Miracle-dz/UniFAR-FTUs huggingface dataset:
Advances in targeted proteomics and applications to biomedical research

Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074–1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data‐independent acquisition (DIA) with targeted data extraction on fast scanning high‐resolution accurate‐mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large‐scale quantification of hundreds of target proteins are discussed.
Accuracy enhancement of collaborative filtering recommender system for blogs using latent semantic indexing

The selection of an interesting blog is becoming ever increasingly tough work for most users as the number of blogs is exponentially increasing every day. A Recommender System (RS) can help the user to find out the blog of his choice or based on parameters specified by him. The accuracy of RS to find out the right blogs for a particular user gets enhanced, if the text of blog is analyzed using semantic analysis. The RS uses the classification of blogs to find out the right blogs for a user. The information with respect to blogs like blog's title, tags given by blogger, blog image etc., provides good information to classify the blogs. A classification of text can be done using Part of Speech (POS) text analyzer. POS tagger of text provides information about the blogs that can be used to find the similarity between two blogs. The similar types of blogs can be kept together to provide better indexing in the set of large blogs. The paper finds the better accuracy of Collaborative Filtering Recommender System (CF RS) for bloggers when the blogs are processed with different text analysis using semantic information of blogs. The observation is addressed by computing various measures like Precision, Recall and F1.
Development and thermo‐mechanical behavior of nanocomposite epoxy adhesives

Two kinds of organo-modified (OM) clays were dispersed in an epoxy resin for the preparation of nanocomposite adhesives at various filler amounts. XRD tests evidenced the formation of intercalated structures, increasing the intercalation degree with the clay hydrophilicity. The original transparency of the samples was retained up to a filler content of 3 wt%, and then decreased due to filler agglomeration. The glass transition temperature of nanocomposites filled with the more hydrophilic clay (30B) raised up to a filler content of 3 wt% and then decreased, probably because of the concurrent and contrasting effects of the physical chain blocking and reduction of the cross-linking degree. Also elastic modulus, stress at break, and fracture toughness were sensibly improved by nanoclay addition up to filler loadings of 0.5–1 wt%. For higher concentrations the positive contribution of clay nanoplatelets was counterbalanced by the presence of agglomerated tactoids in the matrix. Mechanical tests on single-lap composite (epoxy/glass) bonded joints evidenced an enhancement of the shear strength by about 25% for an optimal filler content of 1 wt%. Therefore, it was concluded that the addition of a proper amount of OM clay to epoxy adhesives could represent an effective way to improve the shear resistance of adhesively bonded composite structures. Copyright © 2011 John Wiley & Sons, Ltd.
Swirling Flow and Wall Shear: Evaluating the BioMimics 3D Helical Centerline Stent for the Femoropopliteal Segment

The BioMimics 3D self-expanding nitinol stent represents a strategy for femoropopliteal intervention that is alternative or complementary to deployment of drug-coated stents or balloons. Whereas conventional straight stents reduce arterial curvature and disturb blood flow, creating areas of low wall shear, where neointimal hyperplasia predominantly develops, the helical centerline geometry of the BioMimics 3D maintains or imparts arterial curvature, promotes laminar swirling blood flow, and elevates wall shear to protect against atherosclerosis and restenosis. In the multicenter randomized MIMICS trial, treatment of femoropopliteal disease with the BioMimics 3D (n = 50) significantly improved 2-year primary patency (log-rank test p = 0.05) versus a control straight stent (n = 26), with no cases of clinically driven target lesion revascularization between 12 and 24 months (log-rank test p = 0.03 versus controls). In geometric X-ray analysis, the BioMimics stent was significantly more effective in imparting a helical shape even when the arterial segment was moderately to severely calcified. Computational fluid dynamics analysis showed that average wall shear was significantly higher with the helical centerline stent (1.13 ± 0.13 Pa versus 1.06 ± 0.12 Pa, p = 0.05). A 271-patient multicenter international MIMICS-2 trial and a 500-patient real-world MIMICS-3D registry are underway.
Inotropes and vasopressors

Inotropic agents are used to increase myocardial contraction while vasopressors are used to increase vascular tone. They are often used for treatment of patients whose tissue perfusion is insufficient to meet metabolic requirements. Therefore, these agents are usually administered in intensive care units where continuous and invasive monitoring of cardiac function can be applied. Inotropic agents can be divided into those that increase cAMP levels and those that do not. Adrenergic receptor agonists and phosphodiesterase inhibitors (PDEi) increase cAMP levels and are currently the mainstay of positive inotropic therapy. Levosimendan acts as calcium sensitizer and increases myocardial contraction force without increasing intracellular calcium levels. In addition to existing inotropic agents, new promising inotropes are being developed. These include sarcoplasmic reticulum calcium pump (istaroxime), cardiac myosin activators (omecamtivmecarbil), gene therapy, nitroxyl donors and ryanodine receptor stabilizers. Current treatments of heart failure are aimed at prolonging survival and not just alleviating symptoms. This review provides a short description of the physiology of myocardial contraction and adrenergic receptors. We also provide a short description of commonly used inotropic agents and vasopressor drugs as well as a short review of agents that are expected are in use in the future. Inotropes are agents used to increase myocardial contractility, while vasopressors are administered to increase vascular tone (1). Their use ismostly confined to critically ill patients whose hemodynamic impairment is such that tissue perfusion is insufficient to meet metabolic requirements (2). Patients in need of inotropic or vasopressor support are often presented with septic or cardiogenic shock and severe heart failure, and are victims of major trauma or undergoing major surgery.These drugs are therefore administered usually to patients treated in intensive care settings where continuous monitoring of cardiac rhythm, arterial oxygenation, urine output and other invasive hemodynamic monitoring can be applied.Inotropic and vasopressor drugs should be administered through a central venous catheter via infusion pumps that can deliver precise flow rates. These agents are mostly short acting with rapid onset and offset of action. Therefore, they can be used without an initial bolus and can be titrated frequently. Abrupt discontinuation should be avoided because of possible hypotension.
Fine-Grained MSR Specifications for Quantitative Security Analysis

The traditional Dolev-Yao model of security limits attacks to “computationally feasible” operations. We depart from this model by assigning a cost to protocol actions, both of the Dolev-Yao kind as well as non traditional forms such as computationally-hard operations, guessing, principal subversion, and failure. This quantitative approach enables evaluating protocol resilience to various forms of denial of service, guessing attacks, and resource limitation. While the methodology is general, we demonstrate it through a low-level variant of the MSR specification language.
Multiple sets resistance training: Effects of Condensed versus circuit models on muscular strength, endurance and body composition.

Arazi H, Asadi A. Multiple sets resistance training: Effects of Condensed versus circuit models on muscular strength, endurance and body composition. J. Hum. Sport Exerc. Vol. 7, No. 4, pp. 733-740, 2012. The purpose of this study was to examine the effects of condensed multiple-set resistance training and circuit multiple-set resistance training on muscular strength, endurance, body composition and arm and thigh circumference in healthy males. Twenty seven healthy males volunteered to participate in this study and assigned into three groups; according to; condensed multiple-set group (COM; n=9), circuit multiple-set group (CIM; n=8) and control group (CON; n=10). Subjects in the COM performed resistance training exercises for 3 sets continuously; whereas subjects in the CIM performed resistance training program for 1 set of each exercise and come back to the first exercise and this approach was performed 3 times each training session. Pre and post 8 weeks of training, one repetition maximum (1RM) and muscle endurance (60% of 1RM) for leg press and bench press, body weight, arm and thigh circumference and body composition were measured. No significant differences in body mass, arm and thigh circumference and muscular strength for the bench press exercise were observed for any group during the 8 weeks of training period (p > 0.05). A significant increase in muscular strength for the leg press exercise was observed for COM after 8 weeks of training (p < 0.05). Both the COM and CIM groups showed significant improvement compared with pre training and CON in muscular endurance for the bench press and leg press exercises (p < 0.05). In conclusion, it can be recommended that, COM is better for improving muscle strength and both
Changing Tetra Pak: From Waste to Resource

In recent years, the problem caused by Tetra Pak waste (TPW) has became a topic of great concern to scientists and environmentalists, and commercial companies have also begun to take an interest in developing processes for tackling this issue. In this article, the challenges in the recycling of TPW are described. This article presents the major conclusions of previously published works focussed on the utilisation of TPW for energy and material purposes. The commercial utilisation of TPW is also described. Some suggestions for better recycling of TPW are given in the latter part of this work.
RNA Binding Domain of Telomerase Reverse Transcriptase

ABSTRACT Telomerase is a ribonucleoprotein reverse transcriptase that extends the ends of chromosomes. The two telomerase subunits essential for catalysis in vitro are the telomerase reverse transcriptase (TERT) and the telomerase RNA. Using truncations and site-specific mutations, we identified sequence elements of TERT and telomerase RNA required for catalytic activity and protein-RNA interaction for Tetrahymena thermophila telomerase. We found that the TERT amino and carboxyl termini, although evolutionarily poorly conserved, are nonetheless important for catalytic activity. In contrast, high-affinity telomerase RNA binding requires only a small region in the amino terminus of TERT. Surprisingly, the TERT region necessary and sufficient for telomerase RNA binding is completely separable from the reverse transcriptase motifs. The minimalTetrahymena TERT RNA binding domain contains two sequence motifs with ciliate-specific conservation and one TERT motif with conservation across all species. With human TERT, we demonstrate that a similar region within the TERT amino terminus is essential for human telomerase RNA binding as well. Finally, we defined theTetrahymena telomerase RNA sequences that are essential for TERT interaction. We found that a four-nucleotide region 5′ of the template is critical for TERT binding and that the 5′ end of telomerase RNA is sufficient for TERT binding. Our results reveal at least one evolutionarily conserved molecular mechanism by which the telomerase reverse transcriptase is functionally specialized for obligate use of an internal RNA template.
Tissue Factor: An Enzyme Cofactor and a True Receptor

Summary Tissue factor is considered to be the physiologic trigger of the blood clotting system in normal hemostasis and in many – perhaps most – thrombotic diseases. A wealth of new knowledge is available regarding the structure and assembly of the TF:VIIa complex and the role of factor VIIa and tissue factor in hypercoagulable states. The exciting recent finding that tissue factor can function as a signaling receptor, and suggestions that tissue factor may have important, non-hemostatic roles, will be the subject of much additional study in the near future.
Optimal generation of Fock states in a weakly nonlinear oscillator

We apply optimal control theory to determine the shortest time in which an energy eigenstate of a weakly anharmonic oscillator can be created under the practical constraint of linear driving. We show that the optimal pulses are beatings of mostly the transition frequencies for the transitions up to the desired state and the next leakage level. The time of the shortest possible pulse for a given nonlinearity scales with the nonlinearity parameter δ as a power law δ−α with α≃0.73±0.029. This is a qualitative improvement relative to the value α=1 suggested by a simple Landau–Zener argument.
Comparison of the performance and stability of two torsional vibration dampers for variable‐speed wind turbines

Alleviation of excess fatigue loads due to vibrations in the drive-train of wind turbines can be achieved through the use of torsional vibration dampers. Two torsional dampers based on different design approaches were designed and assessed: the first employs a conventional band-pass filter technique, whereas the second involves an alternative model-based approach. Frequency domain analyses were carried out on the system with the two dampers for the cases with and without model uncertainty. The system using the band-pass filter-based damper showed deterioration in stability and performance when subjected to uncertainty in the model and had to be re-tuned to recover a good damping performance. Conversely, the system employing the model-based damper maintained good stability and superior damping performance in the presence of model uncertainties. These attributes can ensure that the damper exhibits a good performance even if the wind turbine parameters vary during operation, such as when ice forms on the blades. Time domain simulations were carried out to verify the frequency domain analyses. © 2014 The Authors. Wind Energy published by John Wiley & Sons, Ltd.
Complex scheduling problems using an optimization methodology

Scheduling operations problems arise in diverse areas such as flexible manufacturing, production planning and scheduling, logistics, supply chain problem, etc. A common feature of many of these problems is that no efficient solution algorithms are known that solve each instance to optimality in a time bounded polynomially in the size of the problem, Dorndorf and Pesch [22]. Discrete optimization can help to overcome these difficulties. This paper presents an optimization approach to solve the complex scheduling problem in a job shop environment. This problem is also known as the Job Shop Scheduling Problem (JSSP). The JSSP is a difficult problem in combinatorial optimization for which extensive investigation has been devoted to the development of efficient algorithms. The proposed approach is based on a genetic algorithm technique. Genetic algorithms are an optimization methodology based on a direct analogy to Darwinian natural selection and mutations in biological reproduction. The scheduling rules such as SPT and MWKR are integrated into the process of genetic evolution. The chromosome representation of the problem is based on random keys. The schedules are constructed using a priority rule in which the priorities and delay times of the operations are defined by the genetic algorithm. Schedules are constructed using a procedure that generates parameterized active schedules. After a schedule is obtained a local search heuristic is applied to improve the solution. The approach is tested on a set of standard instances taken from the literature and compared with other approaches. The computation results validate the effectiveness of the proposed approach.
Do flowers wave to attract pollinators? A case study with Silene maritima

To answer the question whether flowers wave to attract pollinators, we determine: (1) the heritability of floral mobility; (2) whether wavy flowers attract more insects; (3) does the duration of pollination affect seed set; and (4) the relationship between seed set and floral mobility. The pollination ecology of Silene maritima was investigated. Flowers on stalks of different waviness were used to investigate the effect of floral movement on pollinator visits. There is heritable variation in both direct and indirect estimates of floral mobility. The highest insect total visitation times were associated with medium length thin stalks that were visited more frequently and by more insect species. Although mean individual visit durations were less than those of less mobile flowers, this was compensated for by increased visits. Observations of controlled pollinations show that when the visit times are low, so is seed set and therefore low and high mobility flowers might suffer from reduced fitness. Combining these observations provides a mechanism that could be driving stabilizing selection for flower stalk traits, with a trade‐off applying between waving to attract pollinators and not being too mobile as to prevent effective pollination. Further evidence for stabilizing selection is provided by the relationship observed in the field between seed set and floral mobility where the highest levels of fitness was associated with intermediate levels of floral waving.
DNA Template Dependent Accuracy Variation of Nucleotide Selection in Transcription

It has been commonly assumed that the effect of erroneous transcription of DNA genes into messenger RNAs on peptide sequence errors are masked by much more frequent errors of mRNA translation to protein. We present a theoretical model of transcriptional accuracy. It uses experimentally estimated standard free energies of double-stranded DNA and RNA/DNA hybrids and predicts a DNA template dependent transcriptional accuracy variation spanning several orders of magnitude. The model also identifies high-error as well a high-accuracy transcription motifs. The source of the large accuracy span is the context dependent variation of the stacking free energy of pairs of correct and incorrect base pairs in the ever moving transcription bubble. Our model predictions have direct experimental support from recent single molecule based identifications of transcriptional errors in the C. elegans transcriptome. Our conclusions challenge the general view that amino acid substitution errors in proteins are mainly caused by translational errors. It suggests instead that transcriptional error hotspots are the dominating source of peptide sequence errors in some DNA template contexts, while mRNA translation is the major cause of protein errors in other contexts.
Load adaptive modulation method for all-metal induction heating application

Induction heating (IH) load made from a non-ferromagnetic material have not been a target of an IH cooktop application, because a small resistance of the non-ferromagnetic material induces large resonant current on a series resonant converter. However, heating capability for various pot materials is essential to improve the functionality of IH products. In this paper, a load adaptive modulation is proposed to heat the pot of non-ferromagnetic and ferromagnetic materials. The proposed control method can change the magnitude of input voltage and operational frequency of power converter according to the pot resistance. The operational principle and design method are analyzed to implement the proposed control method. The validity is experimentally verified using a 2-kW prototype series resonant converter.
GENERATION OF TRANSITION CLASS MODELS FROM FORMAL QUEUEING NETWORK DESCRIPTIONS

A main feature of a novel tool is described, the algorthmic translation of formal queueing network descriptions into transition class models. Transition classes are a highlevel modelling paradigm for the structured and compact denition of Markov chains. Transition class models can be solved with many known solution techniques for Markov chains, exact and approximate, and simulation, even hybrid analysis is possible. The queueing network description language and the translator are extensible with respect to new network features, for example new node types. The tool is extensible with respect to new modelling paradigms and new solvers. Models can be multi-paradigm.
CYK4 Promotes Antiparallel Microtubule Bundling by Optimizing MKLP1 Neck Conformation

Centralspindlin, a constitutive 2:2 heterotetramer of MKLP1 (a kinesin-6) and the non-motor subunit CYK4, plays important roles in cytokinesis. It is crucial for the formation of central spindle microtubule bundle structure. Its accumulation at the central antiparallel overlap zone is key for recruitment and regulation of downstream cytokinesis factors and for stable anchoring of the plasma membrane at the midbody. Both MKLP1 and CYK4 are required for efficient microtubule bundling. However, the mechanism by which CYK4 contributes to this is unclear. Here we performed structural and functional analyses of centralspindlin using high-speed atomic force microscopy, Fӧrster resonance energy transfer analysis, and in vitro reconstitution. Our data reveal that CYK4 binds to a globular mass in the atypically long MKLP1 neck domain between the catalytic core and the coiled coil and thereby reconfigures the two motor domains in the MKLP1 dimer to be suitable for antiparallel microtubule bundling. Our work provides insights into the microtubule bundling during cytokinesis and into the working mechanisms of the kinesins with non-canonical neck structures.
Do media influence learning? Revisiting the debate in the context of distance education

In this article Vicki Carter, Instructional Programmer at The Pennsylvania State University, reviews the academic literature of distance education which has considered whether the media and technologies of education affect the learning which takes place. She finds that the conventional answer, especially from a North American perspective, is in the negative, despite a minority who assert the contrary. While the author argues in conclusion for the second of these positions, she suggests that the frames of reference used by distance education have been too narrow, and that valuable insights can be found in the fields of neurology and mass communications, as well as in feminist approaches to the situated nature of knowledge.