Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudomonas stutzeri Has Two Closely RelatedpilA Genes (Type IV Pilus Structural Protein) with Opposite Influences on Natural Genetic Transformation

ABSTRACT Pseudomonas stutzeri has type IV pili for which the pilA gene (here termed pilAI) provides the structural protein and which are required for DNA uptake and natural genetic transformation. Downstream of pilAIwe identified a gene, termed pilAII, coding for a deduced protein with a size similar to that of PilAI with 55% amino acid sequence identity and with a typical leader peptide including a leader peptidase cleavage site. Fusions to lacZ revealed that pilAII is expressed only about 10% compared topilAI, although the genes are cotranscribed as shown by reverse transcription-PCR. Surprisingly, insertional inactivation ofpilAII produced a hypertransformation phenotype giving about 16-fold-increased transformation frequencies. Hypertransformation also occurred in pilAI pilAII double mutants expressing heterologous pilA genes of nontransformable bacteria, like Pseudomonas aeruginosa or Dichelobacter nodosus. The overexpression of pilAII decreased transformation up to 5,000-fold compared to that of thepilAII mutant. However, neither inactivation ofpilAII nor its overexpression affected the amounts of [3H]thymidine-labeled DNA that were competence-specifically bound and taken up by the cells. In thepilAII mutant, the transformation by purified single-stranded DNA (which depends on comA andexbB, as does transformation by duplex DNA) was also increased 17-fold. It is concluded that PilAII suppresses a step in transformation after the uptake of duplex DNA into the cell and perhaps before its translocation into the cytoplasm. The idea that the degree of the transformability of cells could be permanently adjusted by the expression level of an antagonistic protein is discussed.
Overcoming Problems in the Measurement of Biological Complexity

In a genetic algorithm, fluctuations of the entropy of a genome over time are interpreted as fluctuations of the information that the genome's organism is storing about its environment, being this reflected in more complex organisms. The computation of this entropy presents technical problems due to the small population sizes used in practice. In this work we propose and test an alternative way of measuring the entropy variation in a population by means of algorithmic information theory, where the entropy variation between two generational steps is the Kolmogorov complexity of the first step conditioned to the second one. As an example application of this technique, we report experimental differences in entropy evolution between systems in which sexual reproduction is present or absent.
Two-step channel selection-a novel technique for reconfigurable multistandard transceiver front-ends

This paper starts with a review of the prevailing channel-selection techniques utilized so far in the design of wireless transceiver analog front-ends before describing a novel two-step channel-selection technique, which handles the traditionally unwanted image, in radio frequency-to-intermediate frequency (RF-to-IF) or IF-to-RF frequency conversion, as a useful adjacent channel of the desired one, and selects deliberately either of them from IF to baseband (or baseband to IF). Thus, one more channel-selection possibility is created for both low-IF receivers and two-step-up transmitters. The consequential benefits of introducing channel selection at IF consist of two. First, many design specifications (such as phase noise and settling time) of the RF frequency synthesizer and local oscillator can be substantially relaxed. Second, a low-IF/zero-IF reconfigurable receiver and a direct-up/two-step-up reconfigurable transmitter can be synthesized to match better with narrowband-wideband-mixed multistandard systems. The operating principles of such architectures are presented in easy-to-understand complex-signal spectral-flow illustrations, and their practicability is demonstrated in the design of a Bluetooth/IEEE 802.11FH/HomeRF multistandard receiver. SPECTRE simulation results validate the reconfigurable functionalities mainly implemented by a triple-mode channel-select filter and a multifunctional sampling-mixer scheme.
Parallel Hybrid Preconditioning: Incomplete Factorization with Selective Sparse Approximate Inversion

We consider parallel preconditioning to solve large sparse linear systems $Ax=b$ using conjugate gradients when $A$ is symmetric and positive definite. We develop a preconditioner that can be viewed as a hybrid of incomplete factorization and sparse approximate inversion schemes. Such a hybrid can potentially enable fast and reliable solution through a preconditioner with low memory requirements that allows latency-tolerant construction and application on multiprocessor systems. We propose a parallel hybrid scheme which yields a preconditioner as a tree-structured aggregate of sparse incomplete factors and inverses of selected submatrices. We analyze the computation and communication costs of our hybrid preconditioner and report on its parallel performance on some well-known test matrices. Our results indicate that our hybrid has significant advantages over sparse approximate inverse preconditioners and incomplete Cholesky preconditioners using either drop-threshold or zero-level-of-fill schemes.
Design of Orthogonal UWB Pulse Waveform for Wireless Multi-Sensor Applications

In this work we propose an orthogonal pulse waveform for wireless ultra wideband (UWB) transmission. The design is based on an ideal low-pass prototype filter having a windowed sinc impulse response. The frequency response of the prototype filter is transferred to the high frequency region using a specific sign modulator. The UWB pulse waveform comprises of the weighted summation of the left singular vectors of the impulse response matrix. The power spectral density of the pulse waveform fulfils the FCC constraint (allowed frequency band 3.1-10.6 GHz) for unlicensed UWB transmission. Applications of the UWB pulse waveform in multi-channel wireless sensor networks are considered.
Time and Frequency Synchronization for Power Line OFDM Systems with Colored Noise

A pilot aided joint symbol timing and frequency offset estimator for OFDM systems over power line channel (PLC) with colored noise is proposed in this paper. In the proposed estimator, the received time domain OFDM samples are first divided into groups where noise samples are approximately independent. Initial maximum likelihood (ML) based symbol timing and frequency offset estimates are obtained based on each group and final estimate is then derived by combining the initial estimates. We further simplify the proposed estimator to a practical one which does not require the knowledge of PLC fading profile, noise profile and signal-to-noise-ratio (SNR). The simulation results show that, under the presence of colored noise, the proposed practical symbol timing estimator achieves performance gain in terms of correct synchronization probability, around 2dB at SNR=15dB, and with improved mean square error (MSE) performance, compared to the widely adopted estimator in [6], . With the knowledge of the statistics of colored noise, another algorithm is also proposed to further improve the estimation performance.
Middleware based data replication providing snapshot isolation

Many cluster based replication solutions have been proposed providing scalability and fault-tolerance. Many of these solutions perform replica control in a middleware on top of the database replicas. In such a setting concurrency control is a challenge and is often performed on a table basis. Additionally, some systems put severe requirements on transaction programs (e.g., to declare all objects to be accessed in advance). This paper addresses these issues and presents a middleware-based replication scheme which provides the popular snapshot isolation level at the same tuple-level granularity as database systems like PostgreSQL and Oracle, without any need to declare transaction properties in advance. Both read-only and update transactions can be executed at any replica while providing data consistency at all times. Our approach provides what we call "1-copy-snapshot-isolation" as long as the underlying database replicas provide snapshot isolation. We have implemented our approach as a replicated middleware on top of PostgreSQL replicas. By providing a standard JDBC interface, the middleware is completely transparent to the client program. Fault-tolerance is provided by automatically reconnecting clients in case of crashes. Our middleware shows good performance in terms of response times and scalability.
Frame distance array algorithm parameter tune-up for TIMIT corpus automatic speech segmentation

This work is related to unsupervised automatic speech segmentation. An experiment was carried out on the Frame Distance Array (FDA) algorithm with a main goal of the algorithm parameter tune-up. The experiment was carried out by applying the algorithm on TIMIT corpus and by using MFCC as the speech signal features. The parameters tuned up in this work are the frame length, the frame increment, the number of test frames and the test frame step size. The best combination of values was chosen based on the observations on the detection rate, the miss rate and the false boundary rate. The best parameter tune-up found at 23 ms, 1.5 ms, 9 frames and 2 frames for the frame length, the frame increment, the number of test frames and the test frame step size respectively.
Structure Preserving Non-negative Feature Self-Representation for Unsupervised Feature Selection

Inspired by the importance of self-representation and structure-preserving ability of features, in this paper, we propose a novel unsupervised feature selection algorithm named structure-preserving non-negative feature self-representation (SPNFSR). In this algorithm, each feature in high-dimensional data can be represented by the linear combination of other features. Then, to exploit the structure-preserving ability of features, we construct a low-rank representation graph, which takes the local and global structures into consideration to maintain the intrinsic structure of the data space. Finally, an l2,1-norm regularization and the non-negative constraint are imposed on the representation coefficient matrix with the goal of achieving feature selection in the batch mode. Moreover, we provide a simple yet efficient iterative update algorithm to solve SPNFSR, as well as the convergence analysis of the proposed algorithm. The performance of the proposed approach is illustrated by six publicly available databases. In comparison with the state-of-the-art approaches, the extensive experimental results show the advantages and effectiveness of our approach.
1.4 Quantum computing - the next challenge in circuit and system design

The challenge of quantum computing is that quantum bits are extremely fragile and their state is easily perturbed by environmental fluctuations. However, recent theoretical and experimental advances have made it clear that the resulting errors can in principle be corrected. What it takes is a system containing thousands or millions of quantum bits operating at ultra-low temperatures, that must be interfaced using complex classical mixed-signal and microwave circuits for read-out and control. By comparison, today’s practical demonstrations involve no more than a dozen quantum bits controlled by bulky instrumentation that is not scalable.
Organization of the Paper

Process migration is the act of transferring a process between two machines. It enables dynamic load distribution, fault resilience, eased system administration, and data access locality. Despite these goals and ongoing research efforts, migration has not achieved widespread use. With the increasing deployment of distributed systems in general, and distributed operating systems in particular, process migration is again receiving more attention in both research and product development. As high-performance facilities shift from supercomputers to networks of workstations, and with the ever-increasing role of the World Wide Web, we expect migration to play a more important role and eventually to be widely adopted. This survey reviews the field of process migration by summarizing the key concepts and giving an overview of the most important implementations. Design and implementation issues of process migration are analyzed in general, and then revisited for each of the case studies described: MOSIX, Sprite, Mach and Load Sharing Facility. The benefits and drawbacks of process migration depend on the details of implementation and therefore this paper focuses on practical matters. This survey will help in understanding the potentials of process migration and why it has not caught on.
Integrated multiplatform method for in vitro quantitative assessment of cellular uptake for fluorescent polymer nanoparticles

Studies of cellular internalization of nanoparticles (NPs) play a paramount role for the design of efficient drug delivery systems, but so far they lack a robust experimental technique able to quantify the NP uptake in terms of number of NPs internalized in each cell. In this work we propose a novel method which provides a quantitative evaluation of fluorescent NP uptake by combining flow cytometry and plate fluorimetry with measurements of number of cells. Single cell fluorescence signals measured by flow cytometry were associated with the number of internalized NPs, exploiting the observed linearity between average flow cytometric fluorescence and overall plate fluorimeter measures, and previous calibration of the microplate reader with serial dilutions of NPs. This precise calibration has been made possible by using biocompatible fluorescent NPs in the range of 20–300 nm with a narrow particle size distribution, functionalized with a covalently bonded dye, Rhodamine B, and synthesized via emulsion free-radical polymerization. We report the absolute number of NPs internalized in mouse mammary tumor cells (4T1) as a function of time for different NP dimensions and surface charges and at several exposure concentrations. The obtained results indicate that 4T1 cells incorporated 103–104 polymer NPs in a short time, reaching an intracellular concentration 15 times higher than the external one.
Clinical efficacy of paroxetine in resistant depression

The antidepressant effects of a specific reuptake inhibitor of 5-hydroxytryptamine (5-HT), paroxetine, were tested in 24 patients with resistant depression who had failed to respond to conventional antidepressants after at least 4 weeks of treatment. A novel exper imental design was chosen in which all patients had 12 weeks of treatment beginning and ending with placebo therapy with 6 weeks of active drug treatment at some point in between. Ratings of depressive symptoms were made using the Hamilton rating scale (HRS) for depression, and the checklist for unwanted effects and their severity was also recorded before and during treatment at 2 week intervals. The change from placebo to active paroxetine therapy was made using a double-blind procedure. Patients who made a significant placebo response in the first 2 weeks of treatment were excluded from further analysis; 20 patients completed the study and satisfied all criteria for inclusion. Both groups of showed a significant improvement in symptoms after 4 weeks of paroxetine therapy. There were no significant treatment differences between the groups, but improvement in symptoms occurred sig nificantly later in the patients who had a longer period of initial placebo therapy. The experimental design also allowed study of withdrawal effects after stopping active treatment. There was no increase in adverse effects, including a subgroup associated with withdrawal problems, either during treatment with paroxetine or after the drug was stopped. The results suggest that paroxetine is probably an effective antidepressant, is well tolerated and has few adverse effects.
Real-time audiovisual laughter detection

Laughter detection is an essential aspect towards effective human-computer interaction. This work primarily addresses the problem of laughter detection in a real-time environment. We utilize annotated audio and visual data collected from a Kinect sensor to identify discriminative features for audio and video, separately. We show how the features can be used with classifiers such as support vector machines (SVM). The two modalities are then fused into a single output to form a decision. We test our setup by emulating real-time data with Kinect sensor, and compare the results with the offline version of the setup. Our results indicate that our laughter detection system gives a promising performance for a real-time human-computer interactions.
New algorithms for preserving differential privacy

In this thesis, we consider the problem of how one should perform computations on private data. We specifically consider algorithms which preserve the recent formalization of privacy known as differential privacy. The fundamental tradeoff that we consider is that of privacy and utility. For which tasks can we perform useful computations while still preserving privacy, and what exactly is the tradeoff between usefulness and privacy? We study this tradeoff for statistical query release, both offline and online, as well as for many standard combinatorial optimization tasks.
Theoretical Validation and Case Study of Requirements Management Measures

The quality of software systems depends on early activities in the software development process, of which the management of requirements is one. When requirements are not managed well, a project can fail or become more costly than intended, and the quality of the software developed can decrease. Among the requirements management practices, it is particularly important to quantify and predict requirements volatility, i.e., how much the requirements are likely to change over time. Software measures can help in quantifying and predicting requirements attributes like volatility. However, few measures have yet been defined, due to the fact that the early phases are hard to formalise. Furthermore, very few requirements measures have been validated, which would be needed in order to demonstrate that they are useful. The approach to requirements management in this thesis is quantitative, i.e. to monitor the requirements management activities and requirements volatility through software measurement. In this thesis, a set of 45 requirements management measures is presented. The measures were defined using the goal question metrics framework for the two predefined goals of the requirements management key process area of the capability maturity model for software. A subset of these measures was validated theoretically and empirically in four case studies. Furthermore, an analysis of validated measures in the literature was performed, showing that there is a lack of validated process, project, and requirements measures in software engineering. The studies presented in this thesis show that size measures are good estimators of requirements volatility. The important result is that size is relevant: increasing the size of a requirements document implies that the number of changes to requirements increases as well. Furthermore, subjective estimations of volatility were found to be inaccurate assessors of requirements volatility. These results suggest that practitioners should complement the subjective estimations for assessing volatility with the objective ones. Requirements engineers and project managers will benefit from the research presented in this thesis because the measures defined, proved to be predictors of volatility, can help in understanding how much requirements will change. By deploying the measures, the practitioners would be prepared for possible changes in the schedule and cost of a project, giving them the possibility of creating alternative plans, new cost estimates, and new software development schedules.
Preimplantation genetic diagnosis for Down syndrome pregnancy

ObjectiveTo evaluate the effect of preimplantation genetic diagnosis (PGD) conducted for women who had Down syndrome pregnancy previously.MethodsTrisomy 21 was diagnosed by using fluorescence in site hybridization (FISH) before embryo transfer in two women who had Down syndrome pregnancies. Each received one or two PGD cycles respectively.ResultsCase 1: one PGD cycle was conducted, two oocytes were fertilized and biopsied. One embryo is of trisomy 21 and the other of monosomy 21. No embryo was transferred. Case 2: two PGD cycles were conducted, in total, sixteen oocytes were fertilized and biopsied. Four embryos were tested to be normal, six of trisomy 21, and one of monosomy 21. Five had no signal. Four normal embryos were transferred but no pregnancy resulted.ConclusionFor couples who had pregnancies with Down syndrome previously, PGD can be considered, and has been shown to be an effective strategy.
A Practical Certified E-Mail System with Temporal Authentication Based on Transparent TSS

In this paper, we present a certified e-mail system providing non-repudiation, fairness, confidentiality and temporal authentication service based on transparent TSS (time stamping server). Scheme in this paper follows the generic messaging model as defined in the X.400 message handling system (CCITT, 1988) and the Internet mail system (Crocker, 1982). Compared with other schemes for certified e-mail, this scheme is more practical.
Decoding billions of integers per second through vectorization

In many important applications—such as search engines and relational database systems—data are stored in the form of arrays of integers. Encoding and, most importantly, decoding of these arrays consumes considerable CPU time. Therefore, substantial effort has been made to reduce costs associated with compression and decompression. In particular, researchers have exploited the superscalar nature of modern processors and single‐instruction, multiple‐data (SIMD) instructions. Nevertheless, we introduce a novel vectorized scheme called SIMD‐BP128⋆ that improves over previously proposed vectorized approaches. It is nearly twice as fast as the previously fastest schemes on desktop processors (varint‐G8IU and PFOR). At the same time, SIMD‐BP128⋆ saves up to 2 bits/int. For even better compression, we propose another new vectorized scheme (SIMD‐FastPFOR) that has a compression ratio within 10% of a state‐of‐the‐art scheme (Simple‐8b) while being two times faster during decoding. © 2013 The Authors. Software: Practice and Experience Published by John Wiley & Sons, Ltd.