Miracle-dz/UniFAR-FTUs huggingface dataset:
to infer gene regulatory interactions Integrative analysis of C . elegans modENCODE ChIP-seq data sets Material Supplemental

Material Supplemental http://genome.cshlp. org/content/suppl/2013/04/16/gr.152876. 112.DC1. html References http://genome.cshlp. org/content/23/6/941.full. html#ref-list-1 This article cites 69 articles, 27 of which can be accessed free at: License Commons Creative . http://creativecommons.org/licenses/by-nc/3.0/ described at a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as ). After six months, it is available under http://genome.cshlp. org/site/misc/terms.xhtml first six months after the full-issue publication date (see This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the
Expanding Television’s Cultural Forum in the Digital Era: Prime Time Television, Twitter, and Black Lives Matter

Twitter updates and expands television’s cultural forum model by letting viewers speak to current events such as the Black Live Matter (BLM) movement. This article analyzes 1,985 tweets in response to three television episodes (Law & Order: SVU, The Good Wife, and Scandal) that dramatized BLM, and identifies five common themes in how viewers address these representations: thematic appropriateness, timing, producers’ qualifications, institutional critiques, and the purpose of entertainment television. This study concludes that Twitter facilitates a meta-commentary, which expands traditional discussions of entertainment programming, and that these programs transcend “mere” entertainment to become critiques of larger social movements.
High-Level Test Generation for Gate-Level Fault Coverage

In this paper we introduce a spectral method of register transfer level (RTL) test generation for sequential circuits. We dene RTL faults as stuck-at faults on all primary inputs, primary outputs, and ip-op terminals. Test vectors generated to cover the RTL faults are analyzed using Hadamard matrices. The analysis determines the amplitudes of prominent Walsh functions and the random noise level for each primary input. That information is then used to generate vectors for any gate-level implementation. At the gate-level, a fault simulator and an integer linear program (ILP) are used to compact the test sequence. We give results for three ITC’99 and four ISCAS’89 benchmark circuits. Each ITC’99 circuit was synthesized two ways, separately for area and delay optimization. The RTL spectral vectors performed equally well on both implementations. When compared to a gatelevel ATPG, the coverages of RTL vectors were similar and in many cases RTL vectors produced equal or higher coverage in shorter CPU time.
Global Analysis of Differentially Expressed Genes and Proteins in the Wheat Callus Infected by Agrobacterium tumefaciens

Agrobacterium-mediated plant transformation is an extremely complex and evolved process involving genetic determinants of both the bacteria and the host plant cells. However, the mechanism of the determinants remains obscure, especially in some cereal crops such as wheat, which is recalcitrant for Agrobacterium-mediated transformation. In this study, differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were analyzed in wheat callus cells co-cultured with Agrobacterium by using RNA sequencing (RNA-seq) and two-dimensional electrophoresis (2-DE) in conjunction with mass spectrometry (MS). A set of 4,889 DEGs and 90 DEPs were identified, respectively. Most of them are related to metabolism, chromatin assembly or disassembly and immune defense. After comparative analysis, 24 of the 90 DEPs were detected in RNA-seq and proteomics datasets simultaneously. In addition, real-time RT-PCR experiments were performed to check the differential expression of the 24 genes, and the results were consistent with the RNA-seq data. According to gene ontology (GO) analysis, we found that a big part of these differentially expressed genes were related to the process of stress or immunity response. Several putative determinants and candidate effectors responsive to Agrobacterium mediated transformation of wheat cells were discussed. We speculate that some of these genes are possibly related to Agrobacterium infection. Our results will help to understand the interaction between Agrobacterium and host cells, and may facilitate developing efficient transformation strategies in cereal crops.
A terminology for talking about privacy by data minimization: Anonymity, Unlinkability, Undetectability, Unobservability, Pseudonymity, and Identity Management

Based on the nomenclature of the early papers in the field privacy by data minimization, we develop a terminology which is both expressive and precise. More particularly, we define anonymity, unlinkability, linkability, undetectability, unobservability, pseudonymity (pseudonyms and digital pseudonyms, and their attributes), identifiability, identity, partial identity, digital identity and identity management. In addition, we describe the relationships between these terms, give a rationale why we define them as we do, and sketch the main mechanisms to provide for the properties defined.
A Study on Stress Level and Coping Strategies among Undergraduate Students

Feelings of stress are a part of university students’ life. Stress is simply the body's response to changes that create taxing demands. There is a difference between eustress, which is a term for positive stress, and distress, which refers to negative stress. Coping mechanism plays a significant part to overcome or reduce the stress experienced by individuals. People use different types of coping strategies to overcome their stress. The purpose of the study was to study the relationship between stress and coping strategies among university students. Eighty- six university students participated in the study. A quantitative study utilizing a cross sectional non-probability sampling research design was used to gather data. The data was collected using a questionnaire with the addition of Perceived Stress Scale (PSS) and the Adolescent Coping Scale (ACS) were administered. The result of this study indicated that majority of the university students have moderate level of stress. There was a significant inverse relationship between stress level and coping strategies among undergraduates. In conclusion, some levels of stress can be good, as the right kind of stress encourages them towards change and growth. However, when students are unable to cope with stress, they can become a burden. It is recommended that students should be encouraged to take part in extra-curricular activities such as sports to reduce stress. Keywords: Stress; coping strategies; university students
Is Trade Liberalization Poverty Worsening in Tunisia? A General Equilibrium Assessment ┴

The effects of trade liberalization on poverty in Tunisia are examined in a dynamic computable general equilibrium model (DCGE). The DCGE model endogenously generates the evolution of prices and, for each household group, income paths under protection and freer trade assumptions. These results are then used to assess the equivalent income of each household using a sample from 1995 household survey, and so the effects of the simulated changes on poverty. Dominance tests are also used to avoid the arbitrariness of choosing a poverty line and a poverty measure. Simulation results show that although trade openness slowdowns the downward trend of poverty in the short-run, it enhances poverty reduction in the longrun.
SPEAKER - INDEPENDENT VISUAL LIP ACTIVITY DETECTION FOR HUMAN - COMPUTER INTERACTION

Recently there is an increased interest in using th e visual features for improved speech processing. L ip reading plays a vital role in visual speech processing. In this paper, a new a pproach for lip reading is presented. Visual speech recognition is applied in mobile phone applications, human-computer interacti on and also to recognize the spoken words of hearin g impaired persons. The visual speech video is taken as input for face dete ction module which is used to detect the face regio n. The mouth region is identified based on the face region of interest (RO I). The mouth images are applied for feature extrac tion process. The features are extracted using every 10th coordinate, every 16 th coordinate, 16 point + Discrete Cosine Transform (DCT) method and Lip DCT method. Then, these features are applied as inp uts for recognizing the visual speech using Hidden Markov Model. Out of the different feature extraction methods, the DCT metho d gives the experimental results of better performa nce accuracy. 10 participants were uttered 35 different isolated wor ds. For each word, 20 samples are collected for tra ining and testing the process.
Multiuser MIMO in Distributed Antenna Systems With Out-of-Cell Interference

Distributed antenna systems (DAS) augment the base station's transmit capability by adding multiple remote radio units, connected to the base station via a high bandwidth and low latency link. With DAS, the base station operates as if it had multiple antennas, but the antennas happen to be in different geographic locations. DAS have been shown to enhance coverage and capacity in cellular systems, in a variety of different configurations. This paper proposes, analyzes, and compares several downlink multiuser multiple input multiple output (MIMO) DAS strategies in terms of per-user throughput and area spectral efficiency. Zero-forcing transmit beamforming is used for transmission, the remote radio units may have one or more antennas, and the subscriber has a single receive antenna. Techniques considered include beamforming across all remote radio units (full transmission), using the same beamforming vector for each remote radio unit (simplified transmission), and selecting a subset of remote radio units. To facilitate rapid simulation and design space exploration, approximations of the ergodic rate are proposed for each technique assuming path-loss, small-scale Rayleigh fading, and out-of-cell interference. Simulations accounting for multiple interfering cells are used to compare the different transmission techniques. Full transmission is found to have the best performance even accounting for out-of-cell interference, though gains diminish for higher numbers of active users. Simplified transmission improves over no DAS but performance degrades with more active remote radio units.
The DDMKCC decision support architecture in the light of case studies

What makes the development of decision support systems (DSS) particularly challenging is the change dynamics of the design space, the instability of initial specifications, and the lack of an adequate model of the decision making process. Facing these, one can appreciate a methodology that can drive the designer's creative effort within a particular decision context. The paper aims to outline the origin and the evolution of research on the DSS architecture commenced by Sprague and Carlson and carried on under the auspices of the International Federation for Information Processing (IFIP) and the International Society for Decision Support Systems (ISDSS)1. In particular, the paper presents insights, findings, recommendations and conclusions derived from case studies conducted in domestic medium-sized and large enterprises.
A meta-model assisted coprocessor synthesis framework for compiler/architecture parameters customization

Hardware coprocessors are extensively used in modern heterogeneous systems-on-chip (SoC) designs to provide efficient implementation of application-specific functions. Customized coprocessor synthesis exploits design space exploration to derive Pareto optimal design configurations for a set of targeted metrics. Existing exploration strategies for coprocessor synthesis have been focused on either time consuming iterative scheduling approaches or ad-hoc sampling of the solution space guided by the designer's experience. In this paper, we introduce a meta-model assisted exploration framework that eliminates the aforementioned drawbacks by using response surface models (RSMs) for generating customized coprocessor architectures. The methodology is based on the construction of analytical delay and area models for predicting the quality of the design points without resorting to costly architectural synthesis procedures. Various RSM techniques are evaluated with respect to their accuracy and convergence. We show that the targeted solution space can be accurately modeled through RSMs, thus enabling a speedup of the overall exploration runtime without compromising the quality of results. Comparative experimental results, over a set of real-life benchmarks, prove the effectiveness of the proposed approach in terms of quality improvements of the design solutions and exploration runtime reductions. An MPEG-2 decoder case study describes how the proposed approach can be exploited for customizing the architecture of two hardware accelerated kernels.
FINDING SMALL HIGH PERFORMANCE SUBSETS OF INDUCED RULE SETS: EXTENDED SUMMARY

Models consisting of decision rules – such as those produced by methods from Pawlak’s rough set theory – generally have a white-box nature, but in practice induced models are too large to be inspected. Here, we investigate methods for simplifying complex models while retaining predictive performance. The approach taken is rule filtering, i.e. post-pruning of complete rules. Two methods for finding high-performance subsets of a set of rules are investigated. One method is to use a genetic algorithm to search the space of subsets. Another method is to create an ordering of a rule set by sorting the rules according to a quality measure for individual rules. A rule set with a particular cardinality and expected good predictive performance can then be constructed by taking the first rules in the ordering. Algorithms for the two methods have been implemented in the ROSETTA system. Predictive performance is estimated using ROC analysis, and compared using statistical hypothesis testing. Ten different formulae from the literature that can be used to define rule quality are compared. Experiments on real-world data show that models often can be dramatically simplified without significant performance loss.
Senescence Delay of Human Diploid Fibroblast Induced by Anti-sense p16INK4a Expression*

p16INK4a, a tumor suppressor gene that inhibits cyclin-dependent kinase 4 and cyclin-dependent kinase 6, is also implicated in the mechanisms underlying replicative senescence, because its RNA and protein accumulate as cells approach their finite number of population doublings in tissue culture. To further explore the involvement of p16INK4a in replicative senescence, we constructed a retroviral vector containing antisense p16INK4a, pDOR-ASp16, and introduced it into early passages of human diploid fibroblasts. The introduction of this construct significantly suppressed the expression of wild-type p16INK4a. It also imposed a finite increase in proliferative life span and significant delay of several other cell senescent features, such as cell flattening, cell cycle arrest, and senescence-associated β-galactosidase positivity. Moreover, telomere shortening and decline in DNA repair capacity, which normally accompany cell senescence, are also postponed by the ASp16 transfection. The life span of fibroblasts was significantly extended, but the onset of replicative senescence could not be totally prevented. Telomerase could not be activated even though telomere shortening was slowed. These observations suggest that the telomere pathway of senescence cannot be bypassed by ASp16 expression. These data not only strongly support a role for p16INK4a in replicative senescence but also raise the possibility of using the antisense p16INK4atherapeutically.
Incremental Nonparametric Weighted Feature Extraction for OnlineSubspace Pattern Classification

In this paper, a new online method based on nonparametric weighted feature extraction (NWFE) is proposed. NWFE was introduced to enjoy optimum characteristics of linear discriminant analysis (LDA) and nonparametric discriminant analysis (NDA) while rectifying their drawbacks. It emphasizes the points near decision boundary by putting greater weights on them and deemphasizes other points. Incremental nonparametric weighted feature extraction (INWFE) is the online version of NWFE. INWFE has advantages of NWFE method such as extracting more than L-1 features in contrast to LDA. It is independent of the class distribution and performs well in complex distributed data. The effects of outliers are reduced due to the nature of its nonparametric scatter matrix. Furthermore, it is possible to add new samples asynchronously, i.e. whenever a new sample becomes available at any given time, it can be added to the algorithm. This is useful for many real world applications since all data cannot be available in advance. This method is implemented on Gaussian and non-Gaussian multidimensional data, a number of UCI datasets and Indian Pine dataset. Results are compared with NWFE in terms of classification accuracy and execution time. For nearest neighbour classifier it shows that this technique converges to NWFE at the end of learning process. In addition, the computational complexity is reduced in comparison with NWFE in terms of execution time.
Potential of Dynamic Binary Parallelization

As core counts continue to grow in modern microarchitectures, automatic parallelization technologies are becoming increasingly important to fill the gap between hardware that has increased parallelism and software that is still designed for sequential execution. In previous research, we have proposed a novel dynamic binary parallelization scheme called T-DBP, which leverages hot traces to provide a large instruction window without introducing spurious control and data dependencies. In this paper, we conduct a limit study to estimate the maximum possible performance of T-DBP on the SPEC CPU2000 benchmark suite. Our results indicate an average speedup of 9.18x and 22.34x over sequential execution for the integer and floating point benchmarks, respectively. We also explain this high speed increase by quantitatively demonstrating that T-DBP uses runtime information to overcome two key handicaps of compile-time parallelization techniques. By artificially emulating the effects of these handicaps in T-DBP, the average speedup shrinks to 4.51x (integer) and 9.36x (floating point), respectively.
Phenotypic Alterations in Hippocampal NPY- and PV-Expressing Interneurons in a Presymptomatic Transgenic Mouse Model of Alzheimer’s Disease

Interneurons, key regulators of hippocampal neuronal network excitability and synchronization, are lost in advanced stages of Alzheimer’s disease (AD). Given that network changes occur at early (presymptomatic) stages, we explored whether alterations of interneurons also occur before amyloid-beta (Aβ) accumulation. Numbers of neuropeptide Y (NPY) and parvalbumin (PV) immunoreactive (IR) cells were decreased in the hippocampus of 1 month-old TgCRND8 mouse AD model in a sub-regionally specific manner. The most prominent change observed was a decrease in the number of PV-IR cells that selectively affected CA1/2 and subiculum, with the pyramidal layer (PY) of CA1/2 accounting almost entirely for the reduction in number of hippocampal PV-IR cells. As PV neurons were decreased selectively in CA1/2 and subiculum, and given that they are critically involved in the control of hippocampal theta oscillations, we then assessed intrinsic theta oscillations in these regions after a 4-aminopyridine (4AP) challenge. This revealed increased theta power and population bursts in TgCRND8 mice compared to non-transgenic (nTg) controls, suggesting a hyperexcitability network state. Taken together, our results identify for the first time AD-related alterations in hippocampal interneuron function as early as at 1 month of age. These early functional alterations occurring before amyloid deposition may contribute to cognitive dysfunction in AD.
Microbiologically Enhanced Mixing across Scales during in-situ Bioremediation of Uranium

Production of nuclear fuels for weapons and electric energy has resulted in groundwater uranium contamination at Department of Energy (DOE) sites. Reduction of uranium by dissimilatory metalreducing bacteria (DMRB) is an effective approach for in-situ bioremediation of these sites. In this process, an organic electron donor is typically delivered through a well into groundwater in order to promote the biological reduction of soluble and toxic U(VI) to insoluble and less toxic U(IV). A key challenge is mixing the organic electron donor with U(VI) in groundwater where laminar flow conditions prevail. A potential solution is to enhance reaction beyond the scale of physical mixing by promoting extracellular electron shuttling. Growing evidence suggests that extracellular electron shuttling can occur by either diffusion of aqueous phase electron shuttles (e.g., H2, quinones) between syntrophs and/or DMRB, or through direct electron transfer between cells through metallic-like appendage (i.e., nanowR. Al c A l d e i n McNa i r Sc h o l a r S re S e a r c h Jo u r N a l 2012 2 ires). In this project, we used pore scale, microfluidic experiments in order to elucidate cell-to-cell electron transport that can potentially enhance U(VI) reduction beyond the scale of physical mixing with an organic electron donor. Batch studies were performed to develop DMRB cultures, and to evaluate their growth with different electron acceptor and donor conditions. DMRB cultures from batch studies were used to inoculate pore scale, microfluidic reactors. The microfluidic experiments allowed direct imaging of microbial growth over various mixing length scales. Anaeromyxobacter dehalogenans Strain K and a mixed ground water culture were used, and we hypothesize that these organisms will enhance reaction beyond physical mixing scales by facilitated electron transfer.
PPCU: Proportional per-packet consistent updates for Software Defined Networks

Per-packet consistency (PPC) is preserved, if during an update to a Software Defined Network (SDN), every packet either matches the new rules added or the old rules to be deleted, but not a combination of both. We propose a general update algorithm called PPCU that preserves PPC, is concurrent and provides an all-or-nothing semantics for an update, irrespective of the execution speeds of switches and links, while confining changes to only the affected switches and affected rules.
Corpus for Probabilisfic Parsing

This paper describes the use of a small but syntactically rich parsed corpus of English in probabilistic parsing. Software has been developed to extract probabilistic systemic-f~nctional grammars (SFGs) from the Polytechnic of Wales Corpus in several formalisms, which could equally well be applied to other parsed corpora. To complement the large probabilistic grammar, we discuss progress in the provision of lexical resources, which range from corpus wordlists to a large lexical database supplemented with word frequencies and SFG categories. The lexicon and grammar resources may be used in a variety of probabilistic parsing programs, one of which is presented in some detail: The Realistic Annealing Parser. Compared to traditional rule-based methods, such parsers usn~ily implement complex algorithms, and are relatively slow, but are more robust in providing analyses to unrestricted and even semi-grammatical English.
On the impact of highpass filtering when using PAM-FDE for visible light communication

A next generation optical wireless communications standard is currently established, denoted as IEEE 802.15. 7r1, targeting data rates between 1 Mbit/s and 10 Gbit/s. Selecting an appropriate transmission scheme is one of the critical tasks. Following this issue, this paper gives a review on PAM-FDE in VLC. Based on PAM-FDE laboratory measurements, we demonstrate the need to include highpass filtering into the propagation model. In this paper, numerical analyses investigate the impact of the resulting baseline wander on the performance. We include a multi-level 5S6S coding technique in order to prepare PAM-FDE for practice. Finally, research topics are summarized.