Miracle-dz/UniFAR-FTUs huggingface dataset:
The Approximate k-List Problem

We study a generalization of the k -list problem, also known as the Generalized Birthday problem. In the k -list problem, one starts with k lists of binary vectors and has to find a set of vectors – one from each list – that sum to the all-zero target vector. In our generalized Approximate k -list problem, one has to find a set of vectors that sum to a vector of small Hamming weight ω . Thus, we relax the condition on the target vector and allow for some error positions. This in turn helps us to significantly reduce the size of the starting lists, which determines the memory consumption, and the running time as a function of ω . For ω = 0, our algorithm achieves the original k -list run-time/memory consumption, whereas for ω = n / 2 it has polynomial complexity. As in the k -list case, our Approximate k -list algorithm is defined for all k = 2 m ,m > 1. Surprisingly, we also find an Approximate 3-list algorithm that improves in the runtime exponent compared to its 2-list counterpart for all 0 < ω < n / 2 . To the best of our knowledge this is the first such improvement of some variant of the notoriously hard 3-list problem. As an application of our algorithm we compute small weight multiples of a given polynomial with more flexible degree than with Wagner’s algorithm from Crypto 2002 and with smaller time/memory consumption than with Minder and Sinclair’s algorithm from SODA 2009.
An Activator Binding Module of Yeast RNA Polymerase II Holoenzyme

ABSTRACT The Mediator complex of Saccharomyces cerevisiae is required for both general and regulated transcription of RNA polymerase II (PolII) and is composed of two stable subcomplexes (Srb4 and Rgr1 subcomplexes). To decipher the function of each Mediator subcomplex and to delineate the functional relationship between the subcomplexes, we characterized the compositions and biochemical activities of PolII-Mediator complexes (holoenzymes) prepared from several Mediator mutant strains of S. cerevisiae. We found that holoenzymes devoid of a functional Gal11 module were defective for activated but not basal transcription in a reconstituted in vitro system. This activation-specific defect was correlated with a crippled physical interaction to transcriptional activator proteins, which could be bypassed by artificial recruitment of a mutant holoenzyme to a promoter. Consistent with this observation, a direct interaction between Gal11 and gene-specific transcriptional activator proteins was detected by far-Western analyses and column binding assays. In contrast, the srb5 deletion mutant holoenzyme was defective for both basal and activated transcription, despite its capacity for activator binding that is comparable to that of the wild-type holoenzyme. These results demonstrate that the Gal11 module of the Rgr1 subcomplex is required for the efficient recruitment of PolII holoenzyme to a promoter via activator-specific interactions, while the Srb4 subcomplex functions in the modulation of general polymerase activity.
Exploring a New Security Framework for Cloud Storage Using Capabilities

We are seeing the deployment of new types of networks such as sensor networks for environmental and infrastructural monitoring, social networks such as facebook, and e-Health networks for patient monitoring. These networks are producing large amounts of data that need to be stored, processed and analysed. Cloud technology is being used to meet these challenges. However, a key issue is how to provide security for data stored in the Cloud. This paper addresses this issue in two ways. It first proposes a new security framework for Cloud security which deals with all the major system entities. Secondly, it introduces a Capability ID system based on modified IPv6 addressing which can be used to implement a security framework for Cloud storage. The paper then shows how these techniques are being used to build an e-Health system for patient monitoring.
Best Practices for the Design of RESTful Web Services

The trend towards creating web services based on the REpresentational State Transfer (REST) is unbroken. Because of this, several best practices for designing RESTful web services have been created in research and practice to ensure a certain level of quality. But, these best practices are often described differently with the same meaning due to the nature of natural language. In addition, they are not collected and presented in a central place but rather distributed across several pages in the World Wide Web, which impedes their application even further. In this article, we identify, collect, and categorize several best practices for designing RESTful web services and illustrate their application on a real system to show their application. For illustration purpose, we apply the best practices on the CompetenceService, an assistance service of the SmartCampus system developed at the Karlsruhe Institute of Technology (KIT). Keywords–REST; RESTful; best practices; collection; catalog; design; quality; research and practice
Validating the defect detection performance advantage of group designs for software reviews: report of a replicated experiment

It is widely accepted that software development technical reviews (SDTRs) are a useful technique for finding defects in software products. The normative SDTR literature assumes that group reviews are better than individual reviews. Recent debates centre around the need for review meetings. This paper presents the findings of a replicated experiment that was conducted to investigate whether group review meetings are needed and why. We found that an interacting group is the preferred choice over the average individual and artificial (nominal) groups. The source of performance advantage of interacting groups is not synergy as was previously thought, but rather in discriminating between true defects and false positives identified by individual reviewers. As a practical implication, nominal groups may be an alternative review design in situations where individuals exhibit a low level of false positives.
Multiview convolutional neural networks for lung nodule classification

To find a better way to screen early lung cancer, motivated by the great success of deep learning, we empirically investigate the challenge of classifying lung nodules in computed tomography (CT) in an end‐to‐end manner. Multi‐view convolutional neural networks (MV‐CNN) are proposed in this article for lung nodule classification. Unlike the traditional CNNs, a MV‐CNN takes multiple views of each entered nodule. We carry out a binary classification (benign and malignant) and a ternary classification (benign, primary malignant, and metastatic malignant) using the Lung Image Database Consortium and Image Database Resource Initiative database. The results show that, for binary or ternary classifications, the multiview strategy produces higher accuracy than the single view method, even for cases that are over‐fitted. Our model achieves an error rate of 5.41 and 13.91% for binary and ternary classifications, respectively. Finally, the receiver operating characteristic curve and t‐distributed stochastic neighbor embedding algorithm are used to analyze the models. The results reveal that the deep features learned by the model proposed in this article have a higher separability than features from the image space and the multiview strategies; therefore, researchers can get better representation. © 2017 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 27, 12–22, 2017
UMMARIZATION OF S OFTWARE A RTIFACTS : A R EVIEW

Summarization of software artifacts is an ongoing field of research among the software engineering community due to the benefits that summarization provides like saving of time and efforts in various software engineering tasks like code search, duplicate bug reports detection, traceability link recovery, etc. Summarization is to produce short and concise summaries. The paper presents the review of the state of the art of summarization techniques in software engineering context. The paper gives a brief overview to the software artifacts which are mostly used for summarization or have benefits from summarization. The paper briefly describes the general process of summarization. The paper reviews the papers published from 2010 to June 2017 and classifies the works into extractive and abstractive summarization. The paper also reviews the evaluation techniques used for summarizing software artifacts. The paper discusses the open problems and challenges in this field of research. The paper also discusses the future scopes in this area for new researchers.
Feasibility study of a combined treatment of electromyography-triggered neuromuscular stimulation and mirror therapy in stroke patients: a randomized crossover trial.

BACKGROUND Mirror therapy (MT) and electromyography-triggered neuromuscular stimulation (ETMS) are both effective treatments for impaired upper limbs following stroke. A combination of these two treatments (ETMS-MT) may result in greater gain than either treatment alone. OBJECTIVES The feasibility and possible effects of ETMS-MT upon upper extremity function were investigated in stroke patients. METHODS Thirteen post-acute stroke patients were randomly assigned to an immediate ETMS-MT group or a delayed ETMS-MT group and then underwent an 8-week training program. The immediate ETMS-MT group received ETMS-MT in addition to physical and occupational therapy (PT+OT) for 4 weeks. They then received only PT+OT for the next 4 weeks. In the delayed ETMS-MT group, interventions were provided in the reverse order. The main outcome measure was the Fugl-Meyer Assessment (FMA). RESULTS The immediate ETMS-MT group showed significantly greater gain in FMA in the first 4 weeks. The delayed ETMS-MT group showed significantly greater gain in active range of motion during the latter 4 weeks. No adverse effects were reported following ETMS-MT. CONCLUSION ETMS-MT might be as effective as independent MT or ETMS without causing any side effects. Future research should focus upon the direct comparisons between independent and combined interventions.
A Drop-on-Demand-Based Electrostatically Actuated Microdispenser

This paper presents a noncontact drop-on-demand three-layer microdroplet generator based on electrostatic actuation. The dispenser is actuated via a deformable membrane that isolates the electrical field from the working fluid. The dispenser controlled droplet formation, frequency, size, and velocity within the ranges tested. Prototypes were fabricated using three-step deep reactive-ion etching and polydimethylsiloxane (PDMS) plasma activated bonding. Experiments verified stable droplet dispensing with a variance in subsequent droplet volume of less than 15% between droplets. The frequency of stable generation was 20 Hz, and the average volume of dispensed droplet was 1 nL. The dispenser operating range and the nondestructive actuation make it suitable for biological applications.
A secure hardware-software solution based on RISC-V, logic locking and microkernel

In this paper we present the first generation of a secure platform developed by following a security-by-design approach. The security of the platform is built on top of two pillars: a secured hardware design flow and a secure microkernel. The hardware design is protected against the insertion of hardware Trojans during the production phase through netlist obfuscation provided by logic locking. The software stack is based on a trustworthy and verified microkernel. Moreover, the system is expected to work in an environment which does not allow physical access to the device. Therefore, on-the-field attacks are only possible via software. We present a solution whose security has been achieved by relying on simple and open hardware and software solutions, namely a RISC-V processor core, open-source peripherals and an seL4--based operating system.
Value and Financial Toxicity of New Cancer Drugs

By now you’ve read Karen Herold’s excellent overview of the CLEOPATRA study in the January/February issue of JADPRO (2016). CLEOPATRA confirmed that PDT (pertuzumab [Perjeta], docetaxel, and trastuzumab [Herceptin]) was superior to docetaxel and trastuzumab (DT) to improve progression-free and overall survival for patients with HER2+ metastatic breast cancer (Baselga et al., 2012; Swain et al., 2015). However, Durkee and colleagues (2016) examined value and financial toxicity associated with PDT—issues not addressed in any CLEOPATRA publications. During CLEOPATRA, investigators would not know the future price of pertuzumab, although trastuzumab cost approximately $70,000 a year. Durkee and others (2016) carried out Markov analyses to predict the “cost of progress. ” Averaged across treatment, the cost to insurers and patients receiving PDT would be $4,649 per week. For a median survival of 39.4 months for DT and 56.9 months for PDT, drug costs of $347,627 and $805,449, respectively, were predicted—plus other drugs, administration, laboratory, etc. If all 17,450 patients diagnosed with advanced HER2+ breast cancer each year got PDT or DT, now recommended by the National Comprehensive Cancer Network (NCCN, 2016) as first-line treatment for metastatic, HER2+ breast cancer, yearly costs would be billions, which Durkee concluded is not sustainable in the United States.
Proper evaluation of alignment-free network comparison methods

Motivation: Network comparison is a computationally intractable problem with important applications in systems biology and other domains. A key challenge is to properly quantify similarity between wiring patterns of two networks in an alignment-free fashion. Also, alignment-based methods exist that aim to identify an actual node mapping between networks and as such serve a different purpose. Various alignment-free methods that use different global network properties (e.g. degree distribution) have been proposed. Methods based on small local subgraphs called graphlets perform the best in the alignment-free network comparison task, due to high level of topological detail that graphlets can capture. Among different graphlet-based methods, Graphlet Correlation Distance (GCD) was shown to be the most accurate for comparing networks. Recently, a new graphlet-based method called NetDis was proposed, which was claimed to be superior. We argue against this, as the performance of NetDis was not properly evaluated to position it correctly among the other alignment-free methods. Results: We evaluate the performance of available alignment-free network comparison methods, including GCD and NetDis. We do this by measuring accuracy of each method (in a systematic precision-recall framework) in terms of how well the method can group (cluster) topologically similar networks. By testing this on both synthetic and real-world networks from different domains, we show that GCD remains the most accurate, noise-tolerant and computationally efficient alignment-free method. That is, we show that NetDis does not outperform the other methods, as originally claimed, while it is also computationally more expensive. Furthermore, since NetDis is dependent on the choice of a network null model (unlike the other graphlet-based methods), we show that its performance is highly sensitive to the choice of this parameter. Finally, we find that its performance is not independent on network sizes and densities, as originally claimed. Contact: natasha@imperial.ac. uk Supplementary information: Supplementary data are available at Bioinformatics online.
Contact Forces between Single Metal Oxide Nanoparticles in Gas-Phase Applications and Processes

In this work we present a comprehensive experimental study to determine the contact forces between individual metal oxide nanoparticles in the gas-phase using atomic force microscopy. In addition, we determined the amount of physisorbed water for each type of particle surface. By comparing our results with mathematical models of the interaction forces, we could demonstrate that classical continuum models of van der Waals and capillary forces alone cannot sufficiently describe the experimental findings. Rather, the discrete nature of the molecules has to be considered, which leads to ordering at the interface and the occurrence of solvation forces. We demonstrate that inclusion of solvation forces in the model leads to quantitative agreement with experimental data and that tuning of the molecular order by addition of isopropanol vapor allows us to control the interaction forces between the nanoparticles.
Introduction to artificial neural networks for physicians: Taking the lid off the black box

Over the past 5 years, a steady stream of publications has discussed the use of artificial neural networks (ANNs) for urologic and other medical applications. The pace of this research has increased recently, and deployed products based on this technology are now appearing. Before these tools can be widely accepted by clinicians and researchers, a deeper level of understanding of ANNs is necessary. This article attempts to lay some of the groundwork needed to facilitate this familiarity.
Person x situation interactions in body dissatisfaction.

OBJECTIVE The aim of the study was to investigate the interaction between personal and situational variables in the determination of body satisfaction. METHOD Participants were asked to imagine themselves in each of four hypothetical scenarios while completing measures of body image. RESULTS A main effect for situation was found on both global body dissatisfaction and body esteem, whereby participants rated themselves as more dissatisfied in the body-focused situations (Beach, Dressing room) than in the non-body-focused situations (Refectory, Home). In addition, there was a main effect of self-esteem. Of more interest, there were also significant Situation x Body Mass Index (BMI), Situation x Dietary Restraint, and Situation x BMI x Social Comparison interactions. DISCUSSION This study has demonstrated situational effects, person effects, and Person x Situation interactions within the one framework. As such, it contributes to an increasingly complex and dynamic view of body image.
Plume source localization for AUV based autonomous hydrothermal vent discovery

Hydrothermal vent systems are the plumbing systems of the deep ocean, spewing heat and minerals from Earth's interior while supporting unique ecosystems and offering clues about the geological processes that regulate the formation of oceanic crust. Locating and mapping the distribution of hydrothermal plumes near the venting sources assists the geochemists optimize their efforts to study the evolution of dissolved and particulate components of vent emissions by helping them determine the best locations and depths to take water samples. This paper presents an effective hydrothermal plume mapping and search algorithms for using on AUVs to locate the hydrothermal venting source location. AUVs use hydrothermal chemical signature as a guide to navigate and track in the unknown environments. The mapping algorithms are based on Bayesian inference theory. The planning algorithms are based on artificial potential field methods. This methodology results in algorithms for predicting likelihood of vent location versus position. The AUV would then optimize a desired trajectory to navigate in the hydrothermal plume and locate the hydrothermal vent.
Daptomycin treatment of Staphylococcus aureus experimental chronic osteomyelitis.

BACKGROUND Infection due to methicillin-resistant Staphylococcus aureus (MRSA) is increasingly common in nosocomial and community settings. Daptomycin is a cyclic lipopeptide anti-infective with activity against MRSA, approved for treatment of complicated skin and skin structure infections. Daptomycin may be useful in systemic or local treatment of chronic osteomyelitis. METHODS We measured mechanical strength of daptomycin- and vancomycin-loaded polymethylmethacrylate (PMMA), assayed in vivo release of daptomycin and vancomycin from daptomycin- and vancomycin-loaded PMMA, respectively, and compared the efficacy of two systemic doses of daptomycin with that of vancomycin, each with or without the respective anti-infective loaded into PMMA, using a rat model of MRSA chronic osteomyelitis. RESULTS Neither tensile nor compressive strength of PMMA was impacted by impregnation with these antimicrobials at a concentration of 7.5% by weight. The peak concentrations of daptomycin and vancomycin in rat tibial bone surrounding a 7.5% daptomycin- and vancomycin-loaded 3 mm PMMA bead were 178 and 49 mg/L, respectively. In the treatment of experimental osteomyelitis, rats assigned to no treatment, daptomycin 50 mg/kg subcutaneously twice daily, daptomycin 60 mg/kg subcutaneously twice daily, and vancomycin 50 mg/kg intraperitoneally twice daily had 6.4, 4.1, 4.0 and 4.5 median log10 cfu/g of bone at the end of 21 days of therapy. All systemic anti-infectives studied were more active than was no treatment. Daptomycin- or vancomycin-loaded PMMA did not, however, exhibit microbiological efficacy alone or adjunctively, as assessed 21 days after implantation. CONCLUSIONS Daptomycin is released from PMMA in vivo at a rate similar to that of vancomycin. Systemic daptomycin is as active as vancomycin in a rat model of chronic MRSA experimental osteomyelitis.
The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags

Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define ≈23,500 genes, of which only ≈1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that <1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.
Distributed Optimal Dispatch of Virtual Power Plant via Limited Communication

In this letter, a distributed optimal dispatch method based on the distributed primal-dual sub-gradient algorithm is proposed. By coordinating individual decision-making of distributed energy resources (DERs) in the virtual power plant (VPP) via limited communication, the profit of VPP can be maximized. It can be proven that the proposed distributed algorithm has similar performance to the centralized dispatch.