Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Uhp1, a Ubiquitinated Histone-like Protein, as a Target/Mediator of Rhp6 in Mating-type Silencing in Fission Yeast*

Mating-type silencing inSchizosaccharomyces pombe is brought about by cooperative interactions between cis-acting DNA sequences flankingmat2P and mat3M and the trans-acting factors, namely Swi6, Clr1–Clr4, Clr6, and Rik1. In addition, DNA repair generhp6, which plays a role in post-replication DNA repair and ubiquitination of proteins including histones, is also involved in silencing, albeit in a unique way; its effect on silencing and chromatin structure of the donor loci is dependent on their switching competence. Earlier, we hypothesized the existence of a mediator of Rhp6 that plays a role in reestablishment of the chromatin structure coincidentally with DNA replication associated with mating-type switching. Here we report the identification of a 22-kDa protein as anin vivo target and mediator of Rhp6 in mating-type silencing. The level of this protein is greatly elevated insng1-1/rhp6− mutant andrhp6Δ as compared with wild type strain. Both the deletion and overexpression of the gene encoding this protein elicit switching-dependent loss of silencing. Furthermore, the 22-kDa protein undergoes Rhp6-dependent multiubiquitination and associates with mat2 locus during S phase in wild type cells. Interestingly, it contains a histone-fold motif similar to that of histone H2A, and like histone H2A, it interacts strongly with histone H2B in vitro. These results indicate that the 22-kDa protein, renamed as the ubiquitinated histone-like protein Uhp1, is an in vivo target/mediator of Rhp6 in silencing. Thus, regulation of association of Uhp1 with chromatin and ubiquitination followed by degradation may play a role in reestablishment of inactive chromatin structure at the silent mating-type loci.
Comparison of a Brain-Based Adaptive System and a Manual Adaptable System for Invoking Automation

Objective: Two experiments are presented examining adaptive and adaptable methods for invoking automation. Background: Empirical investigations of adaptive automation have focused on methods used to invoke automation or on automation-related performance implications. However, no research has addressed whether performance benefits associated with brain-based systems exceed those in which users have control over task allocations. Method: Participants performed monitoring and resource management tasks as well as a tracking task that shifted between automatic and manual modes. In the first experiment, participants worked with an adaptive system that used their electroencephalographic signals to switch the tracking task between automatic and manual modes. Participants were also divided between high-and low-reliability conditions for the system-monitoring task as well as high- and low-complacency potential. For the second experiment, participants operated an adaptable system that gave them manual control over task allocations. Results: Results indicated increased situation awareness (SA) of gauge instrument settings for individuals high in complacency potential using the adaptive system. In addition, participants who had control over automation performed more poorly on the resource management task and reported higher levels of workload. A comparison between systems also revealed enhanced SA of gauge instrument settings and decreased workload in the adaptive condition. Conclusion: The present results suggest that brain-based adaptive automation systems may enhance perceptual level SA while reducing mental workload relative to systems requiring user-initiated control. Application: Potential applications include automated systems for which operator monitoring performance and high-workload conditions are of concern.
SIMD programming by expansion.

Since its advent 30 years ago, single-instruction multiple-data (SIMD) functional units continue to provide an opportunity for high performance at a low hardware cost. However, a general consensus is that only a class of well-formed computations is suitable for SIMD execution. We believe that the boundary of the class should be pushed so that more applications can get the benefit of SIMD parallelism. Our goal is to provide programmers tools that will allow easier access to SIMD functional units. In this paper, we describe a new method to generate SIMD instructions automatically. Unlike the current approaches that target either loops or basic blocks, our approach targets a whole function. Instead of trying to keep the sequential execution semantics, we semantically transform the given input function by replacing the operators and operands with their SIMD counterparts. The output functions generated this way take vector arguments and return a vector value. We have implemented the new method in a compiler, called EXPAND, and show how to use it for user applications. To demonstrate the effectiveness of the new method, we apply the EXPAND compiler to 12 GNU math library intrinsic functions. When measured on a PowerPC G5, the transformed output codes achievemore » speedups ranging from 2.05 to 11.37 over the scalar baseline. « less
Acid adaptation of Escherichia coli : a genetic study

Department of Biochemistry and Biophysics, Faculty of Natural Sciences of Vilnius University, M. K. Èiurlionio 21, Vilnius LT-01513, Lithuania. E-mail: edita.suziedeliene@gf.vu. lt E. coli log-phase cells are capable of inducing of log-phase acid tolerance response (ATR), but stationary-phase cells do not exhibit this adaptive ability. To study the genetic systems responsible for the induction of log-phase ATR, we investigated E. coli mutants deficient in the known acid resistance systems. Our results show that RpoS-dependent oxidative and arginine decarboxylase systems are not induced during acid adaptation of log-phase cells. Glutamate decarboxylases were found to be induced during adaptation and result in a more efficient acid-protection. However, our study shows that other highly efficient protection mechanisms are induced, operate and play the main role in log-phase ATR.
Effects of partial extraction of troponin complex upon the tension-pCa relation in rabbit skeletal muscle. Further evidence that tension development involves cooperative effects within the thin filament

Partial extraction of troponin C (TnC) decreases the Ca2+ sensitivity of tension development in mammalian skinned muscle fibers (Moss, R. L., G. G. Giulian, and M. L. Greaser. 1985. Journal of General Physiology. 86:585), which suggests that Ca2+-activated tension development involves molecular cooperativity within the thin filament. This idea has been investigated further in the present study, in which Ca2+- insensitive activation of skinned fibers from rabbit psoas muscles was achieved by removing a small proportion of total troponin (Tn) complexes. Ca2+-activated isometric tension was measured at pCa values (i.e., -log[Ca2+]) between 6.7 and 4.5: (a) in control fiber segments, (b) in the same fibers after partial removal of Tn, and (c) after recombination of Tn. Tn removal was accomplished using contaminant protease activity found in preparations of LC2 from rabbit soleus muscle, and was quantitated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and scanning densitometry. Partial Tn removal resulted in the development of a Ca2+-insensitive active tension, which varied in amount depending on the duration of the extraction, and concomitant decreases in maximal Ca2+-activated tensions. In addition, the tension-pCa relation was shifted to higher pCa values by as much as 0.3 pCa unit after Tn extraction. Readdition of Tn to the fiber segments resulted in the reduction of tension in the relaxing solution to control values and in the return of the tension-pCa relation to its original position. Thus, continuous Ca2+-insensitive activation of randomly spaced functional groups increased the Ca2+ sensitivity of tension development in the remaining functional groups along the thin filament. In addition, the variation in Ca2+-insensitive active tension as a function of Tn content after extraction suggests that only one- third to one-half of the functional groups within a thin filament need to be activated for complete disinhibition of that filament to be achieved.
Use of a platelet-rich fibrin membrane to repair traumatic tympanic membrane perforations: a comparative study

Abstract Objectives: (1) To evaluate the effects of a platelet-rich fibrin (PRF) membrane in the repair of traumatic tympanic membrane (TM) perforations; and (2) to compare the use of a PRF membrane with the paper patch technique with regard to recovery rates, healing time, and correction of the mean air–bone gap. Methods: A randomized, prospective analysis was performed for 60 patients who were treated for traumatic TM perforations using one of the two methods. Closure rate, speed of healing, and hearing gain were compared between the PRF (Group 1) and paper patch (Group 2) groups. Results: Closure was obtained in 28 (93%) perforations in Group 1 and 25 (83%) perforations in Group 2 (p > 0.05). On day 10, full closure of the TM was observed in 24 (80%) patients in Group 1 and 16 (53%) patients in Group 2 (p < 0.05). The improvement in the mean air–bone gap was 14.1 dB in Group 1 and 12.4 dB in Group 2 on post-operative day 45 (p < 0.05). Conclusions: In comparison with the paper patch method, PRF, a new method, provided more rapid healing with more successful audiological results, and with no requirement for a second procedure.
Continuous Neonatal Blood Gas Monitoring Using a Multiparameter Intra-arterial Sensor

AIMS To compare arterial blood gas (ABG) readings obtained with a multiparameter intra-arterial sensor with those from an ABG analyser. METHODS An MPIAS with the ability to measure continuously pH, PaCO2, and PaO2 was introduced via an umbilical arterial catheter in 27 neonates requiring intensive care. They underwent 3260 hours of MPIAS monitoring, during which 753 ABG readings were performed. RESULTS Overall bias (mean difference: MPIAS–ABG) and precision (standard deviation of differences) values were: −0.002 and 0.022, respectively, for pH; +0.26 and 0.52 for PaCO2 (kPa); and −0.19 and 0.99 for PaO2 (kPa). This gave 95% limits of agreement as: −0.047 to +0.042 for pH, −0.76 to +1.28 kPa for PaCO2, and −2.13 to +1.75 kPa for PaO2. For each variable, precision across readings from the same individual was better than overall precision for all data. No complications related to the use of the catheter were observed. CONCLUSIONS Continuous MPIAS ABG monitoring is an exciting development, with the potential to reduce blood transfusions and improve ABG homeostasis.
Bioaccumulation of Heavy metals in different tissues of some commercially important fish species from Warri River, Niger Delta, Nigeria

Levels of seven heavy metals (Fe, Pb, Zn, Cu, Ni, Cr and Cd) in muscles, gill, kidney, liver and tissues of some commercial fish species caught between August 2005 – September 2007 from Warri River, Niger Delta, Nigeria were assessed. Analysis was carried out using Flame Atomic absorption spectrometry for the heavy metal analysis of the different tissues. Concentration levels of Fe and Zn in the different tissues of the fishes were higher in most cases. Apart from Cu, the level of heavy metals in the different tissues of the fish species exceeded the maximum permissible limit specified by statutory authorities such Food and Agricultural Organization/World Health Organization, Median International Standard and European Union for food fish consumed by human. The order of heavy metals are Fe>Zn>Pb>Ni>Cr>Cu>Cd in gills and Fe>Zn>Pb>Ni>Cu>Cr>Cd in kidneys, livers and muscles. The concentration of the heavy metals in the different tissues were in the order; liver> kidney>gill>muscle. The concentrations of all the heavy metals in each of the tissues were statistically different (P<0.05) among the different fish species. Hence consumption of fish from the Warri River poses a health risk to the consumers due to accumulation of high levels of Pb, Cd, Fe, Cr, Ni and Zn in fish through biotransfer of metals especially through water phase. Bioaccumulation of metals by humans has the potency to cause diverse ailments such as insomnia, brain damage and cancer. We, therefore, recommended that industrial and domestic effluent discharged into the Warri River be treated, controlled and monitored
Individualized ROI Optimization via Maximization of Group-wise Consistency of Structural and Functional Profiles

Functional segregation and integration are fundamental characteristics of the human brain. Studying the connectivity among segregated regions and the dynamics of integrated brain networks has drawn increasing interest . A very controversial, yet fundamental issue in these studies is how to determine the best functional brain regions or ROIs (regions of interests) for individuals. Essentially, the computed connectivity patterns and dynamics of brain networks are very sensitive to the locations, sizes, and shapes of the ROIs. This paper presents a novel methodology to optimize the locations of an individual's ROIs in the working memory system. Our strategy is to formulate the individual ROI optimization as a group variance minimization problem, in which group-wise functional and structural connectivity patterns, and anatomic profiles are defined as optimization constraints. The optimization problem is solved via the simulated annealing approach. Our experimental results show that the optimized ROIs have significantly improved consistency in structural and functional profiles across subjects, and have more reasonable localizations and more consistent morphological and anatomic profiles.
Aalborg Universitet Closed-loop Identification for Control of Linear Parameter Varying Systems

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MidiNet: A Convolutional Generative Adversarial Network for Symbolic-Domain Music Generation

Most existing neural network models for music generation use recurrent neural networks. However, the recent WaveNet model proposed by DeepMind shows that convolutional neural networks (CNNs) can also generate realistic musical waveforms in the audio domain. Following this light, we investigate using CNNs for generating melody (a series of MIDI notes) one bar after another in the symbolic domain. In addition to the generator, we use a discriminator to learn the distributions of melodies, making it a generative adversarial network (GAN). Moreover, we propose a novel conditional mechanism to exploit available prior knowledge, so that the model can generate melodies either from scratch, by following a chord sequence, or by conditioning on the melody of previous bars (e.g. a priming melody), among other possibilities. The resulting model, named MidiNet, can be expanded to generate music with multiple MIDI channels (i.e. tracks). We conduct a user study to compare the melody of eight-bar long generated by MidiNet and by Google's MelodyRNN models, each time using the same priming melody. Result shows that MidiNet performs comparably with MelodyRNN models in being realistic and pleasant to listen to, yet MidiNet's melodies are reported to be much more interesting.
A Multi-Objective Transmission Expansion Planning Framework in Deregulated Power Systems With Wind Generation

Integration of renewable energy resources into the power system has increased the financial and technical concerns for the market-based transmission expansion planning. This paper proposes a stochastic framework for transmission grid reinforcement studies in a power system with wind generation. A multi-stage multi-objective transmission network expansion planning (TNEP) methodology is developed which considers the investment cost, absorption of private investment and reliability of the system as the objective functions. A non-dominated sorting genetic algorithm (NSGA II) optimization approach is used in combination with a probabilistic optimal power flow (POPF) to determine the Pareto optimal solutions considering the power system uncertainties. Using a compromise-solution method, the best final plan is then realized based on the decision-maker preferences. The proposed methodology is applied to the IEEE 24-bus Reliability Tests System (RTS) to evaluate the feasibility and practicality of the developed planning strategy.
Can deterministic replay be an enabling tool for mobile computing?

Deterministic record and replay is fast becoming a vital technology in desktop and server computing environments. Yet, the applicability of this technology to computation run on small, mobile devices such as cell phones has not yet been explored. We argue that there are several potential uses of replay that are especially beneficial when applied to mobile phones: dual execution on cloud or cloudlet computers to reduce latency and possibly phone energy use, operation shipping for file synchronization, and offloading of expensive security and reliability checks to remote servers. In this paper, we explore these potential uses, as well as some of the unique challenges posed by implementing replay on phones.
Maintenance of data cubes and summary tables in a warehouse

Data warehouses contain large amounts of information, often collected from a variety of independent sources. Decision-support functions in a warehouse, such as on-line analytical processing (OLAP), involve hundreds of complex aggregate queries over large volumes of data. It is not feasible to compute these queries by scanning the data sets each time. Warehouse applications therefore build a large number of summary tables, or materialized aggregate views, to help them increase the system performance. As changes, most notably new transactional data, are collected at the data sources, all summary tables at the warehouse that depend upon this data need to be updated. Usually, source changes are loaded into the warehouse at regular intervals, usually once a day, in a batch window, and the warehouse is made unavailable for querying while it is updated. Since the number of summary tables that need to be maintained is often large, a critical issue for data warehousing is how to maintain the summary tables efficiently. In this paper we propose a method of maintaining aggregate views (the summary-delta table method), and use it to solve two problems in maintaining summary tables in a warehouse: (1) how to efficiently maintain a summary table while minimizing the batch window needed for maintenance, and (2) how to maintain a large set of summary tables defined over the same base tables. While several papers have addressed the issues relating to choosing and materializing a set of summary tables, this is the first paper to address maintaining summary tables efficiently.
On the Semantics of Purpose Requirements in Privacy Policies

Privacy policies often place requirements on the purposes for which a governed entity may use personal information. For example, regulations, such as HIPAA, require that hospital employees use medical information for only certain purposes, such as treatment. Thus, using formal or automated methods for enforcing privacy policies requires a semantics of purpose requirements to determine whether an action is for a purpose or not. We provide such a semantics using a formalism based on planning. We model planning using a modified version of Markov Decision Processes, which exclude redundant actions for a formal definition of redundant. We use the model to formalize when a sequence of actions is only for or not for a purpose. This semantics enables us to provide an algorithm for automating auditing, and to describe formally and compare rigorously previous enforcement methods. This research was supported by the US Army Research Office under grants DAAD19-02-1-0389 and W911NF09-1-0273 to CyLab and by the National Science Foundation (NSF) grant CCF0424422. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of any sponsoring institution, the U.S. government or any other entity. ∗ On May 10, 2012, the above funding acknowledgements were corrected. No other changes were made. This manuscript was submitted to the 24th IEEE Computer Security Foundations Symposium.
Reduction of the mutual coupling between two planar inverted-F antennas working in close radiocommunication standards

This paper presents a solution to reduce the mutual coupling between two planar inverted-F antennas (PIFA's) working in close radiocommunication standards: DCS1800 (1710-1880 MHz) and UMTS (1920-2170 MHz). These antennas are positioned on the corner of a limited ground plane whose size is representative of the printed circuit board (PCB) of a typical mobile phone. Three antennas are designed and several arrangements are numerically studied. Prototypes are then fabricated and measured to validate our proposed solution which consists in inserting a suspended line between the PIFA's to neutralize the electromagnetic coupling
Improving dynamic performance and efficiency of a resonant switched-capacitor converter based on phase-shift control

This paper presents the output voltage regulation characteristics and the dynamic performance of an RSCC using a phase-shift control. The proposed phase-shift control realizes soft switching operation even if the output voltage was changed, and it achieves a higher conversion efficiency. A theoretical analysis shows that the RSCC can reduce its inductor volume compared with a buck converter when its output voltage range is limited within 19–81% of its input voltage. Experimental results verify the operation characteristics of the proposed method and show the improved conversion efficiency more than 99%.
Knapsack Constrained Contextual Submodular List Prediction with Application to Multi-document Summarization

We study the problem of predicting a set or list of options under knapsack constraint. The quality of such lists are evaluated by a submodular reward function that measures both quality and diversity. Similar to DAgger (Ross et al., 2010), by a reduction to online learning, we show how to adapt two sequence prediction models to imitate greedy maximization under knapsack constraint problems: CONSEQOPT (Dey et al., 2012) and SCP (Ross et al., 2013). Experiments on extractive multi-document summarization show that our approach outperforms existing state-of-the-art methods.
A numerical scheme for space-time fractional advection-dispersion equation

In this paper, we develop a numerical resolution of the space-time fractional advection-dispersion equation. After time discretization, we utilize collocation technique and implement a product integration method in order to simplify the evaluation of the terms involving spatial fractional order derivatives. Then utilizing Bernstein polynomials as basis, the problem is transformed into a linear system of algebraic equations. Error analysis and order of convergence for the proposed method are also discussed. Some numerical experiments are presented to demonstrate the effectiveness of the proposed method and to confirm the analytic results.
A simple wrapped core linking module for SoC test access

For a system-on-a-chip (SoC) comprised of multiple IP cores, various design techniques have been proposed to provide diverse test link configurations. In this paper we introduce a simple flag based wrapped core linking module (WCLM) that enables systematic integration of IEEE 1149.1 TAP'd cores and P1500 wrapped cores. Compared with other state-of-art techniques, our technique requires no modification to each core, uses less area, and provides more diverse link configurations.