Miracle-dz/UniFAR-FTUs huggingface dataset:
A proof‐of‐principle gel‐free proteomics strategy for the identification of predictive biomarkers for the onset of pre‐eclampsia

Objective Progress in the prevention and treatment of women at risk of pre‐eclampsia (PE) still remains hindered by the lack of clinical screening tools that can accurately predict which mothers are at risk. The identification and validation of predictive biomarkers is therefore seen as a critical milestone towards improved healthcare provision and the clinical testing of new therapeutic strategies. Gel‐free proteomic technologies offer the capability of analysing hundreds of plasma proteins simultaneously, but as yet these methods have not been applied to pregnancy complications. To assess the feasibility of such an approach to plasma biomarker research in pregnancy we have applied the technique to samples from women with PE to gestation‐matched controls.
Channel aware MAC scheme based on CSMA/CA

The knowledge of channel states can improve the performance of wireless communications systems, and its benefits are outstanding where the channel states vary rapidly with time. The fast feedback of channel information was realized in the downlink of cdma2000 1/spl times/EV-DO system and it shows great enhancement in terms of total average throughput. However, it does not scale well since the burden of feedback channels increases proportionally with the increase of users in number. We propose a multiple access scheme based on CSMA/CA, which gives high priority to users in the good channel by assigning small backoff counters. Since the channel gain is used to choose the backoff counter locally, it is not sent back to the central controller, thereby achieving low overhead and complexity. Our proposed channel aware MAC scheme adapts to traffic conditions dynamically by changing the size of contention window when collision occurs.
Social Knowledge Awareness Map for Computer Supported Ubiquitous Learning Environment

Social networks are helpful for people to solve problems by providing useful information. Therefore, the importance of mobile social software for learning has been supported by many researches. In this research, a model of personalized collaborative ubiquitous learning environment is designed and implemented in order to support learners doing learning tasks or activities. It utilizes RFID technology to detect the surrounding environmental objects and then provides social knowledge awareness map for peer helpers dynamically according to the detected objects. The map visualizes the learners’ surrounding objects, peer helpers and the strength of the relation in the social network perspective. It is experimentally tested and evaluated in a small special community. The quantitative and qualitative data of the experiment indicate the important role of the map in augmenting the collaboration between the learners.
Research on model of knowledge transfer in outsourced software projects

In this paper, we firstly explored the attributes of knowledge embedded in outsourced software projects. We identified three attributes of knowledge by a review of literature and referred to these as codifiability, complexity and novelty. Drawing on organizational controls, social capital and knowledge transfer literature, this paper presented a model demonstrating the role of particular organizational controls (outcome, process and social) in knowledge transfer between client and vendor characterized by different knowledge attribute. Especially, we examined how social capital dimensions (structural, cognitive and relational) affect the transfer of knowledge between client and vendor. We also showed the role and impact of information and communications technology (ICT) on outsourced software projects especially on offshore projects which faced with cultural differences, language differences, time zone differences, geographic distance and other challenges. Results showed from the perspective of vendor, in order to acquire and transfer knowledge from client more effectively, Chinese enterprises should make full use of ICTs to built social capital with client.
A thermodynamically compatible model for describing asphalt binders: solutions of problems

In this sequel to the first paper (Málek et al., 2014. International Journal of Pavement Engineering), in which we identified a generalisation of the model due to Burgers which was corroborated against two sets of experiments, including a challenging one showing distinctly different relaxation times for shear and normal stresses, we solve several time-dependent boundary value problems wherein the boundary of the material is deforming, that have relevance to applications involving asphalt. Problems wherein the boundary is subject to time-varying compressive loads such as those due to moving automobiles and the attendant rutting, and the compaction due to rollers are considered in additions to other problems.
End User Comparison of Anatomically Matched 3-Dimensional Printed and Virtual Haptic Temporal Bone Simulation

Objective Simulation has assumed a prominent role in education. It is important to explore the effectiveness of different modalities. In this article, we directly compare surgical resident impression of 2 distinct temporal bone simulations (physical and haptic). Study Design Research Ethics Board–approved prospective cohort study. Setting A haptic voxel-based virtual model (VM) and a physical 3-dimensional printed temporal bone model (PBM) were developed. Participants rated each construct on a number of parameters and performed a direct comparison of the simulations using a survey instrument that employed a 7-point Likert scale and rank lists. Subjects and Methods Ten otolaryngology residents dissected anatomically identical, matched physical and virtual models. Data for both simulations originated from 10 unique cadaveric micro–computed tomography images. Results Subjects rated the PBM drill quality as being more similar to cadaveric temporal bone than the VM (cortical bone mean: 5.5 vs 3.2, P = .011; trabecular bone mean: 5.2 vs 2.8, P = .004) and with better air cell system representation (mean: 5.4 vs 4.5, P = .003). Subjects strongly agreed that both simulations are effective educational tools, but they rated the PBM higher (mean: 6.7 vs 5.4, P = .019). Notably, subjects agreed that both modalities should be integrated into training, but they were more favorably inclined toward the PBM (mean: 7.0 vs 5.5, P = .002). In direct comparison, the PBM was the preferred simulation in 7 of 9 educational domains. Conclusions Appraisal of a PBM and a VM found both to have perceived educational benefit. However, the PBM was considered to have more realistic physical properties and was considered the preferred training instrument.
Temporal activation of p70 S6 kinase and Akt1 by insulin: PI 3-kinase-dependent and -independent mechanisms.

Several studies have suggested that activation of p70 ribosomal S6 kinase (p70 S6 kinase) by insulin may be mediated by the phosphatidylinositol 3-kinase (PI 3-kinase)-Akt pathway. However, by temporal analysis of the activation of each kinase in L6 muscle cells, we report that the activation of the two serine/threonine kinases (Akt and p70 S6 kinase) can be dissociated. Insulin stimulated p70 S6 kinase in intact cells in two phases. The first phase (5 min) of stimulation was fully inhibited by wortmannin (IC50 = 20 nM) and LY-294002 (full inhibition at 5 μM). After this early inhibition, p70 S6 kinase was gradually stimulated by insulin in the presence of 100 nM wortmannin. After 30 min, the stimulation was 65% of the maximum attained in the absence of wortmannin. The IC50 of wortmannin for inhibition of this second phase was ∼150 nM. In contrast, activation of Akt1 by insulin was completely inhibited by 100 nM wortmannin at all time points investigated. Inhibition of mitogen-activated protein kinase/extracellular signal-regulated protein kinase kinase with PD-098059 (10 μM) or treatment with the protein kinase C inhibitor bisindolylmaleimide (10 μM) had no effect on the late phase of insulin stimulation of p70 S6 kinase. We have previously shown that GLUT-1 protein synthesis in these cells is stimulated by insulin via the mTOR-p70 S6 kinase pathway, based on its sensitivity to rapamycin. We therefore investigated whether the signals leading to GLUT-1 synthesis correlated with the early or late phase of stimulation of p70 S6 kinase. GLUT-1 synthesis was not inhibited by wortmannin (100 nM). In summary, insulin activates p70 ribosomal S6 kinase in L6 muscle cells by two mechanisms, one dependent on and one independent of the activation of PI 3-kinase. In addition, activation of Akt1 is fully inhibited by wortmannin, suggesting that Akt1 does not participate in the late activation of p70 S6 kinase. Wortmannin-sensitive PI 3-kinases and Akt1 are not required for insulin stimulation of GLUT-1 protein biosynthesis.
Splitting (complicated) surfaces is hard

Let M be an orientable combinatorial surface without boundary. A cycle on M is splitting if it has no self-intersections and it partitions M into two components, neither of which is homeomorphic to a disk. In other words, splitting cycles are simple, separating, and non-contractible. We prove that finding the shortest splitting cycle on a combinatorial surface is NP-hard but fixed-parameter tractable with respect to the surface genus. Specifically, we describe an algorithm to compute the shortest splitting cycle in gO(g)n log n time.
Performance Evaluation of Some Clustering Algorithms and Validity Indices

In this article, we evaluate the performance of three clustering algorithms, hard K-Means, single linkage, and a simulated annealing (SA) based technique, in conjunction with four cluster validity indices, namely Davies-Bouldin index, Dunn's index, Calinski-Harabasz index, and a recently developed index I. Based on a relation between the index I and the Dunn's index, a lower bound of the value of the former is theoretically estimated in order to get unique hard K-partition when the data set has distinct substructures. The effectiveness of the different validity indices and clustering methods in automatically evolving the appropriate number of clusters is demonstrated experimentally for both artificial and real-life data sets with the number of clusters varying from two to ten. Once the appropriate number of clusters is determined, the SA-based clustering technique is used for proper partitioning of the data into the said number of clusters.
Robust web content extraction

We present an empirical evaluation and comparison of two content extraction methods in HTML: absolute XPath expressions and relative XPath expressions. We argue that the relative XPath expressions, although not widely used, should be used in preference to absolute XPath expressions in extracting content from human-created Web documents. Evaluation of robustness covers four thousand queries executed on several hundred webpages. We show that in referencing parts of real world dynamic HTML documents, relative XPath expressions are on average significantly more robust than absolute XPath ones.
In search of the molecular basis of memory loss in Alzheimer disease.

One of the problems in understanding diseases of the brain is that it is so hard to examine the physical characteristics of a disease—what goes wrong inside the brain—while people are suffering from it. To draw a relationship between memory problems and what is happening structurally inside the brain, medical researchers needed an animal model that would develop the memory problems and the physical characteristics of Alzheimer disease. Ten years ago, by inserting into a normal mouse a human gene that had been identified as causing Alzheimer’s, my laboratory invented just such an animal model. With this animal, called Tg2576, we and other researchers could begin to study how the disease develops in the brain, and how that corresponds to the very mild memory problems that the mouse exhibits. We have discovered a molecule in the brain, called amyloid-beta star (Ab*), that we have proven causes memory loss. We adopted a 3-step strategy to discover Ab*. First, identification of candidate Ab* molecules. Second, purification of candidate Ab* molecules. And third, application of purified Ab* in normal subjects. This is the first time that a substance in an Alzheimer brain or Alzheimer model has been identified, isolated and, when applied to healthy animal subjects, shown to cause memory loss. We propose that Ab* starts to form long before memory problems are clinically apparent, and that it causes memory problems without killing neurons or forming visible aggregates called amyloid plaques. We are working now to design the tools that would allow a person to have a simple test to detect this molecule. At the same time, we are starting down the path of designing a drug or a vaccine that would block Ab* in the hopes of stopping Alzheimer disease even before it begins. About 5 years ago, we developed a different mouse that could develop very severe memory problems, equivalent to having a fairly advanced stage of Alzheimer Copyright r 2006 by Lippincott Williams & Wilkins From the *Edmund Wallace and Anne Marie Tulloch Chairs in Neurology and Neuroscience, Department of Neurology, Center for Memory Research and Care, University of Minnesota Medical School; and wGRECC, Minneapolis VA Medical Center. Dr Ashe received royalties for patents related to the subject of this study in excess of $10,000 a year. Reprints: Karen Hsiao Ashe, MD, PhD, University of Minnesota Medical School, Mayo Mail Code 295, 420 Delaware St. S.E. , Minneapolis, MN 55455-0323 (e-mail: hsiao005@umn.edu). 2006 POTAMKIN PRIZE
Encouraging an Active Lifestyle with Personal Mobile Devices: Motivational Tools and Techniques

nd methods of allowing people to monitor their own activity levels and hence allow them to alter their lifestyle in such a way as they become more active. It is possible to achieve this aim through a number of methods, ranging for individual personal devices to making use of social groups and social feedback in order to further encourage physical activity through the notion that friends can also monitor our progress. In this review paper we look at some of the work undertaken in understanding the desire of those who wish to become more active, paying particular attention to those with sedentary lifestyles. We also take a look at the technologies and methods utilised to aid and motivate these people in achieving their goals.
Elucidation of time-dependent systems biology cell response patterns with time course network enrichment

Advances in OMICS technologies emerged both massive expression data sets and huge networks modelling the molecular interplay of genes, RNAs, proteins and metabolites. Network enrichment methods combine these two data types to extract subnetwork responses from case/control setups. However, no methods exist to integrate time series data with networks, thus preventing the identification of time-dependent systems biology responses. We close this gap with Time Course Network Enrichment (TiCoNE). It combines a new kind of human-augmented clustering with a novel approach to network enrichment. It finds temporal expression prototypes that are mapped to a network and investigated for enriched prototype pairs interacting more often than expected by chance. Such patterns of temporal subnetwork co-enrichment can be compared between different conditions. With TiCoNE, we identified the first distinguishing temporal systems biology profiles in time series gene expression data of human lung cells after infection with Influenza and Rhino virus. TiCoNE is available online (this https URL) and as Cytoscape app in the Cytoscape App Store (this http URL).
Nerve Crush Injuries—A Model for Axonotmesis

Nerve crush is a commonly used experimental model in the rat; however, a standard method of inducing this injury has not been defined. This study examined six crush techniques that are frequently used and characterized the subsequent nerve injury. Five types of nerve crush using a No. 5 jeweler's forceps and a sixth using a 30-s single crush with a serrated hemostat were studied in the posterior tibial nerve of the Lewis rat. Regeneration was evaluated using serial walking track assessments at 1, 2, 4, 6, and 8 weeks postoperatively. Nerve conduction studies and histological examination were performed at 2 days, 2 weeks, and 8 weeks. Blood-nerve barrier breakdown was observed at 2 days and recovered by 2 weeks. By 4 weeks normal walking track patterns were obtained in all groups. A pattern of Wallerian degeneration and axonal regeneration was noted at 2 weeks, with histological recovery in all groups by 8 weeks. Nerve crush, induced by any of the six methods tested, was similar and provides a reliable model of axonotmesis.
How useful is region-based classification of remote sensing images in a deep learning framework?

In this paper, we investigate the impact of segmentation algorithms as a preprocessing step for classification of remote sensing images in a deep learning framework. Especially, we address the issue of segmenting the image into regions to be classified using pre-trained deep neural networks as feature extractors for an SVM-based classifier. An efficient segmentation as a preprocessing step helps learning by adding a spatially-coherent structure to the data. Therefore, we compare algorithms producing superpixels with more traditional remote sensing segmentation algorithms and measure the variation in terms of classification accuracy. We establish that superpixel algorithms allow for a better classification accuracy as a homogenous and compact segmentation favors better generalization of the training samples.
Proteoglycan-mediated inhibition of A beta proteolysis. A potential cause of senile plaque accumulation.

Senile plaques of Alzheimer's disease brain contain, in addition to beta amyloid peptide (A beta), multiple proteoglycans. Systemic amyloidotic deposits also routinely contain proteoglycan, suggesting that these glycoconjugates are generally involved in amyloid plaque formation and/or persistence. We demonstrate that heparan sulfate proteoglycan (HSPG) and chondroitin sulfate proteoglycan (CSPG) inhibit the proteolytic degradation of fibrillar, but not non-fibrillar, A beta at physiological pH. In accordance with the proteolysis studies, high affinity binding of proteoglycans to fibrillar A beta(1-40) and A beta(1-42) is observed from pH 4 to 9, whereas appreciable binding of HSPG or CSPG to non-fibrillar peptide is only seen at pH < 6. This differing pH dependence of binding suggests that a lysine residue is involved in proteoglycan association with fibrillar A beta, whereas a protonated histidine appears to be needed for binding of the glycoconjugates to non-fibrillar peptide. Scatchard analysis of fibrillar A beta association with proteoglycans indicates a single affinity interaction, and the binding of both HSPG and CSPG to fibrillar A beta is completely inhibited by free glycosaminoglycan chains. This implies that these sulfated carbohydrate moieties are primarily responsible for proteoglycan.A beta interaction. The ability of proteoglycans to bind fibrillar A beta and inhibit its proteolytic degradation suggests a possible mechanism of senile plaque accumulation and persistence in Alzheimer's disease.
Sequence analysis of wheat grain allergens separated by two‐dimensional electrophoresis with immobilized pH gradients

Micropreparative two‐dimensional (2‐D) gel electrophoresis with immobilized pH gradients (4–8) in the first dimension (IPG‐DALT) was optimized for the separation of salt‐soluble wheat grain proteins associated with bakers' asthma disease. The resolved polypeptides were electroblotted onto a polyvinylidene difluoride (PVDF) membrane and incubated with the pooled sera from four asthmatic bakers. Bound IgE was demonstrated by alkaline phosphatase conjugated anti‐human IgE. Major IgE binding was detected in the 27 kDa, 37 kDa and, to a lesser extent, in the 14–18 kDa area of the 2‐D immunoblots, respectively. Since the main purpose of our study was to determine the N‐terminal amino acid sequences of the major wheat grain allergens, N‐terminal sequencing was performed for six out of a total of eleven major allergens located in the 27 kDa area, for one out of two 37 kDa allergens, and for two out of four 14–18 kDa allergens. Our results revealed that two of the 27 kDa polypeptides are clearly related to several Acyl‐CoA oxidase variants of barley and rice, whereas no significant homologies were found for the remaining four 27 kDa allergens analyzed. The N‐terminus of the 37 kDa allergen appeared to be blocked so that no sequence information was obtained, while the two 14–18 kDa allergens analyzed were identified as members of the wheat α‐amylase‐inhibitor family.
A Framework for A Graph- and Queuing System-Based Pedestrian Simulation

With a growing trend in usage of mobile navigation devices, there is also a need for an intelligent pedestrian navigation system. As an example, one might think of a visit to a large commercial center or a theme park, where the visitor must be efficiently guided to accomplish his tasks. In order to efficiently schedule a visit in such a scenario, the system not only needs to simulate and determine the waiting times across each destination, but also to integrate the entire system into the geometry of the scenario, to provide spatial context to non-spatial data. In this paper, we present a framework for a pedestrian simulation that models the movement of pedestrians by embedding the simulation into a geometric context. The resulting model considers the dimensions and architectural constraints of the scenario, simulates the pedestrian movement over a 3D graph network and gives an overall view of the congestions along the paths, waiting times at the destinations, etc.
Improving Document Ranking in Information Retrieval Using Ordered Weighted Aggregation and Leximin Refinement

Classical information retrieval (IR) methods often lose valuable information when aggregating weights, which may diminish the discriminating power between documents. To cope with this problem, the paper presents an approach for ranking documents in IR, based on a vector-based ordering technique already considered in fuzzy logic for multiple criteria analysis purpose. Moreover, the proposed approach uses a possibilistic framework for encoding the retrieval status values. The approach, applied to a benchmark collection, has been shown to improve IR precision w.r. t. classical approaches.
Topic models for RFID data modeling and localization

Topic Modeling, widely used and associated with text-mining applications, is a methodology that may be applied to other domains where the data generation process may be treated as a mixture model, and the underlying data objects modeled similarly to unigrams in the text-mining context. In this paper, we consider the application of topic-modeling to the RFID data generation process, and show how the resulting topics from topic-modeling are applicable to the RFID localization problem — particularly in challenging environments that have significant signal reflections or multi-path.
Studies on the Interaction Mechanism of 1,10-Phenanthroline Cobalt(II) Complex with DNA and Preparation of Electrochemical DNA Biosensor

Fluorescence spectroscopy and ultraviolet (UV) spectroscopy techniques coupled with cyclic voltammetry (CV) were used to study the interaction between salmon sperm DNA and 1,10-Phenanthroline cobalt(II) complex, [Co(phen)2(Cl)(H2O)]Cl·H2O, where phen = 1,10-phenanthroline. The interaction between [Co(phen)2(Cl)(H2O)]+ and double-strand DNA (dsDNA) was identified to be intercalative mode. An electrochemical DNA biosensor was developed by covalent immobilization of probe single-strand DNA (ssDNA) related to human immunodeficiency virus (HIV) on the activated glassy carbon electrode (GCE). With [Co(phen)2(Cl)(H2O)]+ being the novel electrochemical hybridization indicator, the selectivity of ssDNA-modified electrode was investigated and selective detection of complementary ssDNA was achieved using differential pulse voltammetry (DPV).