Miracle-dz/UniFAR-FTUs huggingface dataset:
GNG Motifs Can Replace a GGG Stretch during G-Quadruplex Formation in a Context Dependent Manner

G-quadruplexes are one of the most commonly studied non-B DNA structures. Generally, these structures are formed using a minimum of 4, three guanine tracts, with connecting loops ranging from one to seven. Recent studies have reported deviation from this general convention. One such deviation is the involvement of bulges in the guanine tracts. In this study, guanines along with bulges, also referred to as GNG motifs have been extensively studied using recently reported HOX11 breakpoint fragile region I as a model template. By strategic mutagenesis approach we show that the contribution from continuous G-tracts may be dispensible during G-quadruplex formation when such motifs are flanked by GNGs. Importantly, the positioning and number of GNG/GNGNG can also influence the formation of G-quadruplexes. Further, we assessed three genomic regions from HIF1 alpha, VEGF and SHOX gene for G-quadruplex formation using GNG motifs. We show that HIF1 alpha sequence harbouring GNG motifs can fold into intramolecular G-quadruplex. In contrast, GNG motifs in mutant VEGF sequence could not participate in structure formation, suggesting that the usage of GNG is context dependent. Importantly, we show that when two continuous stretches of guanines are flanked by two independent GNG motifs in a naturally occurring sequence (SHOX), it can fold into an intramolecular G-quadruplex. Finally, we show the specific binding of G-quadruplex binding protein, Nucleolin and G-quadruplex antibody, BG4 to SHOX G-quadruplex. Overall, our study provides novel insights into the role of GNG motifs in G-quadruplex structure formation which may have both physiological and pathological implications.
Social Farming in the Promotion of Social-Ecological Sustainability in Rural and Periurban Areas

Rural areas are facing a spectrum of landscape changes and vulnerability as a consequence of financial and environmental crises. Innovative approaches are required to maintain the provision of social services and manage ecosystem services in these areas. We explore the capacity of social farming to create viable and sustainable rural and periurban areas according to a social-ecological perspective. We use the key elements of social-ecological systems under social farming practices to analyse (1) the role of local communities and non-formal institutions; (2) the involvement of target stakeholders; and (3) the explicit connection between agroecosystems and human wellbeing. To do so, we selected and described four cases of local social farming initiatives in terms of the key elements of social-ecological systems and conducted a literature review to provide an overview of the explicit impact of social farming on the quality of life. We found that social farming illustrates hybrid governance solutions beyond market instruments that could be applied for the governance of agroecosystems. It can also provide a range of other wellbeing and cultural ecosystem services to rural and urban inhabitants. Greater cooperation between social farming and ecosystem service science could rebound in rural landscape sustainability.
A Type III restriction–modification system in Mycoplasma mycoides subsp. capri

The sequenced genome of Mycoplasma mycoides subsp. capri revealed the presence of a Type III restriction–modification system (MmyCI). The methyltransferase (modification) subunit of MmyCI (M.MmyCI) was shown to recognize the sequence 5′-TGAG-3′ and methylate the adenine. The coding region of the methyltransferase gene contains 12 consecutive AG dinucleotide repeats that result in a translational termination at a TAA codon immediately beyond the repeat region. This strain does not have MmyCI activity. A clone was found with 10 AG repeats such that the gene is in frame, and this strain has MmyCI activity, suggesting that the expression of the MmyCI methyltransferase may be phase variable.
Using non-rigid image registration and Thin-Plate Spline warping for lung cancer progression assessment

Among different types of cancer the lung cancer is the most aggressive and best practice to its accurate prognosis is the determination of the current stage of the disease. Three main factors in cancer staging are primary tumor, regional lymph nodes and metastasis. Accurate determination of the cancer stage is not a trivial task, however utilization of computerized diagnostic tools can help the cancer experts to better diagnose the cancer status. Image registration is one of the main tools used for cancer diagnosis by experts. In this paper a new approach based on image registration is proposed to help the experts in better diagnosis of the lung cancer which is an improved method based on a previously proposed approach by the authors. In a multistep process the similarity between a pair of images acquired during past and current cancer stages is maximized with regards to the fact that tumor changes should be preserved during the deformation process. The similarity measure used during the registration process is Normalized Mutual Information. In the non-rigid image registration phase constraints are enforced on the optimization criteria, number of iterations and number of B-Spline grid nodes to preserve the tumor change. Control points which are transformation parameters for the Thin-Plate Spline warping are extracted from edge detected images in a semiautomatic manner. In the final step subtraction of sequential CT images is performed to detect the changes in the lung including the tumor change. Using the Insight Toolkit framework improved the quality of the final results and also ensured a more robust application. Experiments conducted on 8 pairs of CT lung volumes proved to have a satisfactory quality for change detection of the lung cancer.
A Consideration on Compression Level Control for Dynamic Compressed Data Transfer Method

Recently, large amount of data is transferred over network. The available bandwidth of network varies momently, so it is important to realize the efficient data transfer by fully utilizing the time-varying network bandwidth. We are developing the method of efficient data communication by dynamically compressing data, assuming the use of the high performance of multi-core processors. Our method can dynamically switch the compression method according to the network condition, to keep the balance of the compression speed and the transfer speed. In this paper, we examine the configuration of the global compression level that is the most important control parameter in our method. Our evaluation results confirmed that the configuration of the global compression level adopted in our previous research is reasonable.
Is Combining Classifiers Better than Selecting the Best One

We empirically evaluate several state-of-theart methods for constructing ensembles of heterogeneous classifiers with stacking and show that they perform (at best) comparably to selecting the best classifier from the ensemble by cross validation. We then propose a new method for stacking, that uses multi-response model trees at the meta-level, and show that it clearly outperforms existing stacking approaches and selecting the best classifier by cross validation.
Leveraging corporate influence

Abstract Movement scholars have become increasingly interested in the way in which social movement actors target non-state entities, particularly corporations. The reason for this is quite simple: globalization, neoliberal policies adopted by the state, and new legal protections via court rulings have allowed businesses to exert considerable influence across all facets of society. In light of these changes, movements have found targeting the state less effective than directly pressuring business interests. Scholarship suggests that one of the most effective ways to ensure that corporations attend to movement concerns is through market pressures. While negatively impacting stock returns is perhaps the most effective means of achieving such pressure, there is surprisingly little empirical research linking stock price outcomes to movement success. Here, we use Qualitative Comparative Analysis and examine 35 labor strikes to determine if the ability of the union to negatively impact stock price affected their ability to win new gains for members (or, to prevent concessions). Our findings reveal that it is the characteristics of the targeted firm, not the actions of the unions themselves, that is most closely associated with success.
Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain E19, Isolated from a Horse in Chile

ABSTRACT Corynebacterium pseudotuberculosis is related to several diseases infecting horses and small ruminants, causing economic losses to agribusiness. Here, we present the genome sequence of C. pseudotuberculosis strain E19. The genome includes one circular chromosome 2,367,956 bp (52.1% G+C content), with 2,112 genes predicted, 12 rRNAs, and 48 tRNAs.
What do the young people think about the possibility to solve the problems of the contemporary world in the future? An introductory report

Within the framework of the theory of future time perspective, the author discusses the empirical findings from the students of military colleges in Poland on their predictions of solution to various global problems within the next 25, 50, 100 years. The problems refer to political, ecological, health, social, economic, cultural, psychological and religious matters. Overall their predictions were pessimistic and their pessimism was greater than among students of social sciences.
Practical Coding-Aware Mechanism for Opportunistic Routing in Wireless Mesh Networks

Opportunistic routing and network coding have been considered as effective strategies for improving the throughput of wireless mesh networks (WMN). However, most existing work studied opportunistic routing and network coding separately. This has largely limited the ability of the above strategies from effectively improving the network performance. To achieve improved network throughput, in this paper, we propose a coding-aware opportunistic routing mechanism for WMNs. The design goal is achieved by effectively integrating the above two strategies such that decision on each packet forwarding is made with the awareness of potential coding opportunities. Simulation results show that our proposed mechanism can remarkably improve the network throughput.
Ethnomethodology as an Influence on Community-Centred Design

Social norms are integral to the success of online communities. This success is predicated on social norms reinforcing accepted community behaviour, marshalling effective communication and, from a semiotic perspective, providing a foundation for the interpretation of signs. Accepting Stamper's ontological position, we propose ethnomethodology as a theoretical basis for community-centred design. Ethnomethodology is the study of social order and has over the last decade gained much currency as a precursor to technology innovation. The only assumption underlying ethnomethodology is that social order is concrete and observable. Thus, social visualisations, that draw inspiration from ethnomethodology, are proposed as means to render social order accountable. Through reflection, the community is enabled to observe ongoing social processes and activate policy decisions accordingly. This socio-technical framework conceives of the community and supporting infrastructure as a complete information system. Finally, we present the Community Management Framework (CMF), a system, which encourages self-management through ongoing reflection and community-based policy management (CBPM).
Separating stages in the continuation-passing style transformation

The continuation-passing style (CPS) transformation is powerful but complex. Our thesis is that this transformation is in fact compound, and we set out to stage it. We factor the CPS transformation into several steps, separating aspects in each step: (1) Intermediate values are named; (2) Continuations are introduced; (3) Sequencing order is decided and administrative reductions are performed. Step 1 determines the evaluation order (e.g., call-by-name or call-by-value). Step 2 isolates the introduction of continuations and is expressed with local, structure-preserving rewrite rules — a novel aspect standing in sharp contrast with the usual CPS transformations. Step 3 determines the ordering of continuations (e.g., left-to-right or right-to-left evaluation) and leads to the familiar-looking continuation-passing terms. Step 2 is completely reversible and Steps 1 and 3 form Galois connections. Together they lead to the direct style (DS) transformation of our earlier work (including first-class continuations): (1) Intermediate continuations are named and sequencing order is abstracted; (2) Second-class continuations are eliminated; (3) Administrative reductions are performed. A subset of these transformations can leverage program manipulation systems: CPS-based compilers can modify sequencing to improve e.g., register allocation; static program analyzers can yield more precise results; and overspecified CPS programs can be rescheduled. Separating aspects of the CPS transformation also enables a new programming style, with applications to nondeterministic programming. As a byproduct, our work also suggests a new continuation semantics for unspecified sequencing orders in programming languages (e.g., Scheme).
Development of a Measure of Personal Web Usage in the Workplace

This research develops a measurement model representing personal web usage activities (PWU) in the workplace. A series of activities are used to identify potential items and validate three personal web usage dimensions. These dimensions of activity include personal external business, personal external socializing, and personal external interest and research. First and second order confirmatory factor analyses are used to validate the instrument. The results recommend the use of personal web usage construct in both investigating the factors that lead to personal web usage in the workplace and in providing advice for practitioners of potential consequences of these personal web usage dimensions.
LAppDesigner: The Design of a Database Application Customizing Tool Based on Linux

Due to the problem of the often changes of users' requirements leading to many modifications of code, on basis of several technologies such as visual development, Persistent object and design patterns, using object-oriented analysis and design and development methods, we design LAppDesigner (Linux Application Designer): the database application customizing tool based on Linux driven by database with functions of visual customizing and dynamic making of simple database application, to create prototype system adapting to limited changes of user’s requirements. We implement most of functions of LAppDesigner in this paper by using development tool Delphi for Linux.
A Theory of As ; ' llshronous Processes

A theory of asynchronous processes (nondeterministic data florv net-rvorks) is presented. It consists of a mathematical model and a process algebra. The intention is to provide a better theoretical underpinning to the Jackson System Development metirod. The model is so constructed as to be compatible rvith the failures modei of Hoare's Communicating Sequential Processes. The process algebra describes the laws that govern a collection of CSP-like operators, convenient for constructing asynchronous process networks from their components. The operators are defined in terms of the model and so their algebraic properties can be verified. As in CSP, the laws are suffi.ciently complete to transform every netrvork r^ r qpnrrpnria.l form This is imnort;r.nt fnr a dpsion rncfhod like JSD, rvhefe the LU 4 JEqUE]LLI@ lVLfrlt rllfr IJ lutl,va resulting programs must be implemented on a traditional sequential computer.
The Chalcolithic Radiocarbon Record and Its Use in Southern Levantine Archaeology

Archaeological evidence suggests that the Chalcolithic period (5th–4th millennium BCE) in the southern Levant was a time of significant settlement expansion and increasing social complexity. Important technological and social developments during this era set the stage for the later rise of fortified sites and nascence of urbanization in the Early Bronze Age. Controversy surrounding the chronology of Chalcolithic settlement and the reconstruction of social trajectories has stimulated an interest in building a database of radiocarbon dates to measure the tempo of change and help resolve these issues. To facilitate social evolutionary research, this paper reviews and updates published 14C data for the southern Levantine Chalcolithic. The now-substantial database supports the generally accepted time frame for this archaeological period and allows synchronic comparisons across diverse geographic subregions in the southern Levant. In addition, it helps to temporally place the emergence of sophisticated technologies and the development of complex social institutions within the Chalcolithic period. However, radiometrically based attempts at pan-regional internal periodization of the Chalcolithic and fine-tuning of protohistoric events such as site establishment and abandonment are frustrated by the lack of precision in 14C dates, which limits their ability to resolve chronological sequence. Improved delineation of Chalcolithic social trajectories can be achieved most effectively by focussing research efforts on stratigraphic and typological investigations of deeply-stratified settlement sites such as Teleilat Ghassul and Shiqmim within their local contexts.
Using the LASSO's Dual for Regularization in Sparse Signal Reconstruction from Array Data

Waves from a sparse set of source hidden in additive noise are observed by a sensor array. We treat the estimation of the sparse set of sources as a generalized complex-valued LASSO problem. The corresponding dual problem is formulated and it is shown that the dual solution is useful for selecting the regularization parameter of the LASSO when the number of sources is given. The solution path of the complex-valued LASSO is analyzed. For a given number of sources, the corresponding regularization parameter is determined by an order-recursive algorithm and two iterative algorithms that are based on a further approximation. Using this regularization parameter, the DOAs of all sources are estimated.
Computationally Efficient Predictive Robot Control

Conventional linear controllers (PID) are not really suitable for the control of robot manipulators due to the highly nonlinear behavior of the latter. Over the last decades, several control methods have been proposed to circumvent this limitation. This paper presents an approach to the control of manipulators using a computationally-efficient-model-based predictive control scheme. First, a general predictive control law is derived for position tracking and velocity control, taking into account the dynamic model of the robot, the prediction and control horizons, and also the constraints. However, the main contribution of this paper is the derivation of an analytical expression for the optimal control to be applied that does not involve a numerical procedure, as opposed to most predictive control schemes. In the last part of the paper, the effectiveness of the approach for the control of a nonlinear plant is illustrated using a direct-drive pendulum, and then, the approach is validated and compared to a PID controller using an experimental implementation on a 6-DOF cable-driven parallel manipulator.
Enhancing deep extreme learning machines by error backpropagation

We present an extension to a previously proposed Deep ELM architecture, and make the network end-to-end trainable using backpropagation. This significantly increases the network's performance for lower numbers of hidden units, and hence is well suited for resource constrained applications. The new architecture offers classification results of over 98% on the MNIST handwritten digits dataset for hidden layer sizes of 200. This compares favourably with previous results. We achieve the same performance of a network with a total of 12,000 hidden units, but only using 5,000 hidden units. Therefore the execution times of the original Deep ELM have been significantly reduced, whilst maintaining performance.
Anxiety, language use and linguistic competence in an immigrant context: a vicious circle?

ABSTRACT By exploring two novel concepts, heritage language anxiety (HLA) and majority language anxiety (MLA), this study draws attention to the hitherto neglected topic of language anxiety in immigrant and minority contexts. Based on semi-structured interviews with three generations of Turkish immigrants in the Netherlands (n = 30), we investigate why members of an immigrant community experience language anxiety and how it affects them. Findings suggest that language anxiety in the immigrant context, in both its HLA and MLA manifestations, can be attributed to linguistic and socioemotional causes. These linguistic and socioemotional causes, however, are occasionally difficult to isolate and they often interact in bringing about a number of negative consequences. Immigrants may ultimately avoid using the language about which they feel anxious, which will in turn cause further problems in terms of conflicted identities and reduced proficiency in the language concerned. We thus propose that there is a vicious circle that connects bilinguals’ language knowledge, language use and language anxiety.
A spatialized additive synthesizer

In virtual auditory environments, sound generation is typically based on a two-stage approach: synthesizing a monophonic signal, implicitly equivalent to a point source, and simulating the acoustic space. The directivity, spatial distribution and position of the source can be simulated thanks to signal processing applied to the monophonic sound. A one-stage synthesis/spatialization approach, taking into account both timbre and spatial attributes of the source as low-level parameters, would achieve a better computational efficiency essential for real-time audio synthesis in interactive environments. Such approach involves a careful examination of sound synthesis and spatialization techniques to reveal how they can be connected together. This paper concentrates on the sinusoidal sound model and 3D positional audio rendering methods. We present a real-time algorithm that combines Inverse Fast Fourier Transform (FFT-1) synthesis and directional encoding to generate sounds whose sinusoidal components can be independently positioned in space. In addition to the traditional frequency-amplitude-phase parameter set, partials positions are used to drive the synthesis engine. Audio rendering can be achieved on a multispeaker setup, or in binaural over headphones, depending on the available reproduction system.
YAP:Ce scintillator characteristics for neutron detection

YAP: Ce (YAlO3:Ce+, Yttrium Aluminum Perovskite, Ce+ doped) crystals with appropriate converters seem like prospective scintillators for neutron detection. An important aspect for neutron detection with inorganic scintillators is the ability to discriminate neutron radiation from gamma radiation by pulse height of signals. For a detailed measurement of the aspect, a YAP: Ce crystal scintillator with lithium or hydrogen converters and a photomultiplier was used. A plutonium-beryllium neutron source and horizontal neutron channel beams of the LVR-15 research reactor were used as neutron sources. The measurement confirmed the possibility to use the YAP: Ce scintillator for neutron radiation detection. The degree of discrimination between neutron and gamma radiation for different detection configurations was studied.