Miracle-dz/UniFAR-FTUs huggingface dataset:
Does Coronary Endarterectomy Increase Early Mortality and Morbidity Compared with Coronary Artery Bypass Surgery Alone-Single Centre Experience

Background: With increasing incidence of coronary artery disease (CAD) in Saudi Arabia and its fatal co-morbidity, this has resulted in a more complex pool of cases referred to cardiac surgeons. In selected cases, achieving optimal revascularization of diffuse CAD necessitates adjunctive techniques such as coronary endarterectomy (CE). The aim of our study is to evaluate the early mortality and post-operative morbidity related to CE. Method: Retrospective study from Jan 2009 to Dec 2010. Inclusion of 186 patients: 38 patients had CABG with CE and 148 patients had CABG alone. Results: Pre-operative percutaneous coronary intervention (PCI) was higher in the CE with CABG group (25.8%) compared with CABG alone (8.9%) (p = 0.009). Intra-operative data showed a higher mean cardiopulmonary bypass time (CBT) of 160 minutes and a mean cross-clamp time (XCT) of 109 minutes in the CE with CABG, compared to a mean CBT of 129 minutes and a mean XCT of 87 minutes in the CABG alone group (p = 0.001). The most common vessel endarterectomized was left anterior descending artery (LAD) (47%) followed by right coronary artery (RCA) (22%). Post-operatively, the mortality amongst the CE with CABG group (7.9%) was higher than CABG only group (1.4%), however it wasn’t statistically significant (p = 0.06). With regards to morbidity, hemodynamic instability requiring intra aortic balloon pump (HIR-IABP) was higher in the CE with CABG group (10.5%) compared to the CABG only group (1.4%) (p = 0.018). Conclusion: Our study showed that CE when combined with CABG wasn’t associated with a higher mortality rate when compared with CABG alone.
Differences in Proinflammatory Cytokines and Monocyte Subtypes in Older as Compared With Younger Kidney Transplant Recipients

Background The number of elderly patients with end-stage kidney disease requiring kidney transplantation continues to grow. Evaluation of healthy older adults has revealed proinflammatory changes in the immune system, which are posited to contribute to age-associated illnesses via “inflamm-aging. ” Immunologic dysfunction is also associated with impaired control of infections. Whether these immunologic changes are found in older kidney transplant recipients is not currently known, but may have important implications for risk for adverse clinical outcomes. Methods Three months after transplant, innate immune phenotype was evaluated by flow cytometry from 60 kidney transplant recipients (22 older [≥60 years] and 38 younger [<60 years old]). Multiplex cytokine testing was used to evaluate plasma cytokine levels. Younger patients were matched to older patients based on transplant type and induction immune suppression. Results Older kidney transplant recipients demonstrated decreased frequency of intermediate monocytes (CD14++CD16+) compared with younger patients (1.2% vs 3.3%, P = 0.007), and a trend toward increased frequency of proinflammatory classical monocytes (CD14++CD16−) (94.5% vs 92.1%) (P = 0.065). Increased levels of interferon-gamma (IFN-&ggr;) were seen in older patients. Conclusions In this pilot study of kidney transplant recipients, we identified differences in the innate immune system in older as compared with younger patients, including increased levels of IFN-&ggr;. This suggests that age-associated nonspecific inflammation persists despite immune suppression. The ability to apply noninvasive testing to transplant recipients will provide tools for patient risk stratification and individualization of immune suppression regimens to improve outcomes after transplantation.
Transdisciplinary Pedagogical Templates and Their Potential for Adaptive Reuse.

This article explores the use and usefulness of carefully designed transdisciplinary pedagogical templates (TPTs) aligned to different learning theories. The TPTs are based on the Learning Design Framework outlined in the Larnaca Declaration (Dalziel et al. in this collection). The generation of pedagogical plans or templates is not new. However, the creation and sharing of web-based pedagogical templates is underpinned by a re-use philosophy and the notion that such material can be adopted or adapted for various purposes by learning designers and developers. This article will exemplify the importance of pedagogical clarity by showcasing how different teacher and learner roles are instantiated in different TPTs that subscribe to behaviourist, cognitivist, or social learning theories. A key goal is to demonstrate that the TPTs constructed based on the Learning Design Framework (LD-F) introduced in the Larnaca Declaration, are easy to be re-used or modified to suit specific learning situations and contexts.
Learning from Irregularly Sampled Data with Deep Nadaraya–Watson Kernel Regression Networks (NWNet): Application to Endomicroscopy Image Reconstruction

Probe-based Confocal Laser Endomicroscopy (pCLE) enables more accurate diagnosis via optical biopsy. pCLE probes relay on of fibres bundles, which generate irregularly sampled signals. Current pCLE reconstruction is based on interpolating irregular signals onto an over-sampled Cartesian grid, using a sub-optimal Delaunay triangulation based linear interpolation scheme. High-quality reconstruction with improved information representation should be possible with the use of Deep Convolutional Neural Networks (CNNs). However, classical CNNs are limited to take as an input only Cartesian images, not irregular data. In this work, we propose to embed Nadaraya-Watson (NW) kernel regression into the CNN framework as a novel trainable CNN layer that allows for processing of irregularly sampled data represented as sparse data on a Cartesian grid. We design a new NWNet architecture in conjunction with examplar-based super-resolution CNN, which allows reconstructing high-quality pCLE images from the irregularly sampled input data. Models were trained on a database of 8806 images from 238 pCLE video sequences. The results were validated through an image quality assessment based on a composition of the following metrics: PSNR, SSIM, GCF. Our analysis indicates that the proposed solution unlocks the potential of CNNs for sparse data processing. NW layer is the main contribution of our end-to-end model performing pCLE image reconstruction directly from sparse imaging input to high-resolution cartesian images. Our method outperforms the reconstruction method in current clinical use.
ARM: ANN-based ranking model for privacy and security analysis in smartphone ecosystems

Smartphone ecosystems are considered as a unique source due to the large number of apps which in turn makes an extensive use of personal data. Currently, there is no privacy and security preservation mechanism in smartphone ecosystems to enable users to compare apps in terms of privacy and security protection level, and to alarm them regarding the invasive issues (in terms of privacy and security) of apps before installing them. In this paper, we exploit user comments on app stores as an important source to extract privacy and security invasive (PSI) claims corresponding to apps. Thus, we propose an artificial neural network (ANN)-based ranking model (ARM) in order to classify user comments with privacy and security concerns. Our ranking model is based on three main features namely privacy and security, sentiment, and lifetime analyses as the input of the ranking model along with a novel mathematical formulation in such a way as to maximise the differentiation between comments. The performance results show that ARM is able to classify and predict PSI user comments with accuracy as high as 93.3%. Our findings confirm that due to the functionality of ARM, it has the potential to be widely adopted in smartphone ecosystems.
Commentary on clinical utility of whole genome sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

3The present study is commentary and aims to evaluate the practical application of Whole Genome Sequencing (WGS) and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) in clinical microbiology. The MALDI-TOF MS method has been replaced cultural and biochemical tests for species identification in most laboratories worldwide. Moreover, WGS has elevated the discriminatory power by detection of single nucleotide polymorphisms (SNPs), and helped with the identification of microorganisms that were misidentified by previous culture and biochemical tests. Moreover, WGS can be used in epidemiological studies (e.g. clinical outbreaks) by tracking of phylogenetic maps and analyzing SNP distance; antimicrobial resistance studies such as the study of antimicrobial resistance genes, e.g. CTX-M, NDM, KPC, or OXA; and the study of recombination of plasmid or insertion sequence (IS) elements to elucidate the mechanism of antimicrobial resistance. MALDI-TOF technology is used for bacterial or fungal species identification in most laboratories. VITEK MS (bioMerieux) and Biotyper (Bruker Daltonics) are examples of commercially available MALDI-TOF MS systems. The technique has been used for direct identification of organisms from blood culture bottles, markedly shortening the identification time. Beta-lactamases or carbapenemases have been detected by analyzing specific protein peaks using MALDI-TOF MS. Shiga toxin-producing Escherichia coli, Salmonella serotype, and Vibrio phenotypes can also be detected.
Acoustic communication in two freshwater gobies: ambient noise and short-range propagation in shallow streams.

Noise is an important theoretical constraint on the evolution of signal form and sensory performance. In order to determine environmental constraints on the communication of two freshwater gobies Padogobius martensii and Gobius nigricans, numerous noise spectra were measured from quiet areas and ones adjacent to waterfalls and rapids in two shallow stony streams. Propagation of goby sounds and waterfall noise was also measured. A quiet window around 100 Hz is present in many noise spectra from noisy locations. The window lies between two noise sources, a low-frequency one attributed to turbulence, and a high-frequency one (200-500 Hz) attributed to bubble noise from water breaking the surface. Ambient noise from a waterfall (frequencies below 1 kHz) attenuates as much as 30 dB between 1 and 2 m, after which values are variable without further attenuation (i.e., buried in the noise floor). Similarly, courtship sounds of P. martensii attenuate as much as 30 dB between 5 and 50 cm. Since gobies are known to court in noisy as well as quiet locations in these streams, their acoustic communication system (sounds and auditory system) must be able to cope with short-range propagation dictated by shallow depths and ambient noise in noisy locations.
A Systematic Review and Meta-Analysis of Risk Factors for Sexual Transmission of HIV in India

Background Approximately 2.4 million people are living with HIV in India. This large disease burden, and potential for epidemic spread in some areas, demands a full understanding of transmission in that country. We wished to quantify the effects of key sexual risk factors for HIV infection for each gender and among high- and low-HIV risk populations in India. Methodology We conducted a systematic review of sexual risk factors for HIV infection from 35 published studies. Risk factors analyzed were: male circumcision/religion, Herpes Simplex Virus 2, syphilis, gonorrhoea, genital ulcer, multiple sexual partners and commercial sex. Studies were included if they met predetermined criteria. Data were extracted and checked by two researchers and random-effects meta analysis of effects was conducted. Heterogeneity in effect estimates was examined by I2 statistic. Publication bias was tested by Begg's test and funnel plots. Meta regression was used to assess effect modification by various study attributes. Results All risk factors were significantly associated with HIV status. The factor most strongly associated with HIV for both sexes was HSV-2 infection (ORmen: 5.87; 95%CI: 2.46–14.03; ORwomen: 6.44; 95%CI: 3.22–12.86). The effect of multiple sexual partners was similar among men (OR = 2.46; 95%CI: 1.91–3.17,) and women (OR = 2.02; 95%CI: 1.43–2.87) and when further stratified by HIV-risk group. The association between HSV-2 and HIV prevalence was consistently stronger than other STIs or self-reported genital ulcer. If the strong associations between HSV-2 and HIV were interpreted causally, these results implied that approximately half of the HIV infections observed in our study population were attributable to HSV-2 infection. Conclusions The risk factors examined in our analysis should remain targets of HIV prevention programs. Our results confirm that sexual risk factors for HIV infection continue to be an important part of Indian HIV epidemic 26 years after it began.
Novel ATPase Cu2+ Transporting Beta Polypeptide Mutations in Chinese Families with Wilson's Disease

Wilson's disease (WD) is an autosomal recessive inherited disorder caused by mutations in the ATPase Cu2+ transporting beta polypeptide gene (ATP7B). The detailed metabolism of copper-induced pathology in WD is still unknown. Gene mutations as well as the possible pathways involved in the ATP7B deficiency were documented. The ATP7B gene was analyzed for mutations in 18 Chinese Han families with WD by direct sequencing. Cell viability and apoptosis analysis of ATP7B small interfering RNA (siRNA)-treated human liver carcinoma (HepG2) cells were measured by 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) assay and Hoechst 33342 staining. Finally, the expression of B-cell CLL/lymphoma 2 (BCL2), BCL2-associated X protein (BAX), sterol regulatory element binding protein 1 (SREBP1), and minichromosome maintenance protein 7 (MCM7) of ATP7B siRNA-treated cells were tested by real-time polymerase chain reaction (real-time PCR) and Western blot analysis. Twenty different mutations including four novel mutations (p.Val145Phe, p.Glu388X, p.Thr498Ser and p.Gly837X) in the ATP7B gene were identified in our families. Haplotype analysis revealed that founder effects for four mutations (p.Arg778Leu, p.Pro992Leu, p.Ile1148Thr and p.Ala1295Val) existed in these families. Transfection of HepG2 cells with ATP7B siRNA resulted in decreased mRNA expression by 86.3%, 93.1% and 90.8%, and decreased protein levels by 58.5%, 85.5% and 82.1% at 24, 48 and 72 hours, respectively (All P<0.01). In vitro study revealed that the apoptotic, cell cycle and lipid metabolism pathway may be involved in the mechanism of WD. Our results revealed that the genetic cause of 18 Chinese families with WD and ATP7B deficiency-induce apoptosis may result from imbalance in cell cycle and lipid metabolism pathway.
A narrative-based collaborative writing tool for constructing coherent technical documents

FACULTY OF ENGINEERING, SCIENCE AND MATHEMATICS SCHOOL OF ELECTRONICS AND COMPUTER SCIENCE Doctor of Philosophy A narrative-based collaborative writing tool for constructing coherent technical documents by Nishadi H. De Silva One important feature of an effective document that makes it easy to read and understand is known as coherence. Technical documents produced collaboratively are often incoherent due to a lack of group consensus and misaligned contributions by the individual authors. However, current document planning techniques and writing tools do not provide explicit support for improving coherence. The goal of this research, therefore, is to develop and evaluate a new technique and tool that helps teams of authors to structure coherent technical documents. The coherence of a document can be attributed to the story (or narrative) it conveys to the reader. If this story is consistent and coherent, the same can be said about the document. A discourse theory such as Rhetorical Structure Theory (RST) that has been developed by linguists helps further to analyse and improve a narrative. RST explains the coherence of a text by virtue of relationships (such as “paragraph A justifies paragraph B”) between parts of the text. This research has combined the ideas from these parallel strands of research to develop a new document planning technique called narrative-based writing. The method involves writing down an explicit precis of the story (called a document narrative or DN) and then analysing it using RST. The DN and RST analysis are then used to structure the eventual document. To extend the usability of narrative-based writing to geographically-dispersed authors, I have designed and implemented a collaborative tool that allows co-authors to edit, analyse and review DNs. The thorough design for the tool uses a combination of three models (conceptual, business process and functional) culminating in a set of functions that enable collaborative narrative-based writing. This dissertation discusses how, in the future, these functions could be incorporated in existing collaborative writing tools. Implementing this tool, albeit in its current prototypic state, has been invaluable in understanding the complexities of modelling and manipulating DNs and RST structures. Initial investigations using the new technique and tool have been positive, encouraging me to continue the research and evaluation in this field.
Social influence analysis and application on multimedia sharing websites

Social media is becoming popular these days, where users necessarily interact with each other to form social networks. Influence network, as one special case of social network, has been recognized as significantly impacting social activities and user decisions. We emphasize in this article that the inter-user influence is essentially topic-sensitive, as for different tasks users tend to trust different influencers and be influenced most by them. While existing research focuses on global influence modeling and applies to text-based networks, this work investigates the problem of topic-sensitive influence modeling in the multimedia domain. According to temporal data justification, we propose a multimodal probabilistic model, considering both users' textual annotation and uploaded visual images. This model is capable of simultaneously extracting user topic distributions and topic-sensitive influence strengths. By identifying the topic-sensitive influencer, we are able to conduct applications, like collective search and collaborative recommendation. A risk minimization-based general framework for personalized image search is further presented, where the image search task is transferred to measure the distance of image and personalized query language models. The framework considers the noisy tag issue and enables easy incorporation of social influence. We have conducted experiments on a large-scale Flickr dataset. Qualitative as well as quantitative evaluation results have validated the effectiveness of the topic-sensitive influencer mining model, and demonstrated the advantage of incorporating topic-sensitive influence in personalized image search and topic-based image recommendation.
TALC-sef A Manually-Revised POS-TAgged Literary Corpus in Serbian, English and French

In this paper, we present a parallel literary corpus for Serbian, English and French, the TALC-sef corpus. The corpus includes a manually-revised pos-tagged reference Serbian corpus of over 150,000 words. The initial objective was to devise a reference parallel corpus in the three languages, both for literary and linguistic studies. The French and English sub-corpora had been pos-tagged from the onset, using TreeTagger (Schmid, 1994), but the corpus lacked, until now, a tagged version of the Serbian sub-corpus. Here, we present the original parallel literary corpus, then we address issues related to pos-tagging a large collection of Serbian text: from the conception of an appropriate tagset for Serbian, to the choice of an automatic pos-tagger adapted to the task, and then to some quantitative and qualitative results. We then move on to a discussion of perspectives in the near future for further annotations of the whole parallel corpus.
The Association between KCNQ1 Gene Polymorphism and Type 2 Diabetes Risk: A Meta-Analysis

Background KCNQ1 (potassium voltage-gated channel KQT-like sub-family, member 1) encodes a pore-forming subunit of a voltage-gated K+ channel (KvLQT1) that plays a key role for the repolarization of the cardiac action potential as well as water and salt transport in epithelial tissues. Recently, genome-wide association studies have identified KCNQ1 as a type 2 diabetes (T2D) susceptibility gene in populations of Asian descent. After that, a number of studies reported that the rs2237892 and rs2237895 polymorphism in KCNQ1 has been implicated in T2D risk. However, studies on the association between these polymorphism and T2D remain conflicting. To investigate this inconsistency, we performed this meta-analysis. Methods Databases including Pubmed, EMBASE, Web of Science and China National Knowledge Infrastructure (CNKI) were searched to find relevant studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association. Potential sources of heterogeneity were also assessed by subgroup analysis and meta-regression. Results A total of 25 articles involving 70,577 T2D cases and 99,068 controls were included. Overall, the summary odds ratio of C allele for T2D was 1.32 (95% CI 1.26–1.38; P<10−5) and 1.24 (95% CI: 1.20–1.29; P<10−5) for KCNQ1 rs2237892 and rs2237895 polymorphisms, respectively. Significant results were also observed using co-dominant, dominant and recessive genetic models. After stratifying by ethnicity, sample size, and diagnostic criteria, significant associations were also obtained. Conclusions This meta-analysis suggests that the rs2237892 and rs2237895 polymorphisms in KCNQ1 are associated with elevated type 2 diabetes susceptibility.
Fast exact toffoli network synthesis of reversible logic

The research in the field of reversible logic is motivated by its application in low-power design, optical computing and quantum computing. Hence synthesis of reversible logic has become a very important research area in the last years. In this paper exact algorithms for the synthesis of generalized Toffoli networks are considered. We present an improvement of an existing synthesis approach that is based on Boolean Satisfiability. Furthermore, the principle limits of the original and the improved approach are shown. Then, we propose a new method using problem specific knowledge during the synthesis process to overcome these limits. Experimental results demonstrate improvements of the overall synthesis time up to four orders of magnitude.
A Frugal Auction Technique for Data Replication in Large Distributed Computing Systems

Fine-grained data replication over the Internet allows duplication of frequently accessed data objects, as opposed to entire sites, to certain locations so as to improve the performance of large-scale content distribution systems. In a distributed system, agents representing their sites try to maximize their own benefit since they are driven by different goals such as to minimize their communication costs, latency, etc. In this paper, we will use game theoretical techniques and in particular auctions to identify a bidding mechanism that encapsulates the selfishness of the agents, while having a controlling hand over them. In essence, the proposed game theory based mechanism is the study of what happens when independent agents act selfishly and how to control them to maximize the overall performance. A bidding mechanism asks how one can design systems so that agents’ selfish behavior results in the desired systemwide goals. Experimental results reveal that this mechanism provides excellent solution quality, while maintaining fast execution time. The comparisons are recorded against some well known techniques such as greedy, branch and bound, game theoretical auctions and