Miracle-dz/UniFAR-FTUs huggingface dataset:
McPAT-PVT: Delay and Power Modeling Framework for FinFET Processor Architectures Under PVT Variations

As technology has moved into the deep-submicrometer regime, the shrinking feature size has placed a considerable stress on CMOS fabrication due to short-channel effects (SCEs) and excessive leakage. Although many research efforts have been devoted to seeking system-level solutions, underlying transistor-level solutions are still urgently required to overcome these obstacles. FinFETs have emerged as promising substitutes for conventional CMOS due to their superior control of SCEs and process scalability. However, FinFETs still face lithographic and workfunction engineering challenges, in addition to those posed by supply voltage and temperature variations across the integrated circuit (IC). These lead to process, supply voltage, and temperature (PVT) variations in FinFET ICs, which, in turn, lead to large spreads in delay and leakage. In this paper, we present a multicore power, area, and timing (McPAT)-PVT, an integrated framework for the simulation of power, delay, as well as PVT variations of FinFET-based processors. McPAT-PVT uses a FinFET design library, consisting of logic and memory cells, to model circuit-level characteristics as well as their PVT variation trends. It is based on macromodels, derived from very accurate TCAD device simulations that characterize various functional units in a processor under PVT variations, making yield analysis for timing and power for processor components possible. McPAT-PVT can model both shorted-gate (SG) and asymmetric-workfunction shorted-gate (ASG) FinFET-based processors. Combining these macromodels with a FinFET-based CACTI-PVT cache model and an ORION-PVT on-chip network model, McPAT-PVT is able to simulate a delay and power consumption of all processor components under PVT variations. We present extensive simulation results to demonstrate its efficacy, including for an alpha-like processor and multicore simulations based on Princeton Application Repository for Shared-Memory Computers benchmarks. Results show that the ASG FinFET-based processor implementation has 73× lower leakage power and 2.6× lower total power relative to the SG FinFET-based processor implementation for the same performance, with <;1% area penalty.
Sec16B is involved in the endoplasmic reticulum export of the peroxisomal membrane biogenesis factor peroxin 16 (Pex16) in mammalian cells

Sec16 plays a key role in the formation of coat protein II vesicles, which mediate protein transport from the endoplasmic reticulum (ER) to the Golgi apparatus. Mammals have two Sec16 isoforms: Sec16A, which is a longer primary ortholog of yeast Sec16, and Sec16B, which is a shorter distant ortholog. Previous studies have shown that Sec16B, as well as Sec16A, defines ER exit sites, where coat protein II vesicles are formed in mammalian cells. Here, we reveal an unexpected role of Sec16B in the biogenesis of mammalian peroxisomes. When overexpressed, Sec16B was targeted to the entire ER, whereas Sec16A was mostly cytosolic. Concomitant with the overexpression of Sec16B, peroxisomal membrane biogenesis factors peroxin 3 (Pex3) and Pex16 were redistributed from peroxisomes to Sec16B-positive ER membranes. Knockdown of Sec16B but not Sec16A by RNAi affected the morphology of peroxisomes, inhibited the transport of Pex16 from the ER to peroxisomes, and suppressed expression of Pex3. These phenotypes were significantly reversed by the expression of RNAi-resistant Sec16B. Together, our results support the view that peroxisomes are formed, at least partly, from the ER and identify a factor responsible for this process.
Frequency Domain capture of light fields using Heterodyning: Analysis of Aliasing

We analyze the modulation of a light-field via non-refracting attenuators. The d esign first proposed in [ 8] exploits frequency-domain modulation to achieve a more efficient encodin g . We study the aliasing in the sensed light field and discuss the effects of aliasing on mask based heterodyning lig ht field camera.
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships

MOTIVATION The prediction of protein-protein interactions is currently an important issue in bioinformatics. The mirror tree method uses evolutionary information to predict protein-protein interactions. However, it has been recognized that predictions by the mirror tree method lead to many false positives. The incentive of our study was to solve this problem by improving the method of extracting the co-evolutionary information regarding the protein pairs. RESULTS We developed a novel method to predict protein-protein interactions from co-evolutionary information in the framework of the mirror tree method. The originality is the use of the projection operator to exclude the information about the phylogenetic relationships among the source organisms from the distance matrix. Each distance matrix was transformed into a vector for the operation. The vector is referred to as a 'phylogenetic vector'. We have proposed three ways to extract the phylogenetic information: (1) using the 16S rRNA from the same source organisms as the proteins under consideration, (2) averaging the phylogenetic vectors and (3) analyzing the principal components of the phylogenetic vectors. We examined the performance of the proposed methods to predict interacting protein pairs from Escherichia coli, using experimentally verified data. Our method was successful, and it drastically reduced the number of false positives in the prediction. AVAILABILITY The R script for the prediction of protein-protein interactions reported in this manuscript is available at http://timpani.genome. ad.jp/~proj/ CONTACT sato@kuicr.kyoto-u.ac. jp SUPPLEMENTARY INFORMATION The information is also available at the same site as the R script.
Pseudomonas aeruginosa Bacteriophage PA1Ø Requires Type IV Pili for Infection and Shows Broad Bactericidal and Biofilm Removal Activities

ABSTRACT We isolated a new lytic Pseudomonas aeruginosa phage that requires type IV pili for infection. PA1Ø has a broad bactericidal spectrum, covering Gram-positive and Gram-negative bacteria, and can eradicate biofilm cells. PA1Ø may be developed as a therapeutic agent for biofilm-related mixed infections with P. aeruginosa and Staphylococcus aureus.
The Art of Artificial Intelligence: Themes and Case Studies of Knowledge Engineering

The knowledge engineer practices the art of bringing the principles and tools of AI research to bear on difficult applications problems requiring experts' knowledge for their solution. The technical issues of acquiring this knowledge, representing it, and using it appropriately to construct and explain lines-of-reasoning, are important problems in the design of knowledge-based systems. Various systems that have achieved expert level performance in scientific and medical inference illuminate the art of knowledge engineering and its parent science, Artificial Intelligence.
Serotonin Stimulates Phosphorylation of AplysiaSynapsin and Alters Its Subcellular Distribution in Sensory Neurons

Only a small fraction of neurotransmitter-containing synaptic vesicles (SVs), the readily releasable pool, is available for fast Ca2+-induced release at any synapse. Most SVs are sequestered at sites away from the plasma membrane and cannot be exocytosed directly. Recruitment of SVs to the releasable pool is thought to be an important component of short-term synaptic facilitation by serotonin (5-HT) at Aplysia sensorimotor synapses. Synapsins are associated with SVs and hypothesized to play a central role in the regulation of SV mobilization in nerve terminals.Aplysia synapsin was cloned to examine its role in synaptic plasticity at the well characterized sensorimotor neuron synapse of this animal. Acute 5-HT treatment of ganglia induced synapsin phosphorylation. Immunohistochemical analyses of culturedAplysia neurons revealed that synapsin is distributed in distinct puncta in the neurites. These puncta are rapidly dispersed after treatment of the neurons with 5-HT. The dispersion of synapsin puncta by 5-HT was fully reversible after washout of the modulator. Both 5-HT-induced phosphorylation and dispersion of synapsin were mediated, at least in part, by cAMP-dependent protein kinase and mitogen-activated protein kinase. These experiments indicate that synapsin and its regulation by 5-HT may play an important role in the modulation of SV trafficking in short-term synaptic plasticity.
A Metamorphic Testing Approach for Online Testing of Service-Oriented Software Applications

Testing the correctness of services assures the functional quality of service-oriented applications. A service-oriented application may bind dynamically to its supportive services. For the same service interface, the supportive services may behave differently. A service may also need to realize a business strategy, like best pricing, relative to the behavior of its counterparts and the dynamic market situations. Many existing works ignore these issues to address the problem of identifying failures from test results. This article proposes a metamorphic approach for online services testing. The off-line testing determines a set of successful test cases to construct their corresponding follow-up test cases for the online testing. These test cases will be executed by metamorphic services that encapsulate the services under test as well as the implementations of metamorphic relations. Thus, any failure revealed by the metamorphic testing approach will be due to the failures in the online testing mode. An experiment is included. Copyright
USING fMRI IN CARTOGRAPHIC RESEARCH

In this paper we summarize findings to date from a project that had subjects performing navigational map tasks on a computer and again while they were being scanned in a magnetic resonance imaging machine. By comparing activity levels in each voxel with an expected function, the images were converted to functional ones (fMRI), and involvement or non-involvement of the brain area in doing the task was indicated. We will raise some fundamental questions that arise in such research, including "Should cartographers be collaborating with colleagues in other disciplines to carry out work of this sort? " and "So what? " We argue that yes, we should be so involved, even if in the end we find little useful. There could be important implications for some very hard questions that overlap between psychology, physiology, and cartography/GIS such as which tasks use similar brain regions even though the tasks themselves seem to be very different or which tasks use different brain regions even though the tasks seem to be very similar. INTRODUCTION AND BACKGROUND: For years, cartographers and psychologists conducted research in the area of map reading and spatial abilities. But, until recently, collaborative research was rare. Arguably, such collaborative research brings together the strengths of each discipline, resulting in more meaningful, reliable, and valid results. Similar to the beginning of spatial/map abilities research, fMRI based experiments are currently not commonly conducted collaboratively. But, such collaboration would likely improve the breadth and depth of the research. Any review of fMRI-related spatial abilities research would reveal many results that address map related issues. However, in many cases, even though the study questions may mirror similar ones asked by cartographers, the test instruments do not include maps. Therefore, results may be generalized to suggest they may potentially be related to similar cartographic questions; but, unless the test instruments include maps and the questions address cartographic research, the extent to which results may be generalized is unproven. One way to bring the map or cartographic questions into the body of fMRI research is for cartographers to include this technology in their research. Arguably, map-related research may be considerably more fruitful when undertaken by collaborative teams. In the case of fMRI research, such teams may involve more than the cartographic/psychological groupings that are becoming more common in cognitive map research. Because of the technology and processes involved in fMRI studies, radiology and physiology researchers are part of the research team. Each participant potentially brings to the project a unique and valuable perspective.
Mycoplasma tullyi sp. nov., isolated from penguins of the genus Spheniscus.

A mycoplasma isolated from the liver of a dead Humboldt penguin (Spheniscus humboldti) and designated strain 56A97T, was investigated to determine its taxonomic status. Complete 16S rRNA gene sequence analysis indicated that the organism was most closely related to Mycoplasma gallisepticum and Mycoplasma imitans(99.7 and 99.9 % similarity, respectively). The average DNA-DNA hybridization values between strain 56A97T and M. gallisepticum and M. imitans were 39.5 and 30 %, respectively and the Genome to Genome Distance Calculator gave results of 29.10 and 23.50 %, respectively. The 16S-23S rRNA intergenic spacer was 72-73 % similar to M. gallisepticum strains and 52.2 % to M. imitans. A partial sequence of rpoB was 91.1-92 % similar to M. gallisepticum strains and 84.7 % to M. imitans. Colonies possessed a typical fried-egg appearance and electron micrographs revealed the lack of a cell wall and a nearly spherical morphology, with an electron-dense tip-like structure on some flask-shaped cells. The isolate required sterol for growth, fermented glucose, adsorbed and haemolysed erythrocytes, but did not hydrolyse arginine or urea. The strain was compared serologically against 110 previously described Mycoplasma reference strains, showing that, except for M. gallisepticum, strain 56A97T is not related to any of the previously described species, although weak cross-reactions were evident. Genomic information, serological reactions and phenotypic properties demonstrate that this organism represents a novel species of the genus Mycoplasma, for which the name Mycoplasma tullyi sp. nov. is proposed; the type strain is 56A97T (ATCC BAA-1432T, DSM 21909T, NCTC 11747T).
D-Coil: A Hands-on Approach to Digital 3D Models Design

We introduce D-Coil, a new digital 3D modeling approach using wax coiling to bring tangibility to the design of digital models. After defining a shape to extrude, the users follow the lead of a hand-held actuated extruder to instantiate the actual extrusion using wax. The tangibility of the wax extrusion sets the stage to create the next components until the digital model is completed. The digital model affords all digital attributes (ease of transformation, distribution, and 3D printing) while the wax artifact can be discarded or kept as a one-of-a-kind memento. We present a proof-of-concept implementation of D-Coil and showcase how this additive approach can also be extended to a subtractive process using a digitally actuated cutter. By adding a 6DOF mouse, users can also include scaling, rotation, and bending effects to create a wide variety of shapes often difficult for novices to produce in standard CAD software.
Jamming Detection of Smartphones for WiFi Signals

In this paper, we investigate the impact of jamming attacks on the performance of smartphones regarding their WiFi access and propose a real-time jamming detection method based on the received signal strength indicator and the packet loss rate of WiFi signals, which can be easily implemented on Android smartphones. Experiments are performed to evaluate the proposed jamming detection method, in which universal software radio peripherals are used as jammers to block the WiFi signals between smartphone phones and wireless routers. Experimental results show that the proposed application can detect jamming attacks with small false alarm rate and miss detection raaaaaate.
The Next Stage of Operational Business Intelligence: Creating New Challenges for Business Process Management

Current practices in the area of business intelligence (BI) and business performance management (BPerM) confirm the need for better integration of BI and business processes (BPs). This is especially the case with operational BI that aims to unify strategic and tactical decision making, by integrating BI solutions with organisation's constantly evolving BPs. However, operational BI has a very limited view of BP and business process management (BProM) systems. In essence, it focuses on a limited number of core, transactional BPs that are, by definition, highly structured and repetitive. This paper argues that in order to support customer-facing employees in service-oriented industries, it is necessary to consider knowledge intensive BPs and their possible integration with operational BI. This paper offers a critical analysis of case-handling BPs in the context of operational BI. It then identifies a number of research challenges related to a new type of case-handling BProM system
On event-triggered adaptive robust control

In this work, an event-triggered adaptive robust controller (ET-ARC) design is considered for a continuous-time nonlinear system combined with structural uncertainties and parameter uncertainties. In the event-trigger scheme, the controller only can obtain the sampled date of the output measurement at some certain instants determined by the designed triggering condition and therefore the performance of the ET-ARC depends on the triggering condition directly. Thus, in this work, for the adaptive robust control scheme, an event-triggered transmission strategy is proposed, which relies on the output measurement of the nonlinear system. Then, based on this strategy, the design idea of the adaptive robust controller is presented such that the tracking performance is guaranteed. Furthermore, based on a more general assumption, we provide a possible formation of control signal which satisfies the requirement proposed.
Tailored Mechanical Properties and Residual Stresses of a-C:H:W Coatings

In this study, three different a-C:H:W coatings with predefined hardness values, ranging from 10 up to 16 GPa, were deposited by adjusting bias voltage according to a previously created regression model. For this purpose, the influence of the main process parameters of the used reactive unbalanced magnetron sputtering process on the mechanical properties of the a-C:H:W coating was investigated previously by nanoindentation. For a systematical evaluation of the single effects, parameters were varied according to a central composite design. The three coating variants of this study were investigated in terms of microstructure, mechanical properties and residual stresses. It turned out, that by the use of the regression model, a-C:H:W coatings with tailored mechanical properties can be deposited. Residual stresses were measured by means of focused ion beam milling of a double-slit geometry, which causes the internal stresses to relax, and mapping of the resultant relief strain by digital image correlation. A linear relation between the applied bias voltage and the hardness, the modulus of the coating as well as the determined relief strain was observed. Thus, residual stresses of the coatings increase disproportionately with applied bias voltage. The obtained results can be helpful for tailored coating design and further optimization of a-C:H:W coatings.
On the Feasibility of a Consistent and Fault-Tolerant Data Store for SDNs

Maintaining a strongly consistent network view in a Software Defined Network has been usually proclaimed as a synonym of low performance. We disagree. To support our view, in this paper we argue that with the use of modern distributed systems techniques it is possible to build a strongly consistent, fault-tolerant SDN control framework that achieves acceptable performance. The central element of our architecture is a highly-available, strongly consistent data store. We describe a prototype implementation of a distributed controller architecture integrating the Floodlight controller with a data store implemented using a state-of-the-art replication algorithm. We evaluate the feasibility of the proposed design by analyzing the workloads of real SDN applications (a learning switch, a load balancer and a device manager) and showing that the data store is capable of handling them with adequate performance.
Formation of DNA Replication Structures in Herpes Virus-Infected Cells Viral DNA Binding Protein Requires a

Eukaryotic DNA synthesis is thought to occur in multienzyme complexes present at numerous discrete sites throughout the nucleus. We demonstrate here that cellular DNA replication sites identified by bromodeoxyuridine labeling are relocated in cells infected with herpes simplex virus such that they correspond to viral prereplicative structures containing the HSV DNA replication protein, ICP8. Thus components of the cellular DNA replication apparatus are present at viral prereplicative sites. Mutant virus strains expressing defective ICP8 do not alter the pattern of host cell DNA replication sites, indicating that functional ICP8 is required for the redistribution of cellular DNA replication complexes. This demonstrates that a specific protein molecule can play a role in the organixation of DNA replication proteins at discrete sites within the cell nucleus.
Making distortions comprehensible

This paper discuses visual information representation from the perspective of human comprehension. The distortion viewing paradigm is an appropriate focus for this discussion as its motivation has always been to create more understandable displays. While these techniques are becoming increasingly popular for exploring images that are larger than the available screen space, in fact users sometimes report confusion and disorientation. We provide an overview of structural changes made in response to this phenomenon and examine methods for incorporating visual cues based on human perceptual skills.
Neuropharmacology of Vestibular System Disorders

This work reviews the neuropharmacology of the vestibular system, with an emphasis on the mechanism of action of drugs used in the treatment of vestibular disorders. Otolaryngologists are confronted with a rapidly changing field in which advances in the knowledge of ionic channel function and synaptic transmission mechanisms have led to the development of new scientific models for the understanding of vestibular dysfunction and its management. In particular, there have been recent advances in our knowledge of the fundamental mechanisms of vestibular system function and drug mechanisms of action. In this work, drugs acting on vestibular system have been grouped into two main categories according to their primary mechanisms of action: those with effects on neurotransmitters and neuromodulator receptors and those that act on voltage-gated ion channels. Particular attention is given in this review to drugs that may provide additional insight into the pathophysiology of vestibular diseases. A critical review of the pharmacology and highlights of the major advances are discussed in each case.
Interactive remote exploration of massive cityscapes

We focus on developing a simple and efficient unified level-of-detail structure for networked urban model viewers. At the core of our approach is a revisitation of the BlockMap [CDG*07] data structure, originally introduced for encoding coarse representations of blocks of buildings to be used as direction-independent impostors when rendering far-away city blocks. The contribution of this paper is manifold: we extend the BlockMap representation to support sloped surfaces and input-sensitive sampling of color; we introduce a novel sampling strategy for building accurate BlockMaps; we show that BlockMaps can be used as a versatile and robust way to parameterize the visible surface of a highly complex model; we improve the expressiveness of urban models rendering by integrating an ambient occlusion term in the representation and describe an efficient method for computing it; we illustrate the design and implementation of a urban models streaming and visualization system and demonstrate its efficiency when browsing large city models in a limited bandwidth setting.