Miracle-dz/UniFAR-FTUs huggingface dataset:
Extrachromosomal Control of Methicillin Resistance and Toxin Production in Staphylococcus aureus

All of 41 naturally occurring coagulase-positive methicillin-resistant strains of Staphylococcus aureus isolated in various laboratories were resistant to several antibiotics and were lipase-negative. Most strains produced hemolysins, and 38 strains produced enterotoxin B. Acriflavine treatment of four strains resulted in elimination of resistance to methicillin and mercury; in one strain, resistance to cadmium was also lost. Production of enterotoxin B and β-hemolysin was eliminated in all four strains and penicillinase production was eliminated in one strain. In transduction experiments, methicillin resistance and enterotoxin B production were transferred together at a frequency of 0.2 × 10−8 to 1.1 × 10−8 by use of ultraviolet-induced phage lysates from naturally lysogenic methicillin-resistant strains. Cotransductions of resistance to mercury and cadmium, as well as production of penicillinase and β-hemolysin, were obtained to some extent. The extrachromosomal character of these determinants and their possible genetic association are discussed.
Exploration in relational domains for model-based reinforcement learning

A fundamental problem in reinforcement learning is balancing exploration and exploitation. We address this problem in the context of model-based reinforcement learning in large stochastic relational domains by developing relational extensions of the concepts of the E3 and R-MAX algorithms. Efficient exploration in exponentially large state spaces needs to exploit the generalization of the learned model: what in a propositional setting would be considered a novel situation and worth exploration may in the relational setting be a well-known context in which exploitation is promising. To address this we introduce relational count functions which generalize the classical notion of state and action visitation counts. We provide guarantees on the exploration efficiency of our framework using count functions under the assumption that we had a relational KWIK learner and a near-optimal planner. We propose a concrete exploration algorithm which integrates a practically efficient probabilistic rule learner and a relational planner (for which there are no guarantees, however) and employs the contexts of learned relational rules as features to model the novelty of states and actions. Our results in noisy 3D simulated robot manipulation problems and in domains of the international planning competition demonstrate that our approach is more effective than existing propositional and factored exploration techniques.
Restricting Dosage Compensation Complex Binding to the X Chromosomes by H2A.Z/HTZ-1

Dosage compensation ensures similar levels of X-linked gene products in males (XY or XO) and females (XX), despite their different numbers of X chromosomes. In mammals, flies, and worms, dosage compensation is mediated by a specialized machinery that localizes to one or both of the X chromosomes in one sex resulting in a change in gene expression from the affected X chromosome(s). In mammals and flies, dosage compensation is associated with specific histone posttranslational modifications and replacement with variant histones. Until now, no specific histone modifications or histone variants have been implicated in Caenorhabditis elegans dosage compensation. Taking a candidate approach, we have looked at specific histone modifications and variants on the C. elegans dosage compensated X chromosomes. Using RNAi-based assays, we show that reducing levels of the histone H2A variant, H2A.Z (HTZ-1 in C. elegans), leads to partial disruption of dosage compensation. By immunofluorescence, we have observed that HTZ-1 is under-represented on the dosage compensated X chromosomes, but not on the non-dosage compensated male X chromosome. We find that reduction of HTZ-1 levels by RNA interference (RNAi) and mutation results in only a very modest change in dosage compensation complex protein levels. However, in these animals, the X chromosome–specific localization of the complex is partially disrupted, with some nuclei displaying DCC localization beyond the X chromosome territory. We propose a model in which HTZ-1, directly or indirectly, serves to restrict the dosage compensation complex to the X chromosome by acting as or regulating the activity of an autosomal repellant.
Localization of a herpes simplex virus neurovirulence gene dissociated from high-titer virus replication in the brain

Previous studies with the herpes simplex virus type 1 X type 2 intertypic recombinant RS6 suggested that the genomic region from 0.11 to 0.14 map units is involved in neurovirulence (R. T. Javier, R. L. Thompson, and J. G. Stevens, J. Virol. 61:1978-1984, 1987). To study this further, we isolated an RS6-derived herpes simplex virus intertypic recombinant (R13-1) which has a genetic defect within this area. After inoculation into mouse brains, R13-1 was found to be approximately 10,000-fold less neurovirulent than either the wild-type type 1 or type 2 parental virus. However, R13-1 replicated in the mouse brain to titers resembling those of the wild-type parents. Further comparisons with wild-type counterparts indicated that R13-1 expressed equivalent levels of the enzyme thymidine kinase and replicated to intermediate levels in primary mouse embryo fibroblasts maintained at the normal body temperature for mice. Using marker rescue techniques combined with in vivo selection, we found that recombination between unit-length R13-1 DNA and a cloned type 1 DNA fragment spanning the region from 0.11 to 0.14 map units (EcoRI-d, 0.079 to 0.192 map units) generated viruses with a wild-type neurovirulence phenotype. To further refine the genomic region of interest, we performed marker rescue experiments using two EcoRI-d subclones, EcoRI/BamHI dc (0.079 to 0.143 map units) and BamHI/EcoRI and (0.143 to 0.192 map units), representing the left and right halves of the EcoRI d fragment, respectively. In these experiments the EcoRI/BamHI dc clone, but not the BamHI/EcoRI ad clone, yielded recombinant viruses exhibiting wild-type neurovirulence. These results show that at least one herpes simplex virus gene function associated with neurovirulence is located within a 9.1-kilobase region at 0.079 to 0.143 map units of the viral genome. Perhaps more significantly, the results indicate that this neurovirulence property functions independently of high-titer virus replication in the brain.
Text Classification Using WordNet Hypernyms

This paper describes experiments in Machine Learning for text classification using a new representation of text based on WordNet hypernyms. Six binary classification tasks of varying difficulty are defined, and the Ripper system is used to produce discrimination rules for each task using the new hypernym density representation. Rules are also produced with the commonly used bag-of-words representation, incorporating no knowledge from WordNet. Experiments show that for some of the more difficult tasks the hypernym density representation leads to significantly more accurate and more comprehensible rules.
Hydrosedimentological Modelling of a Small, Trained Tidal Inlet System, Currumbin Creek, Southeast Queensland, Australia

ABSTRACT Shaeri, S. ; Strauss, D. ; Etemad-Shahidi, A. , and Tomlinson, R. , 2018. Hydrosedimentological modelling of a small, trained tidal inlet system, Currumbin Creek, southeast Queensland, Australia. Small tidal inlets with an entrance width of less than 50 m or a cross-sectional area of less than 100 m2 have not been investigated as often as their larger counterparts. To discern the major processes responsible for entrance infilling in a small inlet system, the hydrosedimentological processes in the annually dredged Currumbin Creek (Australia) inlet system were investigated. Delft3D was applied and validated using local field measurements and regional data. A standalone regional hydrodynamic model and three nested standalone wave models provided detailed data for the offshore boundary of the more detailed creek entrance model, which was a coupled, local flow–wave–sediment transport model. The noncohesive sediment transport module was calibrated based on the volume of dredging and the net annual volume of longshore transport. The results of this hindcast model provided insight into the dominant processes responsible for the inlet's current configuration (i.e. significant refraction of incident waves to a nearly shore normal direction; a noteworthy onshore-offshore transfer of sediments; channel infilling induced by wave-induced currents; very limited sediment transport within the back-barrier lagoon because of an absence of wave-induced currents, as well as weak tide-induced currents; and infilling of the dredged area because of immersed slope stability, rather than hydrodynamic processes). Overall, the adopted modelling approach and the selected model setups proved to be a suitable combination of the available resources and tools to forecast the influence of any alteration to the current maintenance strategy. Accordingly, the identified physical processes and findings can be applied to similar cases with narrow inlet entrance widths and small back barriers with limited circulation.
Transition-state structure of neisseria meningitides 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

5‘-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is a bacterial enzyme that is involved in quorum sensing pathways and a potential target for the design of antibiotics. Kinetic isotope effects (KIEs) and computer modeling using density functional theory were used to determine the transition state of N. meningitides MTAN. KIEs were measured for hydrolysis of 5‘- methylthioadenosine (MTA) and were corrected for forward commitment to catalysis to obtain intrinsic KIEs for [1‘-3H], [9-15N], [1‘-14C], [2‘-3H], [4‘-3H], [5‘-3H2], and [Me-3H3] MTAs. KIEs support an early SN1 transition state unlike the dissociative transition states of other MTANs. Computational modeling of intrinsic KIEs places the leaving group adenine at 1.68 A from the anomeric carbon, a Pauling bond order of 0.50, and no participation of the hydroxide nucleophile. The N7 of adenine is protonated and the leaving group is cationic owing to the significant bond order to the C1‘−N9 bond at the transition state. The 3‘-OH is not.
Evaluation of deep neural networks for single image super-resolution in a maritime context

High resolution imagery is of crucial importance for the performance on visual recognition tasks. Super-resolution (SR) reconstruction algorithms aim to enhance the image resolution beyond the capability of the image sensor being used. Traditional SR algorithms approach this inverse problem using physical models for the image formation combined with a regularization function to prevent instabilities in the solution. Recently deep neural networks have been put forward as an alternative approach to the SR reconstruction problem. They learn a mapping from low resolution images to their high resolution counterparts from pairs of training images, which allows them to capture more specific information about the space of possible solutions than traditional regularization functions. These networks have achieved state-of-the-art performance on single image SR for sets of generic test images. Here we investigate whether the same performance can be realized when these neural networks for single image SR are applied specifically in the maritime domain. In particular we investigate their ability to reconstruct undersampled images of ships at sea, and demonstrate that the performance is similar to what is achieved on generic test images. In addition we quantify the gain in performance that is achieved when the networks are trained specifically on images of ships, which allows the networks to capture more prior knowledge about the space of possible solutions. Finally we show that the performance deteriorates when the resolution of test images is limited by image blur, for example due to diffraction, rather than undersampling. This highlights the importance of using representative training data that account for the part of the image formation process that limits the resolution in the sensor data.
Indoor Environment Quality, Design, and the Value of Facility Ecology

Actions Towards Sustainable Outcomes Environmental Issues/Principal Impacts • Poor office Indoor Environment Quality (IEQ) costs tenants in terms of occupant wellbeing, performance and productivity. • Recent overseas research indicates the payback time for improved IEQ in the commercial sector is generally below two years. • The release of new Australian guidelines and rating tools is expected in 2007/8 which will further increase the focus on IEQ in office and public facilities.
Sample compression schemes for VC classes

Sample compression schemes were defined by Littlestone and Warmuth (1986) as an abstraction of the structure underlying many learning algorithms. Roughly speaking, a sample compression scheme of size k means that given an arbitrary list of labeled examples, one can retain only k of them in a way that allows to recover the labels of all other examples in the list. They showed that compression implies PAC learnability for binary-labeled classes, and asked whether the other direction holds. We answer their question and show that every concept class C with VC dimension d has a sample compression scheme of size exponential in d. The proof uses an approximate minimax phenomenon for binary matrices of low VC dimension, which may be of interest in the context of game theory.
Where is the length effect? A cross-linguistic study.

Many models of speech production assume that one cannot begin to articulate a word before all its segmental units are inserted into the articulatory plan. Moreover, some of these models assume that segments are serially inserted from left to right. As a consequence, latencies to name words should increase with word length. In a series of five experiments, however, we showed that the time to name a picture or retrieve a word associated with a symbol is not affected by the length of the word. Experiments 1 and 2 used French materials and participants, while Experiments 3, 4 and 5 were conducted with English materials and participants. These results are discussed in relation to current models of speech production, and previous reports of length effects are reevaluated in light of these findings. We conclude that if words are encoded serially, then articulation can start before an entire phonological word has been encoded.
Vintage Organization Capital

We study 114 years of U.S. stock market data and find That there are large cohort effects in stock prices, effects that we label 'organization capital,' That cohort effects grew at a rate of 1.75% per year, That the debt-equity ratio of all vintages declined, That three big technological waves took place: electricity (1895-1930), a 'World War II' wave (1945-1970), and information technology (1971-), and That organization capital tends to grow fastest during the second half of a technological wave.
Order barriers and characterizations for continuous mono-implicit Runge-Kutta schemes

The mono-implicit Runge-Kutta (MIRK) schemes, a subset of the family of implicit Runge-Kutta (IRK) schemes, were originally proposed for the numerical solution of initial value ODEs more than fifteen years ago. Dur- ing the last decade, a considerable amount of attention has been given to the use of these schemes in the numerical solution of boundary value ODE prob- lems, where their efficient implementation suggests that they may provide a worthwhile alternative to the widely used collocation schemes. Recent work in this area has seen the development of some software packages for bound- ary value ODEs based on these schemes. Unfortunately, these schemes lead to algorithms which provide only a discrete solution approximation at a set of mesh points over the problem interval, while the collocation schemes provide a natural continuous solution approximation. The availability of a continuous solution is important not only to the user of the software but also within the code itself, for example, in estimation of errors, defect control, mesh selection, and the provision of initial solution estimates for new meshes. An approach for the construction of a continuous solution approximation based on the MIRK schemes is suggested by recent work in the area of continuous extensions for explicit Runge-Kutta schemes for initial value ODEs. In this paper, we describe our work in the investigation of continuous versions of the MIRK schemes: (i) we give some lower bounds relating the stage order to the minimal number of stages for general continuous IRK schemes, (ii) we establish lower bounds on the number of stages needed to derive continuous MIRK schemes of orders 1 through 6, and (iii) we provide characterizations of these schemes having a minimal number of stages for each of these orders.
Expression and Contribution of Three Different Isoforms of Prostaglandin E Synthase in the Bovine Endometrium1

Abstract Prostaglandins are involved in the regulation of several reproductive processes such as ovulation, luteolysis, and establishment of pregnancy. Prostaglandin E2 (PGE2) appears to favor establishment of pregnancy in most mammals studied so far. The primary enzymes involved in the production of PGE2 from arachidonic acid are cyclooxygenases and prostaglandin E synthases (PGES). Three PGES have been identified in humans, but in the bovine, microsomal PGES2 and cytosolic PGES genes have neither been cloned nor associated to any physiological processes. The present study was undertaken to clone bovine MPGES2 and CPGES and to report on their regulation in the endometrium during the estrous cycle. CPGES mRNA expression declines progressively during the cycle; its protein is not modulated according to a precise pattern. MPGES2 mRNA and protein expression decrease from the beginning of the cycle until Days 13–15 and then increase until ovulation. Immunohistochemical analysis reveals that both enzymes are located in luminal epithelial and glandular epithelial cells and at a lower level in stromal cells. In addition, using the bovine endometrial cell line BEND, where higher accumulation of PGE2 is observed following treatment with phorbol 12-myristate 13-actetate (PMA) and tumor necrosis factor-α (TNF-α), we have found an associated increase of MPGES1 and COX2 but not CPGES or MPGES2 protein expression. Together, our results suggest that MPGES1 is not the only PGES present in the bovine endometrium but is the main enzyme associated with increased PGE2 production in vitro.
MDCT appearance of gastrointestinal stromal tumors after therapy with imatinib mesylate.

OBJECTIVE Our objective was to determine the MDCT appearance of gastrointestinal stromal tumors (GISTs) after treatment with imatinib mesylate. CONCLUSION Cystic changes within primary and metastatic GISTs seen on MDCT in patients after imatinib mesylate therapy are evidence of disease response. Calcification may also occur in lesions that respond to therapy.
Brief Report: Identification of MTMR3 as a Novel Susceptibility Gene for Lupus Nephritis in Northern Han Chinese by Shared‐Gene Analysis With IgA Nephropathy

Several novel susceptibility genes for systemic lupus erythematosus (SLE) and IgA nephropathy have been identified in recent genome‐wide association studies. Since both lupus nephritis and IgA nephropathy are autoimmune diseases of the kidney, they may share common disease mechanisms that overlap with genetic susceptibility. To test this hypothesis, we sought to identify genetic variants associated with IgA nephropathy in lupus nephritis.
Health and Masculinities Shaped by Agency within Structures among Young Unemployed Men in a Northern Swedish Context

Aim The aim of our paper was to explore expressions of life choices and life chances (aspects of agency within structures) related to power and experiences of health among early unemployed adolescent young men during the transition period to adulthood. These expressions of agency within structure were interpreted in the light of Cockerham’s Health Lifestyles Theory. Furthermore, social constructions of masculinities were addressed in our analysis. Methods Repeated interviews with ten young men in a cohort of school leavers were analyzed with qualitative content analysis. Results and Discussion Cockerham’s model was useful for interpreting our findings and we found disposition to act to be a crucial theoretical tool to capture the will and intentions of participants in relation to health. We developed the model in the following ways: structure and socialization were visualized as surrounding the whole model. Analyses of what enhances or restricts power are important. In addition to practices of health lifestyles, we added experiences of health as outcome as well as emotional aspects in disposition to act. We interpret our findings as constructions of masculinities within certain structures, in relation to choices, habitus and practices. Conclusions Qualitative research could contribute to develop the understanding of the agency within structure relationships. Future studies need to pay attention to experiences of health among young people at the margin of the labor market in various milieus – and to analyze these in relation to gender constructions and within the frame-work of agency within structure.
Neural Circuits Original Research Article a Model Combining Oscillations and Attractor Dynamics for Generation of Grid Cell Firing

Different models have been able to account for different features of the data on grid cell firing properties, including the relationship of grid cells to cellular properties and network oscillations. This paper describes a model that combines elements of two major classes of models of grid cells: models using interactions of oscillations and models using attrac-tor dynamics. This model includes a population of units with oscillatory input representing input from the medial septum. These units are termed heading angle cells because their connectivity depends upon heading angle in the environment as well as the spatial phase coded by the cell. These cells project to a population of grid cells. The sum of the heading angle input results in standing waves of circularly symmetric input to the grid cell population. Feedback from the grid cell population increases the activity of subsets of the heading angle cells, resulting in the network settling into activity patterns that resemble the patterns of firing fields in a population of grid cells. The properties of heading angle cells firing as conjunctive grid-by-head-direction cells can shift the grid cell firing according to movement velocity. The pattern of interaction of oscillations requires use of separate populations that fire on alternate cycles of the net theta rhythmic input to grid cells.