Miracle-dz/UniFAR-FTUs huggingface dataset:
31P magnetization transfer measurements of Pi→ATP flux in exercising human muscle

Fundamental criticisms have been made over the use of 31P magnetic resonance spectroscopy (MRS) magnetization transfer estimates of inorganic phosphate (Pi)→ATP flux (VPi-ATP) in human resting skeletal muscle for assessing mitochondrial function. Although the discrepancy in the magnitude of VPi-ATP is now acknowledged, little is known about its metabolic determinants. Here we use a novel protocol to measure VPi-ATP in human exercising muscle for the first time. Steady-state VPi-ATP was measured at rest and over a range of exercise intensities and compared with suprabasal oxidative ATP synthesis rates estimated from the initial rates of postexercise phosphocreatine resynthesis (VATP). We define a surplus Pi→ATP flux as the difference between VPi-ATP and VATP. The coupled reactions catalyzed by the glycolytic enzymes GAPDH and phosphoglycerate kinase (PGK) have been shown to catalyze measurable exchange between ATP and Pi in some systems and have been suggested to be responsible for this surplus flux. Surplus VPi-ATP did not change between rest and exercise, even though the concentrations of Pi and ADP, which are substrates for GAPDH and PGK, respectively, increased as expected. However, involvement of these enzymes is suggested by correlations between absolute and surplus Pi→ATP flux, both at rest and during exercise, and the intensity of the phosphomonoester peak in the 31P NMR spectrum. This peak includes contributions from sugar phosphates in the glycolytic pathway, and changes in its intensity may indicate changes in downstream glycolytic intermediates, including 3-phosphoglycerate, which has been shown to influence the exchange between ATP and Pi catalyzed by GAPDH and PGK.
Towards a framework for end-to-end control of a simulated vehicle with spiking neural networks

Spiking neural networks are in theory more computationally powerful than rate-based neural networks often used in deep learning architectures. However, unlike rate-based neural networks, it is yet unclear how to train spiking networks to solve complex problems. There are still no standard algorithms and it is preventing roboticists to use spiking networks, yielding a lack of Neurorobotics applications. The contribution of this paper is twofold. First, we present a modular framework to evaluate neural self-driving vehicle applications. It provides a visual encoder from camera images to spikes inspired by the silicon retina (DVS), and a steering wheel decoder based on an agonist antagonist muscle model. Secondly, using this framework, we demonstrate a spiking neural network which controls a vehicle end-to-end for lane following behavior. The network is feed-forward and relies on hand-crafted feature detectors. In future work, this framework could be used to design more complex networks and use the evaluation metrics for learning.
Multifrontal Sparse Matrix Factorization on Graphics Processing Units

For many finite element problems, when represented as sparse matrices, iterative solvers are found to be unreliable because they can impose computational bottlenecks. Early pioneering work by Duff et al, explored an alternative strategy called multifrontal sparse matrix factorization. This approach, by representing the sparse problem as a tree of dense systems, maps well to modern memory hierarchies. Furthermore, it promotes the effective use of highly-tuned dense matrix arithmetic kernels, especially on novel and specialized hardware. The graphics processing units (GPUs) are architected differently than general-purpose hosts and offer an order of magnitude more processing power. This paper explores the hypothesis that GPUs can accelerate the speed of a multifrontal linear solver, even when only processing a small number of the largest frontal matrices. We show that GPUs can more than double the throughput of the sparse matrix factorization. This, in turn, promises to offer a very cost-effective speedup to many science and engineering problems in disciplines such as Mechanical Computer Aided Engineering (MCAE).
Optimal Carry Save

A general theory is developed for constructing the asymptotically shallowest networks and the asymptotically smallest networks (with respect to formula size) for the carry save addition of n numbers using any given basic carry save adder as a building block. Using these optimal carry save addition networks the shallowest known multiplication circuits and the shortest formulae for the majority function (and many other symmetric Boolean functions) are obtained. In this paper, simple basic carry save adders are described, using which multiplication circuits of depth 3:71 log n (the result of which is given as the sum of two numbers) and majority formulae of size O(n 3:21) are constructed. Using more complicated basic carry save adders, not described here, these results could be further improved. Our best bounds are currently 3:57 log n for depth and O(n 3:13) for formula size.
Arguing about Recommendations in Social Networks

In social networks every user could act as an individual recommender for its neighbours. However, the information spread across the network change quickly over time. There is a need for a recommendation mechanism able to manage this dynamicity and to provide users with up-to-date and suitable recommendations. This paper proposes a well-known concept of argumentation theory, dialogue games, as a mechanism to manage collaborative recommendation in social networks. Dialogue games allow agents to argue about several available recommendations and thus, to get better results from the recommendation process.
Varying Cardinality in Metonymic Extensions to Nouns

Meaning shifting phenomena such as metonymy have recently attracted increasing interest of researchers. Though these phenomena have been addressed by plenty of computational methods, the impacts of cardinalities of metonymically related items have been widely ignored in all of them. Motivated by this lack of analysis, we have developed a method for representing expectations and knowledge about the cardinalities of metonymically related entities and for exploiting this information to build logical forms expressing metonymic relations, the entities related, and their cardinalities. The representation of lexically motivated knowledge is realized as an enhancement to Pustejovsky's Generative Lexicon, and the process of building logical forms takes into account overwriting of default information and mismatch of cardinality requirements. Our method enables a precise attachment of sentence complements, and it supports reference resolution in the context of metonymic expressions.
Enhancement of Rhinovirus Plaque Formation in Human Heteroploid Cell Cultures by Magnesium and Calcium

Fiala, Milan (University of Washington, Seattle), and George E. Kenny. Enhancement of rhinovirus plaque formation in human heteroploid cell cultures by magnesium and calcium. J. Bacteriol. 92:1710–1715. 1966. —A reproducible macroplaque assay for six M and three H strains of rhinoviruses has been developed in several human heteroploid cell lines. Plaques were produced only with suitable solidifying agents: purified agar (Ionagar, Agarose) or methylcellulose. Plaque development was greatly enhanced by increasing Mg+2 to 30 to 40 mm. Diethylaminoethyl (DEAE) dextran also increased plaque sizes, and the effects of Mg+2 and DEAE dextran were additive. In addition, Ca+2 substituted for Mg+2. The suitability of human heteroploid cell lines for rhinovirus plaque assay varied greatly, ranging from insensitivity through partial to complete sensitivity. This assay was six to seven times more sensitive than an end point tube assay. These results indicate that potentiation of plaque formation by Mg+2 known for some enteroviruses can also be extended to the rhinovirus group of picornaviruses.
Enhanced Visual Clustering by Reordering of Dimensions in Parallel Coordinates

The high dimensional dataset presents a serious challenge of visualization techniques such as Parallel Coordinates. The order and arrangement of dimensions in Parallel Coordinates has a major impact on the user analysis task. Therefore we need to find an expressive and effective order that helps the user to explore and analyze visualdisplay of data mining results. This problem is the key motivation of our work. In this paper, we extended the concept of relative entropy measure like distance measure between dimensions. After the application of the proposed measure on datasets, the obtained results demonstrate that this measure is able to reorder dimensions, while the set of clusters are reorganized to help the user to detect where the clusters' behavior are similar and different. Moreover, it shows clearly the user the most important dimensions that can be used to analyze data mining results using Parallel Coordinates.
A texttiling based approach to topic boundary detection in meetings

Our goal is to automatically detect boundaries between discussions of different topics in meetings. Towards this end we adapt the TextTiling algorithm [1] to the context of meetings. Our features include not only the overlapped words between adjacent windows, but also overlaps in the amount of speech contributed by each meeting participant. We evaluate our algorithm by comparing the automatically detected boundaries with the true ones, and computing precision, recall and f–measure. We report average precision of 0.85 and recall of 0.59 when segmenting unseen test meetings. Error analysis of our results shows that although the basic idea of our algorithm is sound, it breaks down when participants stray from typical behavior (such as when they monopolize the conversation for too long).
High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes

In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep sequencing and computational methods to identify, profile and analyze non-conserved MIRNA genes in Arabidopsis thaliana. 48 non-conserved MIRNA families, nearly all of which were represented by single genes, were identified. Sequence similarity analyses of miRNA precursor foldback arms revealed evidence for recent evolutionary origin of 16 MIRNA loci through inverted duplication events from protein-coding gene sequences. Interestingly, these recently evolved MIRNA genes have taken distinct paths. Whereas some non-conserved miRNAs interact with and regulate target transcripts from gene families that donated parental sequences, others have drifted to the point of non-interaction with parental gene family transcripts. Some young MIRNA loci clearly originated from one gene family but form miRNAs that target transcripts in another family. We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks.
Up‐regulation of c‐Jun NH2‐terminal kinase‐interacting protein 3 (JIP3) contributes to BDNF‐enhanced neurotransmitter release

Brain‐derived neurotrophic factor (BDNF) has been implicated in the potent modulation of synaptic plasticity at both pre‐synaptic and post‐synaptic sites. However, the molecular mechanism underlying BDNF‐mediated pre‐synaptic modulation remains incompletely understood. Here, we report that BDNF treatment for over 4 h could significantly enhance the expression of c‐Jun NH2‐terminal kinase‐interacting protein 3 (JIP3) in cultured hippocampal neurons. This enhancement could be blocked by the Trk inhibitor K252a or by a cAMP response element‐binding protein (CREB) inhibitor. In addition, chromatin immunoprecipitation (ChIP) assays revealed that CREB could bind with the JIP3 promoter region and the BDNF treatment could increase this binding. Using dual‐luciferase assays we further characterized the cAMP response element (CRE) site in the JIP3 promoter. Finally, we found that BDNF‐increased JIP3 expression contributes to the BDNF‐induced modulation of neurotransmitter release. Together, our studies reveal that in hippocampal neurons BDNF up‐regulates JIP3 expression via CREB activation, which contributes to the enhancement of neurotransmitter release; thus, we have identified a novel mechanism that BDNF modulates pre‐synaptic transmission.
Testing the Limits of Optimizing Dual-Task Performance in Younger and Older Adults

Impaired dual-task performance in younger and older adults can be improved with practice. Optimal conditions even allow for a (near) elimination of this impairment in younger adults. However, it is unknown whether such (near) elimination is the limit of performance improvements in older adults. The present study tests this limit in older adults under conditions of (a) a high amount of dual-task training and (b) training with simplified component tasks in dual-task situations. The data showed that a high amount of dual-task training in older adults provided no evidence for an improvement of dual-task performance to the optimal dual-task performance level achieved by younger adults. However, training with simplified component tasks in dual-task situations exclusively in older adults provided a similar level of optimal dual-task performance in both age groups. Therefore through applying a testing the limits approach, we demonstrated that older adults improved dual-task performance to the same level as younger adults at the end of training under very specific conditions.
Efficacy of silver-releasing rubber for the prevention of Pseudomonas aeruginosa biofilm formation in water

Abstract The aim of the present study was to evaluate the efficacy of Elastoguard™ silver-releasing rubber in preventing Pseudomonas aeruginosa biofilm formation in water. Biofilm formation by P. aeruginosa under various conditions in an in vitro model system was compared for silver-releasing and conventional rubber. Under most conditions tested, the numbers of sessile cells attached to silver-releasing rubber were considerably lower with reference to conventional rubber, although the effect diminished with increasing volumes. The release of silver also resulted in a decrease in planktonic cells. By exposing both materials simultaneously to conditions for biofilm growth, it became obvious that the antibiofilm effect was due to a reduction in the number of planktonic cells, rather than to contact-dependent killing of sessile cells. The data demonstrate that the use of silver-releasing rubber reduces P. aeruginosa biofilm in water and reduces the number of planktonic cells present in the surrounding solution.
Adaptable components

The key to viable software reuse is the ability to rapidly retrieve and tailor software components for new uses. An adaptable component is a representation of a family of similar software components which supports tailoring as an intrinsic aspect of retrieval. Differences among the instances of a family are conceived as a set of feature decisions and represented as parameters of adaptability. Organized into a domain-specific taxonomy of architectural categories, adaptable components provide for rapid retrieval of components tailored to suit each particular use.
A Novel Strategy to Improve the Therapeutic Efficacy of Gemcitabine for Non-Small Cell Lung Cancer by the Tumor-Penetrating Peptide iRGD

Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, comprising approximately 75–80% of all lung cancers. Gemcitabine is an approved chemotherapy drug for NSCLC. The objective of this study was to develop a novel strategy to improve the therapeutic efficacy of Gemcitabine for NSCLC by the co-administered iRGD peptide. We showed that the rates of positive expression of αvβ3, αvβ5 and NRP-1 in the A549 cell line were 68.5%, 35.3% and 94.5%, respectively. The amount of Evans Blue accumulated in the tumor of Evans Blue+iRGD group was 2.5 times that of Evans Blue group. The rates of growth inhibition of the tumors of the iRGD group, the Gemcitabine group and the Gemcitabine+iRGD group were 8%, 59.8% and 86.9%, respectively. The results of mechanism studies showed that PCNA expression in the Gemcitabine+iRGD group decreased 71.5% compared with that in Gemcitabine group. The rate of apoptosis in the Gemcitabine+iRGD group was 2.2 time that of the Gemcitabine group. Therefore, the tumor-penetrating Peptide iRGD can enhance the tumor-penetrating ability and therapeutic efficacy of Gemcitabine in the A549 xenograft. The combined application of Gemcitabine with iRGD may be a novel strategy to enhance the clinical therapeutic efficacy of Gemcitabine in patients with NSCLC.
Current Trends in Sensors Based on Conducting Polymer Nanomaterials

Conducting polymers represent an important class of functional organic materials for next-generation electronic and optical devices. Advances in nanotechnology allow for the fabrication of various conducting polymer nanomaterials through synthesis methods such as solid-phase template synthesis, molecular template synthesis, and template-free synthesis. Nanostructured conducting polymers featuring high surface area, small dimensions, and unique physical properties have been widely used to build various sensor devices. Many remarkable examples have been reported over the past decade. The enhanced sensitivity of conducting polymer nanomaterials toward various chemical/biological species and external stimuli has made them ideal candidates for incorporation into the design of sensors. However, the selectivity and stability still leave room for improvement.
The role of TLR activation in inflammation

The Toll‐like receptor family was originally identified in Drosophila, where it provides important developmental and immunological signalling. In mammals, the developmental signal appears to have been lost, but the immunological defence role of these receptors has been expanded to provide broad recognition of bacterial, fungal, viral and parasitic pathogens. There is increasing evidence that these receptors go beyond the recognition of microbial molecules to sense host tissue damage. Recognition of host molecules and commensal microbes is also involved in the restoration of normal tissue architecture after injury and in maintenance of epithelial health. Recent developments in the TLR field highlight the importance of these molecules to human health and disease and demonstrate that their targeting, to boost immunity or inhibit inflammation, is both feasible and also potentially challenging. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Successful Attack on an FPGA-based Automatically Placed and Routed WDDL+ Crypto Processor.

In this paper, we report the first successful attack on a DES crypto co-processor protected by the ``Positive'' Wave Dynamic Differential Logic (WDDL+) and embedded in a Field Programmable Gates Array (FPGA). This attack is unambigous as the full key is retrieved. We experimentally show that this countermeasure resists to Differential Power Analysis (DPA), but can be broken by a totally non-invasive Electro-Magnetic Analysis (EMA) method. The method relies on two stages, the first being a localisation phase by means of cartography, and the second being the EMA attack on the most relevant area.
A Clinical Comparison Study of Attention Deficit/Hyperactivity Disorder (DSM-IV) and Hyperkinetic Disorder (ICD-10) in Indian children and Adolescents

Aims: To compare the usefulness of DSM IV and ICD-10 DCR criteria in clinic children presenting with the symptoms of inattention and hyperactivityimpulsivity. Methods: 62 children (54 boys and 8 girls) participated in the study. Children were assessed on Kiddie schedule for affective disorders and schizophrenia present and lifetime version and then diagnosed as attention deficit/hyperactivity disorder (ADHD) or hyperkinetic disorder (HKD) as per DSM IV or ICD-10 DCR criteria. Comorbidities were diagnosed as per DSM IV criteria. Severity of symptoms was rated using Hillside Behavior Rating Scale (HBRS) while global assessment of functioning was assessed on Children’s Global assessment Scale (CGAS). Results: All could be diagnosed with ADHD however, only 44 (71%) could be diagnosed as HKD. There was no statistically significant difference in most sociodemographic variables, severity of illness on HBRS and impairment on CGAS of the subjects diagnosed with ADHD and HKD and subjects with ADHD but not HKD (non-HKD-ADHD). Conclusions: DSM IV should be used because it diagnoses more children with impairing symptoms of inattention and hyperactivity-impulsivity as compared to ICD-10 DCR. Also, there is a significant overlap in between ADHD and HKD.
Resource placement and assignment in distributed network topologies

We consider the problem of how to place and efficiently utilize resources in network environments. The setting consists of a regionally organized system which must satisfy regionally varying demands for various resources. The operator aims at placing resources in the regions as to minimize the cost of providing the demands. Examples of systems falling under this paradigm are 1) A peer supported Video on Demand service where the problem is how to place various video movies, and 2) A cloud-based system consisting of regional server-farms, where the problem is where to place various contents or end-user services. The main challenge posed by this paradigm is the need to deal with an arbitrary multi-dimensional (high-dimensionality) stochastic demand. We show that, despite this complexity, one can optimize the system operation while accounting for the full demand distribution. We provide algorithms for conducting this optimization and show that their complexity is pretty small, implying they can handle very large systems. The algorithms can be used for: 1) Exact system optimization, 2) deriving lower bounds for heuristic based analysis, and 3) Sensitivity analysis. The importance of the model is demonstrated by showing that an alternative analysis which is based on the demand means only, may, in certain cases, achieve performance that is drastically worse than the optimal one.
An Evaluation of Self‐report Physical Activity Instruments Used in Studies Involving Cardiac Patients

PURPOSE Given the importance of physical activity (PA) in cardiac rehabilitation and prevention, measuring it in a valid and reliable manner is a practical challenge. Measuring self-reported PA in elderly cardiac patients can be problematic because of the need to assess many activities of short duration that may occur as part of routine daily functions. The primary purpose of this article was to identify and evaluate instruments that have been used over the last 15 years in studies of cardiac patients. METHODS A comprehensive MEDLINE search was carried out to identify articles from studies undertaken to assess PA in cardiac patients. The self-report PA instruments were subjected to evaluation concerning suitability for use with cardiac patients. RESULTS The initial electronic and hand searches yielded 203 articles. After removing articles that did not meet the inclusion criteria, a total of 86 articles were selected. Twenty-three self-report instruments were identified for evaluation. Most of the instruments had problems associated with inadequate validation methods or suitability for cardiac patients. Many of the instruments failed to demonstrate adequate validity or reliability, particularly when measuring low-intensity PA. CONCLUSIONS Some instruments are more suited to epidemiologic research than to clinical interventions where responsiveness to interventions is crucial. Recommendations for the constituents of an acceptable self-report PA instrument for cardiac patients are presented and the most suitable existing instruments are identified.