Miracle-dz/UniFAR-FTUs huggingface dataset:
Catalytic Specificity of Human Protein Tyrosine Kinases Revealed by Peptide Substrate Profiling

Out of the 90 human protein tyrosine kinases, 81 were assayed with short peptides derived from well-characterized [CDK1(Tyr15), IRS1(Tyr983), and JAK1(Tyr1023)] or generic [polyGlu:Tyr(4:1) and poly-Glu:Ala:Tyr(1:1:1)] substrates. As expected, the CDK1 peptide is a substrate for all Src family kinases. On the other hand, some of the activities are novel and lead to a better understanding of the function of certain kinases. Specifically, the CDK1 peptide is a substrate for many of the Eph family members. Interestingly, profiling of nearly all the human protein tyrosine kinases revealed a distinct pattern of selectivity towards the CDK1 and IRS1 peptides.
What Is STEM? A Discussion About Conceptions of STEM in Education and Partnerships

Educational reformation has proceeded slowly despite the many calls to improve science and mathematics for our students. The acronym STEM (science, technology, engineering, and mathematics) has been adopted by numerous programs as an important focus for renewed global competitiveness for the United States, but conceptions of what STEM entails often vary among stakeholders. This paper examines the conceptions of STEM held by faculty members from a public Research I institution in the middle of a regional “STEM movement. ” Faculty members responded to two open-ended questions: (1) What is STEM? and (2) How does STEM influence and/or impact your life? Although 72% of these faculty members possessed a relevant conception of STEM, the results suggest that they do not share a common conceptualization of STEM. Their conception is most likely based on their academic discipline or how STEM impacts their daily lives. STEM faculty members were likely to have a neutral or positive conception where non-STEM faculty members often had negative feelings about STEM.
The CpG Dinucleotide Adjacent to a κB Site Affects NF-κB Function through Its Methylation

NF-κB is an important transcription factor that plays critical roles in cell survival, proliferation, inflammation, and cancers. Although the majority of experimentally identified functional NF-κB binding sites (κB sites) match the consensus sequence, there are plenty of non-functional NF-κB consensus sequences in the genome. We analyzed the surrounding sequences of the known κB sites that perfectly match the GGGRNNYYCC consensus sequence and identified the nucleotide at the -1 position of κB sites as a key contributor to the binding of the κB sites by NF-κB. We demonstrated that a cytosine at the -1 position of a κB site (-1C) could be methylated, which thereafter impaired NF-κB binding and/or function. In addition, all -1C κB sites are located in CpG islands and are conserved during evolution only when they are within CpG islands. Interestingly, when there are multiple NF-κB binding possibilities, methylation of -1C might increase NF-κB binding. Our finding suggests that a single nucleotide at the -1 position of a κB site could be a critical factor in NF-κB functioning and could be exploited as an additional manner to regulate the expression of NF-κB target genes.
Enhancing Reflective Teaching Practices: Implications for Faculty Development Programs

Refl ecting on one’s teaching practice is often an implicit goal for faculty development programs. Yet very little has been documented how programs for diverse groups of university teachers actually engage faculty in such refl ection. This paper examines how theoretical constructs of refl ective practice were applied in the context of an 8-month UBC Faculty Certifi cate Program on Teaching and Learning in Higher Education (FCP). The Teaching Perspectives Inventory (TPI) was particularly useful for providing faculty cohort members with a means of looking more deeply at the underlying values and assumptions that constituted their philosophical orientations to teaching. Furthermore, a change in faculty members’ TPI scores indicate that participants refl ected more comprehensively on their teaching at the end of the program, than they did at the beginning of the program. Barriers to facilitating refl ection included inadequate time allocation, unclear expectations and goals for refl ection activities, and varying cultural norms for refl ective teaching practices within academe.
Decreasing information technology expenses by using emulators on Windows and Linux platforms

The two most popular operating systems (continues: OS) nowadays are Windows (wide range of products) and Linux (various distributions). Every OS has different development history, aimed application and different hardware implementation. The popularity of Windows operating systems is on a very high level but, today, Linux has proved that high quality software doesn't necessarily have to be commercial software. Linux and Windows operating systems and their applications are not compatible because of kernel and file systems differences and program code execution. That means that the users have to decide which OS they will use depending on economical and financial possibilities. The problem of using applications under different operating systems can be solved by emulator programs on both of Windows and Linux platforms. Most widely used emulators today are Wine (on Linux platforms) and VMware (on both platforms). Emulators offer the possibility to execute different applications (even installation of operating systems) on a platform that they were not previously written for. By choosing less expensive (or free) operating systems and appropriate emulators the overall information technology expenses can be significantly decreased.
For review purpose only 1 MODULAR FEATURE SELECTION USING RELATIVE IMPORTANCE FACTORS

Feature selection plays an important role in finding relevant or irrelevant features in classification. Genetic algorithms (GAs) have been used as conventional methods for classifiers to adaptively evolve solutions for classification problems. In this paper, we explore the use of feature selection in modular GA-based classification. We propose a new feature selection technique, Relative Importance Factor (RIF), to find irrelevant features in the feature space of each module. By removing these features, we aim to improve classification accuracy and reduce the dimensionality of classification problems. Benchmark classification data sets are used to evaluate the proposed approaches. The experiment results show that RIF can be used to determine irrelevant features and help achieve higher classification accuracy with the feature space dimension reduced. The complexity of the resulting rule sets is also reduced which means the modular classifiers with irrelevant features removed will be able to classify data with a higher throughput.
Reduction of allergic skin weal responses by sexual intercourse in allergic patients

Effect of sexual intercourse on allergen- and histamine-induced skin weal responses was studied. In normal subjects, house dust mite or Japanese cedar pollen allergen did not induce skin weal responses, while histamine induced skin weal responses. In contrast, in patients with allergic rhinitis or atopic dermatitis, who were allergic to Japanese cedar pollen and house dust mite, these allergens as well as histamine induced skin weal responses. Sexual intercourse had no effect on skin weal responses induced by histamine in normal subjects. In contrast, sexual intercourse significantly reduced skin weal responses induced by Japanese cedar pollen or house dust mite, while it did not reduce skin weal responses induced by histamine in allergic patients. This is the first report that sexual intercourse reduces specifically allergen-induced responses in allergic patients. These finding may have some implications for the pathophysiological effect of sexual intercourse on allergic diseases.
Perchance to Dream: Art, Mathematics, and Shakespeare

Visual representation of textual works has often aided in the understanding of sophisticated concepts [3]. In the Digital Age this is particularly true, given the advent of natural language processing, the ubiquity of general programming languages, and the maturation of digital visualization. In this article, we eschew the traditional disciplinary boundaries to view and analyze Shakespeare’s works in various ways. Our point of departure is Hamlet , where we ﬁrst examine the play as a unity — both graphically and analytically. We then focus on Act III, Scene 1, where we analyze one of the most famous passages in English Literature: Hamlet’s famous “To be or not to be” soliloquy. We study this passage with a sequence of progressively sophisticated content analysis software packages, each of which renders a useful artistic visual representation of the text. In these studies, we have gathered preliminary sets of context-free content data which allow us to give illustrations of a wide range of analytic tools. Throughout our explorations, we use new modes of linguistic exploration, synthesized from elements of philosophy, literature, mathematics, computer science, psychology, and the arts. Many of the methods, which help to form these new modes of exploration, may appear individually as Cartesian in nature, yet when collectively synthesized into a holism, form a fundamentally phenomenological study of human creativity.
Image deblurring using empirical Wiener filter in the curvelet domain and joint non-local means filter in the spatial domain

Abstract In this paper, an efficient image deblurring algorithm is proposed. This algorithm restores the blurred image by incorporating a curvelet-based empirical Wiener filter with a spatial-based joint non-local means filter. Curvelets provide a multidirectional and multiscale decomposition that has been mathematically shown to represent distributed discontinuities such as edges better than traditional wavelets. Our method restores the image in the frequency domain to obtain a noisy result with minimal loss of image components, followed by an empirical Wiener filter in the curvelet domain to attenuate the leaked noise. Although the curvelet-based methods are efficient in edge-preserving image denoising, they are prone to producing edge ringing which relates to the structure of the underlying curvelet. In order to reduce the ringing, we develop an efficient joint non-local means filter by using the curvelet deblurring result. This filter could suppress the leaked noise while preserving image details. We compare our deblurring algorithm with a few competitive deblurring techniques in terms of improvement in signal-to-noise-ratio (ISNR) and visual quality.
Dynamic travel time provision for road networks

The application domain of intelligent transportation is plagued by a shortage of data sources that adequately assess traffic situations. Typically, to provide routing and navigation solutions map attributes in the form of static weights as derived from road categories and speed limits used for road networks. With the advent of Floating Car Data (FCD) and specifically the GPS-based tracking data component, a means was found to derive accurate and up-to-date travel times, i.e., qualitative traffic information. FCD is a by-product in fleet management applications and given a minimum number and uniform distribution of vehicles, this data can be used for accurate traffic assessment and also prediction. This work showcases a system that facilitates the collection of FCD, produces dynamic travel time information, and provides value-added services based on the dynamic travel times. The essential components that will be discussed are a Web-services-based data collection approach, sophisticated map-matching algorithms, a data management architecture and an online visualization platform.
Free-energy landscape of ion-channel voltage-sensor–domain activation

Significance Voltage-gated cation channels (VGCCs) shape cellular excitability. Their working cycle involves the complex conformational change of modular protein units called voltage sensor domains (VSDs). For over 40 y, these rearrangements have been recorded as “gating” currents, the intensities and kinetics of which are unique signatures of VGCC function. We show that the atomistic description of VSD activation obtained by molecular dynamics simulations and free-energy calculations is consistent with the phenomenological models adopted to account for the macroscopic observables measured by electrophysiology. Our findings pave the way for in silico studies of the VGCC electrophysiological response and hold promise to uncover the molecular underpinnings of inherited channelopathies and modulation of VGCCs by drugs and toxins. Voltage sensor domains (VSDs) are membrane-bound protein modules that confer voltage sensitivity to membrane proteins. VSDs sense changes in the transmembrane voltage and convert the electrical signal into a conformational change called activation. Activation involves a reorganization of the membrane protein charges that is detected experimentally as transient currents. These so-called gating currents have been investigated extensively within the theoretical framework of so-called discrete-state Markov models (DMMs), whereby activation is conceptualized as a series of transitions across a discrete set of states. Historically, the interpretation of DMM transition rates in terms of transition state theory has been instrumental in shaping our view of the activation process, whose free-energy profile is currently envisioned as composed of a few local minima separated by steep barriers. Here we use atomistic level modeling and well-tempered metadynamics to calculate the configurational free energy along a single transition from first principles. We show that this transition is intrinsically multidimensional and described by a rough free-energy landscape. Remarkably, a coarse-grained description of the system, based on the use of the gating charge as reaction coordinate, reveals a smooth profile with a single barrier, consistent with phenomenological models. Our results bridge the gap between microscopic and macroscopic descriptions of activation dynamics and show that choosing the gating charge as reaction coordinate masks the topological complexity of the network of microstates participating in the transition. Importantly, full characterization of the latter is a prerequisite to rationalize modulation of this process by lipids, toxins, drugs, and genetic mutations.
Liberal Safety for Answer Set Programs with External Sources

Answer set programs with external source access may introduce new constants that are not present in the program, which is known as value invention. As naive value invention leads to programs with infinite grounding and answer sets, syntactic safety criteria are imposed on programs. However, traditional criteria are in many cases unnecessarily strong and limit expressiveness. We present liberal domain-expansion (de-) safe programs, a novel generic class of answer set programs with external source access that has a finite grounding and allows for value invention. De-safe programs use so-called term bounding functions as a parameter for modular instantiation with concrete—e.g., syntactic or semantic or both—safety criteria. This ensures extensibility of the approach in the future. We provide concrete instances of the framework and develop an operator that can be used for computing a finite grounding. Finally, we discuss related notions of safety from the literature, and show that our approach is strictly more expressive.
Use of Irreversible Antagonists to Determine the Relative Efficacy of μ-Opioids in a Pigeon Drug Discrimination Procedure: Comparison of β-Funaltrexamine and Clocinnamox

The use of irreversible antagonists to assess opioid efficacy has proven fruitful for classifying opioids on the basis of high or low efficacy, but few studies have provided quantitative estimates of efficacy. The purpose of this study was to use β-funaltrexamine (β-FNA) and clocinnamox (C-CAM) in a drug discrimination procedure to examine the efficacy of fentanyl, morphine, l-methadone, sufentanil, and etorphine. In pigeons trained to discriminate 0.12 mg/kg fentanyl from water, dose-effect curves were determined for each opioid alone and after pretreatment with β-FNA and C-CAM. Using quantitative analyses according to an extended model of Black and Leff (1983), apparent efficacy (τ) and affinity (KA) of each opioid was determined, as well as the degree of receptor inactivation (q) produced by each dose of each antagonist. β-FNA and C-CAM produced dose- and time-dependent, rightward shifts in the dose-effect curves of each opioid, and analyses based on dose-ratios and τ values suggest a rank order of efficacy of etorphine > sufentanil = l-methadone > fentanyl = morphine. Marked differences in the profiles of antagonism produced by β-FNA and C-CAM were also apparent, as C-CAM, but not β-FNA, produced insurmountable antagonism. The q values for each antagonist were consistent with these data in indicating that C-CAM and β-FNA can inactivate nearly 100 and 75% of the receptor population, respectively. In tests conducted in pigeons chronically treated with morphine, doses of β-FNA that produced parallel, rightward shifts in untreated pigeons flattened the morphine dose-effect curve in morphine-treated pigeons. These results indicate that β-FNA and C-CAM can differentiate opioids with high relative efficacy and yield comparable estimates of efficacy for various opioids. There are, however, limitations in the proportion of the receptor population that can by eliminated by β-FNA.
Characterizing Neutral Aggregation on Restricted Domains

Sen [6] proved that by confining voters to value restricted (acyclic) domains voting paradoxes (intransitive relations) can be avoided in aggregation by majority. We generalize this result to any neutral monotone aggregation. In addition, we show that acyclicity is neither necessary nor sufficient for transitivity for neutral non-monotone aggregation: we construct a cyclic transitive domain and introduce strong acyclicity as a sufficient condition for transitivity. We also show that strong acyclicity is necessary if repeated transitivity is sought. Finally, we present a cyclic domain repeatedly transitively aggregatable by a non neutral function.
Quaternary Pattern of Freshwater Fishes in Europe: Comparative Phylogeography and Conservation Perspective

The phylogeographic studies of unrelated species that share overlapping distributions lead to new perspectives. Indeed, if different species with similar distributions shared the same phylogeographic pattern, then a common extrinsic cause could be proposed, involving some important issues for species conservation. Considering different mitochondrial studies of European freshwater fishes (threatened or not), it will be possible to perform such a comparative phylogeographic analyses. However, we illustrated how similar mitochondrial patterns can be due to different demographic models or evolutionary scenarios inducing numerous pitfalls. In this review, we present some major theoretical and practical challenges on phylogeography that need to be overcome before the inference of a global scenario. More than the evolution of the phylogeography discipline, estimation of the history of populations/species and their relationships is one of the most important challenges for conservation managers.
Competing Ideas of Social Justice and Space: Locating Critiques of Housing Renewal in Theory and in Practice

Abstract This article considers the experience of the English government's policy of Housing Market Renewal from the perspective of spatial justice. The paper first proposes an analytical framework that situates competing notions of territorial social justice within a space of complex sociospatial relations. The dialectic of two formulations of social justice is first set up, comparing ‘procedural’ or deontological forms of justice and the distributional justice of outcomes. Soja's formulation of spatial justice is advanced as an appropriate balance between spatial and socio-historic contexts for the justice question. Drawing on the literature on sociospatial relations, concrete critiques and justifications of HMR are then positioned in terms of the intersection of structuring principles and policy fields. The role of demolition in urban restructuring programmes is used to explore the differential spatialities involved in different justicial perspectives. It is concluded that ‘gentrification’ critiques of HMR are only partial in their evaluation of justice and lack normative power. Some practical implications for the design of urban restructuring policies are offered.
Resource management in interference channels with asynchronous users

We consider a two-user interference channel where the users are not synchronous meaning there exists a delay between their transmitted codes. Assuming no user is aware of the location of the interference burst on its code, no interference cancellation is performed, i.e., users treat each other as noise. By the same token, the interference is no longer Gaussian as a result of the ambiguity on the start of the interference burst. We propose a stationary channel model for this setup for which we are able to derive the achievable rates based on upper and lower bounds on the mutual information between the input and output of the channel. These bounds meet each other as the code length grows to infinity. We define the outage capacity for each user as the largest transmission rate such that the outage probability is ensured to be below a certain threshold. In case the users are sharing a certain number of frequency sub-bands, we propose to divide the spectrum among the users to maximize the outage capacity for each user. We demonstrate that depending on the probabilistic parameters of the delay model and the value of the outage threshold, there are cases where the best strategy is to assign both private and common frequency sub-bands to the users.
Group Size and Cooperation

To compare the effects of group size on cooperation, we introduce a class of simple multiperson games. These games can be regarded as n-person generalizations of the two-person prisoner's dilemma with expected value payoffs. In order to ensure that identical expected-value monetary alternatives are available to players in different-sized groups, we introduced a certain formal constraint on payoffs. Results of an experimental study comparing three-and seven-person groups show that the smaller-sized group is markedly more cooperative than the larger group. The primary emphasis of this paper is methodological. It demonstrates a technique to measure cooperation as a function of group size unconfounded by role-playing and utility considerations.
Achieving Computational I/O Efficiency in a High Performance Cluster Using Multicore Processors

Cluster computing has become one of the most popular platforms for high-performance computing today. The recent popularity of multicore processors provides a Flexible way to increase the computational capability of clusters. Although the system performance may improve with multicore processors in a cluster, I/O requests initiated by multiple cores may saturate the I/O bus, and furthermore increase the latency by issuing multiple non-contiguous disk accesses. In this paper, we propose an asymmetric collective I/O for multicore processors to improve multiple non-contiguous accesses. In our configuration, one core in each multicore processor is designated as the coordinator, and others serve as computing cores. The coordinator is responsible for aggregating I/O operations from computing cores and submitting a contiguous request. The coordinator allocates contiguous memory buffers on behalf of other cores to avoid redundant data copies.