Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum lipids in children 3 to 5 years after kidney, liver, and heart transplantation

Although dyslipidaemia is common after solid organ transplantation (Tx), there are few long-term studies in children. We investigated the prevalence of dyslipidaemia up to 5 years after Tx in 125 children on triple immunosuppression with one of three different well-functioning grafts, kidney, liver, and heart, and 181 controls. Total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and triglyceride (TG) concentrations were measured annually. Low-density lipoprotein cholesterol concentrations were also calculated. The risk factors for dyslipidaemia were determined at 3 years. There was a high prevalence of hypertriglyceridaemia in all three groups, 50% in the kidney transplantation (KTx) and heart transplantation (HTx) groups and 30% in the liver transplantation (LTx) group. In addition, 50% of KTx patients had high TC. In the Tx groups taken together, the following independent associations were observed: KTx and high pre-Tx TC were associated with high TC, high trough concentration of blood cyclosporine with low HDL-C, and older age at Tx accounted for higher TG. Dyslipidaemia, especially hypertriglyceridaemia, was common 3–5 years after Tx. The aetiology is multifactorial and depends on the transplanted organ.
A Visualization Framework for Task-Oriented Modeling Using UML

The UML is a collection of 13 diagram notations to describe different views of a software system. The existing diagram types display model elements and their relations. Software engineering is becoming more and more model-centric, such that software engineers start using UML models for more tasks than just describing the system. Tasks such as analysis or prediction of system properties require additional information such as metrics of the UML model or from external sources, e.g. a version control system. In this paper we identify tasks of model-centric software engineering and information that is required to fulfil these tasks. We propose views to visualize the information to support fulfilling the tasks. This paper reports on industrial case studies and a light-weight user experiment to validate the usefulness of the proposed views that are implemented in our MetricView evolution tool
The Semantic Web for Complex Network Analysis in Biomedical Domain

Complex networks of direct relevance to biomedicine have not yet been fully mapped largely due to the incompleteness, isolation, and heterogeneity of data. The Semantic Web, by providing a technical framework for the integration and sharing of heterogeneous databases in different domains, can potentially enable more effective complex network mapping and analysis. However, the feasibility of using the Semantic Web for biomedical complex network analysis should be further investigated. In this paper, we propose the semantic graph mining methodology that uses the semantic graph model to integrate graph mining and ontology reasoning for better analyzing biomedical complex networks. We also present reference architecture and a set of recommended biomedical use cases in order to implement this methodology.
Loss of caveolin‐3 induced by the dystrophy‐associated P104L mutation impairs L‐type calcium channel function in mouse skeletal muscle cells

Caveolins are membrane scaffolding proteins that associate with and regulate a variety of signalling proteins, including ion channels. A deficiency in caveolin‐3 (Cav‐3), the major striated muscle isoform, is responsible for skeletal muscle disorders, such as limb‐girdle muscular dystrophy 1C (LGMD 1C). The molecular mechanisms leading to the muscle wasting that characterizes this pathology are poorly understood. Here we show that a loss of Cav‐3 induced by the expression of the LGMD 1C‐associated mutant P104L (Cav‐3P104L) provokes a reduction by half of the maximal conductance of the voltage‐dependent L‐type Ca2+ channel in mouse primary cultured myotubes and fetal skeletal muscle fibres. Confocal immunomiscrocopy indicated a colocalization of Cav‐3 and Cav1.1, the pore‐forming subunit of the L‐type Ca2+ channel, at the surface membrane and in the developing T‐tubule network in control myotubes and fetal fibres. In myotubes expressing Cav‐3P104L, the loss of Cav‐3 was accompanied by a 66% reduction in Cav1.1 mean labelling intensity. Our results suggest that Cav‐3 is involved in L‐type Ca2+ channel membrane function and localization in skeletal muscle cells and that an alteration of L‐type Ca2+ channels could be involved in the physiopathological mechanisms of caveolinopathies.
Rating Endorsements using Generalized Linear Models BLINDED

Insurance policies often contain optional insurance coverages known as endorsements. Because these additional coverages are typically inexpensive relative to primary coverages and data can be sparse (coverages are optional), rating of endorsements is often done in ad hoc manner after a primary analysis has been conducted. This paper describes a study of the Wisconsin Local Government Property Insurance Fund where it is desirable to have a formal mechanism for rating endorsements. Our goal is to provide prediction algorithms that are transparent and that promote equity among policyholders by determining rates that reflect the appropriate level and amount of uncertainty of each risk. To accommodate potentially conflicting goals of data complexity and algorithmic transparency, we utilize shrinkage techniques to moderate the effects of endorsements with penalized likelihoods. We find that the rating algorithms using shrinkage techniques have a predictive accuracy that are comparable to unbiased generalized linear model techniques and provide relativities for endorsements that are consistent with sound economic, risk management, and actuarial practice.
Markov Random Fields for Super-resolution and Texture Synthesis

Suppose we want to digitally enlarge a photograph. The input is a single, low-resolution image, and the desired output is an estimate of the high-resolution version of that image. This problem can be phrased as one of “image interpolation”: we seek to interpolate the pixel values bet ween our observed samples. Image interpolation is sometimes called super-resolution, since we are estimatin g data at a resolution beyond that of the image samples. In contrast with multi-image super-resolution methods, wh ere a high-resolution image is inferred from a video sequence, we are interested in estimating high-resolution images from a single low-resolution example [10].
Insulin‐like Growth Factor‐1 Rescues the Mutated FGF Receptor 3 (G380R) Expressing ATDC5 Cells From Apoptosis Through Phosphatidylinositol 3‐Kinase and MAPK

An activated mutation in the FGFR3 gene causes ACH. To examine the effects of IGF‐1, which is an important mediator of GH, on apoptosis, we analyzed a chondrogenic cell line expressing the FGFR3 mutants. Our findings that IGF‐1 prevented the apoptosis through P13K and MAPK pathways may explain how GH treatment improves the disturbed bone growth in ACH.
Changes in Serological Immunology Measures in UK and Kenyan Adults Post-controlled Human Malaria Infection

Background: The timing of infection is closely determined in controlled human malaria infection (CHMI) studies, and as such they provide a unique opportunity to dissect changes in immunological responses before and after a single infection. The first Kenyan Challenge Study (KCS) (Pan African Clinical Trial Registry: PACTR20121100033272) was performed in 2013 with the aim of establishing the CHMI model in Kenya. This study used aseptic, cryopreserved, attenuated Plasmodium falciparum sporozoites administered by needle and syringe (PfSPZ Challenge) and was the first to evaluate parasite dynamics post-CHMI in individuals with varying degrees of prior exposure to malaria. Methods: We describe detailed serological and functional immunological responses pre- and post-CHMI for participants in the KCS and compare these with those from malaria-naïve UK volunteers who also underwent CHMI (VAC049) (ClinicalTrials.gov NCT01465048) using PfSPZ Challenge. We assessed antibody responses to three key blood-stage merozoite antigens [merozoite surface protein 1 (MSP1), apical membrane protein 1 (AMA1), and reticulocyte-binding protein homolog 5 (RH5)] and functional activity using two candidate measures of anti-merozoite immunity; the growth inhibition activity (GIA) assay and the antibody-dependent respiratory burst activity (ADRB) assay. Results:Clear serological differences were observed pre- and post-CHMI by ELISA between malaria-naïve UK volunteers in VAC049, and Kenyan volunteers who had prior malaria exposure. Antibodies to AMA1 and schizont extract correlated with parasite multiplication rate (PMR) post-CHMI in KCS. Serum from volunteer 110 in KCS, who demonstrated a dramatically reduced PMR in vivo, had no in vitro GIA prior to CHMI but the highest level of ADRB activity. A significant difference in ADRB activity was seen between KCS volunteers with minimal and definite prior exposure to malaria and significant increases were seen in ADRB activity post-CHMI in Kenyan volunteers. Quinine and atovaquone/proguanil, previously assumed to be removed by IgG purification, were identified as likely giving rise to aberrantly high in vitro GIA results. Conclusions: The ADRB activity assay is a promising functional assay that warrants further investigation as a measure of prior exposure to malaria and predictor of control of parasite growth. The CHMI model can be used to evaluate potential measures of naturally-acquired immunity to malaria.
Xenon Combined with Therapeutic Hypothermia Is Not Neuroprotective after Severe Hypoxia-Ischemia in Neonatal Rats

Background Therapeutic hypothermia (TH) is standard treatment following perinatal asphyxia in newborn infants. Experimentally, TH is neuroprotective after moderate hypoxia-ischemia (HI) in seven-day-old (P7) rats. However, TH is not neuroprotective after severe HI. After a moderate HI insult in newborn brain injury models, the anesthetic gas xenon (Xe) doubles TH neuroprotection. The aim of this study was to examine whether combining Xe and TH is neuroprotective as applied in a P7 rat model of severe HI. Design/Methods 120 P7 rat pups underwent a severe HI insult; unilateral carotid artery ligation followed by hypoxia (8% O2 for 150min at experimental normothermia (NT-37: Trectal 37°C). Surviving pups were randomised to immediate NT-37 for 5h (n = 36), immediate TH-32: Trectal 32°C for 5h (n = 25) or immediate TH-32 plus 50% inhaled Xe for 5h (n = 24). Pups were sacrificed after one week of survival. Relative area loss of the ligated hemisphere was measured, and neurons in the subventricular zone of this injured hemisphere were counted, to quantify brain damage. Results Following the HI insult, median (interquartile range, IQR) hemispheric brain area loss was similar in all groups: 63.5% (55.5–75.0) for NT-37 group, 65.0% (57.0–65.0) for TH-32 group, and 66.5% (59.0–72.0) for TH-32+Xe50% group (not significant). Correspondingly, there was no difference in neuronal cell count (NeuN marker) in the subventricular zone across the three treatment groups. Conclusions Immediate therapeutic hypothermia with or without additional 50% inhaled Xe, does not provide neuroprotection one week after severe HI brain injury in the P7 neonatal rat. This model aims to mimic the clinical situation in severely asphyxiated neonates and treatment these newborns remains an ongoing challenge.
Horde of Bandits using Gaussian Markov Random Fields

The gang of bandits (GOB) model \cite{cesa2013gang} is a recent contextual bandits framework that shares information between a set of bandit problems, related by a known (possibly noisy) graph. This model is useful in problems like recommender systems where the large number of users makes it vital to transfer information between users. Despite its effectiveness, the existing GOB model can only be applied to small problems due to its quadratic time-dependence on the number of nodes. Existing solutions to combat the scalability issue require an often-unrealistic clustering assumption. By exploiting a connection to Gaussian Markov random fields (GMRFs), we show that the GOB model can be made to scale to much larger graphs without additional assumptions. In addition, we propose a Thompson sampling algorithm which uses the recent GMRF sampling-by-perturbation technique, allowing it to scale to even larger problems (leading to a "horde" of bandits). We give regret bounds and experimental results for GOB with Thompson sampling and epoch-greedy algorithms, indicating that these methods are as good as or significantly better than ignoring the graph or adopting a clustering-based approach. Finally, when an existing graph is not available, we propose a heuristic for learning it on the fly and show promising results.
Enhance Vitamin B 12 Production by Online CO 2 Concentration Control Optimization in 120 m 3 Fermentation

Great amounts of carbon dioxide generated by Pseudomonas denitrificans during high aerobic vitamin B12 fermentation, while the influence of CO2 concentration on vitamin B12 production remains unclear. In this paper, we present parallel experiments to investigate various levels of inlet CO2 fractions on the physiological metabolism of P. denitrificans in laboratory scale fermentation. The results demonstrated that the oxygen transfer rate, cell growth and glucose consumption were inhibited with CO2 fraction elevated from 0.03% to 8.86 ± 0.24%, while the most exciting results showed that the specific vitamin B12 production rate and the yield to glucose were greatly stimulated when dissolved CO2 increased to 8.86 ± 0.24%. Therefore, the optimal exhausted CO2 fraction control strategy in 120 m 3 fermenter was established. With the exhaust CO2 concentration was well controlled at 7.5 ± 0.25% on-line, vitamin B12 production greatly improved to 223.7 ± 3.7 mg/L, which was 11.2% higher than that of control. This strategy was proved to be significant necessary and effective for successfully scale up optimization in industrial vitamin B12 fermentation. Enhance Vitamin B12 Production by Online CO2 Concentration Control Optimization in 120 m3 Fermentation
Modeling for surge control of centrifugal compressors: comparison with experiment

A dynamic model based on the thermo- and fluid-mechanic processes taking place in a centrifugal compressor is validated. The background for this is the need for an energy based model including the rotational speed as a state in order to perform energy based active surge control. The response of the model is compared with experimental results from the Energy Technology Laboratory at Eindhoven University of Technology. Both the calculated compressor characteristic and transient responses for set point changes and in-surge response were compared to experiment with good results.
Parallelism and messaging services in a J 2 EE-based e-commerce brokering platform . Experiences in European projects

This article presents different experiences carried out in the connectivity layer of several e-commerce mediation and brokering projects: ABS and ABROSE (supported by the European Programme on Advanced Communications, Technologies, and Services, ACTS) and Smart-EC project (supported by the European Programme on Information Society Technologies, IST). Project prototypes were implemented using Java, but in order to allow distributed communications, different techniques were used. While in the first two projects CORBA was considered the best choice for the communication infrastructure, the arrival of J2EE at the same time as the beginning of Smart-EC, led this project to move from CORBA to this new technology. This article will begin by summarising the first two approaches in order to finally concentrate on J2EE communication issues: parallelism, synchronous and asynchronous communications, blocking calls, deadlocks, control flow, multi-threading, etc. The last part of the article presents Smart-EC project as a use case, showing some different communication problems that were found and the different solutions that were taken.
Cognitive Access Policies under a Primary ARQ Process via Forward-Backward Interference Cancellation

This paper introduces a novel technique for access by a cognitive Secondary User (SU) using best-effort transmission to a spectrum with an incumbent Primary User (PU), which uses Type-I Hybrid ARQ. The technique leverages the primary ARQ protocol to perform Interference Cancellation (IC) at the SU receiver (SUrx). Two IC mechanisms that work in concert are introduced: Forward IC, where SUrx, after decoding the PU message, cancels its interference in the (possible) following PU retransmissions of the same message, to improve the SU throughput; Backward IC, where SUrx performs IC on previous SU transmissions, whose decoding failed due to severe PU interference. Secondary access policies are designed that determine the secondary access probability in each state of the network so as to maximize the average long-term SU throughput by opportunistically leveraging IC, while causing bounded average long-term PU throughput degradation and SU power expenditure. It is proved that the optimal policy prescribes that the SU prioritizes its access in the states where SUrx knows the PU message, thus enabling IC. An algorithm is provided to optimally allocate additional secondary access opportunities in the states where the PU message is unknown. Numerical results are shown to assess the throughput gain provided by the proposed techniques.
Chinese students making sense of problem-based learning and Western teaching – pitfalls and coping strategies

Culturally different imaginations of student and teacher roles, incongruent perceptions of academic standards, and diverging conceptualizations of learning may cause ‘difficult times’ for institutions and individual learners involved in international education. Universities practicing alternative approaches to teaching and learning, for example problem-based learning (PBL), may face even larger challenges because of the unfamiliarity of international students with such approaches. This study explores the difficult times experienced by Chinese students in a PBL setting at a Danish University. The main result of the study is an increased understanding of these students’ remarkable ‘survival’ skills, coping strategies, and learning outcomes gained from the challenging immersion in a Danish PBL environment.
ECM-Based Materials in Cardiovascular Applications: Inherent Healing Potential and Augmentation of Native Regenerative Processes

The in vivo healing process of vascular grafts involves the interaction of many contributing factors. The ability of vascular grafts to provide an environment which allows successful accomplishment of this process is extremely difficult. Poor endothelisation, inflammation, infection, occlusion, thrombosis, hyperplasia and pseudoaneurysms are common issues with synthetic grafts in vivo. Advanced materials composed of decellularised extracellular matrices (ECM) have been shown to promote the healing process via modulation of the host immune response, resistance to bacterial infections, allowing re-innervation and reestablishing homeostasis in the healing region. The physiological balance within the newly developed vascular tissue is maintained via the recreation of correct biorheology and mechanotransduction factors including host immune response, infection control, homing and the attraction of progenitor cells and infiltration by host tissue. Here, we review the progress in this tissue engineering approach, the enhancement potential of ECM materials and future prospects to reach the clinical environment.
Scalar timing in animals and humans

Abstract John Gibbon's lifetime work provided a deep understanding of the mechanisms whereby the time sense indexes the passage of time (its accumulation) and records, that is, stores, relevant time intervals in memory, enabling behavior to occur at the right time. The Scalar Expectancy Theory (SET; Gibbon, 1977) remains the most prominent of the theoretical accounts of animal and human timing. SET deals with the three principle psychophysical properties of timing data: flexible accuracy, multiplicative variance, and ratio comparisons. It differs from many other timing theories in its emphasis on scalar variability, a term that refers to the linear increase in the standard deviation of timing errors as a task's criterion time increases. Recently, research based on the conceptual framework and analytic tools of SET in John Gibbon's lab was expanded from a decades-long focus on nonhuman species to an assessment of timing performance in “normal” and brain-diseased human subjects, aimed at understanding the functional and neural mechanisms underlying interval timing in humans. This review is aimed at showing that animal and human data obtained with a variety of timing paradigms are both amenable to analyses of accuracy and scalar variability under the SET framework. In the second part of this report we discuss advances made in our understanding of neurobiological mechanisms underlying interval timing by taking advantage of the SET framework. Issues awaiting new theoretical developments in modeling time production and perception, as revealed by psychophysical findings of recent clinical research that are still not well understood (i.e., sources of nonscalar variability), are raised at the end.
Development of a Component-Based Modeling Framework for Agricultural Water-Resource Management

Because hydrologic responses of an agricultural watershed are influenced by many natural and man-made factors including pond/reservoir, management practices, and/or irrigation/drainage, strategies of hydrological modeling for the watershed must be case-dependent and thus carefully designed to effectively reflect their roles as critical hydrologic components in simulation processes. In this study, we propose a component-based modeling framework that accommodates a flexible modeling approach to consider a variety of hydrologic processes and management practices, especially irrigation-reservoir operation and paddy-farming practices, in watershed-scale modeling. The objectives of this study are twofold: to develop a COmponent-based Modeling Framework for Agricultural water-Resources Management (COMFARM) using an object-oriented programming technique, and to evaluate its applicability as a modeling tool to predict the responses of an agricultural watershed characterized with diverse land uses in a case study. COMFARM facilitates quick and easy development of watershed-specific hydrologic models by providing multiple interchangeable simulation routines for each hydrologic component considered. COMFARM is developed with the JAVA programming language, using Eclipse software. The framework developed in this study is applied to simulating hydrologic processes of the Seon-Am irrigation-district watershed consisting primarily of reservoir-irrigated rice paddies in South Korea. The application study clearly demonstrates the applicability of the framework as a convenient method to build models for hydrologic simulation of an agricultural watershed. The newly developed modeling framework, COMFARM is expected to serve as a useful tool in watershed management planning by allowing quick development of case-oriented analysis tools and evaluation of management scenarios customized to a specific watershed.