Miracle-dz/UniFAR-FTUs huggingface dataset:
G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G‐LoSA. G‐LoSA aligns protein local structures in a sequence order independent way and provides a GA‐score, a chemical feature‐based and size‐independent structure similarity score. Our benchmark validation shows the robust performance of G‐LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure‐centric comparative biology studies. In particular, G‐LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G‐LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer‐aided drug design. We hope that G‐LoSA can be a useful computational method for exploring interesting biological problems through large‐scale comparison of protein local structures and facilitating drug discovery research and development. G‐LoSA is freely available to academic users at http://im.compbio. ku.edu/GLoSA/.
Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase

Protein structure modeling using a homologous template is one of many routines that accompany the molecular dynamics simulation for biological material. There are currently two protocols of protein modeling available in Accelrys Discovery Studio 2.1, Build Mutants and Build Homology Modeling protocols. Both are template-based modeling, but with a different process. In this study, two different templates, 3CKZ and 274Y, have been used to see how much the differences will be made by those two protocols if the templates has significant percentage of identity. Evaluation of structure models has been performed using DOPE score, 3D-profile, and PROCHECK. The results indicated that Build Mutants Protocols produces more stable structures but has a low reliability values and low quality of stereochemistry when using a template that has a lower percentage of identity. The results also yield more stable, reliable, and higher percentage of residues in most favoured and additionally allowed region for the usage of Build Homology Modeling Protocol on both templates. These observations suggest that Build Homology Modeling protocol is recommended for protein modeling.
Striosome–dendron bouquets highlight a unique striatonigral circuit targeting dopamine-containing neurons

Significance The dopamine-containing nigrostriatal system and its return striatonigral pathway form a loop–circuit crucial for the functions of dopamine in modulating movement and mood. Here we identify a specialized subsystem within this loop. With new mouse models and tissue expansion to allow nanoscale imaging, we demonstrate that striatonigral fibers originating in striosomes form bouquet-like arborizations innervating clusters of dopamine-containing neurons and their ventrally extending, tightly bundled dendrites. Within these formations (termed “striosome–dendron bouquets”), striosomal axons and dopamine-containing dendrites are intimately intertwined, as are other afferent and glial elements. The stunning selectivity of striosomal output to the bouquets suggests that the bouquets could exert powerful and focused control over elements of the dopamine system in normal and abnormal states. The dopamine systems of the brain powerfully influence movement and motivation. We demonstrate that striatonigral fibers originating in striosomes form highly unusual bouquet-like arborizations that target bundles of ventrally extending dopamine-containing dendrites and clusters of their parent nigral cell bodies. Retrograde tracing showed that these clustered cell bodies in turn project to the striatum as part of the classic nigrostriatal pathway. Thus, these striosome–dendron formations, here termed “striosome–dendron bouquets,” likely represent subsystems with the nigro–striato–nigral loop that are affected in human disorders including Parkinson’s disease. Within the bouquets, expansion microscopy resolved many individual striosomal fibers tightly intertwined with the dopamine-containing dendrites and also with afferents labeled by glutamatergic, GABAergic, and cholinergic markers and markers for astrocytic cells and fibers and connexin 43 puncta. We suggest that the striosome–dendron bouquets form specialized integrative units within the dopamine-containing nigral system. Given evidence that striosomes receive input from cortical regions related to the control of mood and motivation and that they link functionally to reinforcement and decision-making, the striosome–dendron bouquets could be critical to dopamine-related function in health and disease.
Automatic 3D modelling of craniofacial form

Three-dimensional models of craniofacial variation over the general population are useful for assessing pre- and post-operative head shape when treating various craniofacial conditions, such as craniosynostosis. We present a new method of automatically building both sagittal profile models and full 3D surface models of the human head using a range of techniques in 3D surface image analysis; in particular, automatic facial landmarking using supervised machine learning, global and local symmetry plane detection using a variant of trimmed iterative closest points, locally-affine template warping (for full 3D models) and a novel pose normalisation using robust iterative ellipse fitting. The PCA-based models built using the new pose normalisation are more compact than those using Generalised Procrustes Analysis and we demonstrate their utility in a clinical case study.
Changes in the Microvasculature after Mechanical Pressure on the Hamster Cheek Pouch

The reaction of the microvasculature in the periodontal ligament to mechanical pressure is considered a very important phenomenon with respect to the biological background to orthodontic tooth movement. For clarification of the microvascular reaction to mechanical pressure, an experimental model that incorporated a hamster cheek pouch was established. This in vivo model solves some of the problems of other experimental models of the microvasculature of the periodontal ligament. Blood plasma permeation in this model was examined by means of a blue dye (pontamine sky blue), and histological observation was performed by light and transmission electron microscopy. Increased vascular permeability was observed within 30 min after removal of the mechanical stimulation. The threshold weight resulting in dye leakage was between 1 and 5 g applied for 60 min. From the histological observations, some large gaps between the endothelial cells in venules were found, while most basement membranes remained undisturbed. These observations suggest that the plasma leakage was due to mild traumatic injury to the endothelial cells. Both leukocytes and platelets were observed in the gaps between the endothelial cells in the venule. These types of microvascular reactions to mechanical pressure could initiate tissue changes in the periodontal ligament during orthodontic tooth movement.
Introduction of Nickel Coated Silicon Carbide Particles in Aluminum Metal Matrix Hardfaced by MIG/TIG Processes on Precoated Flux Layer

The aim of the study was to investigate an aluminium metal matrix surface layer hardfaced by shielded gas metal arc welding processes applying either metal inert gas (MIG) or tungsten inert gas (TIG), with standard wire filler onto the precoated flux layer – a baked resistant film containing electroless nickel coated micro/nano SiC particles. During baking, the components of the flux (MgCl2, NaCl, KCl and Na3AlF6) form a low melting eutectic, which: protects the hardfaced surface from oxidation, provides electrical conductance and keeps the particles on the surface during welding, as well as facilitates particles wettability and their interfacial bonding with the molten metal into the weld puddle. The hardfaced layers were studied by NDT, SEM and EDX, as well as nanoindentation and wear resistance tests. The results from the nondestructive radiographic test show lack of imperfections, porosity and slag inclusions only after TIG hardfaced using nano SiC particles. The wear resistance increased from 25 % (TIG) up to 71 % (MIG), which was due to the presence of the incorporated in the hardfaced layer reinforced phase of electroless nickel coated micro/nano SiC particles. The obtained wear resistance test results correspond to the obtained hardness test values. © 2018 Published by Faculty of Engineering Corresponding author: V. Kamburov Technical University of Sofia 8 Kl. Ohridski Blvd 1786 Sofia, Bulgaria E-mail: vvk@tu-sofia.bg
Effective capacity of imperfect adaptive wireless communication systems

This paper presents a model for the link service capacity that an imperfect adaptive radio link provides to upper layers. As the main contribution of this paper, the model includes a number of imperfections in the link adaptation chain, as well as implementation implications. The average goodput is expressed also in compact form and its dependence on the impairments is discussed using analytical, numerical, and simulations results. The model, to be used for analyses at upper layers, integrates physical channel, transceiver characteristics, and imperfections in a flexible way, by independent, separate matrices
On Bounding the Delay of a Critical Path

Process variations cause different behavior of timing-dependent effects across different chips. In this work, we analyze one example of timing-dependent effects, cross-coupling capacitance, and the complex problem space created by considering coupling and process variations together. The delay of a critical path under these conditions is difficult to bound for design and test. We develop a methodology that analyzes this complex space by decomposing the problem space along three dimensions: the aggressor space, test space, and sample space. For design, we utilize an OBDD-based approach to prune the aggressor space based on logical constraints, which can be combined with a worst-case timing window simulator to prune based on both logical and timing constraints. After pruning, the reduced aggressor space can be used to derive a more accurate timing bound. Solving the problems in the test and sample spaces is postponed to the post-silicon stage, where we propose a test selection methodology for bounding the delay of every sample. This methodology is based on probability density estimation and has a tradeoff between the number of tests to apply and the tightness of the delay bound obtained. Experimental results based on benchmark examples are presented to show the effectiveness of the proposed methodology
Sub-nanometer narrow bandwidth gratings using deeply etched SOI rib waveguides

We report the design and analysis of a novel sub nanometer narrow bandwidth grating using sidewall corrugated SOI rib waveguide. Wavelength filters with narrow bandwidth, smaller device footprint, lesser complexity and higher fabrication tolerance are essential for on-chip Wavelength Division Multiplexing (WDM) applications. In this paper, we propose a simple and effective method to obtain ultra-narrow bandwidth. The design consists of a deeply etched rib waveguide with slab sidewall corrugation for index modulation. In order to understand the device characteristics, numerical investigations were employed. With a corrugation width of 60 nm, narrow 3-dB bandwidth of 0.5 nm at 1550 nm was achieved. Our results also serve as the precursor for a Dense WDM architecture with channel spacing of 0.8 nm, realizable by varying the grating pitch.
Metadata of the chapter that will be visualized in SpringerLink

The evolution of network services is closely connected to the understanding and modeling of their corresponding traffic. The obtained conclusions are related to a wide range of applications, like the design of the transfer lines’ capacity, the scalar taxing of customers, the security violations and the spotting of errors and anomalies. Intrusion Detection Systems (IDS) monitor and analyze the events in traffic, to locate indications for potential intrusion and integrity violation attacks, resulting in the violation of trust and availability of information resources. They act in a complimentary mode with the existing security infrastructure, aiming in the early warning of the administrator, offering him details that will let him reach proper decisions and correction actions. This paper proposes a network-based online system, which uses minimum computational power to analyze only the basic characteristics of network flow, so as to spot the existence and the type of a potential network anomaly. It is a Hybrid Machine Learning Anomaly Detection System (HMLADS), which employs classification performed by Evolving Spiking Neural Networks (eSNN), in order to properly label a Potential Anomaly (PAN) in the net. On the other hand it uses a Multi-Layer Feed Forward (MLFF) ANN to classify the exact type of the intrusion.
Four-Year Cumulative Radiation Exposure in Patients Undergoing Computed Tomography Angiography for Suspected Pulmonary Embolism

Purpose. The objective of this study was to determine the estimated effective radiation dose of pulmonary CT angiography (CTA) for suspected pulmonary embolism (PE) contributing to total medical radiation exposure over a 4-year period. Materials and Methods. This investigation retrospectively reviewed 300 patients who presented to the emergency department and received a pulmonary CTA scan for suspected PE. We evaluated these patients' electronic medical record to determine their estimated radiation exposure to CT scans during the following four years. Using DLP to E conversion coefficients, we calculated the cumulative effective radiation dose each subject received. Results. A total of 900 CT scans were reviewed in this study. Pulmonary CTA delivered an average effective radiation dose of 10.7 ± 2.5 mSv and accounted for approximately 65% of subjects' 4-year cumulative medical radiation dose. Only 6.3% of subjects had a positive acute PE according to their radiology report. Conclusion. Pulmonary CTA accounted for the majority of subjects' medically related effective radiation dose over a 4-year period. With only a minority of subjects having positive findings for acute PE, increased efforts should be made to clinically assess pretest probability before the consideration of imaging.
Magnesium Attenuates Phosphate-Induced Deregulation of a MicroRNA Signature and Prevents Modulation of Smad1 and Osterix during the Course of Vascular Calcification

Vascular calcification (VC) is prevalent in patients suffering from chronic kidney disease (CKD). High phosphate levels promote VC by inducing abnormalities in mineral and bone metabolism. Previously, we demonstrated that magnesium (Mg2+) prevents inorganic phosphate- (Pi-) induced VC in human aortic vascular smooth muscle cells (HAVSMC). As microRNAs (miR) modulate gene expression, we investigated the role of miR-29b, -30b, -125b, -133a, -143, and -204 in the protective effect of Mg2+ on VC. HAVSMC were cultured in the presence of 3 mM Pi with or without 2 mM Mg2+ chloride. Total RNA was extracted after 4 h, 24 h, day 3, day 7, and day 10. miR-30b, -133a, and -143 were downregulated during the time course of Pi-induced VC, whereas the addition of Mg2+ restored (miR-30b) or improved (miR-133a, miR-143) their expression. The expression of specific targets Smad1 and Osterix was significantly increased in the presence of Pi and restored by coincubation with Mg2+. As miR-30b, miR-133a, and miR-143 are negatively regulated by Pi and restored by Mg2+ with a congruent modulation of their known targets Runx2, Smad1, and Osterix, our results provide a potential mechanistic explanation of the observed upregulation of these master switches of osteogenesis during the course of VC.
The Wavelength of the Cardiac Impulse and Reentrant Arrhythmias in Isolated Rabbit Atrium: The Role of Heart Rate, Autonomic Transmitters, Temperature, and Potassium

We measured the wavelength of the cardiac impulse, defined as the distance traveled by the depolarization wave during the functional refractory period, in isolated narrow strips of rabbit atrium. During control, wavelength was 42 mm during pacing with 2 Hz, and was 28 mm at the maximum pacing rate; early premature beats had a wavelength as short as 23 mm. Administration of carbamylcholine (4 ± 10−7 g/ml) shortened the wavelength to 21 mm during 2 Hz, 18 mm at the maximum pacing rate Fmax and 16 mm during an early premature impulse, respectively. The effects of epinephrine (6 ± 10−7 M) were strongly rate dependent. At slow heart rates, epinephrine clearly prolonged the wavelength (58 mm), whereas, during maximum pacing, wavelength remained unchanged (28 mm). Hypokalemia (2 mM) decreased the length of the impulse at all stimulation frequencies. Moderate hyperkalemia (5.6 and 7.0 mM) did not modify wavelength because refractoriness and conduction velocity were affected proportionally. Above 7.0 mM potasssium, the wavelength became progressively prolonged because of the development of post-repolarization refractoriness. Cooling to 27°C resulted in a slight lengthening of the impulse. At lower temperatures, however, wavelength prolonged significantly because of a relatively strong prolongation of the refractory period. In separate experiments in 15 ± 20 mm segments of atrium, reentrant tachyarrhythmias were induced and the circuit size compared with the wavelength. The size of intraatrial circuits was similar to the magnitude of the measured wavelength during maximum pacing. Carbamylcholine and hypokalemia, both of which shorten the impulse length, also clearly decreased the size of reentrant circuits. Cooling to 27°C, which affects both refractoriness and conduction velocity, only slightly prolonged the wavelength; accordingly, the size of reentrant circuits at 27°C was only slightly longer than at 37°C. These experiments emphasize the importance of the wavelength of the cardiac impulse in relation to the occurrence of intramyocardial reentry.
Thin-film multiferroic phase shifter based on a slot transmission line

A microwave phase shifter based on a thin-film multiferroic metamaterials has been investigated. The thin-film structure was composed of a ferrite film, a ferroelectric film, and a slot transmission line. It was shown that the developed phase shifter is electrically and magnetically tunable. The dual tunability is due to a hybridization of the spin wave in the ferrite film with the electromagnetic wave in the slot-line. Performance characteristics of the phase shifter are presented.
System-of-Systems Perspective and Exploratory Modeling to Support the Design of Adaptive Policy for Reducing Carbon Emission

Reducing carbon emissions is needed to tackle climate change. However, despite the large uncertainties surrounding the issue, most policy design processes employ a predict-then-act approach. This paper applies a system-of-systems perspective and exploratory modeling method to support the design of an adaptive policy. Using a case in the Dutch residential sector, we use the SoS perspective as a way to decompose the policy issue into interdependent relevant policy systems. This representation of the policy system provides a framework to test a large number of hypotheses about the evolution of the system's behavior by way of computational experiments, which form the core of the exploratory modeling method. As some of the system uncertainties are resolved, policies am adapted so that policy goals can still be met. In particular, in a situation in which the realized emission level misses the target, a new set of conditions can be identified to bring the level back to the intended target.
A Counter-example to Karlin's Strong Conjecture for Fictitious Play

Fictitious play is a natural dynamic for equilibrium play in zero-sum games, proposed by Brown [6], and shown to converge by Robinson [33]. Samuel Karlin conjectured in 1959 that fictitious play converges at rate O(t-1/2) with respect to the number of steps t. We disprove this conjecture by showing that, when the payoff matrix of the row player is the n × n identity matrix, fictitious play may converge (for some tie-breaking) at rate as slow as Ω(t-1/n).
Nucleic Acid Supercoiling as a Means for Ionic Switching of DNA–Nanoparticle Networks

Oligomeric nanoparticle networks, generated by the self‐assembly of bis‐biotinylated double‐stranded DNA fragments and streptavidin, have been studied by scanning force microscopy (SFM). SFM imaging revealed the presence within the networks of irregular thick DNA molecules, which were often associated with distinct, Y‐shaped structural elements. Closer analysis revealed that the Y structures are formed by condensation (thickening and shortening) of two DNA fragments, most likely through the supercoiling of two DNA molecules bound to adjacent binding sites of the streptavidin particle. The frequency of supercoiling was found to be dependent on the ionic strength applied during the immobilization of the oligomeric networks on mica surfaces. Potential applications of the structural changes as a means for constructing ion‐dependent molecular switches in nanomaterials are discussed.
Acid-Sensing Ion Channel-2 Is Not Necessary for Sour Taste in Mice

The acid-sensitive cation channel acid-sensing ion channel-2 (ASIC2) is widely believed to be a receptor for acid (sour) taste in mammals on the basis of its physiological properties and expression in rat taste bud cells. Using reverse transcriptase-PCR, we detected expression of ASIC1 and ASIC3, but not ASIC4, in mouse and rat taste buds and nonsensory lingual epithelium. Surprisingly, we did not detect mRNA for ASIC2 in mouse taste buds, although we readily observed its expression in rat taste buds. Furthermore, in Ca2+ imaging experiments, ASIC2 knock-out mice exhibited normal physiological responses (increases in intracellular Ca2+ concentrations) to acid taste stimuli. Our results indicate that ASIC2 is not required for acid taste in mice, and that if a universal mammalian acid taste transduction mechanism exists, it likely uses other acid-sensitive receptors or ion channels.
On the birth-and-assassination process, with an application to scotching a rumor in a network

We give new formulas on the total number of born particles in the stable birth-and-assassination process, and prove that it has a heavy-tailed distribution. We also establish that this process is a scaling limit of a process of rumor scotching in a network, and is related to a predator-prey dynamics.