Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient

Identification of loci with adaptive importance is a key step to understand the speciation process in natural populations, because those loci are responsible for phenotypic variation that affects fitness in different environments. We conducted an AFLP genome scan in populations of ocellated lizards (Lacerta lepida) to search for candidate loci influenced by selection along an environmental gradient in the Iberian Peninsula. This gradient is strongly influenced by climatic variables, and two subspecies can be recognized at the opposite extremes: L. lepida iberica in the northwest and L. lepida nevadensis in the southeast. Both subspecies show substantial morphological differences that may be involved in their local adaptation to the climatic extremes. To investigate how the use of a particular outlier detection method can influence the results, a frequentist method, DFDIST, and a Bayesian method, BayeScan, were used to search for outliers influenced by selection. Additionally, the spatial analysis method was used to test for associations of AFLP marker band frequencies with 54 climatic variables by logistic regression. Results obtained with each method highlight differences in their sensitivity. DFDIST and BayeScan detected a similar proportion of outliers (3–4%), but only a few loci were simultaneously detected by both methods. Several loci detected as outliers were also associated with temperature, insolation or precipitation according to spatial analysis method. These results are in accordance with reported data in the literature about morphological and life‐history variation of L. lepida subspecies along the environmental gradient.
Ketosynthase domain probes identify two subclasses of fungal polyketide synthase genes.

Analysis of fungal polyketide synthase gene sequences suggested that these might be divided into two subclasses, designated WA-type and MSAS-type. Two pairs of degenerate PCR primers (LC1 and LC2c, LC3 and LC5c) were designed for the amplification of ketosynthase domain fragments from fungal PKS genes in each of these subclasses. Both primer pairs were shown to amplify one or more PCR products from the genomes of a range of ascomycetous Deuteromycetes and Southern blot analysis confirmed that the products obtained with each pair of primers emanated from distinct genomic loci. PCR products obtained from Penicillium patulum and Aspergillus parasiticus with the LC1/2c primer pair and from Phoma sp. C2932 with both primer pairs were cloned and sequenced; the deduced protein sequences were highly homologous to the ketosynthase domains of other fungal PKS genes. Genes from which LC1/2c fragments were amplified (WA-type) were shown by a phylogenetic analysis to be closely related to fungal PKS genes involved in pigment and aflatoxin biosynthetic pathways, whereas the gene from which the LC3/5c fragment was amplified (MSAS-type) was shown to be closely related to genes encoding 6-methylsalicylic acid synthase (MSAS). The phylogenetic tree strongly supported the division of fungal PKS genes into two subclasses. The LC-series primers may be useful molecular tools to facilitate the cloning of novel fungal polyketide synthase genes.
Stimulus‐Dependent Neuronal Oscillations in Cat Visual Cortex: Inter‐Columnar Interaction as Determined by Cross‐Correlation Analysis

We have demonstrated previously that neurons in cat striate cortex, in response to their preferred stimuli, exhibit oscillatory responses in a frequency range of 40–60 Hz. Recently, we obtained evidence that such oscillatory responses can synchronize across columns. We have now performed an extensive analysis of this phenomenon for both unit and field potential responses. In addition, we studied the stimulus conditions leading to intercolumnar synchronization. We recorded both multi‐unit activity and local field potentials from area 17 of adult cats with arrays of several electrodes. Interelectrode distances ranged from 0.4 to 12 mm. For all pairs of unit (n = 200) and field potential (n = 174) recordings, we computed auto‐ and cross‐correlation functions. The modulation of the correlograms was quantified by fitting a damped sine wave (Gabor) function to the data. Cross‐correlation analysis of the unit data revealed that in 90 out of 200 cases the recorded cells established a constant phase‐relationship of their oscillatory responses. This occurred, on average, with no phase difference. If the receptive fields were nonoverlapping, we observed a synchronization primarily between cells with similar orientation preferences. Cells with overlapping receptive fields also showed a high incidence of synchronization if their orientation preferences were different. In this latter group, synchronization occurred even in cases where the stimulus was optimal for only one of the recording sites. Under conditions of monocular instead of binocular stimulation the oscillatory modulation of the responses was attenuated, but the cross‐correlogram still indicated a significant interaction. Similar effects were seen with the application of stationary instead of moving stimuli. A synchronization of oscillatory field potential responses was observed in 136 out of 174 paired recordings. At all distances investigated, the probability of synchronization of field potential responses was independent of the orientation preferences of the cells. However, the strength of interaction decreased with increasing spatial separation. Control experiments showed that the synchronization of field potential responses was not due to volume conduction. The results demonstrate that oscillatory responses at separate cortical sites can transiently synchronize. The probability and strength of synchronization are dependent on the spatial separation of the recorded cells and their orientation preferences. In addition, the cross‐columnar synchronization is influenced by features of the visual stimulus. It is suggested that this synchronization provides a mechanism for the formation of neuronal assemblies in the visual cortex.
Kinetics of inorganic phosphate release during the interaction of p21ras with the GTPase-activating proteins, p120-GAP and neurofibromin.

The rate of GTP hydrolysis on p21ras is accelerated by approximately 10(5) times by the catalytic domains of GTPase-activating proteins (GAPs), p120-GAP (GAP-344) or neurofibromin (NF1-334). The kinetic mechanism of this activation has been investigated by following the release of inorganic phosphate (Pi), using a fluorescent probe that is sensitive to Pi [Brune, M. , Hunter, J., Corrie, J. E. T. , & Webb, M. R. (1994) Biochemistry 33, 8262-8271]. Measurements were made in real time with a stopped-flow apparatus, in which the p21ras complex with the 2',3'-methanthraniloyl analogue of GTP (mantGTP) was mixed with the GAP in the presence of this Pi probe. The results show that Pi release is fast and that the overall hydrolysis is controlled by the cleavage itself or a conformational change preceding the cleavage. The time courses were single exponentials over a range of [GAP-344] and were modeled to show that a single step controlled Pi release. The maximum rate constant was 15 s-1 (all data at 30 degrees C, pH 7.6, low ionic strength) in experiments in which GAP-344 underwent a single turnover, compared with 5 s-1 for multiple-turnover experiments, and possible causes of this discrepancy were investigated and discussed. With NF1-334 the time courses were more complex, showing a lag prior to rapid release of Pi. The results were consistent with a Kd of 0.04 microM for NF1-344 affinity is some 3 orders of magnitude tighter than that of GAP-344. (ABSTRACT TRUNCATED AT 250 WORDS)
Associations of disordered sleep with body fat distribution, physical activity and diet among overweight middle‐aged men

This cross‐sectional study aimed to investigate whether body fat distribution, physical activity levels and dietary intakes are associated with insomnia and/or obstructive sleep apnea among overweight middle‐aged men. Participants were 211 Finnish men aged 30–65 years. Among the 163 overweight or obese participants, 40 had insomnia only, 23 had obstructive sleep apnea only, 24 had comorbid insomnia and obstructive sleep apnea and 76 were without sleep disorder. The remaining 48 participants had normal weight without sleep disorder. Fat mass, levels of physical activity and diet were assessed by dual‐energy X‐ray densitometry, physical activity questionnaire and 3‐day food diary, respectively. Among the overweight participants, we found that: (i) groups with sleep disorders had higher fat mass in trunk and android regions than the group without sleep disorder (P = 0.048–0.004); (ii) the insomnia‐only group showed a lower level of leisure‐time physical activity (436.9 versus 986.5 MET min week−1, P = 0.009) and higher intake of saturated fatty acids (14.8 versus 12.7 E%, P = 0.011) than the group without sleep disorder; and (iii) the comorbid group had a lower level of leisure‐time physical activity (344.4 versus 986.5 MET min week−1, P = 0.007) and lower folate intake (118.9 versus 152.1 μg, P = 0.002) than the group without sleep disorder, which were independent of body mass index. The results suggest that central obesity is associated with insomnia and/or obstructive sleep apnea. In addition, low levels of leisure‐time physical activity and poor dietary intakes are related to insomnia or comorbid insomnia and obstructive sleep apnea among overweight men.
Mathematical Modeling of Regulation of Type III Secretion System in Salmonella enterica Serovar Typhimurium by SirA

Salmonella enterica serovar Typhimurium invades the intestinal epithelial cells using type three secretion system (TTSS) encoded on Salmonella pathogenicity island-1 (SPI-1). The key regulator of this secretion system is HilA, which is in turn regulated by HilD, HilC and RtsA. It is also known that SirA/BarA system, a two-component regulatory system plays a crucial role in regulating HilA. There are two different mechanisms that have been proposed earlier for regulation of HilD-HilC-RtsA-HilA network by SirA. One considers SirA to be acting through HilA and HilC, whereas the other considers SirA to be acting through HilD. In this paper, we have built mathematical models corresponding to both these scenarios and carried out simulations under different gene knock-out conditions. Additionally, since the two proposed mechanisms based on the experimental data are equally likely, we also considered a mechanism which is a combination of the two proposed mechanisms. The simulations were carried out to check the levels of HilA, the factor regulating the virulence, as well as the levels of the intermediate components in the network, namely HilC and RtsA. The simulation results were used to check the consistency of various models and also to suggest the most probable mechanism of hilA regulation. The results of our study show that while most of the mathematical models are able to predict the virulence data, the models considering SirA to regulate through HilA and HilC fail to predict the levels of intermediate components, HilC and RtsA. Nevertheless, one of the models considering regulation of virulence by SirA via HilD was able to predict results comparable to the experimental data. In addition, combination of this model (regulation by SirA via HilD) with the model considering regulation by SirA through HilA and HilC, also predicted results consistent with experimental observations. Our conclusions were further validated by testing the stability of the results against changes in parameter values, thus confirming the relative robustness of the proposed modeling system.
Identification of a novel mechanism for endotoxin‐mediated down‐modulation of CC chemokine receptor expression

In the present study, we explored the molecular mechanisms by which bacterial endotoxin (LPS) mediates the down‐regulation of CCR2 receptors on human monocytes. We found that LPS induced a marked reduction in CCR2 cell surface protein levels which was blocked by pretreatment with the tyrosine kinase inhibitors genistein and herbimycin A. The effector mechanism underlying LPS‐induced CCR2 down‐modulation appears to involve the enzymatic activity of proteinases since Western blot analysis of LPS‐stimulated monocytes revealed the degradation of a 38‐kDa species corresponding to the CCR2B monomer. In RBL cells expressing the CCR2B‐green fluorescent protein (GFP) fusion chemokine receptor, LPS stimulated the internalization and degradation of CCR2. The serine proteinase inhibitor N‐α‐p‐tosyl‐L‐lysine chloromethyl ketone blocked LPS‐induced down‐modulation of CCR2 in monocytes and CCR2B‐GFP in RBL cells. This work describes a previously uncharacterized mechanism for CC chemokine receptor down‐modulation that is dependent upon tyrosine kinase activation and serine proteinase‐mediated receptor degradation and may provide further insight into the mechanisms of leukocyte regulation during immunological and inflammatory responses.
Open Innovation Success or Failure - The Impact of Contextual Factors

This paper examines the contextual factors that influenced an open innovation project failure. To this end the paper adds to the discussion on open innovation in non high-tech settings and highlights the importance of contextual factors as determinants of success or failure within the open innovation paradigm. It is based on a case study performed at PowerDrive, a manufacturer of hydraulic drive systems, and three of its customers, and follows their attempt to co-create new value-adding services through the innovative use of information technology. The study shows that open innovation project success cannot be measured only in terms of coherence with set targets of quality, time, and costs, but also has to include the creation of mutual value and the development of strong inter-organizational relationships. Furthermore, the role and character of information technology has to be considered and accounted for.
A Framework for Network Function Decomposition and Deployment

Network Function Virtualization (NFV) enables fast provisioning of packet processing logic on general purpose CPUs. This approach, however, does not scale well to very high speed traffic. Programmable hardware solutions, including those based on programmable switches, are emerging as an option for accelerating and scaling network functions. Unfortunately, every type of programmable hardware has specific characteristics that do not make it suitable for running all possible functions. We argue that an efficient strategy is decomposing network functions into components that can run on CPUs or that can be offloaded to specific programmable hardware depending on their characteristics.This paper presents a preliminary work on a framework for automating the decomposition and deployment of network functions. The framework includes an orchestrator that chooses the best decomposition according to the traffic demands, the network topology and other constraints. It also provides a tool to combine multiple functions into a single P4 program that can be deployed to a programmable switch. Finally, the framework comprises a set of tools to deploy the network functions either as containers running in a data center or as programs loaded in a programmable switch.We present numerical results to highlight the advantages of partially offloading decomposed VNFs to programmable hardware over a pure software solution. We also highlight the robustness of the approach showing how the model reacts in case of network failures.
Deriving a Data-Based Interspecies Assessment Factor Using the NOAEL and the Benchmark Dose Approach

In deriving human health-based exposure limits from animal data, differences in sensitivity to a compound between animals and humans must be taken into account. These interspecies differences can be caused by differences in toxicokinetics and or toxicodynamics. Apart from that, species differ in body size, and this is usually accounted for by scaling doses to body weight (i.e., expressed as mg/kg body weight1.0/day). Adefault assessmentfactor (AF) of 10 is commonly applied to this dose metric to account for potential toxicokinetic and toxicodynamic differences. However, both proportional body weight (BW)scalingand the defaultAFas often applied are not directly based on empirical findings. Attempts have been made to derive data-based assessment factors and allometric scaling powers using various toxicological values such as no-observedadverse-effect-levels (NOAELs). In thisstudy both the NOAEL approach and the benchmark dose (BMD) approach are applied to deriveNOAEL ratios and BMD ratios from mouse and rat studies and, based on that information, toestimate an allometric scaling power and an interspecies AF. To account for interspecies differences in body size, our results confirm earlier findings that allometric body weight scaling with a power of around 0.7 is appropriate. The factor needed to rescale the dose in terms of mg/kgBWto the allometric dose scale ranges from around 1.7 (for dogs) to 10(for mice), similar to other findings. The additional factor required for taking into account interspecies toxicokinetic and toxicodynamic differences, when based on the 95th percentile of the relevant ratio distribution, would be 3.1 for a lower Confidence limit of theBMD (BMDL), and 8.3 for a NOAEL (to be applied to the allometrically scaled dose). These results indicate that the generally used defaultAFof 10 may not cover potential interspecies differences, in particular when applied to results from smaller test species. Therefore, using the default AF of 10 could lead to human exposure limits that are insufficiently protective. Further, our results show that a data-based AF that would be needed for interspecies extrapolation is smaller when the point of departure is aBMDLrather than a NOAEL. In the context of a probabilistic hazard characterization, our results indicate that the (geometric) SD of the interspecies AF distribution should be around 2.0 when the BMDL (or BMD uncertainty distribution) is used, and around 3.4 when the NOAEL is used as a point of departure for further risk assessment.
Oncogenes induce senescence with incomplete growth arrest and suppress the DNA damage response in immortalized cells

Activation of the Her2 (ErbB2) oncogene is implicated in the development of breast, ovary and other cancers. Here, we show that expression of NeuT, a mutant‐activated rodent isoform of Her2, in immortalized breast epithelial cells, while promoting senescence‐associated morphological changes, up‐regulation of senescence‐associated β‐galactosidase activity, and accumulation of the cyclin‐dependent kinase inhibitor p21, failed to trigger the major senescence end‐point, i.e. permanent growth arrest. Similar senescence‐associated phenotype with incomplete growth arrest, which we dubbed senescence with incomplete growth arrest (SWING), could also be triggered by the expression of the Ras oncogene. SWING phenotype was stable, and persisted in tumor xenografts established from NeuT‐transduced cells. Furthermore, a significant population of cells in SWING state was found in tumors in the MMTV/NeuT transgenic mouse model. SWING cells showed downregulation of histone H2AX, critical for repair of double‐stranded DNA breaks, and impaired activation of Chk1 kinase. Overall, SWING cells were characterized by increased DNA instability and hypersensitivity to genotoxic stresses. We propose that the SWING state could be a stage in the process of cancer development.
Molecular and phylogenetic analyses of 16 novel simian T cell leukemia virus type 1 from Africa: close relationship of STLV-1 from Allenopithecus nigroviridis to HTLV-1 subtype B strains.

A serological survey searching for antibodies reacting with human T-cell leukemia virus type 1 (HTLV-1) antigens was performed on a series of 263 sera/plasma obtained from 34 monkey species or subspecies, originating from different parts of Africa. Among them, 34 samples exhibited a typical HTLV-1 Western blot pattern. Polymerase chain reaction was performed with three primer sets specific either to HTLV-1/STLV-1 or HTLV-2 and encompassing gag, pol, and tax sequences, on genomic DNA from peripheral blood mononuclear cells of 31 animals. The presence of HTLV-1/simian T-cell leukemia virus type 1 (STLV-1) related viruses was determined in the 21 HTLV-1 seropositive animals tested but not in the 10 HTLV-1 seronegative individuals. Proviral DNA sequences from the complete LTR (750 bp) and a portion of the env gene (522 bp) were determined for 16 new STLV-1 strains; some of them originating from species for which no STLV-1 molecular data were available as Allenopithecus nigroviridis and Cercopithecus nictitans. Comparative and phylogenetic analyses revealed that these 16 new sequences belong to five different molecular groups. The A. nigroviridis STLV-1 strains exhibited a very strong nucleotide similarity with HTLV-1 of the subtype B. Furthermore, four novel STLV-1, found in Cercocebus torquatus, C. m. mona, C. nictitans, and Chlorocebus aethipos, were identical to each other and to a previously described Papio anubis STLV-1 strain (PAN 503) originating from the same primate center in Cameroon. Our data extend the range of the African primates who could be permissive and/or harbor naturally STLV-1 and provide new evidences of cross-transmission of African STLV-1 between different monkey species living in the same environment and also of STLV-1 transmissions from some monkeys to humans in Central Africa.
Timeliness of Share Price Discovery – Does Litigation Improve or Hinder It?

Timeliness of share price discovery is the speed at which value-relevant, private information is released and reflected in a firm‟s share price. As shareholder litigation is a common occurrence in the United States, it could affect the speed at which price discovery occurs. Managers can be personally named in securities class action litigation, and the choice to disclose information to the market will be affected by the fear or experience of shareholder litigation. Will the threat of litigation result in quicker or slower disclosure? Will there be more or less disclosure? If there is a significant effect on disclosure, there will be a direct impact on the timeliness of share price discovery. In addition, my research will look at the effect of certain legal events on timeliness. I hope to find that there is a market-wide effect as a result of significant changes in the legal environment. Any comments are extremely welcome and appreciated. Email address: hsuy02@student.uwa. edu.au
Fusion of Infrared-Visible Images in UE-IoT for Fault Point Detection Based on GAN

In the development of modern intelligent Ubiquitous Electric Internet of Things (UE-IoT), infrared thermal imaging always plays an important role in automated early-warning detection of developing failures of critical assets such as transformers, disconnects and capacity banks in electrical power substation non-intrusively. However, the low resolution and contrast of infrared images hinder the subsequent analysis and recognition of fault points. In contrast, visible images present abundant texture details of the equipment without thermal information. In order to assist the detection of fault points, this paper proposes a Generative adversarial networks (GAN) based infrared and visible image fusion method to produce a composite image with enhanced edges and better quality. The edge loss function is added to represent the perceptual edges. In the discriminator, the proposed method improves the texture similarity between fusion image and visible image by minimizing the Wasserstein distance in VGG (Visual Geometry Group network) feature space. The experimental results show that the fault regions become more salient and the details are enhanced. In this way, it can facilitate the detection of fault points both reliably and accurately.