Miracle-dz/UniFAR-FTUs huggingface dataset:
Plastid Genome Sequence of a Wild Woody Oil Species, Prinsepia utilis, Provides Insights into Evolutionary and Mutational Patterns of Rosaceae Chloroplast Genomes

Background Prinsepia utilis Royle is a wild woody oil species of Rosaceae that yields edible oil which has been proved to possess particular benefits for human health and medical therapy. However, the lack of bred varieties has largely impeded exploiting immense potentials for high quality of its seed oil. It is urgently needed to enlarge the knowledge of genetic basis of the species and develop genetic markers to enhance modern breeding programs. Results Here we reported the complete chloroplast (cp) genome of 156,328 bp. Comparative cp sequence analyses of P . utilis along with other four Rosaceae species resulted in similar genome structures, gene orders, and gene contents. Contraction/expansion of inverted repeat regions (IRs) explained part of the length variation in the Rosaceae cp genomes. Genome sequence alignments revealed that nucleotide diversity was associated with AT content, and large single copy regions (LSC) and small single copy regions (SSC) harbored higher sequence variations in both coding and non-coding regions than IRs. Simple sequence repeats (SSRs) were detected in the P . utilis and compared with those of the other four Rosaceae cp genomes. Almost all the SSR loci were composed of A or T, therefore it might contribute to the A-T richness of cp genomes and be associated with AT biased sequence variation. Among all the protein-coding genes, ycf1 showed the highest sequence divergence, indicating that it could accomplish the discrimination of species within Rosaceae as well as within angiosperms better than other genes. Conclusions With the addition of this new sequenced cp genome, high nucleotide substitution rate and abundant deletions/insertions were observed, suggesting a greater genomic dynamics than previously explored in Rosaceae. The availability of the complete cp genome of P . utilis will provide chloroplast markers and genetic information to better enhance the conservation and utilization of this woody oil plant.
An Empirical Analysis of Malware Blacklists

Besides all the advantages and reliefs the Internet brought us over the years, there are also a lot of suspicious and malicious activities taking place. Attackers are constantly developing new techniques to compromise computer systems. Furthermore, there are many malicious servers on the Internet that host, for example, exploits, drive-by download toolkits, or malicious software. We want to track the network locations of these malicious servers by analyzing different kinds of blacklists that provide a listing of suspicious servers. In this article, we present the design and implementation of our blacklist parser system that tracks 49 different blacklists. We have collected more than 2.2 million distinct blacklist entries and more than 410,000 distinct URLs in the first 80 days of running the system. Besides discussing the design, we also provide an overview of the first empirical results of analyzing the collected data. In the future, we plan to extend the system such that it provides a comprehensive overview of malicious activities on the Internet.
The impact of duration of antibiotic exposure on bacterial resistance predictions using in vitro dynamic models.

OBJECTIVES To explore whether the duration of in vitro simulated antibiotic exposure influences bacterial resistance, time-dependent amplification of resistant subpopulations of Staphylococcus aureus was studied in 10 day simulations in a dynamic model with daptomycin as a prototypic agent. METHODS S. aureus ATCC 43300 was exposed to once-daily dosing of daptomycin at subtherapeutic ratios of 24 h area under the curve (AUC(24)) to the MIC (32 and 64 h). To provide an integral presentation of the time course of mutants grown on agar plates containing 2x and 4x the MIC of daptomycin, areas under the bacterial mutant kinetic curves (AUBC(M)s) were calculated. RESULTS Daptomycin-resistant S. aureus mutants were enriched gradually over the entire treatment duration, with systematic increases in AUBC(M) and concomitant decreases in susceptibility. AUBC(M) analyses were also applied to resistance data reported from other studies with S. aureus exposed to daptomycin and garenoxacin over a wide range of AUC(24)/MIC ratios. Although the maximal AUBC(M)s were greater with longer than with shorter exposures, the treatment or observation durations did not influence the predicted anti-mutant AUC(24)/MIC ratios. CONCLUSIONS These findings suggest that the duration of in vitro simulated antibiotic exposure is important for estimates of the maximal enrichment of resistant mutants but not for the prediction of the anti-mutant AUC(24)/MIC ratio.
Revealing the City That We Cannot See

We here investigate the potential of participatory sensor networks derived from location sharing systems, such as Foursquare, to understand the human dynamics of cities. We propose the City Image visualization technique, which builds a transition graph mapping people's movements between location categories, and demonstrate its use to identify similarities and differences of human dynamics across cities by clustering cities according to their citizens' routines. We also analyze centrality metrics of the transition graphs built for different cities, considering transitions between specific venues. We show that these metrics complement the City Image technique, contributing to a deeper understanding of city dynamics.
Freak ” waves and large-scale simulations of surface gravity waves

Can extreme waves on the open ocean, away from bottom influence and current refraction, be explained by state-of-the-art wave statistics, or are there exceptions deserving the names “freak” or “rogue” waves? We believe that some findings from the large scale numerical simulations of Socquet-Juglard et al. (2004) are relevant for answering these questions. The 3D simulations use a computational domain containing typically 10 4 waves, starting from a truncated JONSWAP spectrum with various angular distributions giving both long-crested and short-crested waves. For short-crested waves, the probability distributions of surface elevation and crest height are seen to fit the theoretical distributions found by Tayfun (1980)very well up to 5 standard deviations. After giving a short review of the simulation results, we try to relate them to storm wave data from the Central North Sea.
ENet: A Deep Neural Network Architecture for Real-Time Semantic Segmentation

The ability to perform pixel-wise semantic segmentation in real-time is of paramount importance in mobile applications. Recent deep neural networks aimed at this task have the disadvantage of requiring a large number of floating point operations and have long run-times that hinder their usability. In this paper, we propose a novel deep neural network architecture named ENet (efficient neural network), created specifically for tasks requiring low latency operation. ENet is up to 18$\times$ faster, requires 75$\times$ less FLOPs, has 79$\times$ less parameters, and provides similar or better accuracy to existing models. We have tested it on CamVid, Cityscapes and SUN datasets and report on comparisons with existing state-of-the-art methods, and the trade-offs between accuracy and processing time of a network. We present performance measurements of the proposed architecture on embedded systems and suggest possible software improvements that could make ENet even faster.
Immunization with Alpha-Toxin Toxoid Protects the Cornea against Tissue Damage during Experimental Staphylococcus aureus Keratitis

ABSTRACT Alpha-toxin is a major virulence factor in Staphylococcus aureus keratitis. Active or passive immunization with alpha-toxin toxoid could protect against corneal damage. Results show that either form of immunization did not kill bacteria but did significantly protect against corneal pathology, especially epithelial erosion.
Examination of the change in Assessment of Motor and Process Skills performance in patients with acquired brain injury between the hospital and home environment.

AIM The Assessment of Motor and Process Skills (AMPS) is a standardised, valid, reliable, observational assessment that is sensitive to change over time. This research aimed to examine the change in AMPS performance in patients discharged from a neurosurgical rehabilitation ward to a home-based therapy programme over a four-week time frame. METHODS A total of 15 individuals with acquired brain injury who were participating in rehabilitation were recruited to the study. The AMPS was conducted with each individual during the participant's inpatient rehabilitation and again approximately four weeks later, while participating in home-based rehabilitation. Assessment results were collated using the AMPS computer programme and entered into a statistics package from which data were analysed. RESULTS As a group, no statistically significant change in function was identified between the home and hospital environments; however, individual results did indicate a change in occupational performance for many of the participants. CONCLUSIONS The AMPS was shown to reflect a change in occupational performance for many of the research participants. This research supports previous studies which indicate that some individuals' motor and process skill abilities appear to be affected by the environment in which they perform. This suggests that occupational therapists wishing to know how an individual will perform activities of daily living should evaluate the individual's performance in the environment in which they will be functioning.
Towards Efficient Field Programmable Pattern Matching Array

Pattern matching is used in most of the network security devices in order to detect attacks, threats and malicious network traffic. Many hardware architectures have been designed to accelerate this time-critical operation in order to increase processing speed and achieve multi-gigabit throughput. Recently introduced automata processor is an powerful architecture which represents a new class of field programmable circuits called Field Programmable Pattern Matching Array (FPPMA). In the paper, we propose to improve the FPPMA architecture by Deterministic Units (DU), which have been originally introduced in NFA Split and significantly reduce the amount of required resources for mapping NFA to hardware. Dual position automaton is used to create data structure for the new FPPMA architecture from set of regular expressions. Moreover, we investigate efficiency of DU based on a dual position automation. Since the DU can implement a finite automaton without structural restrictions, we propose to use unrestricted finite automaton for deterministic unit and the dual position automaton for parts mapped to basic FPPMA elements. The results show that the DU based on the unrestricted finite automaton utilizes up to 42.43% less State-Transition elements than the DU based on the dual position automaton. Utilization of DUs provides significant reduction of FPPMA resources. For example, State-transition elements were reduced by more than 71% for the Snort module spyware-put.
Effects of Individual Differences in Working Memory on Plan Presentational Choices

This paper addresses research questions that are central to the area of visualization interfaces for decision support: (RQ1) whether individual user differences in working memory should be considered when choosing how to present visualizations; (RQ2) how to present the visualization to support effective decision making and processing; and (RQ3) how to evaluate the effectiveness of presentational choices. These questions are addressed in the context of presenting plans, or sequences of actions, to users. The experiments are conducted in several domains, and the findings are relevant to applications such as semi-autonomous systems in logistics. That is, scenarios that require the attention of humans who are likely to be interrupted, and require good performance but are not time critical. Following a literature review of different types of individual differences in users that have been found to affect the effectiveness of presentational choices, we consider specifically the influence of individuals' working memory (RQ1). The review also considers metrics used to evaluate presentational choices, and types of presentational choices considered. As for presentational choices (RQ2), we consider a number of variants including interactivity, aggregation, layout, and emphasis. Finally, to evaluate the effectiveness of plan presentational choices (RQ3) we adopt a layered-evaluation approach and measure performance in a dual task paradigm, involving both task interleaving and evaluation of situational awareness. This novel methodology for evaluating visualizations is employed in a series of experiments investigating presentational choices for a plan. A key finding is that emphasizing steps (by highlighting borders) can improve effectiveness on a primary task, but only when controlling for individual variation in working memory.
Competencies Development for Lecturers at Faculty of Letters in Private University

This research was aimed to describe how the real image of the competencies of lecturer at Faculty of Letters and the faculty’s effort in encourage the development of lecturer’s competencies. This research used a qualitative descriptive method. The data were taken by an interview and documentation studies. The results of the research showed that all lecturers of which have master's academic qualifications are 106 publications that have been produced by lecturers in the last three years. Nine lecturers have practical positions issued by the government; nine lecturers have certified lecturers from the government; all lecturers, participating in their personal and systematic development activities. All lecturers have joined in skilled associations. The effort carried out by the faculty is to encourage each lecturer to study further; improve the quality and quantity of research and systematic publication; improve operational position qualifications and obtain a lecturer certification; always develop themselves and their knowledge; active in qualified organizations, and improve information technology skills. The things that need to be improved are the quality and quantity of scientific publication to support functional promotion and lecturer certification. The Support from institutions and the lecturer’s effort are needed to develop their competencies in order to be able to adjust the demands of the dynamic of development and the needs of the world of education. Based on these things, it can be concluded that the lecturers' competencies and the efforts that have been made by the faculty to develop lecturer competencies are good. Keywords— competencies, development, lecturer
Species Richness and the Temporal Stability of Biomass Production: A New Analysis of Recent Biodiversity Experiments

The relationship between biological diversity and ecological stability has fascinated ecologists for decades. Determining the generality of this relationship, and discovering the mechanisms that underlie it, are vitally important for ecosystem management. Here, we investigate how species richness affects the temporal stability of biomass production by reanalyzing 27 recent biodiversity experiments conducted with primary producers. We find that, in grasslands, increasing species richness stabilizes whole-community biomass but destabilizes the dynamics of constituent populations. Community biomass is stabilized because species richness impacts mean biomass more strongly than its variance. In algal communities, species richness has a minimal effect on community stability because richness affects the mean and variance of biomass nearly equally. Using a new measure of synchrony among species, we find that for both grasslands and algae, temporal correlations in species biomass are lower when species are grown together in polyculture than when grown alone in monoculture. These results suggest that interspecific interactions tend to stabilize community biomass in diverse communities. Contrary to prevailing theory, we found no evidence that species’ responses to environmental variation in monoculture predicted the strength of diversity’s stabilizing effect. Together, these results deepen our understanding of when and why increasing species richness stabilizes community biomass.
Evaluating the Harmfulness of Cloning: A Change Based Experiment

Cloning is considered a harmful practice for software maintenance because it requires consistent changes of the entities that share a cloned fragment. However this claim has not been refuted or confirmed empirically. Therefore, we have developed a prototype tool, CloneTracker, in order to study the rate of change of applications containing clones. This paper describes CloneTracker and illustrates its preliminary application on a case study.
Transcriptional neoteny in the human brain

In development, timing is of the utmost importance, and the timing of developmental processes often changes as organisms evolve. In human evolution, developmental retardation, or neoteny, has been proposed as a possible mechanism that contributed to the rise of many human-specific features, including an increase in brain size and the emergence of human-specific cognitive traits. We analyzed mRNA expression in the prefrontal cortex of humans, chimpanzees, and rhesus macaques to determine whether human-specific neotenic changes are present at the gene expression level. We show that the brain transcriptome is dramatically remodeled during postnatal development and that developmental changes in the human brain are indeed delayed relative to other primates. This delay is not uniform across the human transcriptome but affects a specific subset of genes that play a potential role in neural development.
THE RESPIRATION OF THE ISOLATED ROD OUTER LIMB OF THE FROG RETINA

The respiration of the isolated frog rod outer limb has been measured in the Cartesian diver. The outer limbs respire in Ringer solution without the addition of substrates, but the rate of respiration is increased by the addition of fructose diphosphate or succinate. The respiration is cyanide-sensitive, and therefore presumably mediated by the cytochromes. The Q OO2 in 0.01 M fructose diphosphate is –1.0 µl. oxygen per mg. dry weight per hour at 20°C. This is lower than the Q OO2 of whole frog retina, but comparable with it and many other tissues. The respiratory rate is independent of the state of dark adaptation (rhodopsin content) of the outer limbs. The metabolism of the outer limb is probably adequate to provide the DPN required for the maintenance of the rhodopsin concentration necessary for vision.
The Function of the Coding Sequences for the Putative Pheromone Precursors in Podospora anserina Is Restricted to Fertilization

ABSTRACT We cloned the pheromone precursor genes of Podospora anserina in order to elucidate their role in the biology of this fungus. The mfp gene encodes a 24-amino-acid polypeptide finished by the CAAX motif, characteristic of fungal lipopeptide pheromone precursors similar to the a-factor precursor of Saccharomyces cerevisiae. The mfm gene encodes a 221-amino-acid polypeptide, which is related to the S. cerevisiae α-factor precursor and contains two 13-residue repeats assumed to correspond to the mature pheromone. We deleted the mfp and mfm coding sequence by gene replacement. The mutations specifically affect male fertility, without impairing female fertility and vegetative growth. The male defect is mating type specific: the mat+ Δmfp and mat− Δmfm mutants produce male cells inactive in fertilization whereas the mat− Δmfp and mat+ Δmfm mutants show normal male fertility. Genetic data indicate that both mfp and mfm are transcribed at a low level in mat+ and mat− vegetative hyphae. Northern-blot analysis shows that their transcription is induced by the mating types in microconidia (mfp by mat+ and mfm by mat−). We managed to cross Δmfp Δmfm strains of opposite mating type, by complementation and transient expression of the pheromone precursor gene to trigger fertilization. These crosses were fertile, demonstrating that once fertilization occurs, the pheromone precursor genes are unnecessary for the completion of the sexual cycle. Finally, we show that the constitutively transcribed gpd::mfm and gpd::mfp constructs are repressed at a posttranscriptional level by the noncognate mating type.
Robust and flexible response of the Ostreococcus tauri circadian clock to light/dark cycles of varying photoperiod

The green microscopic alga Ostreococcus tauri has recently emerged as a promising model for understanding how circadian clocks, which drive the daily biological rhythms of many organisms, synchronize to the day/night cycle in changing weather and seasons. Here, we analyze translational reporter time series data for the central clock genes CCA1 and TOC1 for a wide range of daylight durations (photoperiods). The variation of temporal expression profiles with day duration is complex, with the two protein peaks tracking different times of the day. Nevertheless, all profiles are accurately reproduced by a simple two‐gene transcriptional loop model whose parameters depend on light only through the photoperiod value. We show that this non‐intuitive behavior allows the circadian clock to combine flexibility and robustness with respect to daylight fluctuations.
Anomalous Reynolds-number scaling in turbulent Rayleigh–Bénard convection

This paper reports measurements of Reynolds numbers Rep corresponding to the turnover time of thermal excitations (‘plumes’) and Reω corresponding to the twisting-oscillation period of the large-scale circulation (LSC) of turbulent Rayleigh–Bénard convection over the Rayleigh-number range and Prandtl-number range for cylindrical samples of aspect ratio Γ = 1. For both periods, and hence both Reynolds numbers, were the same and scaled as Re∼Rγeff with . Here both the σ- and R-dependences were quantitatively consistent with the Grossmann–Lohse (GL) prediction. For R>R* the results could be represented by Rep = 0.138 σ−0.82R0. 493 for the plume turnover time and Reω = 0.17 σ−0.81R0. 480 for the twisting oscillation, both of which differ significantly from the GL prediction as well as from each other. A relatively sharp transition at R* to the large-R regime and the separation of the two Reynolds numbers from each other suggest a qualitative and sudden change that renders the measured quantities inapplicable to the GL prediction. Combining Rep and previously reported measurements of the Nusselt number yielded the kinetic energy-dissipation as a function of Rep. For these results were in excellent agreement with the corresponding GL prediction, and both approached closely to the (Re)3-dependence that is expected at large Re where the bulk contribution to ϵu dominates. For R>R* the data were consistent with . This differs from the expected large-Re behavior and suggests that Rep no longer is the Reynolds number relevant to ϵu.