Miracle-dz/UniFAR-FTUs huggingface dataset:
The msaABCR Operon Regulates Resistance in Vancomycin-Intermediate Staphylococcus aureus Strains

ABSTRACT Vancomycin-intermediate Staphylococcus aureus (VISA) strains present an increasingly difficult problem in terms of public health. However, the molecular mechanism for this resistance is not yet understood. In this study, we define the role of the msaABCR operon in vancomycin resistance in three clinical VISA strains, i.e., Mu50, HIP6297, and LIM2. Deletion of the msaABCR operon resulted in significant decreases in the vancomycin MIC (from 6.25 to 1.56 μg/ml) and significant reductions of cell wall thickness in strains Mu50 and HIP6297. Growth of the mutants in medium containing vancomycin at concentrations greater than 2 μg/ml resulted in decreases in the growth rate, compared with the wild-type strains. Mutation of the msaABCR operon also reduced the binding capacity for vancomycin. We conclude that the msaABCR operon contributes to resistance to vancomycin and cell wall synthesis in S. aureus.
Simulated Annealing for Aiding Genetic Algorithm in Software Architecture Synthesis

AbstractThe dream of software engineers is to be able to automatically producesoftware systems based on their requirements. Automatic synthesis of soft-ware architecture has already been shown to be feasible with genetic algo-rithms. Genetic algorithms, however, easily become very slow if the size ofthe problem and complexity of mutations increase as GAs handle a large pop-ulation with much data. Also, for purely scientiﬁc interest it is worthwhileto investigate how other search algorithms handle the problem of softwarearchitecture synthesis. The present paper studies the possibilities of usingsimulated annealing for synthesizing software architecture. For this purposewe have two goals: 1) to study whether a simpler search algorithm can handlesynthesis and 2) if a seeded algorithm can provide quality results faster than asimple genetic algorithm. We start from functional requirements which forma base architecture and consider three quality attributes, modiﬁability, eﬃ-ciency and complexity. Synthesis is performed by adding design patterns andarchitecture styles to the base architecture. The algorithm thus produces asoftware architecture which fulﬁlls the functional requirements and also corre-sponds to the quality requirements. It is concluded that simulated annealingas such does not produce good architectures, but it is useful for speeding upthe evolution process by quickly ﬁne-tuning a seed solution achieved with agenetic algorithm. The main contribution is thus a new seeded algorithm forsoftware architecture design.Keywords: search-based software engineering, simulated annealing, softwaredesign, genetic algorithm, software architecture
4555-05 August 2005 Is the Accrual Anomaly a Global Anomaly ?

This paper investigates the subsequent return implications of accruals within a sample of large, developed, international equity markets and assesses whether similar institutional features account for the accrual anomaly across countries. I investigate the returns implications of accruals in 17 countries over the 1989 to 2003 time period. In general, the results of country-specific analysis indicate that the accrual anomaly is a global phenomenon. After decomposing total accruals, I find, in general, that accrual mispricing is largest for working capital accruals, specifically current asset accruals. However, the results of further analysis suggest that there is no dominant factor that explains the accrual anomaly internationally. Overall, the results indicate that the accrual anomaly is present in international markets yet the factor(s) driving the accrual anomaly appear to vary across markets. Is the Accrual Anomaly a Global Anomaly?
Five-year results of a prospective, randomized, controlled study evaluating treatment of intra-bony defects with a natural bone mineral and GTR.

BACKGROUND Treatment with a natural bone mineral (NBM) and a guided tissue regeneration (GTR) has been shown to promote periodontal regeneration. However, until now there are only very limited data on the long-term clinical results following this regenerative technique. AIM To present the 5-year results of a prospective, randomized, controlled clinical study evaluating the treatment of deep intra-bony defects either with open flap debridement (OFD) and a combination of an NBM and GTR (test) or OFD alone (control). METHODS Nineteen patients diagnosed with advanced chronic periodontitis, and each of whom displayed one intra-bony defect, received randomly the test or the control treatment. Results were evaluated at baseline, at 1 and at 5 years following therapy. RESULTS No statistically significant differences in any of the investigated parameters were observed at baseline between the two groups. At 1 year after therapy, the test group showed a reduction in mean probing depth (PD) from 9.1+/-1.1 to 3.7+/-0.8 mm (p<0.001) and a change in mean clinical attachment level (CAL) from 10.4+/-1.3 to 6.4+/-1.2 mm (p<0.001). At 5 years, mean PD and CAL measured 4.3+/-0.8 and 6.7+/-1.6 mm, respectively. At 5 years, both PD and CAL were statistically significantly improved compared with baseline (p<0.001) without statistically significant differences between the 1- and 5-year results. In the control group, mean PD was reduced from 8.9+/-1.3 to 4.9+/-1.2 mm (p<0.001) and mean CAL changed from 10.6+/-1.4 to 8.8+/-1.5 mm (p<0.01). At 5 years, mean PD and CAL measured 5.6+/-1.1 and 9.1+/-1.3 mm, respectively, and were still statistically significantly improved compared with baseline (p<0.01). No statistically significant differences were found between the 1- and 5-year results. The test treatment, at both 1 and 5 years, yielded statistically significantly higher CAL gains than the control one (p<0.01). Compared with baseline, at 5 years a CAL gain of > or =3 mm was found in nine defects (90%) of the test group but in none of the defects treated with OFD alone. CONCLUSIONS It was concluded that (i) treatment of intra-bony defects with OFD+NBM+GTR may result in significantly higher CAL gains than treatment with OFD, and (ii) the clinical results obtained after both treatments can be maintained over a period of 5 years.
Significant and Inevitable End-of-Twenty-First-Century Advances in Surface Runoff Timing in California’s Sierra Nevada

AbstractUsing hybrid dynamical–statistical downscaling, 3-km-resolution end-of-twenty-first-century runoff timing changes over California’s Sierra Nevada for all available global climate models (GCMs) from phase 5 of the Coupled Model Intercomparison Project (CMIP5) are projected. All four representative concentration pathways (RCPs) adopted by the Intergovernmental Panel on Climate Change’s Fifth Assessment Report are examined. These multimodel, multiscenario projections allow for quantification of ensemble-mean runoff timing changes and an associated range of possible outcomes due to both intermodel variability and choice of forcing scenario. Under a “business as usual” forcing scenario (RCP8.5), warming leads to a shift toward much earlier snowmelt-driven surface runoff in 2091–2100 compared to 1991–2000, with advances of as much as 80 days projected in the 35-model ensemble mean. For a realistic “mitigation” scenario (RCP4.5), the ensemble-mean change is smaller but still large (up to 30 days). For al.
Autoinhibition of p50 Rho GTPase-activating Protein (GAP) Is Released by Prenylated Small GTPases*

Interaction of p50 Rho GTPase-activating protein (p50RhoGAP) with Rho family small GTPases was investigated in a yeast two-hybrid system, by radioactive GAP assay, and in a Rac-regulated enzymatic reaction, through superoxide production by the phagocytic NADPH oxidase. The yeast two-hybrid system revealed an interaction between the C-terminal GAP domain and the N-terminal part of p50RhoGAP. The first 48 amino acids play a special role both in the stabilization of the intramolecular interaction and in recognition of the prenyl tail of small GTPases. The GAP assay and the NADPH oxidase activity indicate that the GTPase-activating effect of full-length p50RhoGAP is lower on non-prenylated than on prenylated small GTPase. Removal of amino acids 1–48 and 169–197 of p50RhoGAP increases the GAP effect on non-prenylated Rac, whereas prenylated Rac reacts equally well with the full-length and the truncated proteins. We suggest that p50RhoGAP is in an autoinhibited conformation stabilized by the stretches 1–48 and 169–197 and the prenyl group of the small GTPase plays a role in releasing this intramolecular restraint.
Evaluation of holistic sexuality education: A European expert group consensus agreement

Objectives Holistic sexuality education (HSE) is a new concept in sexuality education (SE). Since it differs from other types of SE in a number of important respects, strategies developed for the evaluation of the latter are not necessarily applicable to HSE. In this paper the authors provide a basis for discussion on how to evaluate HSE. Methods First, the international literature on evaluation of SE in general was reviewed in terms of its applicability to HSE. Second, the European Expert Group on Sexuality Education extensively discussed the requirements of its evaluation and suggested appropriate indicators and methods for evaluating HSE. Results The European experience in SE is scarcely represented in the general evaluation literature. The majority of the literature focuses on impact and neglects programme and implementation evaluations. Furthermore, the current literature demonstrates that evaluation criteria predominantly focus on the public health impact, while there is not yet a consensus on sexual well-being criteria and aspects of positive sexuality, which are crucial parts of HSE. Finally, experimental designs are still considered the gold standard, yet several of the conditions for their use are not fulfilled in HSE. Realising that a new evaluation framework for HSE is needed, the European expert group initiated its development and agreed upon a number of indicators that provide a starting point for further discussion. Conclusions Aside from the health impact, the quality of SE programmes and their implementation also deserve attention and should be evaluated. To be applicable to HSE, the evaluation criteria need to cover more than the typical public health aspects. Since they do not register long-term and multi-component characteristics, evaluation methods such as randomised controlled trials are not sufficiently suitable for HSE. The evaluation design should rely on a number of different information sources from mixed methods that are complemented and triangulated to build a plausible case for the effectiveness of SE in general and HSE in particular. 摘要 目的 整体型性教育（HSE）是性教育中一种新的理念，由于整体型性教育在很多重要方面和其他类型性教育不同，所以为后者的评价而发展的策略不一定适用于HSE。 在这篇文章中作者为如何评价HSE的讨论提供了依据。 方法 首先，复习关于性教育评价的国内外文献，评估其对于HSE的适用性。 第二，欧洲性教育专家组广泛讨论整体型性教育评价的要求并且提出评价HSE的适宜的指标和方法。 结果 欧洲在性教育方面的经验几乎可以说是总的关于评价文献的代表。 大多数文献关注性教育活动的影响而忽略了对于计划和执行情况的评价。 另外，目前的文献资料表明，性教育评价标准主要集中在对公众健康的影响，而关于性满意的标准和性生活积极的方面目前尚没有共识，而这正是HSE至关重要的部分。 最后，实验研究设计仍然被看作评价性教育的金标准，但是实验研究设计的一些条件在HSE中不能满足。 意识到需要一个新的针对HSE的评价体系，欧洲专家组开始着手评价体系的发展并且通过一系列的指标，这为进一步的讨论提供了一个起点。 结论 除了对健康的影响以外，性教育方案的质量和方案的实施也值得关注并且应该加以评价。 为了适用于HSE，评价标准需要涵盖比传统的公共健康更多的范畴。 由于像随机对照实验这样的研究方法不注重长期性和多因素等特征，所以并不是很适合HSE。 评价的设计应该依靠很多来自各种方法的不同的信息资源，这些方法互相补充，呈三角形，一起构建一个合理的关于性教育尤其是HSE有效性评价的实例。
Phosphorus Uptake by Pigeon Pea and Its Role in Cropping Systems of the Indian Subcontinent

Pigeon pea was shown to be more efficient at utilizing iron-bound phosphorus (Fe-P) than several other crop species. This ability is attributed to root exudates, in particular piscidic acid and its p-O-methyl derivative, which release phosphorus from Fe-P by chelating Fe3+. Pigeon pea is normally intercropped with cereals under low-input conditions in the Indian subcontinent. Although pigeon pea can utilize the relatively insoluble Fe-P, intercropped cereals must rely on the more soluble calcium-bound phosphorus. This finding suggests that cultivation of pigeon pea increases total phosphorus availability in cropping systems with low available phosphorus.
Parallelism-Aware Batch Scheduling: Enhancing both Performance and Fairness of Shared DRAM Systems

In a chip-multiprocessor (CMP) system, the DRAM system is shared among cores. In a shared DRAM system, requests from a thread can not only delay requests from other threads by causing bank/bus/row-buffer conflicts but they can also destroy other threadspsilaDRAM-bank-level parallelism. Requests whose latencies would otherwise have been overlapped could effectively become serialized. As are sult both fairness and system throughput degrade, and some thread scan starve for long time periods. This paper proposes a fundamentally new approach to designing a shared DRAM controller that provides quality of service to threads,while also improving system throughput. Our parallelism-aware batch scheduler (PAR-BS) design is based on two key ideas. First, PARBS processes DRAM requests in batches to provide fairness and to avoid starvation of requests. Second, to optimize system throughput,PAR-BS employs a parallelism-aware DRAM scheduling policy that aims to process requests from a thread in parallel in the DRAM banks, thereby reducing the memory-related stall-time experienced by the thread. PAR-BS seamlessly incorporates support for system-level thread priorities and can provide different service levels, including purely opportunistic service, to threads with different priorities.We evaluate the design trade-offs involved in PAR-BS and compare it to four previously proposed DRAM scheduler designs on 4-, 8-, and16-core systems. Our evaluations show that, averaged over 100 4-core workloads, PAR-BS improves fairness by 1.11X and system through put by 8.3% compared to the best previous scheduling technique, Stall-Time Fair Memory (STFM) scheduling. Based on simple request prioritization rules, PAR-BS is also simpler to implement than STFM.
Exact Regularization of Convex Programs

The regularization of a convex program is exact if all solutions of the regularized problem are also solutions of the original problem for all values of the regularization parameter below some positive threshold. For a general convex program, we show that the regularization is exact if and only if a certain selection problem has a Lagrange multiplier. Moreover, the regularization parameter threshold is inversely related to the Lagrange multiplier. We use this result to generalize an exact regularization result of Ferris and Mangasarian [Appl. Math. Optim. , 23 (1991), pp. 266-273] involving a linearized selection problem. We also use it to derive necessary and sufficient conditions for exact penalization, similar to those obtained by Bertsekas [Math. Programming, 9 (1975), pp. 87-99] and by Bertsekas, Nedic, and Ozdaglar [Convex Analysis and Optimization, Athena Scientific, Belmont, MA, 2003]. When the regularization is not exact, we derive error bounds on the distance from the regularized solution to the original solution set. We also show that existence of a “weak sharp minimum” is in some sense close to being necessary for exact regularization. We illustrate the main result with numerical experiments on the $\ell_1$ regularization of benchmark (degenerate) linear programs and semidefinite/second-order cone programs. The experiments demonstrate the usefulness of $\ell_1$ regularization in finding sparse solutions.
Incidence and Mortality Trends in German Women with Breast Cancer Using Age, Period and Cohort 1999 to 2008

Longitudinal analysis investigates period (P), often as years. Additional scales of time are age (A) and birth cohort (C) Aim of our study was to use ecological APC analysis for women breast cancer incidence and mortality in Germany. Nation-wide new cases and deaths were obtained from Robert Koch Institute and female population from federal statistics, 1999–2008. Data was stratified into ten 5-years age-groups starting 20–24 years, ten birth cohorts starting 1939–43, and two calendar periods 1999–2003 and 2004–2008. Annual incidence and mortality were calculated: cases to 100,000 women per year. Data was analyzed using glm and apc packages of R. Breast cancer incidence and mortality increased with age. Secular rise in breast cancer incidence and decline in mortality was observed for period1999-2008. Breast cancer incidence and mortality declined with cohorts; cohorts 1950s showed highest incidence and mortality. Age-cohort best explained incidence and mortality followed by age-period-cohort with overall declining trends. Declining age-cohort mortality could be probable. Declining age-cohort incidence would require future biological explanations or rendered statistical artefact. Cohorts 1949–1958 could be unique in having highest incidence and mortality in recent time or future period associations could emerge relatively stronger to cohort to provide additional explanation of temporal change over cohorts.
Graphical Representation and Similarity Analysis of Protein Sequences Based on Fractal Interpolation

A new graphical representation of protein sequences is introduced in this paper. Nine main physicochemical properties of amino acids were used to obtain a 2D discrete point set for protein sequences by applying principal component analysis. The fractal method was then employed to interpolate discrete points in constructing a graphical representation of protein sequences. Fractal dimension of the protein curve was used to analyze the similarity of protein sequences by comparing the distance of vectors representing segments of protein sequences. The Jeffrey's and Matusita distance was modified in the similarity comparison of protein sequences with different lengths. Nine different species from Nicotinamide adenine dinucleotide (NADH) dehydrogenase 5 (ND5) protein sequences were tested as an example to demonstrate our method. Finally, a linear correlation and significance analysis was used to compare our results with other graphical representations referring to the ClustalW result. To confirm the validity of our method, eight species in NADH dehydrogenase 6 (ND6) protein families and twenty-seven species in beta-globin protein families were also analyzed. Experimental results show that the proposed method is effective for the similarity analysis of proteins.
Dynamic Club Formation With Coordination

We present a dynamic model of club formation in a society of identical people. Coalitions consisting of members of the same club can form for one period and coalition members can jointly deviate. The dynamic process is described by a Markov chain defined by myopic optimization on the part of coalitions. We define a Nash club equilibrium (NCE) as a strategy profile that is immune to such coalitional deviations. For single--peaked preferences, we show that, if one exists, the process will converge to a NCE profile with probability one. NCE is unique up to a renaming of players and locations. Further, NCE corresponds to strong Nash equilibrium in the club formation game. Finally, we deal with the case where NCE fails to exist due to a nonbalancedness problem. When the population size is not an integer multiple of an optimal club size, there may be 'left over' players who prevent the process from `settling down'. To treat this case, we define the concept of k-remainder NCE, which requires that all but k players are playing a Nash club equilibrium, where k is defined by the minimal number of left over players. We show that the process converges to an ergodic NCE, that is, a set of states consisting only of k-remainder NCE.
Unifying Task Specification in Reinforcement Learning

Reinforcement learning tasks are typically specified as Markov decision processes. This formalism has been highly successful, though specifications often couple the dynamics of the environment and the learning objective. This lack of modularity can complicate generalization of the task specification, as well as obfuscate connections between different task settings, such as episodic and continuing. In this work, we introduce the RL task formalism, that provides a unification through simple constructs including a generalization to transition-based discounting. Through a series of examples, we demonstrate the generality and utility of this formalism. Finally, we extend standard learning constructs, including Bellman operators, and extend some seminal theoretical results, including approximation errors bounds. Overall, we provide a well-understood and sound formalism on which to build theoretical results and simplify algorithm use and development.
Analytical solution for the evolution of a binary with stable mass transfer from a giant

We derive a simple analytical solution for the evolution of a close binary with nuclear time-scale driven mass transfer from a giant. This solution is based on the well-known fact that the luminosity and the radius of a giant scale to a good approximation as simple power laws of the mass Mc of the degenerate helium core. Comparison with results of numerical calculations by Webbink, Rappaport & Savonije show the analytical solution and the power-law approximation to be quite accurate. The analytical solution presented does also allow (in parametrized form) for non-conservative mass transfer. Furthermore, it is shown that the near constancy of the mass-transfer rate over most of the mass-transfer phase seen in the results by Webbink, Rappaport & Savonije is not a generic feature of this type of evolution but rather a consequence of a particular choice of parameters. The analytical solution also demonstrates that the level of mass transfer is largely set by the core mass of the giant at the onset of mass transfer. Finally, we show that the model is self-consistent and discuss its applicability to low-mass X-ray binaries.
Veneer densification as a tool for shortening of plywood pressing time.

Veneer densifi cation was performed at 105±3 oC under pressure of 1,8 N/mm2 for 30 s. The approach allowed to reduce 20-mm thick plywood pressing time by 12-25 % when compared to the non-densifi ed controls. It was found that densifi cation did not affect shear strength of the plywood which met the requirements of the respective standards.
Respiratory Syncytial Virus Polymerase Can Initiate Transcription from Position 3 of the Leader Promoter

ABSTRACT The mechanisms by which the respiratory syncytial virus (RSV) RNA-dependent RNA polymerase (RdRp) initiates mRNA transcription and RNA replication are poorly understood. A previous study, using an RSV minigenome, suggested that the leader (Le) promoter region at the 3′ end of the genome has two initiation sites, one at position +1, opposite the 3′ terminal nucleotide of the genome, and a second site at position +3, at a sequence that closely resembles the gene start (GS) signal of the RSV L gene. In this study, we show that the +3 initiation site of the Le is utilized with apparently high frequency in RSV-infected cells and yields small RNA transcripts that are heterogeneous in length but mostly approximately 25 nucleotides (nt) long. Experiments with an in vitro assay in which RSV RNA synthesis was reconstituted using purified RdRp and an RNA oligonucleotide showed that nt 1 to 14 of the Le promoter were sufficient to signal initiation from +3 and that the RdRp could access the +3 initiation site without prior initiation at +1. In a minigenome assay, nucleotide substitutions within the Le to increase its similarity to a GS signal resulted in more-efficient elongation of the RNA initiated from position +3 and a reduction in RNA initiated from the NS1 gene start signal at +45. Taken together, these data suggest a new model for initiation of sequential transcription of the RSV genes, whereby the RdRp initiates the process from a gene start-like sequence at position +3 of the Le.