thin films under a zero magnetic field was explained by the following equation, R/sub s/=/spl alpha//spl times/10/sup 7//J/sub c/, where /spl alpha/ is a constant of 1.2, and the units of the R/sub s/ and J/sub c/ are ohm and A/m/sup 2/, respectively. In addition, the R/sub s/ in dc magnetic fields up to 5 T were inversely proportional to the J/sub c/. However, the parameter /spl alpha/, which was fitted from the R/sub s/-J/sub c/ characteristics in each magnetic field, increased slightly with an increase the magnitude of the applied field. These results indicate that the relationship between the R/sub s/ and J/sub c/ in a zero magnetic field may be a general property of HTS thin films and that the /spl alpha/ in DyBCO thin films depends on the magnitude of the applied magnetic field.
Detecting Opinions Using Deep Syntactic Analysis

In this paper, we present an opinion detection system built on top of a robust syntactic pars-er. The goal of this system is to extract opi-nions associated with products but also with characteristics of these products, i.e. to per-form feature-based opinion extraction. To car-ry out this task, and following a rget corpus tastudy, the robust syntactic parser is enriched by associa ting polarities to pertinent lexical elements and by developing generic rules to extract relations of opinions t ogether with their polarity, i.e. positive or negative. These rela-tions are used to feed an opinion representa-tion model. A first evaluation shows very en-couraging results, but numerous perspectives and developments remain to be inve stigated.
Prostate Cancer Pearls for Prostate Cancer Screening

P rostate cancer screening and its effect on disease-specific mortality has been a topic of debate since the early 1990s. In 2009, after publication of the results of two large randomized prostate cancer screening trials showing contradictory results, the debate continued. Meanwhile, based on the huge amount of data from these two trials it became clear there is no one-size-fits-all for prostate cancer screening. Now, with two recent publications, the debate on whether prostate cancer screening affects mortality can finally be ended. The focus is on how to identify those men that can benefit from screening.
Interactive Importance-Driven Visualization Techniques for Medical Volume Data

In this paper we introduce volume visualization techniques developed with the aim to enhance interactive exploration of medical datasets. We present volumetric lenses which can be applied to a volume dataset to interactively focus regions of interest within these datasets. During rendering the parts of a volume dataset intersecting the lens, which is defined by a convex 3D shape, are rendered using a different visual appearance. The lenses proposed in this paper allow to apply non-photorealistic rendering techniques at interactive frame rates to aid comprehension for medical diagnosis. After briefly explaining how convex focus areas can be defined interactively we will explain the proposed lenses and their implementation in detail. Finally, we will give some performance results and conclude the paper.
CPW-fed wideband circularly-polarized antenna

A novel shorted CPW-fed slot antenna with wideband circular polarization characteristic is proposed in this letter. The proposed antenna consists of a bi-directional radiation slot antenna printed on a single substrate and a reflector for unidirectional radiation. A half circle slot and a slim slot are involved to optimize the axial ratio (AR) bandwidth and taper on the feeding line is utilised to further improve the impedance bandwidth. The measured results show that the antenna has the impedance bandwidth (S11 <; -10dB) of 12.6% and the AR bandwidth (AR <; 3dB) of 12.7%. The RHCP gain in the main radiation direction is 7.5 dBi.
Diversification and Performance: Linking Relatedness, Market Structure, and the Decision to Diversify

An extensive empirical literature in strategy and finance studies the performance implications of corporate diversification. Two core debates in the literature concern the existence of a diversification discount and the relative importance of industry relatedness and market structure for the performance of diversifiers. We address these debates by building a formal model in which the extent of diversification is endogenous and depends on the degree of industry relatedness. Firms’ diversification choices affect both their own competitiveness and market structure. We find a nonmonotonic effect of relatedness on performance: whereas greater relatedness increases the competitiveness of diversified firms, it can also spur additional diversification, thereby eroding market structure and performance. In this way, our theory also elucidates how heterogeneity in firm scope strategies can emerge even when firms are initially identical. We use the model to generate data and show how the negative effect of relatednes.
Resource Availability and Competition Shape the Evolution of Survival and Growth Ability in a Bacterial Community

Resource availability is one of the main factors determining the ecological dynamics of populations or species. Fluctuations in resource availability can increase or decrease the intensity of resource competition. Resource availability and competition can also cause evolutionary changes in life-history traits. We studied how community structure and resource fluctuations affect the evolution of fitness related traits using a two-species bacterial model system. Replicated populations of Serratia marcescens (copiotroph) and Novosophingobium capsulatum (oligotroph) were reared alone or together in environments with intergenerational, pulsed resource renewal. The comparison of ancestral and evolved bacterial clones with 1 or 13 weeks history in pulsed resource environment revealed species-specific changes in life-history traits. Co-evolution with S. marcescens caused N. capsulatum clones to grow faster. The evolved S. marcescens clones had higher survival and slower growth rate then their ancestor. The survival increased in all treatments after one week, and thereafter continued to increase only in the S. marcescens monocultures that experienced large resource pulses. Though adaptive radiation is often reported in evolution studies with bacteria, clonal variation increased only in N. capsulatum growth rate. Our results suggest that S. marcescens adapted to the resource renewal cycle whereas N. capsulatum was more affected by the interspecific competition. Our results exemplify species-specific evolutionary response to both competition and environmental variation.
Apathy in patients with Parkinson’s disease following deep brain stimulation of the subthalamic nucleus

Objective Apathy has been reported as a possible adverse effect of deep brain stimulation of the subthalamic nucleus (STN-DBS). We investigated the prevalence and severity of apathy in 22 patients with Parkinson’s disease (PD) who underwent STN-DBS, as well as the effects of apathy on quality of life (QOL). Methods All patients were assessed with the Lille Apathy Rating Scale (LARS), the Apathy Scale (AS), and the Parkinson’s Disease Questionnaire and were compared to a control group of 38 patients on pharmacotherapy alone. Results There were no significant differences in the prevalence or severity of apathy between patients who had undergone STN-DBS and those on pharmacotherapy alone. Significant correlations were observed between poorer QOL and degree of apathy, as measured by the LARS (p<0.001) and the AS (p=0.021). PD-related disability also correlated with both apathy ratings (p<0.001 and p=0.017, respectively). Conclusion Our findings suggest that STN-DBS is not necessarily associated with apathy in the PD population; however, more severe apathy appears to be associated with a higher level of disability due to PD and worse QOL, but no other clinico-demographic characteristics.