Miracle-dz/UniFAR-FTUs huggingface dataset:
Chordet: an efficient and transparent replication for improving availability of peer-to-peer networked systems

In Peer-to-Peer (P2P) networked systems, participating nodes can be frequently disconnected from the networks because of several reasons such as users' intentions, nodes' failures, and network problems. This may increase the loss-ratio of the data and some other routing information; it may spoil the reliability of the whole P2P networks. Several works have been made to improve their reliability and availability based on existing Distributed Hash Tables (DHT) schemes. However, they have some trade-off relation between the performance and the reliability of the P2P networks. In this paper, we present Chordet, which is an efficient and transparent replication scheme for Chord-based P2P networks. Chordet replicates the data stored in the participating nodes so that they are evenly distributed. Using Chordet, the nodes can reduce lookup failure rates and lookup path length. Moreover, not all nodes need to implement proposed replication algorithm. Our simulation results show that Chordet outperforms the previous schemes in terms of both performance and reliability of the whole P2P networks.
C‐terminal domain of gyrase A is predicted to have a β‐propeller structure

Two different type II topoisomerases are known in bacteria. DNA gyrase (Gyr) introduces negative supercoils into DNA. Topoisomerase IV (Par) relaxes DNA supercoils. GyrA and ParC subunits of bacterial type II topoisomerases are involved in breakage and reunion of DNA. The spatial structure of the C‐terminal fragment in GyrA/ParC is not available. We infer homology between the C‐terminal domain of GyrA/ParC and a regulator of chromosome condensation (RCC1), a eukaryotic protein that functions as a guanine‐nucleotide‐exchange factor for the nuclear G protein Ran. This homology, complemented by detection of 6 sequence repeats with 4 predicted β‐strands each in GyrA/ParC sequences, allows us to predict that the GyrA/ParC C‐terminal domain folds into a 6‐bladed β‐propeller. The prediction rationalizes available experimental data and sheds light on the spatial properties of the largest topoisomerase domain that lacks structural information. Proteins 2002;47:258–264. © 2002 Wiley‐Liss, Inc.
Fractal Dimensions of Macromolecular Structures

Quantifying the properties of macromolecules is a prerequisite for understanding their roles in biochemical processes. One of the less‐explored geometric features of macromolecules is molecular surface irregularity, or ‘roughness’, which can be measured in terms of fractal dimension (D). In this study, we demonstrate that surface roughness correlates with ligand binding potential. We quantified the surface roughnesses of biological macromolecules in a large‐scale survey that revealed D values between 2.0 and 2.4. The results of our study imply that surface patches involved in molecular interactions, such as ligand‐binding pockets and protein‐protein interfaces, exhibit greater local fluctuations in their fractal dimensions than ‘inert’ surface areas. We expect approximately 22 % of a protein’s surface outside of the crystallographically known ligand binding sites to be ligandable. These findings provide a fresh perspective on macromolecular structure and have considerable implications for drug design as well as chemical and systems biology.
‘University opened up so many doors for me’: the personal and professional development of graduates from non-traditional backgrounds

ABSTRACT There is a substantial body of quantitative evidence about the benefits of higher education. However there is little qualitative evidence about the extent to which these benefits accrue to graduates from non-traditional backgrounds. This paper contributes to this gap in knowledge by exploring the experiences of a group of 15 graduates 10 years after they had started at university. The cohort was unusual because they had all completed a college-level qualification before going on to study at an elite university. We draw attention to the impact of higher education on their positions in the labour market, as well as to their development of learning identities that supported them to make changes in their personal and professional lives. Although higher education brought real benefits to the cohort, including better employment prospects and the development of confidence in themselves, we show that they were clustered in various caring and public sector professions at the lower end of the graduate labour market.
A yeast screen system for aromatase inhibitors and ligands for androgen receptor: yeast cells transformed with aromatase and androgen receptor.

Endocrine disruptors are hormone mimics that modify hormonal action in humans and animals. It is thought that some endocrine disruptors modify estrogen and androgen action in humans and animals by suppressing aromatase activity. Aromatase cytochrome P450 is the key enzyme that converts C19 androgens to aromatic C18 estrogenic steroids. We have developed a novel aromatase inhibitor screening method that allows us to identify antiaromatase activity of various environmental chemicals. The screen was developed by coexpressing the human aromatase and the mouse androgen receptor in yeast cells, which carry the androgen-responsive ss-galactosidase reporter plasmid. Functional expression of aromatase in yeast has been demonstrated using the [3H]-water release assay with intact cells as well as with yeast microsomes. The aromatase activity could be blocked by known aromatase inhibitors such as aminoglutethimide (AG). Yeast-produced androgen receptors were able to transactivate a yeast basal promoter linked to an androgen-responsive element in response to androgens. The resultant triple yeast transformant responded to the treatment of testosterone, androstenedione, or 5 alpha-dihydrotestosterone (5 alpha-DHT). In the absence of the aromatase inhibitor AG, transcriptional activation was observed only for the nonaromatizable androgen 5 alpha-DHT. However, the two aromatizable androgens (testosterone and androstenedione) induced the reporter activity in the presence of AG. Using this yeast-based assay, we confirmed that two flavones, chrysin and alpha-naphtholflavone, are inhibitors of aromatase. Thus, this yeast system allows us to develop a high-throughput screening method, without using radioactive substrate, to identify aromatase inhibitors as well as new ligands (nonaromatizable androgen mimics) for the androgen receptors. In addition, this screening method also allows us to distinguish nonandrogenic aromatase inhibitors from inhibitors with androgenic activity. This yeast screening method will be useful to screen environmental chemicals for their antiaromatase activity and for their interaction with androgen receptor. ImagesFigure 2Figure 3Figure 4Figure 5Figure 6Figure 7Figure 8Figure 9
ACTIVE LEARNING GUIDED USER INTERACTIONS FOR CONSISTENT IMAGE SEGMENTATION

Interactive techniques leverage the expert knowledge of users to produce accurate image segmentations. However, the segmentation accuracy varies with the users. Furthermore, users require some training with the algorithm and its exposed parameters to obtain the best segmentation with minimal effort. Our work combines active learning with interactive segmentation to (i) achieve the same accuracy as an interactive segmentation alone with significantly lower number of user interactions (on average 50%), and (ii) improves the consistency of segmentation with variable user inputs by iteratively suggesting gestures for labelling to the user. We present extensive experimental evaluation of our results on two different publicly available datasets.
Bridging the Semantic Gap Through Static Code Analysis

The semantic gap is a challenge inherent in all applications of virtual machine introspection (VMI). It describes the disconnect between the low-level state that the hypervisor has access to and its semantics within the guest. A common approach to bridge this gap is to utilize the debugging symbols of an inspected operating system kernel, although it is well understood that this information does not reect the dynamic pointer manipulations that an operating system kernel performs at runtime. In this work, we describe an analysis technique for capturing dynamic pointer manipulations and type casts in C code. Our approach analyzes the unmodied kernel source code to establish used-as relations between pointer types and to extract the arithmetic that is performed to transform a source pointer to a target address. We have implemented this technique in our VMI tool InSight for Linux to augment the type information retrieved from the debugging symbols. With this extended type information, our tool is able to cope with runtime pointer manipulations performed by the Linux kernel in a completely automated fashion and greatly eases the development of new VMI applications.
On Antenna Diversity Exploitation for Non-Coherent Multicarrier On-Off Keying Transmission

The simplicity of the required transmitter-receiver pair and inherent coding ability of non-coherent multicarrier on-off keying (MOOK) are the reasons for its popular choice for a number of communication systems. Among the disadvantages for this technique however are its relative bandwidth inefficiency and its susceptibility to frequency selective fading channels which are often encountered in the wireless environment. The aim of this paper is to investigate and analyse antenna diversity exploitation techniques with the objective to enhance the performance of MOOK transmissions. Two antenna combining techniques are considered at the receiver and their performances are compared in both static and time varying frequency selective fading channels.
FOCA: A Methodology for Ontology Evaluation

Modeling an ontology is a hard and time-consuming task. Although methodologies are useful for ontologists to create good ontologies, they do not help with the task of evaluating the quality of the ontology to be reused. For these reasons, it is imperative to evaluate the quality of the ontology after constructing it or before reusing it. Few studies usually present only a set of criteria and questions, but no guidelines to evaluate the ontology. The effort to evaluate an ontology is very high as there is a huge dependence on the evaluator's expertise to understand the criteria and questions in depth. Moreover, the evaluation is still very subjective. This study presents a novel methodology for ontology evaluation, taking into account three fundamental principles: i) it is based on the Goal, Question, Metric approach for empirical evaluation; ii) the goals of the methodologies are based on the roles of knowledge representations combined with specific evaluation criteria; iii) each ontology is evaluated according to the type of ontology. The methodology was empirically evaluated using different ontologists and ontologies of the same domain. The main contributions of this study are: i) defining a step-by-step approach to evaluate the quality of an ontology; ii) proposing an evaluation based on the roles of knowledge representations; iii) the explicit difference of the evaluation according to the type of the ontology iii) a questionnaire to evaluate the ontologies; iv) a statistical model that automatically calculates the quality of the ontologies.
A new depth camera calibration algorithm

Camera calibration constitutes a basic problem in many robot applications. In this paper two algorithms tailored to the calibration of the parameters of a depth camera are proposed. More precisely, a closed form solution that requires the coordinates of three corresponding points in the world and the camera coordinates systems, for the noise free case is proposed. Moreover, a robust algorithm that can be used for the successful estimation of the parameters in the presence of both uniform noise that models the quantization error along the axes of the “volume”, as well as of a sparse noise component for the modeling of large errors presented in depth measurements, is presented. From the simulation results we have obtained, the proposed methods seem to outperform in terms of the average worst case estimation errors frequently used algorithms for the problem at hand.
Substitution Between (and Motivations for) Charitable Contributions: An Experimental Study

I run a series of laboratory experiments to estimate and describe the extent to which an individual's charitable donation to one cause displaces his or her giving to another cause. The experiments also investigate motivations for giving, including the simple warm-glow and public-goods models, and the desire for influence, reputation, and normalizing behavior. In the first wave of experiments I allow 49 subjects to donate or keep any amount of their 10 'endowment' to any of three charities in each of six stages (with one stage randomly chosen for payments). Some of the stages include 'shocks' (to certain charities), such as an expanded choice set, a higher 'match' rate, and a promotional video. The second wave of experiments (48 subjects) has 13 stages, a larger set of treatments, and a 20 'endowment'. All of the treatments have the hypothesized effect on giving, including the 'price' shock; in contrast to previous experiments, the subjects exhibit price-elastic demand. Subjects also give significantly more when their decisions and identity are observed. The results demonstrate that 'expenditure substitution' among charities can be seen in a laboratory setting. I find large own-price elasticities and very large cross-price elasticities - these charities are gross substitutes in the conventional sense. The substitution is stronger where the charities serve similar purposes, such as UNICEF and Care. In the "reduced form" model, using instrumental variables estimation, I estimate an expenditure substitution coefficient of 37% - when gifts to one charity are increased (or decreased) by a certain amount because of a shock, the sum of gifts to other charities decreases by 37% of this amount. The conditional-on-positive estimate of this substitution is 80%: where gifts to both charities remain positive, the 'crowding out' is 0.80 for every 1.
Computational modelling of cardiac electrophysiological changes in malarial fever

Cardiac function is impaired in severe malarial fever, and ECGs show changes associated with repolarization. These could contribute to mortality via ventricular arrhythmia. The cardiac effects could be due to the malarial parasite load in the heart, specific cardio-toxic effects of the parasite or cardio-toxic effects of antimalarial agents. We construct a simple 1-dimensional electrophysiological model for the physico-chemical changes clinically observed during malarial fever: with temperature, pH and [ionic]plasma changes. The model can quantitatively reproduce the tachycardia and QTc prolongation seen in the adult, and shortening seen in the child during malarial fever.
Quality control and multi-lesion detection in automated retinopathy classification using a visual words dictionary

— Automated identification of diabetic retinopathy has followed a number of paths. For accurate automated lesion detection, the first step is to identify images that are not suitable for automated assessment. This is followed by lesion or disease classification. For appropriate referral of individuals, the accurate recognition of a lesion and the extent of the lesion is important. The extent of a specific lesion and whether there are more than one type of lesion typify disease progression. In this sense, the visual word dictionary analysis allows automated image analysis where no pre-processing of images for specific lesions is required; training can be from different image resolutions, cameras and allows for some noise in the image. We demonstrate that the method when combined with machine learning allows feature fusion that incorporates identification of one or multiple lesions within one image at an appropriate accuracy level for clinical referral. In addition, the same general visual dictionary methodology can be applied to identify blurred images that are not suitable for automated assessment triggering alternative actions from the operator such as acquiring new images or referring to a qualified reader. For the detection of hard exudates, our approach has achieved an area under the curve (AUC) of 94.7%, while for superficial hemorrhages detection, the AUC achieved is 83.2%. The best performance reached for quality analysis is 87.4%.
Hydrogen Sulfide Inhibits High-Salt Diet-Induced Renal Oxidative Stress and Kidney Injury in Dahl Rats

Background. The study was designed to investigate if H2S could inhibit high-salt diet-induced renal excessive oxidative stress and kidney injury in Dahl rats. Methods. Male salt-sensitive Dahl and SD rats were used. Blood pressure (BP), serum creatinine, urea, creatinine clearance rate, and 24-hour urine protein were measured. Renal ultra- and microstructures were observed. Collagen-I and -III contents the oxidants and antioxidants levels in renal tissue were detected. Keap1/Nrf2 association and Keap1 s-sulfhydration were detected. Results. After 8 weeks of high-salt diet, BP was significantly increased, renal function and structure were impaired, and collagen deposition was abundant in renal tissues with increased renal MPO activity, H2O2, MDA, GSSG, and •OH contents, reduced renal T-AOC and GSH contents, CAT, GSH-PX and SOD activity, and SOD expressions in Dahl rats. Furthermore, endogenous H2S in renal tissues was decreased in Dahl rats. H2S donor, however, decreased BP, improved renal function and structure, and inhibited collagen excessive deposition in kidney, in association with increased antioxidative activity and reduced oxidative stress in renal tissues. H2S activated Nrf2 by inducing Keap1 s-sulfhydration and subsequent Keap1/Nrf2 disassociation. Conclusions. H2S protected against high-salt diet-induced renal injury associated with enhanced antioxidant capacity and inhibited renal oxidative stress.
Self-Assembly in Micro- and Nanofluidic Devices: A Review of Recent Efforts

Self-assembly in micro- and nanofluidic devices has been the focus of much attention in recent years. This is not only due to their advantages of self-assembling with fine temporal and spatial control in addition to continuous processing that is not easily accessible in conventional batch procedures, but they have evolved to become indispensable tools to localize and assimilate micro- and nanocomponents into numerous applications, such as bioelectronics, drug delivery, photonics, novel microelectronic architectures, building blocks for tissue engineering and metamaterials, and nanomedicine. This review aims to focus on the most recent advancements and characteristic investigations on the self-assembly of micro- and nanoscopic objects in micro- and nanofluidic devices. Emphasis is placed on the salient aspects of this technology in terms of the types of micro- and nanomaterials being assembled, the principles and methodologies, as well as their novel applications.
Aliasing in Recurrently Sampled Signals With an Application to Synthetic Aperture Imaging

Recurrent sampling is an example of nonuniform sampling that occurs in multichannel systems such as analog-to-digital converters, synthetic aperture radars (SAR), and synthetic aperture sonars (SAS). While sampling theorems have been developed that guarantee that a bandlimited signal can be perfectly reconstructed from its recurrent samples, little has been said about the case where the signal is not perfectly bandlimited. We compare the impact of out-of-band energy for uniform and recurrent sampling. The results are extended to the case of sampling a wide-sense stationary (WSS) random process. An application to multichannel synthetic aperture imaging is also included to illustrate these results.
IMPACT OF RELAY NODES ON VEHICUL AR DELAY TOLERANT NETWORK

Vehicular Delay Tolerant Networks (VDTNs) are networks in which no simultaneous end-to-end path exists. Typically, message delivery experiences long delays due to the disconnected nature of the network. In this type of network our main goal is to deliver the messages to the destination. In this paper we use stable nodes (relay nodes) at cross roads with different number of mobile nodes. With various simulations it was shown that relay nodes improves the message delivery probability ratio.
Unknotting Unknots

Abstract A knot is an embedding of a circle into three-dimensional space. We say that a knot is unknotted if there is an ambient isotopy of the embedding to a standard circle. In essence, an unknot is a knot that may be deformed to a standard circle without passing through itself. By representing knots via planar diagrams, we discuss the problem of unknotting a knot diagram when we know that it is unknotted. This problem is surprisingly difficult, since it has been shown that knot diagrams may need to be made more complicated before they may be simplified. We do not yet know, however, how much more complicated they must get. We give an introduction to the work of Dynnikov, who discovered the key use of arc-presentations to solve the problem of finding a way to detect the unknot directly from a diagram of the knot. Using Dynnikov's work, we show how to obtain a quadratic upper bound for the number of crossings that must be introduced into a sequence of unknotting moves. We also apply Dynnikov's results to find an upper bound for the number of moves required in an unknotting sequence.
The role of a local newspaper after disaster: an intrinsic case study of Ishinomaki, Japan

ABSTRACT The city of Ishinomaki in Miyagi prefecture was devastated by the tsunami that struck Japan’s North East Coast on 11 March 2011. Drawing on fieldwork conducted in Ishinomaki, which included interviews with senior journalists from the city’s two local newspapers, the Ishinomaki Hibi Shimbun and the Ishinomaki Kahoku, this paper presents an intrinsic case study of the role a local newspaper in Ishinomaki after the Great East Japan Disaster. The evidence reveals that in the immediate aftermath of the tsunami journalists recognised how their newspaper could serve the immediate information-needs of the local community by providing essential lifeline information, describing a duty to report, despite the operational difficulties that their newspapers faced. In the longer term recovery phase, interviewees acknowledged how their newspapers have attempted to communicate a message of hope to the city and provide an alternative perspective to the national media, which sometimes gave a false impression of the state of Ishinomaki’s recovery. This paper offers some insights into journalistic role conceptions, illustrating how journalists from the two newspapers embraced the role of information-disseminator after the disaster, and also identifies avenues for further research.