nils-herrmann/clean_scirepeval huggingface dataset:
Calcium chelating alizarin and other anthraquinones inhibit biofilm formation and the hemolytic activity of Staphylococcus aureus
Venue: Scientific reports

Staphylococcal biofilms are problematic and play a critical role in the persistence of chronic infections because of their abilities to tolerate antimicrobial agents. Thus, the inhibitions of biofilm formation and/or toxin production are viewed as alternative means of controlling Staphylococcus aureus infections. Here, the antibiofilm activities of 560 purified phytochemicals were examined. Alizarin at 10 mg/ml was found to efficiently inhibit biofilm formation by three S. aureus strains and a Staphylococcus epidermidis strain. In addition, two other anthraquinones purpurin and quinalizarin were found to have antibiofilm activity. Binding of Ca2+ by alizarin decreased S. aureus biofilm formation and a calcium specific chelating agent suppressed the effect of calcium. These three anthraquinones also markedly inhibited the hemolytic activity of S. aureus, and in line with their antibiofilm activities, increased cell aggregation. A chemical structure activity relationship study revealed that two hydroxyl units at the C 1 and C 2 positions of anthraquinone play important roles in antibiofilm and anti hemolytic activities. Transcriptional analyses showed that alizarin repressed the a hemolysin hla gene, biofilm related genes (psma, rbf, and spa) and modulated the expressions of cid/lrg genes (the holin/antiholin system) These findings suggest anthraquinones, especially alizarin, are potentially useful for controlling biofilm formation and the virulence of S. aureus.
Discovery of Radioiodinated Monomeric Anthraquinones as a Novel Class of Necrosis Avid Agents for Early Imaging of Necrotic Myocardium
Venue: Scientific reports

Assessment of myocardial viability is deemed necessary to aid in clinical decision making whether to recommend revascularization therapy for patients with myocardial infarction (MI) Dianthraquinones such as hypericin (Hyp) selectively accumulate in necrotic myocardium, but were unsuitable for early imaging after administration to assess myocardial viability. Since dianthraquinones can be composed by coupling two molecules of monomeric anthraquinone and the active center can be found by splitting chemical structure, we propose that monomeric anthraquinones may be effective functional groups for necrosis targetability. In this study, eight radioiodinated monomeric anthraquinones were evaluated as novel necrosis avid agents (NAAs) for imaging of necrotic myocardium. All 131I anthraquinones showed high affinity to necrotic tissues and 131I rhein emerged as the most promising compound. Infarcts were visualized on SPECT/CT images at 6 h after injection of 131I rhein, which was earlier than that with 131I Hyp. Moreover, 131I rhein showed satisfactory heart to blood, heart to liver and heart to lung ratios for obtaining images of good diagnostic quality. 131I rhein was a more promising "hot spot imaging" tracer for earlier visualization of necrotic myocardium than 131I Hyp, which supported further development of radiopharmaceuticals based on rhein for SPECT/CT (123I and 99mTc) or PET/CT imaging (18F and 124I) of myocardial necrosis.
Planar object detection from 3D point clouds based on pyramid voxel representation
Venue: Multimedia Tools and Applications

Planar detection is a fundamental task in many computer vision applications. This paper proposed a fast and reliable plane detection method from 3D point clouds to address the high computation cost problem in existing methods. The 3D space is first partitioned into pyramid voxels. Each 3D point is assigned to one voxel at each pyramid layer so that all the 3D points are represented by pyramid voxels. For each voxel, we apply the Eigen value decomposition to analyze 3D points inside and propose an index for fast plane detection. Especially, the plane index is efficiently computed with no explicit Eigen value decomposition to enhance the computation. The detected planar voxels are analyzed and merged for planar object detection based on geometric relationship between voxels. The proposed method uses voxel wise instead of point wise processing of the 3D point clouds so that it can greatly enhance the computation efficiency yet with good detection results. The proposed method has been validated with actual 3D point clouds collected by RGB D sensor of Kinect 1.0 in both indoor and outdoor environments. The results demonstrate that the proposed method can quickly detect single and multiple planar objects in both environments. The precision and the accuracy of the proposed method are 97.1% and 94.5% respectively. Compared to existing methods (e.g. Hough Transform, RANSAC) the proposed method can greatly enhance the computation efficiency in several orders of magnitudes.
Scalable and accurate detection of code clones
Venue: Programming and Computer Software

A detailed description of a method for detection of code clones is described. This method is based on the semantic analysis of programs and on new algorithms that make it scalable without affecting its accuracy. The proposed method involves two phases. In the first phase, the program dependence graph (PDG) is constructed while the program is compiled. LLVM is used as the compilation infrastructure. In the second phase, similar subgraphs of maximum size that represent code clones are detected. Before starting the search for similar subgraphs, the PDG is divided into subgraphs that will be considered as potential clones of each other. To ensure scalability of the search for similar subgraphs, the composition of algorithms is used. The first algorithm checks that a pair of graphs cannot have similar subgraphs of the desired size; this is done in a linear amount of time. If this algorithm fails, another (approximate) algorithm is executed to find similar subgraphs of maximum size. After similar subgraphs have been found, the program code is additionally checked for the position of the code lines corresponding to the detected clone candidates. Tests showed that the developed tool is more accurate than similar tools, such as MOSS, CCFinder, and CloneDR. Results obtained for the projects Linux 2.6, Firefox Mozilla, LLVM/Clang, and OpenSSL are presented.
Kajian Teoritis Aliran Positivisme Hukum, Dihubungkan Dengan Ketentuan Uu No. 24 Tahun 2009 Tentang Bendera, Bahasa Dan Lambang Negara, Serta Lagu Kebangsaan Jo UU Nomor 12 Tahun 2011 Tentang Pembentukan Perundang undangan

Konsep negara hukum yang berlaku di Indonesia adalah sistem hukum warisan kolonial Belanda yang berkembang di Benua Eropa yang dikenal dengan mazhab Eropa Kontinental, yang keberlakuannya didasarkan kepada "azas konkordansi" sebagaimana disebutkan dalam ketentuan peralihan Pasal II UUD RI Tahun 1945 Naskah Asli yang berbunyi "Segala badan negara dan peraturan yang ada masih langsung berlaku, selama belum diadakan yang baru menurut Undang Undang Dasar ini" Salah satu ciri dari sistem hukum dalam mazhab Eropah Kontinental adalah positivisme hukum atau legisme hukum, yang secara umum dapat diartikan bahwa hukum identik dengan undang undang, diluar undang undang tidak ada hukum, untuk terciptanya kepastian hukum, hukum senantiasa harus dibuat oleh pembuat undang undang dan ditempatkan di dalam buku undang undang (kodifikasi) Setiap ketentuan undang undang yang ditetapkan oleh negara harus dipatuhi saja dan semua masyarakat sudah dianggap mengetahuinya. Lahirnya Tap MPRS No. XX/MPRS/1966 Tentang Tertib Hukum dan Perundang undangan serta Tata Urutan Perundang undangan, Tap MPR No. III/MPR/2000 Tentang Tertib Hukum dan Perundang undangan serta Tata Urutan Perundang undangan, UU No. 10 Tahun 2004 Tentang Pembentukan Perundang undangan maupun UU No. 12 Tahun 2011 tentang Pembentukan Perundang undangan, dimaksudkanagar negara Indonesia memiliki ketertiban maupun kepastian di bidang hukum. Namun di dalam prakteknya masih banyak masyarakat yang belum memahami setiap perundang undangan yang ditetapkan oleh negara, sehingga sering terjadi pelanggaran pelanggaran hukum yang dilakukan oleh masyarakat, akan tetapi tidak disadarinya bahwa perbuatan tersebut merupakan suatu pelanggaran hukum. seperti yang saat ini terjadi yaitu pelanggaran hukum atas bendera merah, sebagai,mana yang diatur dalam UU No. 24 Tahun 2009 tentang Bahasa, Bendera dan Lambang Negara. Kesimpulan dari penelitian ini bahwa hukum nasional Indonesia dalam praktik telah dipengaruhi aliran positivisme/legisme hukum dari mazhab Eropah Kontinental. Kata Kunci Positivisme, Konkordansi, Legisme, Kepastian Hukum.
Metacognition as scaffolding for the development of listening comprehension in a social MALL App

This article focuses on the role that metacognition can effectively play in the development of second language listening comprehension, and specifically, how a mobile app can be specified for this end. A social mobile assisted listening app, ANT (Audio News Trainer) is presented as a prototype for exploring the way in which students can be helped to use metacognition to improve relevant linguistic communicative competences. A study has been undertaken with students using ANT to explore the intricate nature of the listening comprehension development process and the main metacognitive strategies that can be successfully applied. Special attention is paid to the implicitly and explicitly applied metacognitive strategies within the app, and related social network, where follow on activities were undertaken, the strategies in question being: focus (a conscious effort on the gradual development of individual skills) engagement (interest is enhanced when a learning activity is enjoyable/successful) interaction (since collective activities seem to enhance emotional and social involvement) reflection (upon what works and does not work for each individual) self regulation (through data about the students' own progress and achievements) and attitude (here a further distinction is made between satisfaction, self confidence and encouragement) The stages of engagement of a student with the app are explored in relation to the metacognitive strategy used and how they can contribute to the overall success of the learning experience. A final reflection is made about how metacognitive strategies offer an effective way to compensate for the lack of teacher presence, support and guidance on a medium/long term basis. However, although the study of the initial use of this social listening training app shows the potential for incorporating 'knowing about knowing' into mobile technology, it is suggested that future research is required to provide further finer grained insights into this process.
Design Patterns for Container based Distributed Systems
Venue: HotCloud

In the late 1980s and early 1990s, object oriented programming revolutionized software development, popularizing the approach of building of applications as collections of modular components. Today we are seeing a similar revolution in distributed system development, with the increasing popularity of microservice architectures built from containerized software components. Containers     are particularly well suited as the fundamental "object" in distributed systems by virtue of the walls they erect at the container boundary. As this architectural style matures, we are seeing the emergence of design patterns, much as we did for objectoriented programs, and for the same reason thinking in terms of objects (or containers) abstracts away the lowlevel details of code, eventually revealing higher level patterns that are common to a variety of applications and algorithms. This paper describes three types of design patterns that we have observed emerging in container based distributed systems: single container patterns for container management, single node patterns of closely cooperating containers, and multi node patterns for distributed algorithms. Like object oriented patterns before them, these patterns for distributed computation encode best practices, simplify development, and make the systems where they are used more reliable.
Progress and prospects for event tourism research

This paper examines event tourism as a field of study and area of professional practice updating the previous review article published in 2008. In this substantially extended review, a deeper analysis of the field's evolution and development is presented, charting the growth of the literature, focussing both chronologically and thematically A framework for understanding and creating knowledge about events and tourism is presented, forming the basis which signposts established research themes and concepts and outlines future directions for research. In addition, the review article focuses on constraining and propelling forces, ontological advances, contributions from key journals, and emerging themes and issues. It also presents a roadmap for research activity in event tourism.
Ciphertext Policy Attribute Based Access Control with Effective User Revocation for Cloud Data Sharing System
Venue: 2016 International Conference on Advanced Cloud and Big Data (CBD)

With the development and benefits of cloud computing, nowadays more and more users outsource their data to third party cloud storage servers for ease of sharing and cost saving. Ciphertext Policy Attribute Based Encryption (CP ABE) is a promising tool for enabling fine grained access control over the shared data in the cloud. However, the practical application of CP ABE in cloud data sharing system also has its own inherent challenge to regard with user revocation. To address this challenge, the paper proposes a CP ABE scheme which supports an effective user revocation mechanism by introducing "the essential attribute" and by considering minimally trusted proxy servers, the essential attribute must be included in both ciphertext and update key. By excluding the revoked users from update key (which is a part of a decryption key) and by re encrypting the only component in ciphertexts, which is associated with the essential attribute, our scheme achieves immediate and complete user revocation mechanism in CP ABE. The proposed scheme enables a scalable and fine grained access control for cloud data sharing system. Our scheme provides more efficiency and security level simultaneously comparing to the existing user revocable CP ABE scheme.
Utilising the Cross Industry Standard Process for Data Mining to Reduce Uncertainty in the Measurement and Verification of Energy Savings
Venue: DMBD

This paper investigates the application of Data Mining (DM) to predict baseline energy consumption for the improvement of energy savings estimation accuracy in Measurement and Verification (M&V) M&V is a requirement of a certified energy management system (EnMS) A critical stage of the M&V process is the normalisation of data post Energy Conservation Measure (ECM) to pre ECM conditions. Traditional M&V approaches utilise simplistic modelling techniques, which dilute the power of the available data. DM enables the true power of the available energy data to be harnessed with complex modelling techniques. The methodology proposed incorporates DM into the M&V process to improve prediction accuracy. The application of multi variate regression and artificial neural networks to predict compressed air energy consumption in a manufacturing facility is presented. Predictions made using DM were consistently more accurate than those found using traditional approaches when the training period was greater than two months.
Self amputation of the hand: issues in diagnosis and general hospital management
Venue: Australasian psychiatry bulletin of Royal Australian and New Zealand College of Psychiatrists

To detail a diagnostic dilemma of intentional hand amputation in a man with a history of substance misuse and associated psychosis, depression and traumatic brain injury and to highlight issues in joint psychiatric and surgical management of such a complex patient in a general hospital setting.  Deliberate limb self amputation is a rare event with the majority of reported cases occurring during an episode of psychosis. This case illustrates the diagnostic utility of the literature supporting that a person who has self inflicted amputation of a limb should be treated as psychotic until proven otherwise. The presence of a traumatic brain injury, with associated cognitive and psychosocial sequelae, affected diagnosis and management. Early and ongoing involvement of consultation liaison psychiatry collaborating with a multidisciplinary general hospital team may improve mental and physical health outcomes for such patients.
The functional impact of a traumatic hand injury: a comparison of rural/remote and metropolitan/regional populations

The aim of this research was to explore the commonalities and differences in the issues associated with the functional recovery and rehabilitation of a traumatic hand injury experienced by people in rural/remote and metropolitan/regional areas of North Queensland, Australia.  Responses to a previously mailed survey exploring the functional impact on a rural/remote population and a metropolitan/regional population were used for analysis and comparison.  Both populations reported a loss of movement, pain and stiffness, and a significantly greater percentage of metropolitan/regional respondents reported a loss of strength. Leisure and work tasks were affected for both groups as a result of their impairment. Rural and remote respondents would have liked more appointments but found that it was expensive to get to them. There was a significant reduction for both populations of respondents reporting their occupation as labourers after having a hand injury. There was also a signi.
Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases
Venue: Nature

The non receptor protein tyrosine phosphatase SHP2, encoded by PTPN11, has an important role in signal transduction downstream of growth factor receptor signalling and was the first reported oncogenic tyrosine phosphatase. Activating mutations of SHP2 have been associated with developmental pathologies such as Noonan syndrome and are found in multiple cancer types, including leukaemia, lung and breast cancer and neuroblastoma. SHP2 is ubiquitously expressed and regulates cell survival and proliferation primarily through activation of the RAS ERK signalling pathway. It is also a key mediator of the programmed cell death 1 (PD 1) and B and T lymphocyte attenuator (BTLA) immune checkpoint pathways. Reduction of SHP2 activity suppresses tumour cell growth and is a potential target of cancer therapy. Here we report the discovery of a highly potent (IC50 0.071 mM) selective and orally bioavailable small molecule SHP2 inhibitor, SHP099, that stabilizes SHP2 in an auto inhibited conformation. SHP099 concurrently binds to the interface of the N terminal SH2, C terminal SH2, and protein tyrosine phosphatase domains, thus inhibiting SHP2 activity through an allosteric mechanism. SHP099 suppresses RAS ERK signalling to inhibit the proliferation of receptor tyrosine kinase driven human cancer cells in vitro and is efficacious in mouse tumour xenograft models. Together, these data demonstrate that pharmacological inhibition of SHP2 is a valid therapeutic approach for the treatment of cancers.
The non uniformity of fossil preservation
Venue: Philosophical Transactions of the Royal Society B: Biological Sciences

The fossil record provides the primary source of data for calibrating the origin of clades. Although minimum ages of clades are given by the oldest preserved fossil, these underestimate the true age, which must be bracketed by probabilistic methods based on multiple fossil occurrences. Although most of these methods assume uniform preservation rates, this assumption is unsupported over geological timescales. On geologically long timescales (more than 10 Myr) the origin and cessation of sedimentary basins, and long term variations in tectonic subsidence, eustatic sea level and sedimentation rate control the availability of depositional facies that preserve the environments in which species lived. The loss of doomed sediments, those with a low probability of preservation, imparts a secular trend to fossil preservation. As a result, the fossil record is spatially and temporally non uniform. Models of fossil preservation should reflect this non uniformity by using empirical estimates of fossil preservation that are spatially and temporally partitioned, or by using indirect proxies of fossil preservation. Geologically, realistic models of preservation will provide substantially more reliable estimates of the origination of clades. This article is part of the themed issue 'Dating species divergences using rocks and clocks'
Interest in child molestation among a community sample of men sexually attracted to children

Research including community samples of men suggests that sexual attraction to children, a significant risk factor for child sex offending behaviour, may not be limited to forensic populations. The present study investigated proclivity for child molestation among two groups of community men: those who reported never acting on their sexual attractions (Not Acted) and those reporting at least one previous sexual encounter with a child (Acted) The Interest in Child Molestation Scale (Gannon O'Connor, 2011) was found to be a reliable measure for use in a community sample of men with self reported sexual attraction to children. Men in the Not Acted group reported less behavioural propensity towards low force scenarios than did men in the Acted group. Overall, the research supports a distinction between sexual attraction towards children and the proclivity to engage in low force child molestation.
Child molestation and psychopathy: a taxometric analysis

Prior taxometric research on child molesters and general sex offenders has produced inconsistent and contradictory results. There are theoretical, practical, and policy reasons, however, to assume that a psychopathy taxon may exist in sex offenders and that a taxometric study might shed light on this issue. The mean above minus below a cut (MAMBAC) maximum covariance (MAXCOV) and latent mode factor analysis (L Mode) taxometric procedures were employed in three overlapping samples: 188 sex offenders with non relative child victims, 555 sex offenders with non relative child or adolescent victims or child incest victims, and a mixed sample of 1404 sex offenders. The taxometric analyses revealed evidence of continuous latent structure in all three samples. These results suggest that psychopathy in sex offenders, child molesters in particular, is organised quantitatively (continuous) rather than qualitatively (categorical)
Preference guided evolutionary algorithms for many objective optimization
Venue: Inf. Sci.

This paper presents a technique that incorporates preference information within the framework of multi objective evolutionary algorithms for the solution of many objective optimization problems. The proposed approach employs a single reference point to express the preferences of a decision maker, and adaptively biases the search procedure toward the region of the Pareto optimal front that best matches its expectations. Experimental results suggest that incorporating preferences within these algorithms leads to improvements in several quality criteria, and that the proposed approach is capable of yielding competitive results when compared against existing algorithms.