Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions between heme d and heme b595 in quinol oxidase bd from Escherichia coli: a photoselection study using femtosecond spectroscopy.

Femtosecond spectroscopy was performed on CO-liganded (fully reduced and mixed-valence states) and O(2)-liganded quinol oxidase bd from Escherichia coli. Substantial polarization effects, unprecedented for optical studies of heme proteins, were observed in the CO photodissociation spectra, implying interactions between heme d (the chlorin ligand binding site) and the close-lying heme b(595) on the picosecond time scale; this general result is fully consistent with previous work [Vos, M. H. , Borisov, V. B. , Liebl, U. , Martin, J.-L. , and Konstantinov, A. A. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 1554-1559]. Analysis of the data obtained under isotropic and anisotropic polarization conditions and additional flash photolysis nanosecond experiments on a mutant of cytochrome bd mostly lacking heme b(595) allow to attribute the features in the well-known but unusual CO dissociation spectrum of cytochrome bd to individual heme d and heme b(595) transitions. This renders it possible to compare the spectra of CO dissociation from reduced and mixed-valence cytochrome bd under static conditions and on a picosecond time scale in much more detail than previously possible. CO binding/dissociation from heme d is shown to perturb ferrous heme b(595), causing induction/loss of an absorption band centered at 435 nm. In addition, the CO photodissociation-induced absorption changes at 50 ps reveal a bathochromic shift of ferrous heme b(595) relative to the static spectrum. No evidence for transient binding of CO to heme b(595) after dissociation from heme d is found in the picosecond time range. The yield of CO photodissociation from heme d on a time scale of < 15 ps is found to be diminished more than 3-fold when heme b(595) is oxidized rather than reduced. In contrast to other known heme proteins, molecular oxygen cannot be photodissociated from the mixed-valence cytochrome bd at all, indicating a unique structural and electronic configuration of the diheme active site in the enzyme.
O6-Methylguanine-DNA Methyltransferase (MGMT) mRNA Expression Predicts Outcome in Malignant Glioma Independent of MGMT Promoter Methylation

Background We analyzed prospectively whether MGMT (O6-methylguanine-DNA methyltransferase) mRNA expression gains prognostic/predictive impact independent of MGMT promoter methylation in malignant glioma patients undergoing radiotherapy with concomitant and adjuvant temozolomide or temozolomide alone. As DNA-methyltransferases (DNMTs) are the enzymes responsible for setting up and maintaining DNA methylation patterns in eukaryotic cells, we analyzed further, whether MGMT promoter methylation is associated with upregulation of DNMT expression. Methodology/Principal Findings Adult patients with a histologically proven malignant astrocytoma (glioblastoma: N = 53, anaplastic astrocytoma: N = 10) were included. MGMT promoter methylation was determined by methylation-specific PCR (MSP) and sequencing analysis. Expression of MGMT and DNMTs mRNA were analysed by real-time qPCR. Prognostic factors were obtained from proportional hazards models. Correlation between MGMT mRNA expression and MGMT methylation status was validated using data from the Cancer Genome Atlas (TCGA) database (N = 229 glioblastomas). Low MGMT mRNA expression was strongly predictive for prolonged time to progression, treatment response, and length of survival in univariate and multivariate models (p<0.0001); the degree of MGMT mRNA expression was highly correlated with the MGMT promoter methylation status (p<0.0001); however, discordant findings were seen in 12 glioblastoma patients: Patients with methylated tumors with high MGMT mRNA expression (N = 6) did significantly worse than those with low transcriptional activity (p<0.01). Conversely, unmethylated tumors with low MGMT mRNA expression (N = 6) did better than their counterparts. A nearly identical frequency of concordant and discordant findings was obtained by analyzing the TCGA database (p<0.0001). Expression of DNMT1 and DNMT3b was strongly upregulated in tumor tissue, but not correlated with MGMT promoter methylation and MGMT mRNA expression. Conclusions/Significance MGMT mRNA expression plays a direct role for mediating tumor sensitivity to alkylating agents. Discordant findings indicate methylation-independent pathways of MGMT expression regulation. DNMT1 and DNMT3b are likely to be involved in CGI methylation. However, their exact role yet has to be defined.
Building a WordNet for Sinhala

Sinhala is one of the official languages of Sri Lanka and is used by over 19 million people. It belongs to the Indo-Aryan branch of the Indo-European languages and its origins date back to at least 2000 years. It has developed into its current form over a long period of time with influences from a wide variety of languages including Tamil, Portuguese and English. As for any other language, a WordNet is extremely important for Sinhala to take it into the digital era. This paper is based on the project to develop a WordNet for Sinhala based on the English (Princeton) WordNet. It describes how we overcame the challenges in adding Sinhala specific characteristics which were deemed important by Sinhala language experts to the WordNet while keeping the structure of the original English WordNet. It also presents the details of the crowdsourcing system we developed as a part of the project consisting of a NoSQL database in the backend and a web-based frontend. We conclude by discussing the possibility of adapting this architecture for other languages and the road ahead for the Sinhala WordNet and Sinhala NLP.
Uniting Control Lyapunov and Control Barrier Functions

In this paper, we propose a nonlinear control design for solving the problem of stabilization with guaranteed safety. The design is based on the merging of a Control Lyapunov Function and a Control Barrier Function. The proposed control method allows us to combine the design of a stabilizer based on CLF and the design of safety control based on CBF. The efficacy of the proposed approach is shown in the simulation results.
Evolving Complex Network for Classification Problems

In this paper, a new automatic method for constructing and evolving complex network is proposed. This method uses the concept of complex networks (mainly scale-free networks) and combines the essence of Immune Programming with Particle Swarm Optimization algorithm. The structure of a complex network genotype is evolved using Immune Programming algorithm with speci¿c parameters, and the ¿ne tuning of the parameters encoded in the structure is accomplished using particle swarm optimization algorithm. The performance of proposed method is compared with Flexible Neural Tree (FNT), Neural Network (NN), and Wavelet Neural Network (WNN) by using the same breast cancer data set. The results of experimental study indicate that the proposed method is efficient.
Recent Experiments on the Properties of the Na Efflux from Squid Axons

The energy-dependent extrusion of internal Na in exchange for external K by the process known as the sodium pump is inhibited very specifically by low concentrations of the cardiac glycoside ouabain, and the use of this drug provides a means of dividing any flux of Na or K into its presumed Na pump and presumed non-Napump components. The purpose of the present paper is to describe the main properties of these two components of the Na effiux from squid axons (summarized in Table I). Throughout this work care was taken to ensure that the concentration of ouabain used was well in excess of that required to effect 100 % inhibition (usually 100 times) and adequate time was always left for inhibition to become complete. In squid axons inhibition by ouabain is not easily reversed (Caldwell and Keynes, 1959). The axons were obtained from Loligo forbesii and were normally stored at 4°C for up to 12 hr before use. They had an average internal Na content of 75 mmoles/kg axoplasm.
A machine learning approach to vehicle occupancy detection

To manage ever increasing traffic volume on modern highways, transportation agencies have introduced special managed lanes where only vehicles with a certain occupancy level are allowed. This encourages highway users to ride together, thus, in theory, more efficiently transporting people through the highway system. In order to be effective, however, adherence to the vehicle occupancy rules has to be enforced. Recent studies have shown that the traditional approach of dispatching traffic law enforcement officers to perform roadside visual inspections is not only expensive and dangerous, but also ineffective for managed lane enforcement. In this paper, we describe an image-based machine learning approach for automatic or semi-automatic vehicle occupancy detection. Our method localizes windshield regions by constructing an elastic deformation model from sets of uniquely defined landmark points along the front windshield. From the localized windshield region, the method calculates image-level feature representations, which are then applied to a trained classifier for classifying the vehicle into violator and non-violator classes.
IAC: Interest-Aware Caching for Unstructured P2P

The simplicity and robustness of unstructured P2P system make it a preferable architecture for constructing real large scale file sharing system. Most of the existing paradigms require more overhead. The trace data analysis shows that the workloads among peers are correlated. The bigger the intersection of workloads, the higher the probability that they share other files is. By exploiting such principle, we propose IAC, an interest-aware resource advertisement caching paradigm for unstructured p2p system. Each peer advertises its resource list. If a peer is interested in the resource advertisement received, it then caches the advertisement. Through local cache search, usually the peer gets more than 50% success rate. If local cache search is failed, the random walk-based search is used. The simulations show that as to the same hit rate, the maintenance and search overheads are low and the search delay is very low.
Male Sex Is Independently Associated with Faster Disability Accumulation in Relapse-Onset MS but Not in Primary Progressive MS

Background Multiple Sclerosis is more common in women than men and females have more relapses than men. In a large international cohort we have evaluated the effect of gender on disability accumulation and disease progression to determine if male MS patients have a worse clinical outcome than females. Methods Using the MSBase Registry, data from 15,826 MS patients from 25 countries was analysed. Changes in the severity of MS (EDSS) were compared between sexes using a repeated measures analysis in generalised linear mixed models. Kaplan-Meier analysis was used to test for sex difference in the time to reach EDSS milestones 3 and 6 and the secondary progressive MS. Results In relapse onset MS patients (n = 14,453), males progressed significantly faster in their EDSS than females (0.133 vs 0.112 per year, P<0.001,). Females had a reduced risk of secondary progressive MS (HR (95% CI) = 0.77 (0.67 to 0.90) P = 0.001). In primary progressive MS (n = 1,373), there was a significant increase in EDSS over time in males and females (P<0.001) but there was no significant sex effect on the annualized rate of EDSS change. Conclusion Among registrants of MSBase, male relapse-onset patients accumulate disability faster than female patients. In contrast, the rate of disability accumulation between male and female patients with primary progressive MS is similar.
An interval algebra for multiprocessor resource allocation

This paper presents an interval algebra created specifically to evaluate timing properties of multiprocessor systems. It models the application load as intervals, and considers allocation and scheduling as algebraic operations over those intervals, aiming to analyse the impact of resource allocation decisions on application response times or schedulability. The theoretical background is introduced informally, followed by the description of a reference implementation of the interval algebra in C++, aiming to appeal to the design practitioner rather than the formalist. Examples of the usage of the proposed algebra are also provided, showing its applicability to the performance evaluation of industrial systems implemented over bus-based and Network-on-Chip multiprocessor platforms. A particular design flow is highlighted, where the interval algebra is used as a fitness function in a genetic algorithm tailored to optimise resource allocation in hard real-time multiprocessors.
Uses and Gratification of Posting Selfies on Social Media

5 Introduction . 6 Theoretical Perspective . 7 Literature Review.9 Research Questions . 11 Methodology . 12 Results . 19 Discussion . 22 Limitations and Directions for Future Studies . 25 Conclusion . 26 References . 28 Appendix . 32 USES AND GRATIFICATION OF SELFIES 5 USES AND GRATIFICATION OF POSTING SELFIES ON SOCIAL MEDIA Amanda Kearney School of Communication College of Liberal Arts Master of Science in Communication & Media Technologies Term Degree Awarded: Spring Semester 2018 (2175) Abstract Selfies have become an easy and instantaneous form of self-expression and communication. Posting selfies to various social media platforms has become wildly popular and socially accepted in the digital age. This study investigated the motivation behind posting selfies to Facebook, Instagram, and Snapchat using the framework of uses and gratification theory. This study also compared differences in gratification sought from individual social media platforms. A cross-sectional survey shared on Facebook using a snowball sampling method recruited participants who post at least one selfie per week (N = 156). Factor analysis revealed five gratifications for posting selfies to social media: attention seeking, escape, entertainment, archiving time, and communication. An independent t-test revealed female selfie-posters seek self-presentation gratification over men. An independent t-test also revealed selfies are posted to Facebook to satisfy entertainment needs, while Instagram selfies satisfy needs of selfpresentation, habit, attention-seeking, entertainment, and status-seeking.
What powers the 3000-day light curve of SN 2006gy?

SN 2006gy was the most luminous supernova (SN) ever observed at the time of its discovery and the first of the newly defined class of superluminous supernovae (SLSNe). The extraordinary energetics of SN 2006gy and all SLSNe (>10^(51) erg) require either atypically large explosion energies (e.g. pair-instability explosion) or the efficient conversion of kinetic into radiative energy (e.g. shock interaction). The mass-loss characteristics can therefore offer important clues regarding the progenitor system. For the case of SN 2006gy, both a scattered and thermal light echo from circumstellar material (CSM) have been reported at later epochs (day ∼800), ruling out the likelihood of a pair-instability event and leading to constraints on the characteristics of the CSM. Owing to the proximity of the SN to the bright host-galaxy nucleus, continued monitoring of the light echo has not been trivial, requiring the high resolution offered by the Hubble Space Telescope (HST) or ground-based adaptive optics (AO). Here, we report detections of SN 2006gy using HST and Keck AO at ∼3000 d post-explosion and consider the emission mechanism for the very late-time light curve. While the optical light curve and optical spectral energy distribution are consistent with a continued scattered-light echo, a thermal echo is insufficient to power the K′-band emission by day 3000. Instead, we present evidence for late-time infrared emission from dust that is radiatively heated by CSM interaction within an extremely dense dust shell, and we consider the implications on the CSM characteristics and progenitor system.
INFORM: a dynamic interest forwarding mechanism for information centric networking

Information Centric Networking is a new communication paradigm where network primitives are based on named-data rather than host identifiers. In ICN, data retrieval is triggered by user requests which are forwarded towards a copy of the desired content item. Data can be retrieved either from a server that permanently provides a content item,or from a temporary item copy opportunistically cached by an in-network node. As the availability of cached items dynamically varies over time, the request forwarding scheme should be adapted accordingly. In this paper we focus on dynamic request forwarding in ICN, and develop an approach, inspired by Q-routing framework, that we show to outperform algorithms currently available in the state of the art.
Compressive sensing using locality-preserving matrices

Compressive sensing is a method for acquiring high dimensional signals (e.g., images) using a small number of linear measurements. Consider an n-pixel image x ∈ Rn, where each pixel p has value xp. The image is acquired by computing the measurement vector Ax, where A is an m x n measurement matrix, for some m << n. The goal is to design the matrix A and the recovery algorithm which, given Ax, returns an approximation to x. It is known that m=O(k log(n/k)) measurements suffices to recover the k-sparse approximation of x. Unfortunately, this result uses matrices A that are random. Such matrices are difficult to implement in physical devices. In this paper we propose compressive sensing schemes that use matrices A that achieve the near-optimal bound of m=O(k log n), while being highly "local". We also show impossibility results for stronger notions of locality.
C 3-symmetric opioid scaffolds are pH-responsive DNA condensation agents

Herein we report the synthesis of tripodal C3-symmetric opioid scaffolds as high-affinity condensation agents of duplex DNA. Condensation was achieved on both supercoiled and canonical B-DNA structures and identified by agarose electrophoresis, viscosity, turbidity and atomic force microscopy (AFM) measurements. Structurally, the requirement of a tris-opioid scaffold for condensation is demonstrated as both di- (C2-symmetric) and mono-substituted (C1-symmetric) mesitylene-linked opioid derivatives poorly coordinate dsDNA. Condensation, observed by toroidal and globule AFM aggregation, arises from surface-binding ionic interactions between protonated, cationic, tertiary amine groups on the opioid skeleton and the phosphate nucleic acid backbone. Indeed, by converting the 6-hydroxyl group of C3-morphine (MC3) to methoxy substituents in C3-heterocodeine (HC3) and C3-oripavine (OC3) molecules, dsDNA compaction is retained thus negating the possibility of phosphate—hydroxyl surface-binding. Tripodal opioid condensation was identified as pH dependent and strongly influenced by ionic strength with further evidence of cationic amine-phosphate backbone coordination arising from thermal melting analysis and circular dichroism spectroscopy, with compaction also witnessed on synthetic dsDNA co-polymers poly[d(A-T)2] and poly[d(G-C)2]. On-chip microfluidic analysis of DNA condensed by C3-agents provided concentration-dependent protection (inhibition) to site-selective excision by type II restriction enzymes: BamHI, HindIII, SalI and EcoRI, but not to the endonuclease DNase I.
Partitioning Trimmed Spline Surfaces into NonSelf-Occluding Regions for Visibility Computation

Computing the visible portions of curved surfaces from a given viewpoint is of great interest in many applications. It is closely related to the hidden surface removal problem in computer graphics, and machining applications in manufacturing. Most of the early work has focused on discrete methods based on polygonization or ray-tracing and hidden curve removal. In this paper we present an algorithm for decomposing a given surface into regions so that each region is either completely visible or hidden from a given viewpoint. Initially, it decomposes the domain of each surface based on silhouettes and boundary curves. To compute the exact visibility, we introduce a notion of visibility curves obtained by projection of silhouette and boundary curves and decomposition of the surface into nonoverlapping regions. These curves are computed using marching methods and we present techniques to compute all the components. The nonoverlapping and visible portions of the surface are represented as trimmed surfaces and we present a representation based on polygon trapezoidation algorithms. The algorithms presented use some recently developed algorithms from computational geometry like triangulation of simple polygons and point location. Given the nonoverlapping regions, we use an existing randomized algorithm for visibility computation. We also present results from a preliminary implementation of our algorithm.
Research of Permission Administration System Based on Access Control Matrix

Access control had always been seen as a complicated work. The traditional access control way can not adapt to the complicated dynamic access control well. The article had introduced how to use the access control matrix to judge user access or operation permission in the permission administration system and explained the meaning of the permission administration model which was based on access control matrix, then, this paper had illustrated the concrete implementation method of using interceptor to control the access. The control was carried on by an access control matrix. This control process was always triggered by a special interceptor when user accessed the system. In practical application, the access control system based on control matrix had eased the server system loading well.
Interconnecting IPv6 wireless sensors with an Android smartphone in the Future Internet

To fulfill the vision of the Future Internet a ubiquitous deployment of IPv6 is a necessity. The work presented in this paper combines networking technologies and mobile software application development to support interworking of mobile devices and smart objects. We report on the implementation of an Android IPv6 smartphone that interworks with Web-enabled wireless sensors in the Internet of Things. This includes a possible network setup for IPv4/IPv6 interworking by using a public tunnel broker service. The demonstrated solution is universal, since the Android device can be connected to any IP network, even where a Network Address Translation (NAT) device is deployed.
VLSI Implementation of a 2.8 Gevent/s Packet-Based AER Interface with Routing and Event Sorting Functionality

State-of-the-art large-scale neuromorphic systems require sophisticated spike event communication between units of the neural network. We present a high-speed communication infrastructure for a waferscale neuromorphic system, based on application-specific neuromorphic communication ICs in an field programmable gate arrays (FPGA)-maintained environment. The ICs implement configurable axonal delays, as required for certain types of dynamic processing or for emulating spike-based learning among distant cortical areas. Measurements are presented which show the efficacy of these delays in influencing behavior of neuromorphic benchmarks. The specialized, dedicated address-event-representation communication in most current systems requires separate, low-bandwidth configuration channels. In contrast, the configuration of the waferscale neuromorphic system is also handled by the digital packet-based pulse channel, which transmits configuration data at the full bandwidth otherwise used for pulse transmission. The overall so-called pulse communication subgroup (ICs and FPGA) delivers a factor 25–50 more event transmission rate than other current neuromorphic communication infrastructures.