Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction of an miRNA-regulated drug-pathway network reveals drug repurposing candidates for myasthenia gravis

Myasthenia gravis (MG) is a rare debilitating autoimmune neuromuscular disorder. Many studies have focused on the mechanism and treatment strategies of MG. However, the exact pathogenesis of MG and effective treatment strategies remain unclear. Recent studies have indicated that microRNAs (miRNAs or miRs) can regulate the pathological pathways of MG, suggesting their potential role in novel treatments. In the present study, we created a comprehensive catalog of experimentally confirmed MG risk genes and miRNAs by manually mining published literature and public databases. Based on these genes and miRNAs, we identified 41 MG risk pathways and 105 approved drugs that can affect these pathways. Some important MG-related pathways, such as hsa04060 (cytokine-cytokine receptor interaction) and hsa05200 (pathway in cancer), were found to be regulated by MG risk miRNAs and drugs. Furthermore, we constructed an miRNA-regulated drug-pathway network and identified miRNAs and drugs that synergistically regulate key MG pathways and biological processes. We developed a drug repurposing strategy to identify 25 drug repurposing candidates for MG; several of these drugs, such as rituximab, adalimumab, sunitinib, and muromonab, have the potential to be novel MG treatment drugs. This study provides novel insight into the pathogenesis of MG and potential drug candidates for MG were identified.
Planning with the STAR(s)

We present our findings on the first application of motion planning methodologies to the recently introduced Sprawl Tuned Autonomous Robot (STAR). The reported results provide a first glimpse on the capabilities of this novel, 3D-printed robot in performing autonomously non-trivial motion planning tasks in environments populated with obstacles. We employ methods from sampling-based motion planning under nonholonomic constraints, and implement in open loop the generated path on the physical robot for various environments of increasing complexity.
Exact solution of a partially asymmetric exclusion model using a deformed oscillator algebra

We study the partially asymmetric exclusion process with open boundaries. We generalize the matrix approach previously used to solve the special case of total asymmetry and derive exact expressions for the partition sum and currents valid for all values of the asymmetry parameter q . Due to the relationship between the matrix algebra and the q -deformed quantum harmonic oscillator algebra we find that q -Hermite polynomials, along with their orthogonality properties and generating functions, are of great utility. We employ two distinct sets of q -Hermite polynomials, one for q 1. It turns out that these correspond to two distinct regimes: the previously studied case of forward bias (q 1) where the boundaries support a current opposite in direction to the bulk bias. For the forward bias case we confirm the previously proposed phase diagram whereas the case of reverse bias produces a new phase in which the current decreases exponentially with system size.
Cardiac Rehabilitation Attendance and Outcomes in Coronary Artery Disease Patients

Background— Cardiac rehabilitation (CR) is an efficacious yet underused treatment for patients with coronary artery disease. The objective of this study was to determine the association between CR completion and mortality and resource use. Methods and Results— We conducted a prospective cohort study of 5886 subjects (20.8% female; mean age, 60.6 years) who had undergone angiography and were referred for CR in Calgary, AB, Canada, between 1996 and 2009. Outcomes of interest included freedom from emergency room visits, hospitalization, and survival in CR completers versus noncompleters, adjusted for clinical covariates, treatment strategy, and coronary anatomy. Hazard ratios for events for CR completers versus noncompleters were also constructed. A propensity model was used to match completers to noncompleters on baseline characteristics, and each outcome was compared between propensity-matched groups. Of the subjects referred for CR, 2900 (49.3%) completed the program, and an additional 554 subjects started but did not complete CR. CR completion was associated with a lower risk of death, with an adjusted hazard ratio of 0.59 (95% confidence interval, 0.49–0.70). CR completion was also associated with a decreased risk of all-cause hospitalization (adjusted hazard ratio, 0.77; 95% confidence interval, 0.71–0.84) and cardiac hospitalization (adjusted hazard ratio, 0.68; 95% confidence interval, 0.55–0.83) but not with emergency room visits. Propensity-matched analysis demonstrated a persistent association between CR completion and reduced mortality. Conclusions— Among those coronary artery disease patients referred, CR completion is associated with improved survival and decreased hospitalization. There is a need to explore reasons for nonattendance and to test interventions to improve attendance after referral.
Investigating the Variation of Personal Network Size Under Unknown Error Conditions

This article estimates the variation in personal network size, using respondent data containing two systematic sources of error. The data are the proportion of respondents who, on average, claim to know zero, one, and two people in various subpopulations, such as “people who are widows under the age of 65” or “people who are diabetics. ” The two kinds of error—transmission error (respondents are unaware that someone in their network is in a subpopulation) and barrier error (something causes a respondent to know more or less than would be expected, in a subpopulation)—are hard to quantify. The authors show how to estimate the shape of the probability density function (pdf) of the number of people known to a random individual by assuming that respondents give what they assume to be accurate responses based on incorrect knowledge. It is then possible to estimate the relative effective sizes of subpopulations and produce an internally consistent theory. These effective sizes permit an evaluation of the shape of the pdf, which, remarkably, agrees with earlier estimates.
Azide as a preservative in assays of aspartate aminotransferase activity.

Azide at an effective antimicrobial concentration, 7.7 mmol/liter, inhibits neither the cytoplasmic or the mitochondrial isoenzymes of human aspartate aminotransferase (EC 2.6.1.1) or porcine malate dehydrogenase (EC 1.1.1.37). It markedly prolongs the usefulness of substrates in assays for estimating aspartate aminotransferase activity (aspartate substrate without azide deteriorates in less than 24 h at 25 °C) and does not affect results obtained in assays in which activity is continuously monitored. It also has no effect on chromophore development or absorption spectra in 2,4-dinitrophenylhydrazine-coupled assays, but it eliminates oxalacetate-diazonium salt chromophore formation, thus making it unsuitable for use in this assay. At concentrations greater than 100 mmol/liter it inhibits activities of both enzymes. Azide also catalyzes the ketoenol tautomerization of oxalacetate.
Expertise ranking in question-answer social network groups

Online social networks have become the major channel for people to maintain relationships, collaborate, and contribute shared information. A social network group can be created as a specific community for people who share an interest in a particular topic. One form of interaction within the group is the question-answer interaction by which the users in the group can ask questions or provide answers to others. A network analysis method, e.g., PageRank, can be used to analyze the interaction patterns between the users in order to identify and rank experts in the group. In this paper, we are interested in experimenting on how the quality of the users' comments can take part in the identification and ranking of experts by a PageRank-like algorithm. The quality factors are community rating, that is given to the answers, and the content-based features of the comments, i.e., length, complexity, and informativeness. We conduct an experiment on a Java Facebook group and evaluate the accuracy of the ranking with and without comment quality consideration against expertise ranking by Java experts.
ELearning Software Maintenance Diagnostic Model supported by a Decision Support System

Elearning projects often give most of their attention to the design of the content of the course, giving less consideration to its maintainability. By omitting this, elearning specialists do not take into account all the software maintenance activities required over time. Maintenance of software accounts for more than 80% of the cost of software over time. Changes of online courses may vary from basic text and graphic changes, editing complex animation and video, to wide-scale translation and localization requirements. Additional to content changes, many technology evolutions may be required over the life time of the course. This research intends to provide elearning specialists with an early software diagnostic model to help them in early identification of software maintainability issues during their elearning initiative. This will allow them to take proactive decisions during the development stage of an online course.
Disability as Difference - A Fictional Representation

This study presents three perspectives about how the life experience of individuals with disabilities is profoundly affected by the attitudes of others. A first perspective is presented by three individuals who had sustained significant, traumatic injuries. They each shared with me their experiences with acceptance and the attitudes of others. A second perspective comes from me, as the author of this article. As a person with a virtually lifelong disability, I have interpreted those experiences through a lens mediated by my own relationship to disability. These interpretations have informed a third perspective, that of a fictional representation of the role that the attitudes of others play in the lives of individuals with disabilities. That representation of attitude is presented as a one-act play. Within an oral history framework of narrative inquiry, the play offers a synthesis and restorying of the meanings inherent in each of these individual stories. Its purpose is to provide the reader/audience with a more intimate understanding of disability, demonstrating the relationship between others’ perceptions of disability and its apparently significant and categorical difference from the mainstream. Finally, the implications of this perception of disability as difference are made specific within the context of the ongoing employment challenges that continue to confront individuals living with disabilities.
Emotion Recognition in the Wild: Incorporating Voice and Lip Activity in Multimodal Decision-Level Fusion

In this paper, we investigate the relevance of using voice and lip activity to improve performance of audiovisual emotion recognition in unconstrained settings, as part of the 2014 Emotion Recognition in the Wild Challenge (EmotiW14). Indeed, the dataset provided by the organisers contains movie excerpts with highly challenging variability in terms of audiovisual content; e.g., speech and/or face of the subject expressing the emotion can be absent in the data. We therefore propose to tackle this issue by incorporating both voice and lip activity as additional features in a decision-level fusion. Results obtained on the blind test set show that the decision-level fusion can improve the best mono-modal approach, and that the addition of both voice and lip activity in the feature set leads to the best performance (UAR=35.27%), with an absolute improvement of 5.36% over the baseline.
Cloning and characterisation of the S . pombe rad 15 gene , a homologue to the S . cerevisiae RAD 3 and human ERCC 2 genes

The RAD3 gene of Saccharomyces cerevlslae encodes an ATP-dependent 5 ' 3 ' DNA helicase, which is involved in excision repair of ultraviolet radiation damage. By hybridisation of a Schlzosaccharomyces pombe genomic library with a RAD3 gene probe we have isolated the S.pombe homologue of RAD3. We have also cloned the rad15 gene of S.pombe by complementation of radiation-sensitive phenotype of the rad15 mutant. Comparison of the restriction map and DNA sequence, shows that the S.pombe rad15 gene is identical to the gene homologous to S.cerevisiae RAD3, identified by hybridisation. The S.pombe rad15.P mutant Is highly sensitive to UV radiation, but only slightly sensitive to ionising radiation, as expected for a mutant defective In excision repair. DNA sequence analysis of the rad15 gene Indicates an open reading frame of 772 amino acids, and this is consistent with a transcript size of 2.6kb as detected by Northern analysis. The predicted rad15 protein has 65% Identity to RAD3 and 55% identity to the human homologue ERCC2. This homology is particularly striking in the regions Identified as being conserved in a group of DNA helicases. Gene deletion experiments indicate that, like the S.cerevisiae RAD3 gene, the S.pombe rad15 gene is essential for viability, suggesting that the protein product has a role in cell proliferation and not solely in DNA repair.
Design and implementation of filter for simulating hearing loss

Objective evaluation methods of hearing aids are currently based on normal hearing case, without considering the different cases of hearing loss. In this paper, the least square method is used to design digital filters according to standard audiograms. Finally, a set of experiments to verify the attenuation effectiveness of the filters are done, and the results show that, the filters in this paper have the same attenuation effect as the standard audiograms. Thus, the filters is feasible, it can be used for measurement and evaluation system of hearing aids to improve the accuracy of the evaluation.
Reconciliation of Gene and Species Trees

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.
Operator-valued Kernels for Learning from Functional Response Data

In this paper we consider the problems of supervised classification and regression in the case where attributes and labels are functions: a data is represented by a set of functions, and the label is also a function. We focus on the use of reproducing kernel Hilbert space theory to learn from such functional data. Basic concepts and properties of kernel-based learning are extended to include the estimation of function-valued functions. In this setting, the representer theorem is restated, a set of rigorously defined infinite-dimensional operator-valued kernels that can be valuably applied when the data are functions is described, and a learning algorithm for nonlinear functional data analysis is introduced. The methodology is illustrated through speech and audio signal processing experiments.
IoT Network Architecture Using Packet Aggregation and Disaggregation

Internet of Things (IoT) is now considered as a key driving force for achieving next generation social systems. Several approaches have been proposed to achieve effective IoT communications, where each device has very limited communication capabilities. One such approach is the introduction of short packets for a lightweight communication protocol by which we can form a local area sensor network dedicated to IoT devices and can achieve effective packet processing, reducing power consumption, and minimizing bandwidth occupancy. The short packet can solve problems regarding local networks but creates another problem for the wide area Internet, where various devices and local networks are converged. We propose an aggregation scheme that makes it possible to reduce power consumption and packet processing loads caused by a huge amount of short packets. We focus on the wide area Internet with our proposed scheme to support IoT traffic more efficiently.
Swarming along the evolutionary branches sheds light on genome rearrangement scenarios

A genome rearrangement scenario describes a series of chromosome fusion, fission, and translocation operations that suffice to rewrite one genome into another. Exact algorithmic methods for this important problem focus on providing one solution, while the set of distance-wise equivalent scenarios is very large. Moreover, no criteria for filtering for biologically plausible scenarios is currently proposed. We present an original metaheuristic method that uses Ant Colony Optimization to randomly explore the space of optimal and suboptimal rearrangement scenarios. It improves on the state of the art both by permitting large-scale enumeration of optimal scenarios, and by labeling each with metrics that can be used for post-processing filtering based on biological constraints.
Prior Experience with Photostimulation Enhances Photo-Induced Reproductive Response in Female House Finches

In vertebrates, reproductive output often increases with age. Unlike older birds, first-year photoperiodic birds lack experience with the reproductively stimulatory effects of long day lengths (photostimulation). We examined whether age-related differences in annual reproductive development could be partially attributed to previous experience with photostimulation in the photoperiodic house finch (Carpodacus mexicanus). By manipulating photoperiod, we generated 2 groups of first-year females: a photo-experienced group that underwent 1 photoperiodically induced cycle of gonadal development and regression and a photo-naïve group exposed to long days since hatch. We transferred both groups from long to short days and then photostimulated and exposed them to male birdsong prior to sacrifice. Following concurrent photostimulation, both groups exhibited similar plasma luteinizing hormone surges and hypothalamic vasoactive intestinal polypeptide immunoreactivity. In contrast, hypothalamic gonadotropin-releasing hormone immunoreactivity and circulating vitellogenin levels were higher in photo-experienced birds, and yolk deposition occurred in only 2 females, both of which were photo-experienced. Our results demonstrate that photo-experience enhances some aspects of early photo-induced reproductive development and raise the hypothesis that photo-experience may account for at least some age-related variation in reproductive output.
Interactions of TCAP-1 and Endocannabinoids with Corticotropin-releasing Factor in Mediating Cocaine- and Anxiety-related Behaviour

The neuropeptide, corticotropin-releasing factor (CRF), plays a critical role in the central regulation of various stress-related behaviours, including those unique to subjects with prior cocaine experience. The three series of experiments presented in this dissertation explored the role of two neurochemical systems, the teneurin C-terminal associated peptides (TCAP) and the endocannabinoids (eCBs), in several cocaineand anxiety-related behaviours induced or mediated by CRF. The first series of experiments examined the effects of TCAP-1 on the reinstatement of cocaine seeking and expression of cocaine-induced behavioural sensitization. Repeated (5day), but not acute, TCAP-1 treatment blocked the reinstatement of cocaine seeking induced by central injections of CRF. TCAP-1 was, however, without effect on footshockor cocaineinduced reinstatement. Repeated TCAP-1 further interfered with the expression of behavioural sensitization to a CRF, but not a cocaine, challenge. These findings suggest that TCAP-1 normalizes CRF signaling dysregulated by cocaine exposure to interfere in the subsequent effects of CRF on cocaine-related behaviours. A parallel series of experiments investigated the role of eCB signaling at CB1 receptors in the reinstatement of cocaine seeking and cocaine-sensitized locomotion. Pretreatment with
Sparse array antenna design based on dolph-chebyshev and genetic algorithms

In this paper an original method for the synthesis of a planar sparse array antenna is presented. The aim is to obtain a planar sparse array antenna starting from a Dolph Chebyshev radiating elements feeding distribution and cancelling feeding for as large a number of elements as possible while maintaining the performances in terms of directivity characteristics, by applying optimization with genetic algorithms. Planar sparse array antennas with square shapes and variable number of elements are analyzed and synthesized using this new method.
1 metaXa and the Future of Reflection

Reflection has attracted considerable attention in recent years. However there are very little systems that fully support reflective programming and are in real use. In this paper we try to understand the reasons for this lacking acceptance of fully reflective systems and explain how our own reflective Java system, metaXa, tries to tackle some of these problems.
Pre-Shared Key Ciphersuites for Transport Layer Security (TLS)

This document specifies three sets of new ciphersuites for the Transport Layer Security (TLS) protocol to support authentication based on pre-shared keys. These pre-shared keys are symmetric keys, shared in advance among the communicating parties. The first set of ciphersuites uses only symmetric key operations for authentication. The second set uses a Diffie-Hellman exchange authenticated with a pre-shared key; and the third set combines public key authentication of the server with pre-shared key authentication of the client.
Is the English Baccalaureate a passport to future success?

Abstract In England accountability measures have often been used to steer school behaviour in pursuit of policy goals. In 2010, the English Baccalaureate (EBacc) was introduced to increase uptake of traditional academic subjects at GCSE. These subjects, it was argued, would enhance students’ future prospects, in part because they are favoured at A-level by high-ranking universities. However, such prospects are only likely to be accessible for students who achieve at least a grade C in these subjects since it is good grades that act as the primary gatekeepers for entry into higher education and employment. Hence, this paper seeks to problematise this claim using multilevel regression models to investigate the relationship between EBacc uptake and attainment. The findings are used to frame a discussion about the merits of encouraging more students to take the EBacc given the growing tension between the need to achieve good grades and the government-held view that all students should be studying this academic core.