Miracle-dz/UniFAR-FTUs huggingface dataset:
Krüppel-associated Box (KRAB)-associated Co-repressor (KAP-1) Ser-473 Phosphorylation Regulates Heterochromatin Protein 1β (HP1-β) Mobilization and DNA Repair in Heterochromatin*

Background: KAP-1 and HP1-β are involved in DNA repair of heterochromatin via chromatin remodeling. Results: Chk2-dependent KAP-1 phosphorylation regulates HP1-β mobilization from chromatin following DNA damage. Conclusion: Regulation of HP1-β mobilization via KAP-1 phosphorylation is required for efficient DNA repair of heterochromatin. Significance: Understanding the regulation of DNA repair and chromatin remodeling pathways can increase our knowledge of tumorigenesis. The DNA damage response encompasses a complex series of signaling pathways that function to regulate and facilitate the repair of damaged DNA. Recent studies have shown that the repair of transcriptionally inactive chromatin, named heterochromatin, is dependent upon the phosphorylation of the co-repressor, Krüppel-associated box (KRAB) domain-associated protein (KAP-1), by the ataxia telangiectasia-mutated (ATM) kinase. Co-repressors, such as KAP-1, function to regulate the rigid structure of heterochromatin by recruiting histone-modifying enzymes, such HDAC1/2, SETDB1, and nucleosome-remodeling complexes such as CHD3. Here, we have characterized a phosphorylation site in the HP1-binding domain of KAP-1, Ser-473, which is phosphorylated by the cell cycle checkpoint kinase Chk2. Expression of a nonphosphorylatable S473A mutant conferred cellular sensitivity to DNA-damaging agents and led to defective repair of DNA double-strand breaks in heterochromatin. In addition, cells expressing S473A also displayed defective mobilization of the HP1-β chromodomain protein. The DNA repair defect observed in cells expressing S473A was alleviated by depletion of HP1-β, suggesting that phosphorylation of KAP-1 on Ser-473 promotes the mobilization of HP1-β from heterochromatin and subsequent DNA repair. These results suggest a novel mechanism of KAP-1-mediated chromatin restructuring via Chk2-regulated HP1-β exchange from heterochromatin, promoting DNA repair.
A circuit implementation of an ultra high speed, low power analog fully programmable MFG

In this article, an analog fully programmable membership function generator (MFG) is presented. It is capable of generating Gaussian, Triangular and Trapezoidal shapes as well as S or Z shapes. For omitting noise disturbances, differential structures are utilized in input and output stages which are in voltage mode and current mode, respectively. In contrast with conventional MFGs which are controlled digitally or by mixed signal approaches, this structure is a fully programmable analog MFG. It is capable of modifying slope, position and height of output's current. The most distinguishing features of this MFG are its capability of generating ultra-high speed outputs reaching speeds as high as 200 MHz and consuming a very low amount of power. Due to the simple structure of this MFG, it consumes a small active area at the size of 20μm×30μm. It is constructed of only 16 transistors. This MFG has been designed in 0. 35μm CMOS technology. The simulations have been done with Hspice using TSMC, BSIM3 (V3.1) model.
Visual security evaluation for video encryption

Video encryption plays an important role in data security guarantee, which is increasingly important with the development of multimedia technology. A great deal of effort has been made in recent years to develop video encryption methods. However, few studies focus on visual security evaluation, which has significant impact in measuring the effectiveness of these methods. In this paper, a new metric for video encryption is proposed, which evaluates visual security based on color and edge features of original and cipher-videos. The metric is easy to be incorporated into video encryption system for visual security based encryption decision. In addition, subjective tests for visual security assessment have been fully carried out. Experiments show that the proposed metric had better correlation with subjective results than others.
A Preliminary Evaluation of a Home-based, Computer-delivered Attention Training Treatment for Anxious Children Living in Regional Communities

Many children with anxiety disorders live in communities with limited access to treatment. Attention bias modification training, a promising computer-based treatment for anxiety disorders, may provide a readily accessible treatment. Recent evidence suggests that a form of ABMT combining visual-search for positive stimuli with features to enhance learning, memory and treatment engagement reduces anxiety in children. The present study builds upon this research by comparing parent-implemented, visual-search attention training to positive stimuli (ATP) (N = 22) with a waitlist control group (WLC) (N = 19) in children living in regional communities. Diagnostic, parent- and child-reports of anxiety and depressive symptoms and broad internalizing and externalizing behaviour problems were assessed pre- and post-condition. Children in the WLC completed visual-search ATP after the wait period and all participants completed a follow-up assessment six-months after treatment. At post-treatment/wait period, children in the ATP condition showed greater improvements on clinician- and parent-report measures compared to children in the WLC. Similar post-treatment outcomes as those found for the ATP condition were observed at the six-month follow-up after all children had received ATP. Moreover, children who showed greater verbalization of explicit attention strategies related to positive search (assessed during treatment) achieved greater reductions in anxiety severity at post-treatment and six-month follow-up. Attention training towards positive stimuli using enhanced visual-search procedures appears to be a promising treatment for reaching anxious children living in regional communities.
Cross-layer design and analysis for FSO links using automatic repeat request and adaptive modulation/coding schemes

This paper introduces a framework for cross-layer management of data transmissions in free-space optical (FSO) systems over atmospheric turbulence channels, in which link layer automatic repeat request (ARQ) and physical layer adaptive modulation and coding (AMC) are integrated to improve the system's spectral efficiency. The system performance is analytically studied in terms of average frame-error rate and average spectral efficiency, for which we derive closed-form expressions. In numerical results, we show how the proposed scheme outperforms a conventional one, and discuss cross-layer designs for parameters' selection in both physical and link layers to optimise the system performance over different atmospheric turbulence conditions.
Lactic acid secretion by human neutrophils. Evidence for an H+ + lactate- cotransport system

The pathway by which L-lactate (Lac) crosses the plasma membrane of isolated human neutrophils was investigated. The influx of [14C]Lac from a 2 mM Lac, 145 mM Cl-, 5.6 mM glucose medium was approximately 1.5 meq/liter of cell water.min and was sensitive to the organomercurial agent mersalyl (apparent Ki approximately 20 microM), to alpha-cyano-4-hydroxycinnamate (CHC), the classical inhibitor of monocarboxylate transport in mitochondria, and to UK-5099 (apparent Ki approximately 40 microM), a more potent analogue of CHC. Transport was also strongly blocked (greater than 80%) by 1 mM of either 3,5- diiodosalicylic acid, MK-473 (an indanyloxyacetate derivative), or diphenyl-amine-2-carboxylate, and by 0.4 mM pentachlorophenol, but not by 1 mM ethacrynic acid, furosemide, or the disulfonic stilbenes SITS or H2DIDS. One-way [14C]Lac efflux from steady-state cells amounted to approximately 6 meq/liter.min and was likewise affected by the agents listed above. Influx, which was membrane potential insensitive and Na+ independent, displayed a strong pH dependence: extracellular acidification enhanced uptake while alkalinization inhibited the process (pK' approximately 5.7 at 2 mM external Lac). The rate of [14C]Lac influx was a saturable function of external Lac, the Km being approximately 7 mM. Steady-state cells exhibited an intracellular Lac content of approximately 5 mM and secreted lactic acid into the bathing medium a a rate of approximately 4 meq/liter.min. Secretion was completely suppressed by 1 mM mersalyl which inactivates the carrier, leading to an internal accumulation of Lac. That the Lac carrier truly mediates an H+ + Lac- cotransport (or formally equivalent Lac-/OH- exchange) was documented by pH-stat techniques wherein an alkalinization of poorly buffered medium could be detected upon the addition of Lac; these pH changes were sensitive to mersalyl. Thus, the Lac carrier of neutrophils possesses several features in common with other monocarboxylate transport systems in erythrocytes and epithelia.
Inferring semantically related software terms and their taxonomy by leveraging collaborative tagging

Many software engineering tasks, such as feature location and duplicate bug report detection, leverages similarities among textual corpora. However, due to the different words used by developers to express the same concept, exact matching of words is insufficient. One document can contain a particular word while the other document may contain another word that is semantically related but is not the same. Such word differences may cause inaccuracies in subsequent software engineering tasks. Recently, tagging has impacted the software engineering community. Developers increasingly use tags to describe important features of a software product. Many project hosting sites allow users to tag various projects with their own words. It becomes increasingly important to understand and relate these tags. Based on the tags available from software project hosting websites, we propose a similarity metric to infer semantically related terms, each of which is a tag, and build a taxonomy that could further describe the relationships among these terms. We have built a sample taxonomy from tens of thousands of projects and their tags. Our user studies show that our proposed similarity metric for tags are indeed related to the semantic similarity of the terms, and the resultant semantic taxonomy among terms is reasonably good.
A wireless computational platform for distributed computing based traffic monitoring involving mixed Eulerian-Lagrangian sensing

This paper presents a new wireless platform designed for an integrated traffic monitoring system based on combined Lagrangian (mobile) and Eulerian (fixed) sensing. The sensor platform is built around a 32-bit ARM Cortex M4 micro-controller and a 2.4GHz 802.15. 4 ISM compliant radio module, and can be interfaced with fixed traffic sensors, or receive data from vehicle transponders. The platform is specially designed and optimized to be integrated in a solar-powered wireless sensor network in which traffic flow maps are computed by the nodes directly using distributed computing. A MPPT circuitry is proposed to increase the power output of the attached solar panel. A self-recovering unit is designed to increase reliability and allow periodic hard resets, an essential requirement for sensor networks. A radio monitoring circuitry is proposed to monitor incoming and outgoing transmissions, simplifying software debug. An ongoing implementation is briefly discussed, and compared with existing platforms used in wireless sensor networks.
Spam filtering using the Kolgomorov complexity analysis

One of the most irrelevant side effects of e-commerce technology is the development of spamming as an e-marketing technique. Spam e-mails (or unsolicited commercial e-mails) induce a burden for everybody having an electronic mailbox: detecting and filtering spam is then a challenging task and a lot of approaches have been developed to identify spam before it is posted in the end user’s mailbox. In this paper, we focus on a relatively new approach whose foundations rely on the works of A. Kolmogorov. The main idea is to give a formal meaning to the notion of ‘information content’ and to provide a measure of this content. Using such a quantitative approach, it becomes possible to define a distance, which is a major tool for classification purposes. To validate our approach, we proceed in two steps: first, we use the classical compression distance over a mix of spam and legitimate e-mails to check out if they can be properly clustered without any supervision. It has been the case to highlight a kind of underlying structure for spam e-mails. In the second step, we have implemented the k-nearest neighbours algorithm providing 85.
Dreams, reality and memory: confabulations in lucid dreamers implicate reality-monitoring dysfunction in dream consciousness

Introduction. Dreams might represent a window on altered states of consciousness with relevance to psychotic experiences, where reality monitoring is impaired. We examined reality monitoring in healthy, non-psychotic individuals with varying degrees of dream awareness using a task designed to assess confabulatory memory errors – a confusion regarding reality whereby information from the past feels falsely familiar and does not constrain current perception appropriately. Confabulatory errors are common following damage to the ventromedial prefrontal cortex (vmPFC). Ventromedial function has previously been implicated in dreaming and dream awareness. Methods. In a hospital research setting, physically and mentally healthy individuals with high (n = 18) and low (n = 13) self-reported dream awareness completed a computerised cognitive task that involved reality monitoring based on familiarity across a series of task runs. Results. Signal detection theory analysis revealed a more liberal acceptance bias in those with high dream awareness, consistent with the notion of overlap in the perception of dreams, imagination and reality. Conclusions. We discuss the implications of these results for models of reality monitoring and psychosis with a particular focus on the role of vmPFC in default-mode brain function, model-based reinforcement learning and the phenomenology of dreaming and waking consciousness.
High-voltage tolerant stimulation monitoring circuit in conventional CMOS process

Design techniques for realizing analog switch and rail-to-rail constant gm opamp with approximately twice the standard supply voltages and signal swings are proposed in this paper. Based on these techniques, a 6V stimulation monitoring circuit for monitoring 8 different stimulator outputs was implemented in a conventional 0. 18µm CMOS process using standard 3.3V I/O devices. Maximum on-resistance for the switches was less than 3. 15kΩ and the variations on the opamp input gm values were less than ±2.9% with a current consumption of 20µA at 6V.
Transforming UML Models to Formal Speci cations

The Uni ed Modeling Language (UML) is considered a signi cant step in the development of object-oriented (OO) notations in that it is based on some of the best OO modeling experiences. In this paper we are considering more speci cally its use in the context of high-quality modeling of complex systems. We believe that the lack of rm semantics for the modeling notations used makes, among others, the identi cation of requirements problems di cult. One approach to making UML more precise and amenable to rigorous analysis is to integrate it with suitable formal notations. In this paper we present the bene ts from a similar approach that is the result of integrating Fusion modeling techniques and the Z formal speci cation notation. The result is a technique that produces highly-structured, graphical, rigorously-analyzable models that facilitates early detection of errors. We believe that UML could gain from this experience. 1 Research motivation In the area of software speci cation we can distinguish two classes of techniques: the informal, structured techniques (ISTs) (e.g., OMT [7], Fusion [2]) which emphasize ease-of-use and understandability, often at the cost of rigor, and the formal speci cation techniques (FSTs) (e.g., Z [9]) which emphasize formality, often at the cost of ease-of-use and understandability. The lack of precise semantics for popular ISTs can lead to the following problems [4]: Understanding of models can be more apparent than real. Developers can waste considerable time resolving disputes over usage and interpretation of notation. Rigorous semantic analysis is di cult. The need for a rigorous basis for OO modeling suggests the use of traditional FSTs, where a FST consists of a notation that directly utilizes mathematical concepts, and provides mechanisms for formally analyzing models expressed in the notation. OO extensions of traditional FSTs attempt to provide a richer set of structuring mechanisms, but such extensions often result in semantics that are more complex. The integration of ISTs and FSTs provides an avenue for transforming an imprecise model into a more precise model. We propose that rather than attempting to extend traditional FSTs with OO concepts, a more workable approach would be to provide a formal basis for the OO modeling notations and concepts that have been shown to be e ective in practice. In other words, the approach we advocate is to make more precise the notations and concepts that are currently perceived as re ecting the best practical experiences in OO modeling. Formalizing such concepts and notation would deepen our understanding of OO modeling and result in OO techniques that are at least rigorous. In this position paper we give an overview of a rst attempt in this direction. Our approach for requirements modeling and analysis, called FuZed, integrates an informal OO analysis technique, Fusion [2], with a formal speci cation notation, Z [9]. In section 2 we detail our
What frequency bandwidth to run cellular network in a given country? — A downlink dimensioning problem

We propose an analytic approach to the frequency bandwidth dimensioning problem, faced by cellular network operators who deploy/upgrade their networks in various geographical regions (countries) with an inhomogeneous urbanization. We present a model allowing one to capture fundamental relations between users' quality of service parameters (mean downlink throughput), traffic demand, the density of base station deployment, and the available frequency bandwidth. These relations depend on the applied cellular technology (3G or 4G impacting user peak bit-rate) and on the path-loss characteristics observed in different (urban, sub-urban and rural) areas. We observe that if the distance between base stations is kept inversely proportional to the distance coefficient of the path-loss function, then the performance of the typical cells of these different areas is similar when serving the same (per-cell) traffic demand. In this case, the frequency bandwidth dimensioning problem can be solved uniformly across the country applying the mean cell approach proposed in [1]. We validate our approach by comparing the analytical results to measurements in operational networks in various geographical zones of different countries.
Signaling Theory, Strategic Interaction, and Symbolic Capital1

Signaling theory provides an opportunity to integrate an interactive theory of symbolic communication and social benefit with materialist theories of individual strategic action and adaptation. This article examines the potential explanatory value of signaling theory for a variety of anthropological topics, focusing on three social arenas in which signaling might plausibly be important: unconditional generosity, wasteful subsistence behavior, and artistic or craft traditions. In each case, it outlines the ways in which the phenomena correspond with the expectations of signaling theory by showing how a given pattern of action might signal particular hidden attributes, provide benefits to both signaler and observers, and meet the conditions for honest communication. The ethnographic evidence suggests that the fundamental conditions for reliable signaling of conditiondependent qualities may exist in many social domains. It appears that signaling theory has considerable promise for generating novel and powerful insights into the ethnographic realm.
SPICKER: A clustering approach to identify near‐native protein folds

We have developed SPICKER, a simple and efficient strategy to identify near‐native folds by clustering protein structures generated during computer simulations. In general, the most populated clusters tend to be closer to the native conformation than the lowest energy structures. To assess the generality of the approach, we applied SPICKER to 1489 representative benchmark proteins ≤200 residues that cover the PDB at the level of 35% sequence identity; each contains up to 280,000 structure decoys generated using the recently developed TASSER (Threading ASSembly Refinement) algorithm. The best of the top five identified folds has a root‐mean‐square deviation from native (RMSD) in the top 1.4% of all decoys. For 78% of the proteins, the difference in RMSD from native to the identified models and RMSD from native to the absolutely best individual decoy is below 1 Å; the majority belong to the targets with converged conformational distributions. Although native fold identification from divergent decoy structures remains a challenge, our overall results show significant improvement over our previous clustering algorithms. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 865–871, 2004