Miracle-dz/UniFAR-FTUs huggingface dataset:
High-level amikacin resistance in Escherichia coli due to phosphorylation and impaired aminoglycoside uptake

Plasmid pMP1-1 in Escherichia coli L-0 encodes aminoglycoside (AG) 3'-phosphotransferase II [APH(3')-II]. This enzyme modifies and confers high-level resistance to kanamycin. Although amikacin is a substrate for APH(3')-II, strain L-0(pMP1-1) is susceptible to amikacin. Plasmid pMP1-2 is a spontaneous mutant of pMP1-1 which determines increased APH(3')-II activity for amikacin, apparently as a result of an increase in the copy number of the plasmid. From amikacin-susceptible, gentamicin-susceptible transformants and transconjugants that bear the APH(3')-II gene on plasmid pMP1-1 or pMP1-2 or cloned into multicopy plasmid pBR322, we selected spontaneous mutants at concentrations of amikacin or gentamicin that were two to four times higher than the MICs of these antibiotics. In each case, whether they were selected by using amikacin or gentamicin, the mutants exhibited modest (two- to eightfold) increases in the MIC of gentamicin and major (64- to 128-fold) increases in the MIC of amikacin. Using these laboratory strains of E. coli, we examined the effects on AG susceptibility of the interaction of AG-modifying enzyme activity and generalized AG uptake. Increasing the level of activity of an AG phosphotransferase in these strains lowered their susceptibility to AGs which were substrates for which the enzyme had low Kms. However, an increase in AG-modifying activity alone did not result in large increases in the MICs for poor substrates of the enzyme. In strains which lacked AG-modifying enzymes, a decrease in the rate of AG uptake increased the MICs modestly for a broad spectrum of AGs. When a strain bore the phosphotransferase, a decrease in generalized AG uptake could raise the MIC further, not only for low-Km substrates, but even for AG substrates for which the enzyme had high Kms. Thus, increased modifying activity, together with a diminished rate of uptake, could produce even higher MICs for poor AG substrates.
An analysis of TCP processing overhead

The transport layer of the protocol suite, especially in connectionless protocols, has considerable functionality and is typically executed in software by the host processor at the end points of the network. It is thus considered a likely source of processing overhead. However, a preliminary examination has suggested to the authors that other aspects of networking may be a more serious source of overhead. To test this proposition, a detailed study was made of the Transmission Control Protocol (TCP), the transport protocol from the Internet protocol suite. In this set of protocols, the functions of detecting and recovering lost or corrupted packets, flow control, and multiplexing are performed at the transport level. The results of that study are presented. It is concluded that TCP is in fact not the source of the overhead often observed in packet processing, and that it could support very high speeds if properly implemented. <<ETX>>
Low-luminosity gamma-ray bursts as a distinct GRB population: a firmer case from multiple criteria constraints

The intriguing observations of the Swift/Burst Alert Telescope (BAT) X-ray flash (XRF) 060218 and the BATSE-BeppoSAX gamma-ray burst GRB 980425, both with much lower luminosity and redshift compared to other observed bursts, naturally lead to the question of how these low-luminosity (LL) bursts are related to high-luminosity (HL) bursts. Incorporating the constraints from both the flux-limited samples observed with Compton Gamma-ray Observatory (CGRO )/BATSE and Swift/BAT and the redshift-known gamma-ray burst (GRB) sample, we investigate the luminosity function for both LL and HL GRBs through simulations. Our multiple criteria, including the log N - log P distributions from the flux-limited GRB sample, the redshift and luminosity distributions of the redshift-known sample and the detection ratio of HL and LL GRBs with Swift/BAT, provide a set of stringent constraints to the luminosity function. Assuming that the GRB rate follows the star formation rate (SFR), our simulations show that a simple power law (PL) or a broken power-law model of luminosity function fails to reproduce the observations and a new component is required. This component can be modelled with a broken power, which is characterized by a sharp increase in the burst number at around L < 10 47 erg s -1 . The lack of detection of moderate-luminosity GRBs at redshift ∼0.3 indicates that this feature is not due to the observational biases. The inferred local rate, p o , of LL GRBs from our model is ∼200 Gpc -3 yr -1 at ∼ 10 47 erg s -1 , much larger than that of HL GRBs. These results imply that LL GRBs could be a separate GRB population from HL GRBs. The recent discovery of a local X-ray transient 080109/SN 2008D would strengthen our conclusion if the observed non-thermal emission has a similar origin as the prompt emission of most GRBs and XRFs.
Why are Put Options so Expensive?

This paper studies the "overpriced puts puzzle" — the finding that historical prices of the S&P 500 put options have been too high and incompatible with the canonical asset-pricing models. To investigate whether put returns could be rationalized by another, possibly non-standard equilibrium model, we implement the model-free methodology of Bondarenko [2003a, Statistical Arbitrage and Securities Prices, Review of Financial Studies 16, 875–919]. The methodology requires no parametric assumptions on investors' preferences. Furthermore, it can be applied even when the sample is affected by certain selection biases (such as the Peso problem) and when investors' beliefs are incorrect. The main finding of the paper is that no model within a studied class of models can possibly explain the put anomaly.
Assessing the Relation Between Satisfaction with Public Service Delivery and Trust in Government. The Impact of the Predisposition of Citizens Toward Government on Evalutations of Its Performance

We study how satisfaction with service delivery affects trust in public agencies in an empirical setting. Our basic assumption is that the causal relation between satisfaction and trust cannot be fruitfully analyzed unless the measures are controlled for a common component, which we identify as the predisposition toward government. The empirical results suggest that the impact of a negative experience with a public agency is much more pronounced than the effect of a positive one. Decreasing the number of disappointed clients will, therefore, have a stronger effect on increasing trust in the public sector than increasing the number of (already) well-pleased clients: Trust comes on foot and goes away on horseback.
The Design of IMF-Supported Programs

This collection of papers examines IMF-supported programs over the period 1995-2000 in both middle-income and low-income countries. In order to seek insights from a comparison across different types of programs, the sections entitled"Objectives and Outcomes," "Policy Formulation and Analytical Frameworks," and "Macroeconomic and Structural Policies" address a number of questions regarding the economic programs for which national authorities seek the IMF’s financial support: the specific goals of IMF-supported programs, and the challenges they face; how programs are formulated; the components of programs; and how program success should be judged.
The opportunities and challenges facing women in senior academic and managerial positions at a particular campus within a merging South African university.

Whilst there has been considerable research that has documented the barriers facing women (Cassimjee, 2003; Holland, 2001; Lyness & Thompson, 2000; De La Rey, 1999;Wood, 1993), little is known about the opportunities facing women, particularly Black women academics/managers, within tertiary institutions. In an attempt to facilitate such insight, the central aim of the study explores the subjective experiences of women academics/managers in terms of their academic development and career trajectory. This qualitative study was conducted within a particular campus within a merging South African university. Using convenience sampling, three women academics (two participants of African descent, one participant of Indian descent) and two managers (one participant of African descent and one of Indian descent) were selected. All interviews were audio taped and transcribed. Inductive thematic analysis was used to analyse the transcribed interviews followed by interpretation of the data, which was informed by the theoretical underpinnings of the study, rooted within the ambit of Social Cognitive Career Theory (SCCT). The analysis of the subjective experiences of women in this study revealed salient factors relating to the patriarchal nature of the institution of study, the legacy of apartheid and the issue of racism. The lack of overall institutional support and the absence of mentorship programmes were also prevalent. In addition, there emerged a shared ideology that 'academic life was a battle' to be fought. The acquisition of knowledge, constant empowerment and goal orientated behaviour with discipline; boundaries and strategies remained an overall theme to manage hierarchical career growth and development. Balancing work, academic and management roles together with the competing needs around family also posed a challenge. In sum, the implication of the study highlights the need to cultivate a non-racist, gender neutral and logistically supportive environment.
Estimating heterozygosity from a low-coverage genome sequence, leveraging data from other individuals sequenced at the same sites

High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites within an individual's genome, which is informative about inbreeding and effective population size. However, in many cases, the available sequence data of an individual is limited to low coverage, preventing the confident calling of genotypes necessary to directly count the proportion of heterozygous sites. Here, we present a method for estimating an individual's genome-wide rate of heterozygosity from low-coverage sequence data, without an intermediate step calling genotypes. Our method jointly learns the shared allele distribution between the individual and a panel of other individuals, together with the sequencing error distributions and the reference bias. We show our method works well, first by its performance on simulated sequence data, and secondly on real sequence data where we obtain estimates using low coverage data consistent with those from higher coverage. We apply our method to obtain estimates of the rate of heterozygosity for 11 humans from diverse world-wide populations, and through this analysis reveal the complex dependency of local sequencing coverage on the true underlying heterozygosity, which complicates the estimation of heterozygosity from sequence data. We show filters can correct for the confounding by sequencing depth. We find in practice that ratios of heterozygosity are more interpretable than absolute estimates, and show that we obtain excellent conformity of ratios of heterozygosity with previous estimates from higher coverage data.
The Use of Combining Ability Analysis to Identify Elite Parents for Artemisia annua F1 Hybrid Production

Artemisia annua is an important medicinal crop used for the production of the anti-malarial compound artemisinin. In order to assist in the production of affordable high quality artemisinin we have carried out an A. annua breeding programme aimed at improving artemisinin concentration and biomass. Here we report on a combining ability analysis of a diallel cross to identify robust parental lines for hybrid breeding. The parental lines were selected based on a range of phenotypic traits to encourage heterosis. The general combining ability (GCA) values for the diallel parental lines correlated to the positive alleles of quantitative trait loci (QTL) in the same parents indicating the presence of beneficial alleles that contribute to parental performance. Hybrids generated from crossing specific parental lines with good GCA were identified as having an increase in both artemisinin concentration and biomass when grown either in glasshouse or experimental field trials and compared to controls. This study demonstrates that combining ability as determined by a diallel cross can be used to identify elite parents for the production of improved A. annua hybrids. Furthermore, the selection of material for breeding using this approach was found to be consistent with our QTL-based molecular breeding approach.
Short time sports exercise boosts motor imagery patterns: implications of mental practice in rehabilitation programs

Motor imagery (MI) is a commonly used paradigm for the study of motor learning or cognitive aspects of action control. The rationale for using MI training to promote the relearning of motor function arises from research on the functional correlates that MI shares with the execution of physical movements. While most of the previous studies investigating MI were based on simple movements in the present study a more attractive mental practice was used to investigate cortical activation during MI. We measured cerebral responses with functional magnetic resonance imaging (fMRI) in twenty three healthy volunteers as they imagined playing soccer or tennis before and after a short physical sports exercise. Our results demonstrated that only 10 min of training are enough to boost MI patterns in motor related brain regions including premotor cortex and supplementary motor area (SMA) but also fronto-parietal and subcortical structures. This supports previous findings that MI has beneficial effects especially in combination with motor execution when used in motor rehabilitation or motor learning processes. We conclude that sports MI combined with an interactive game environment could be a promising additional tool in future rehabilitation programs aiming to improve upper or lower limb functions or support neuroplasticity.
Level design as model transformation: a strategy for automated content generation

This paper frames the process of designing a level in a game as a series of model transformations. The transformations correspond to the application of particular design principles, such as the use of locks and keys to transform a linear mission into a branching space. It shows that by using rewrite systems, these transformations can be formalized and automated. The resulting automated process is highly controllable: it is a perfect match for a mixed-initiative approach to level generation where human and computer collaborate in designing levels. An experimental prototype that implements these ideas is presented.
Galaxy Zoo: the dependence of morphology and colour on environment

We analyse the relationships between galaxy morphology, colour, environment and stellar mass using data for over 105 objects from Galaxy Zoo, the largest sample of visually classified morphologies yet compiled. We conclusively show that colour and morphology fractions are very different functions of environment. Both colour and morphology are sensitive to stellar mass. However, at fixed stellar mass, while colour is also highly sensitive to environment, morphology displays much weaker environmental trends. Only a small part of both the morphology–density and colour–density relations can be attributed to the variation in the stellar-mass function with environment. Galaxies with high stellar masses are mostly red in all environments and irrespective of their morphology. Low stellar-mass galaxies are mostly blue in low-density environments, but mostly red in high-density environments, again irrespective of their morphology. While galaxies with early-type morphology do always have higher red fractions, this is subdominant compared to the dependence of red fraction on stellar mass and environment. The colour–density relation is primarily driven by variations in colour fractions at fixed morphology, in particular the fraction of spiral galaxies that have red colours, and especially at low stellar masses. We demonstrate that our red spirals primarily include galaxies with true spiral morphology, and that they constitute an additional population to the S0 galaxies considered by previous studies. We clearly show there is an environmental dependence for colour beyond that for morphology. The environmental transformation of galaxies from blue to red must occur on significantly shorter time-scales than the transformation from spiral to early-type. We also present many of our results as functions of the distance to the nearest galaxy group. This confirms that the environmental trends we present are not specific to the manner in which environment is quantified, but nevertheless provides plain evidence for an environmental process at work in groups. However, the properties of group members show little dependence on the total mass of the group they inhabit, at least for group masses ≳1013M⊙. Before using the Galaxy Zoo morphologies to produce the above results, we first quantify a luminosity-, size- and redshift-dependent classification bias that affects this data set, and probably most other studies of galaxy population morphology. A correction for this bias is derived and applied to produce a sample of galaxies with reliable morphological-type likelihoods, on which we base our analysis.
Movement Coordination in Human–Robot Teams: A Dynamical Systems Approach

In order to be effective teammates, robots need to be able to understand high-level human behavior to recognize, anticipate, and adapt to human motion. We have designed a new approach to enable robots to perceive human group motion in real time to anticipate future actions and synthesize their own motion accordingly. We explore this within the context of joint action, in which humans and robots move together synchronously. In this paper we present an anticipation method, which takes high-level group behavior into account. We validate the method within a human-robot interaction scenario, in which an autonomous mobile robot observes a team of human dancers and then successfully and contingently coordinates its movements to “join the dance. ” We compared the results of our anticipation method to move the robot with another method that did not rely on high-level group behavior and found that our method performed better both in terms of more closely synchronizing the robot's motion to the team and exhibiting more contingent and fluent motion. These findings suggest that the robot performs better when it has an understanding of high-level group behavior than when it does not. This study will help enable others in the robotics community to build more fluent and adaptable robots in the future.
AFDC Participation across Generations

William Julius Wilson's influential book The Truly Disadvantaged (1987) has sparked a vigorous debate about the existence and causes of an urban underclass. While there is still no clear agreement about definitions, the growing literature on the underclass focuses both on traits of the current generation and the traits of their parents. If an underclass exists, its current members are assumed to live in deteriorating inner cities, to experience long spells of joblessness or welfare dependency, and/or to engage in illegal and antisocial activities. Furthermore, these traits are assumed to be correlated across generations, leading to a cycle of deprivation. In this paper, I focus on one such link across generations by examining the correlation in welfare participation of daughters and their parents. I first present the state of knowledge about the extent to which children of parents who received Aid to Families with Dependent Children (AFDC) are themselves more likely to participate in this welfare program. Second, I discuss the remaining gaps in our understanding and give several contrasting altemative explanations for the observed correlation, each with a different policy implication.
Chlamydia trachomatis Genital Infections

Etiology, transmission and protection: Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infection (STI) globally. However, C. trachomatis also causes trachoma in endemic areas, mostly Africa and the Middle East, and is a leading cause of preventable blindness worldwide. Epidemiology, incidence and prevalence: The World Health Organization estimates 131 million new cases of C. trachomatis genital infection occur annually. Globally, infection is most prevalent in young women and men (14-25 years), likely driven by asymptomatic infection, inadequate partner treatment and delayed development of protective immunity. Pathology/Symptomatology: C. trachomatis infects susceptible squamocolumnar or transitional epithelial cells, leading to cervicitis in women and urethritis in men. Symptoms are often mild or absent but ascending infection in some women may lead to Pelvic Inflammatory Disease (PID), resulting in reproductive sequelae such as ectopic pregnancy, infertility and chronic pelvic pain. Complications of infection in men include epididymitis and reactive arthritis. Molecular mechanisms of infection: Chlamydiae manipulate an array of host processes to support their obligate intracellular developmental cycle. This leads to activation of signaling pathways resulting in disproportionate influx of innate cells and the release of tissue damaging proteins and pro-inflammatory cytokines. Treatment and curability: Uncomplicated urogenital infection is treated with azithromycin (1 g, single dose) or doxycycline (100 mg twice daily x 7 days). However, antimicrobial treatment does not ameliorate established disease. Drug resistance is rare but treatment failures have been described. Development of an effective vaccine that protects against upper tract disease or that limits transmission remains an important goal.
A feasibility open trial of internet-delivered cognitive-behavioural therapy (iCBT) among consumers of a non-governmental mental health organisation with anxiety

Background. To date the efficacy and acceptability of internet-delivered cognitive behavioural treatments (iCBT) has been examined in clinical trials and specialist facilities. The present study reports the acceptability, feasibility and preliminary efficacy of an established iCBT treatment course (the Wellbeing Course) administered by a not-for-profit non-governmental organisation, the Mental Health Association (MHA) of New South Wales, to consumers with symptoms of anxiety. Methods. Ten individuals who contacted the MHA’s telephone support line or visited the MHA’s website and reported at least mild symptoms of anxiety (GAD-7 total scores ≥5) were admitted to the study. Participants were provided access to the Wellbeing Course, which comprises five online lessons and homework assignments, and brief weekly support from an MHA staff member via telephone and email. The MHA staff member was an experienced mental health professional and received minimal training in administering the intervention. Results. All 10 participants completed the course within the 8 weeks. Post-treatment and two month follow-up questionnaires were completed by all participants. Mean within-group effect sizes (Cohen’s d) for the Generalized Anxiety Disorder 7 Item (GAD-7) and Patient Health Questionnaire 9 Item (PHQ-9) were large (i.e., > .80) and consistent with previous controlled research. The Course was also rated as highly acceptable with all 10 participants reporting it was worth their time and they would recommend it to a friend. Conclusions. These results provide support for the potential clinical utility of iCBT interventions and the acceptability and feasibility of employing non-governmental mental health organisations to deliver these treatments. However, further research is needed to examine the clinical efficacy and cost-effectiveness of delivering iCBT via such organisations.