Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring Immune Modulatory Effects of Cyclotide-Enriched Viola tricolor Preparations

Abstract Viola tricolor is a medicinal plant with documented application as an anti-inflammatory herb. The standard of care for the treatment of inflammatory bowel disease is immunosuppressive therapeutics or biologics, which often have undesired effects. We explored V. tricolor herbal preparations that are rich in an emerging class of phytochemicals with drug-like properties, so-called cyclotides. As an alternative to existing inflammatory bowel disease medications, cyclotides have immunomodulatory properties, and their intrinsic stability allows for application in the gastrointestinal tract, for instance, via oral administration. We optimized the isolation procedure to improve the yield of cyclotides and compared the cellular effects of violet-derived organic solvent-extracts, aqueous preparations, and an isolated cyclotide from this plant on primary human T lymphocytes and macrophages, i.e., cells that are crucial for the initiation and progression of inflammatory bowel disease. The hot water herbal decoctions have a stronger immunosuppressive activity towards proliferation, interferon- γ , and interleukin-21 secretion of primary human T cells than a DCM/MeOH cyclotide-enriched extract, and the isolated cyclotide kalata S appears as one of the active components responsible for the observed effects. This effect was increased by a longer boiling duration. In contrast, the DCM/MeOH cyclotide-enriched extract was more effective in reducing the levels of cytokines interleukin-6, interleukin-12, interleukin-23, tumor necrosis factor- α , and C – X-C motif chemokine ligand 10, secreted by human monocyte-derived macrophages. Defined cyclotide preparations of V. tricolor have promising pharmacological effects in modulating immune cell responses at the cytokine levels. This is important towards understanding the role of cyclotide-containing herbal drug preparations for future applications in immune disorders, such as inflammatory bowel disease.
An SEIR Mathematical Model for Dog Rabies; Case Study: Bongo District, Ghana.

A SEIR model for rabies between dogs with vaccination effect is formulated. The basic reproduction ratio for this model is derived using the Next Generation Matrix Method. Graphical solutions of the differential equations are produced using Matlab. Stability analysis is performed and the impact of vaccination is analysed. This thesis was written in LaTeX and MATLAB was used for the programming. Appendix contains the Matlab code used in simulating the model.
Differential and Opposing Effects of Imatinib on LPS-and Ventilator-Induced 1 Lung Injury

Differential and Opposing Effects of Imatinib on LPSand Ventilator-Induced 1 Lung Injury 2 3 E. Letsiou, A.N. Rizzo, S. Sammani, P. Naureckas, J.R. Jacobson, J.G. N. Garcia, 4 S.M. Dudek 5 6 University of Illinois at Chicago, Division of Pulmonary, Critical Care, Sleep, and 7 Allergy, IL, Arizona Health Sciences Center, University of Arizona, AZ 8 9 10 11 12 13 To whom correspondence should be addressed: 14 Steven M. Dudek, M.D. 15 Associate Professor of Medicine 16 Division of Pulmonary, Critical Care, Sleep, and Allergy 17 University of Illinois Hospital & Health Sciences System 18 CSB 915, 840 S. Wood St., Chicago, IL 60612 19 sdudek@uic.edu 20 21 Running header: Imatinib in LPS and VILI experimental models 22 23 24 Articles in PresS. Am J Physiol Lung Cell Mol Physiol (December 5, 2014). doi:10.1152/ajplung.00323. 2014
Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs

Speeding up particle trajectory simulations under moving force fields using GPUs. In this paper, we introduce a GPU-based framework for simulating particle trajectories under both static and dynamic force fields. By exploiting the highly parallel nature of the problem and making efficient use of the available hardware, our simulator exhibits a significant speedup over its CPU-based analog. We apply our framework to a specific experimental simulation: the computation of trapping probabilities associated with micron-sized silica beads in optical trapping workbenches. When evaluating large numbers of trajectories (4096), we see approximately a 356 times speedup of the GPU-based simulator over its CPU-based counterpart. 1 Introduction The simulation of particle movement under general force fields is of interest across many scientific disciplines. For example, biochemists may wish to model stochastic diffusion of glutamate receptors [1], while financial analysts may attempt to simulate point estimates of stock prices based on stochastic models [2]. In this paper, we present a frame
Reduction of Malaria Transmission to Anopheles Mosquitoes with a Six-Dose Regimen of Co-Artemether

Background Resistance of malaria parasites to chloroquine (CQ) and sulphadoxine-pyrimethamine (SP) is increasing in prevalence in Africa. Combination therapy can both improve treatment and provide important public health benefits if it curbs the spread of parasites harbouring resistance genes. Thus, drug combinations must be identified which minimise gametocyte emergence in treated cases, and so prevent selective transmission of parasites resistant to any of the partner drugs. Methods and Findings In a randomised controlled trial, 497 children with uncomplicated falciparum malaria were treated with CQ and SP (three doses and one dose respectively; n = 91), or six doses of artemether in fixed combination with lumefantrine (co-artemether [Coartem, Riamet]) (n = 406). Carriage rates of Plasmodium falciparum gametocytes and trophozoites were measured 7, 14, and 28 d after treatment. The infectiousness of venous blood from 29 children carrying P. falciparum gametocytes 7 d after treatment was tested by membrane-feeding of Anopheles mosquitoes. Children treated with co-artemether were significantly less likely to carry gametocytes within the 4 weeks following treatment than those receiving CQ/SP (30 of 378 [7.94%] versus 42 of 86 [48.8%]; p < 0.0001). Carriers in the co-artemether group harboured gametocytes at significantly lower densities, for shorter periods (0.3 d versus 4.2 d; p < 0.0001) and were less infectious to mosquitoes at day 7 (p < 0.001) than carriers who had received CQ/SP. Conclusions Co-artemether is highly effective at preventing post-treatment transmission of P. falciparum. Our results suggest that co-artemether has specific activity against immature sequestered gametocytes, and has the capacity to minimise transmission of drug-resistant parasites.
Bit-wise All Edge-pairs Coverage

Structural testing is widely used to detect software failures and to assess test suites quality. Without automated support, though, its use on programs developed at industrial settings is hardly feasible. Structural testing is carried out by means of test criteria based on program code coverage. Program code is usually abstracted into a graph, and control flow-based code coverage is determined in terms of graph elements (e.g., nodes and edges). All edge-pairs is a relatively recent criterion when compared to all nodes and all edges criteria. Studies, though, indicate that all edge-pairs shows promising results at detecting failures. We present a novel approach to track edge-pairs based on bit-wise operations that are also applicable to nodes and edges. Empirical data suggest that all edge-pairs adds new paths to be tested at a tracking cost indistinguishable in comparision to any control flow testing requirement, be it nodes or edges, using bit-wise operations. Furthermore, the cost of the novel bit-wise approach is comparable to the cost of production-grade tools that track nodes and edges.
Monosynaptic premotor circuit tracing reveals neural substrates for oro-motor coordination

Feeding behaviors require intricately coordinated activation among the muscles of the jaw, tongue, and face, but the neural anatomical substrates underlying such coordination remain unclear. In this study, we investigate whether the premotor circuitry of jaw and tongue motoneurons contain elements for coordination. Using a modified monosynaptic rabies virus-based transsynaptic tracing strategy, we systematically mapped premotor neurons for the jaw-closing masseter muscle and the tongue-protruding genioglossus muscle. The maps revealed that the two groups of premotor neurons are distributed in regions implicated in rhythmogenesis, descending motor control, and sensory feedback. Importantly, we discovered several premotor connection configurations that are ideally suited for coordinating bilaterally symmetric jaw movements, and for enabling co-activation of specific jaw, tongue, and facial muscles. Our findings suggest that shared premotor neurons that form specific multi-target connections with selected motoneurons are a simple and general solution to the problem of orofacial coordination. DOI: http://dx.doi. org/10.7554/eLife.02511. 001
Adaptive Integration of Categorical and Multi-relational Ontologies with EHR Data for Medical Concept Embedding

Representation learning has been applied to Electronic Health Records (EHR) for medical concept embedding and the downstream predictive analytics tasks with promising results. Medical ontologies can also be integrated to guide the learning so the embedding space can better align with existing medical knowledge. Yet, properly carrying out the integration is non-trivial. Medical concepts that are similar according to a medical ontology may not be necessarily close in the embedding space learned from the EHR data, as medical ontologies organize medical concepts for their own specific objectives. Any integration methodology without considering the underlying inconsistency will result in sub-optimal medical concept embedding and, in turn, degrade the performance of the downstream tasks. In this article, we propose a novel representation learning framework called ADORE (ADaptive Ontological REpresentations) that allows the medical ontologies to adapt their structures for more robust integrating with the EHR data. ADORE first learns multiple embeddings for each category in the ontology via an attention mechanism. At the same time, it supports an adaptive integration of categorical and multi-relational ontologies in the embedding space using a category-aware graph attention network. We evaluate the performance of ADORE on a number of predictive analytics tasks using two EHR datasets. Our experimental results show that the medical concept embeddings obtained by ADORE can outperform the state-of-the-art methods for all the tasks. More importantly, it can result in clinically meaningful sub-categorization of the existing ontological categories and yield attention values that can further enhance the model interpretability.
Atherothrombosis as a Systemic Disease

Atherothrombosis is a generalized disease process that affects large- and medium-diameter arteries throughout the arterial tree. The trigger of the ischaemic clinical events is the complication of a disrupted atherosclerotic plaque by the formation of a platelet-rich thrombus. These thrombotic events are not always clinically manifest; in most cases, the thrombotic reaction remains parietal but contributes to plaque growth by infiltration of the thrombus by smooth muscle cells. In addition, the evolution of the thrombotic reaction destroys the microvasculature of the downstream tissue by subclinical platelet thrombi. Less often, the resulting thrombus leads to partial or total occlusion of the affected artery with subsequent ischaemic clinical manifestations such as ischaemic stroke, unstable angina and Q-wave or non-Q-wave myocardial infarction. The proportion of ischaemic arterial events that is due to atherothrombosis varies according to the vascular bed in which the event occurs, from a near-total dependency for the lower limbs (intermittent claudication) to less than 50% for cerebrovascular events (ischaemic stroke). Occurrence of an arterial ischaemic event due to atherothrombosis implies that other arterial territories may already be affected by a similar pathological process, even if still clinically silent. Treatment of atherothrombotic patients should include the management of cardiovascular risk factors (which aims at the prevention of incidence, evolution and instability of the plaques) and antiplatelet treatment for the prevention of thrombotic complications. Secondary prevention of an ischaemic event in the index territory will provide primary prevention for other arterial territories that are still clinically silent. The aims of antiplatelet therapy are first to prevent the occurrence of acute ischaemic events through inhibition of platelet thrombus formation and second to protect distal tissues through inhibition of microembolization. Due to the systemic nature of the disease, antiplatelet therapy that has shown a proven consistent benefit across all arterial beds is mandatory for optimal prevention of ischaemic events in atherothrombotic patients.
Shear viscosity of pion gas due to ρππ and σππ interactions

We have evaluated the shear viscosity of pion gas taking into account its scattering with the low mass resonances, σ and ρ during propagation in the medium. The thermal width (or collisional rate) of the pions is calculated from πσ and πρ loop diagrams using effective interactions in the real time formulation of finite temperature field theory. A very small value of shear viscosity by entropy density ratio (η/s), close to the KSS bound, is obtained which approximately matches the range of values of η/s used by Niemi et al. [25] in order to fit the RHIC data of elliptic flow.
Reliable Weakly Supervised Learning: Maximize Gain and Maintain Safeness

Weakly supervised data are widespread and have attracted much attention. However, since label quality is often difficult to guarantee, sometimes the use of weakly supervised data will lead to unsatisfactory performance, i.e., performance degradation or poor performance gains. Moreover, it is usually not feasible to manually increase the label quality, which results in weakly supervised learning being somewhat difficult to rely on. In view of this crucial issue, this paper proposes a simple and novel weakly supervised learning framework. We guide the optimization of label quality through a small amount of validation data, and to ensure the safeness of performance while maximizing performance gain. As validation set is a good approximation for describing generalization risk, it can effectively avoid the unsatisfactory performance caused by incorrect data distribution assumptions. We formalize this underlying consideration into a novel Bi-Level optimization and give an effective solution. Extensive experimental results verify that the new framework achieves impressive performance on weakly supervised learning with a small amount of validation data.
Compositional generalization in a deep seq2seq model by separating syntax and semantics

Standard methods in deep learning for natural language processing fail to capture the compositional structure of human language that allows for systematic generalization outside of the training distribution. However, human learners readily generalize in this way, e.g. by applying known grammatical rules to novel words. Inspired by work in neuroscience suggesting separate brain systems for syntactic and semantic processing, we implement a modification to standard approaches in neural machine translation, imposing an analogous separation. The novel model, which we call Syntactic Attention, substantially outperforms standard methods in deep learning on the SCAN dataset, a compositional generalization task, without any hand-engineered features or additional supervision. Our work suggests that separating syntactic from semantic learning may be a useful heuristic for capturing compositional structure.
Genetic Learning of Fuzzy Rule-Based Classi cationSystems Cooperating with Fuzzy Reasoning Methods

In this paper, we present a multi-stage genetic learning process for obtaining linguistic Fuzzy Rule-Based Classiication Systems, that integrates Fuzzy Reasoning Methods cooperating with the fuzzy rule base and learns the best set of linguistic hedges for the linguistic variable terms. We show the application of the genetic learning process to two well known sample bases, and compare the results with those obtained from diierent learning algorithms. The results show the good behaviour of the proposed method maintaining the linguistic description of the fuzzy rules.
Statistical Methods in the Evaluation of Cardio-Respiratory Parameters in Young Childhood Cancer Survivors and Healthy Peers

Abstract This study concerns the problem of late complications of antineo-plastic therapy. Reduced parameters of the cardiorespiratory system in childhood may have a tremendous impact on health. In order to assess the selected parameters, to evaluate physical endurance, and compare the results with those obtained for healthy children, a test was carried out on a treadmill, until 80% of maximum pulse rate was reached. To compare the differences between the treatment group and the control group, three approaches were used. The first one was the classical statistical inference, the second consisted in forming a multidimensional normal model and also involved modelling of the correlation between variables. The unstructured type of the working correlation matrix was chosen to obtain the results and correct standard errors. In the last approach, logistic regression was used to model the relationship between binary outcome and covariates, and to differentiate between the groups of patients on the basis of their cardiovascular parameters.
Understanding Agricultural Price Range Systems as Trade Restraints : Peru – Agricultural Products ( DS 457 )

An agricultural price range system (PRS) aims to stabilize local prices in an open economy via the use of import duties that vary with international prices. The policy is inherently distortionary and welfare-reducing for a small open economy, at least according to the canonical economic model. We offer an explanation for why a government concerned with national welfare may nevertheless implement such a policy when faced with risk aversion and imperfect insurance markets. We also highlight open questions arising out of the Peru – Agricultural Products dispute for the WTO’s Appellate Body to address in order to clarify how a PRS consistent with WTO rules could be designed. Finally, we discuss the possibility that a WTO member might resort to a free trade agreement (FTA) to preserve its flexibility to implement a PRS and how an FTA provision of this sort ought to be treated in WTO litigation.
Offset Surface Light Fields

For producing realistic images, reflection is an important visual effect. Reflections of the environment are important not only for highly reflective objects, such as mirrors, but also for more common objects such as brushed metals and glossy plastics. Generating these reflections accurately at real-time rates for interactive applications, however, is a difficult problem. Previous works in this area have made assumptions that sacrifice accuracy in order to preserve interactivity. I will present an algorithm that tries to handle reflection accurately in the general case for real-time rendering. The algorithm uses a database of prerendered environment maps to render both the original object itself and an additional bidirectional reflection distribution function (BRDF). The algorithm performs image-based rendering in reflection space in order to achieve accurate results. It also uses graphics processing unit (GPU) features to accelerate rendering.
Behavioral and Brain Functions

Background: Existing literature to date suggests a relationship between cognitive attention and working memory (WM), but the relationship between overt inattentive behaviour and WM is less clear. This study examined the relationship between WM and parent-rated inattentive behaviour in a community sample of 140 children aged 7–12 years. Methods: Children completed 2 clinical (laboratory-based) measures of WM (auditory-verbal and visual-spatial) and a measure of real-life WM, designed specifically for this study, while their parents completed questionnaires about their child's inattentive behaviour and other areas of functioning. Results: Findings indicated that poorer performance on WM tasks predicted inattentive behaviour. Conclusion: These results are consistent with previous research linking WM deficits and poor attention in ADHD and normal populations. The present findings support a controlled attention model of WM. Background Working memory (WM) is a cognitive processing resource of limited capacity that allows the temporary storage of information while simultaneously processing the same or other information. Performance on WM measures correlates with performance on higher-order cognitive tasks involving reading comprehension, reasoning, and complex learning [1]. A well-known model of WM is Baddeley and Hitch's model [2,3], in which WM is comprised of two separate systems for the temporary storage of verbal information ('phonological loop') and visual-spatial information ('visuo-spatial sketchpad') and a 'central executive' as a control mechanism that manipulates the information in active storage in order to perform complex cognitive tasks. Many other theoretical perspectives on WM exist [4], but one area of general agreement is the distinction between processes involving storage (e.g., shortterm memory; STM) and those involving greater cognitive control (e.g., central executive). The controlled attention view of WM, proposed by Engle and his colleagues [5], is another model of WM that consists of STM and executive-attention components (consistent with Baddeley and Hitch's storage and central executive). However, instead of emphasizing how large the STM store or WM capacity (i.e., how much WM can hold), the controlled attention perspective views information maintenance in the presence of interference as a critical Published: 23 February 2007 Behavioral and Brain Functions 2007, 3:12 doi:10.1186/1744-9081-3-12 Received: 6 July 2006 Accepted: 23 February 2007 This article is available from: http://www.behavioralandbrainfunctions. com/content/3/1/12 © 2007 Lui and Tannock; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.