Miracle-dz/UniFAR-FTUs huggingface dataset:
Sex‐biased transcriptome divergence along a latitudinal gradient

Sex‐dependent gene expression is likely an important genomic mechanism that allows sex‐specific adaptation to environmental changes. Among Drosophila species, sex‐biased genes display remarkably consistent evolutionary patterns; male‐biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex‐biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex‐specific selection and the evolution of sex‐biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male‐biased genes, there was no overrepresentation of X‐linked genes in males. By contrast, X‐linked divergence was elevated in females, especially for female‐biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro‐ and micro‐ecological spatial scales.
Performance and Optimization of Cooperative Diversity Systems in Generic Noise and Interference 1

Cooperative diversity systems have received significant attention recently as a distributed means of exploiting the inherent spatial diversity of wireless networks. In this paper, we consider a cooperative diversity system consisting of a source, a destination, and multiple single–hop amplify–and–forward relays, and provide a mathematical framework for the asymptotic analysis of this system in generic noise and interference for high signal–to–noise ratios. Assuming independent Rayleigh fading for all links in the network, we obtain simple and elegant closed–form expressions for the asymptotic symbol and bit error rates valid for arbitrary linear modulation formats, arbitrary numbers of relays, and arbitrary types of noise and interference with finite moments including co–channel interference, ultra–wideband interference, impulsive ǫ–mixture noise, generalized Gaussian noise, and Gaussian noise. Furthermore, we exploit the derived analytical error rate expressions to develop power allocation, relay selection, and relay placement schemes that are optimal in environments with generic noise and interference. Simulation results confirm our analysis and illustrate that, in non–Gaussian noise, the proposed power allocation, relay selection, and relay placement schemes lead to large performance gains compared to their conventional counterparts optimized for Gaussian noise.
Growth Determinants of Micro-businesses in Canada Acknowledgments We Thank

for providing very helpful comments and suggestions on earlier drafts of this paper. We also thank David Halabisky for his timely research assistance in the later phase of the project and Patricia Normandeau for her invaluable help with editing. We are indebted to the members of the Small Business Research Advisory Committee, and in particular, Mallet, Don Rumball and Ron Trépanier for providing very useful insights from the outset of this project, including the design of the survey on which this study is based. Any errors in this paper are the sole responsibility of the authors and any opinions expressed are those of the authors and not necessarily those of Industry Canada.
Functional Characterization of a Lipoprotein-Encoding Operon in Campylobacter jejuni

Background Bacterial lipoproteins have important functions in bacterial pathogenesis and physiology. In Campylobacter jejuni, a major foodborne pathogen causing gastroenteritis in humans, the majority of lipoproteins have not been functionally characterized. Previously, we showed by DNA microarray that CmeR, a transcriptional regulator repressing the expression of the multidrug efflux pump CmeABC, modulates the expression of a three-gene operon (cj0089, cj0090, and cj0091) encoding a cluster of lipoproteins in C. jejuni. Methodology/Principal Findings In this work, we characterized the function and regulation of the cj0089-cj0090-cj0091 operon. In contrast to the repression of cmeABC, CmeR activates the expression of the lipoprotein genes and the regulation is confirmed by immunoblotting using anti-Cj0089 and anti-Cj0091 antibodies. Gel mobility shift assay showed that CmeR directly binds to the promoter of the lipoprotein operon, but the binding is much weaker compared with the promoter of cmeABC. Analysis of different cellular fractions indicated that Cj0089 was associated with the inner membrane, while Cj0091 was located on the outer membrane. Inactivation of cj0091, but not cj0089, significantly reduced the adherence of C. jejuni to INT 407 cells in vitro, indicating that Cj0091 has a function in adherence. When inoculated into chickens, the Cj0091 mutant also showed a defect in early colonization of the intestinal tract, suggesting that Cj0091 contributes to Campylobacter colonization in vivo. It was also shown that Cj0091 was produced and immunogenic in chickens that were naturally infected by C. jejuni. Conclusion/Significance These results indicate that the lipoprotein operon is subject to direct regulation by CmeR and that Cj0091 functions as an adhesion mechanism in C. jejuni and contributes to Campylobacter colonization of the intestinal tract in animal hosts.
Optimizing topology in Bit Torrent based networks

In this paper, we discuss the importance of the network connectivities of the peers in Bit Torrent based systems in determining the download performance of the peers. In this context, assuming that the fraction of the peers of each bandwidth are known, we derive optimal connectivities of the peers that help to improve the average latency of the peers. We represent the topology of a Bit Torrent based system as a weighted graph, where the average edge weight of the graph directly relates to the download latency of the peers. We formulate the average edge weight of the whole system as a linear function of the fraction of the edges that connect peers of different bandwidth and derive the topology that maximizes the average edge weight of the network. Simulation results based on the Bit Torrent protocol validates the fact that in the optimal topology, peers have 13% better download latency as compared to topologies formed in the normal Bit Torrent based systems. Further the obtained topology also improves the fairness of the system as compared to normal Bit Torrent significantly.
Abusive interactions with embodied agents

Numerous research groups around the world are attempting to build realistic and believable autonomous embodied agents that attempt to have natural interactions with users. Research into these entities has primarily focused on their potential to enhance human–computer interaction. As a result, there is little understanding of the potential for embodied entities to abuse and manipulate users for questionable purposes. We highlight the potential opportunities for abuse when interacting with embodied agents in virtual worlds and discuss how our social interactions with such entities can contribute to abusive behaviour. Suggestions for reducing such risks are also provided, along with suggestions for important future research areas.
Physical Activities and Playful Learning Using Mobile Games

The combination of informal learning and mobile outdoor games can be seen as a relevant arena for conducting novel learning activities that involve children in different tasks including physical motion, problem solving, inquiry and collaboration. These are activities that support different cognitive and social aspects of learning. Co-design and human centric design practices have been the focus of current research efforts in the field of educational technologies but not as prevalent in mobile games to support learning. In our current research we are exploring which design methods are appropriate for developing innovative ways of learning supported by mobile games. This paper presents all those aspects related to the design and implementation of a mobile game called Skattjakt (Treasure Hunt in Swedish). The outcome of our activities has provided us with valuable results that can help additionally to integrate outside informal learning with more formal classroom activities. Moreover, we believe that involvi.
A system for the delivery of interactive television programming

Interactive television is a technology for delivering television programming on demand to households and businesses. Rather than passively choosing from a predetermined set of programs at scheduled times, the viewer can request programming to be delivered to him individually on demand. This paper describes a system being developed by IBM that is in active use at customer trials. The system supports movies on demand as well as more interactive applications such as home shopping. This system as deployed today on IBM's RS/6000 series of computers supports in the hundreds of viewers, but running on the SP-2 supercomputer and its follow-ons, the system can be scaled to support thousands of interactive viewers.
Sensor correction and radiometric calibration of a 6-band multispectral imaging sensor for UAV remote sensing

Abstract. The increased availability of unmanned aerial vehicles (UAVs) has resulted in their frequent adoption for a growing range of remote sensing tasks which include precision agriculture, vegetation surveying and fine-scale topographic mapping. The development and utilisation of UAV platforms requires broad technical skills covering the three major facets of remote sensing: data acquisition, data post-processing, and image analysis. In this study, UAV image data acquired by a miniature 6-band multispectral imaging sensor was corrected and calibrated using practical image-based data post-processing techniques. Data correction techniques included dark offset subtraction to reduce sensor noise, flat-field derived per-pixel look-up-tables to correct vignetting, and implementation of the Brown- Conrady model to correct lens distortion. Radiometric calibration was conducted with an image-based empirical line model using pseudo-invariant features (PIFs). Sensor corrections and radiometric calibration improve the quality of the data, aiding quantitative analysis and generating consistency with other calibrated datasets.
Personality Traits, Emotional Intelligence, and Multiple Happiness

This study set out to re-examine the predictors of self-reported trait happiness as measured by the Oxford Happiness Inventory (OHI) as well as the predictors of various happiness types proposed by Morris (2004). In all, 120 Cypriot participants completed the 4 questionnaires: OHI, Eysenck Personality Questionnaire (EPQ), Trait Emotional Intelligence Questionnaire (TEIQue-SF), and Morris Multiple Happiness Inventory (MMHI). It was hypothesized that Extraversion and Neuroticism would be, respectively, positively and negatively correlated with happiness and trait EI would be a positive predictor of happiness. Considering Morris' happiness types, it was hypothesized that specific individual difference variables (Extraversion, trait EI, religiousness, Neuroticism) would be predictive of different happiness conditions or motivations (Sensation seeking, Interpersonal happiness, Spiritual happiness and Negative happiness) respectively. All but one hypothesis was confirmed: Neuroticism was not a significant predictor of Negative happiness. This study demonstrated that high trait EI and extraversion are predictive of overall happiness and most happiness types proposed by Morris, although other factors, like religiousness, are also important. Implications for increasing well-being are discussed. © NAJP.
Monetary Policy and the Cyclicality of Risk

We use a DSGE model that generates endogenous movements in risk premia to examine the positive and normative implications of alternative monetary policy rules. As emphasized by the microfinance literature, variation in risk arises because households face fixed costs of transferring cash across financial accounts, implying that some households rebalance their portfolios infrequently. We show that the model can account for the mean returns on equity and the risk-free rate, and in line with empirical evidence generates a decline in the equity premium following an unanticipated easing of monetary policy. An important result that emerges from our analysis is that countercyclical monetary policy generates higher average welfare than constant money growth or zero inflation policies.
Comprehensive Analysis to Improve the Validation Rate for Single Nucleotide Variants Detected by Next-Generation Sequencing

Next-generation sequencing (NGS) has enabled the high-throughput discovery of germline and somatic mutations. However, NGS-based variant detection is still prone to errors, resulting in inaccurate variant calls. Here, we categorized the variants detected by NGS according to total read depth (TD) and SNP quality (SNPQ), and performed Sanger sequencing with 348 selected non-synonymous single nucleotide variants (SNVs) for validation. Using the SAMtools and GATK algorithms, the validation rate was positively correlated with SNPQ but showed no correlation with TD. In addition, common variants called by both programs had a higher validation rate than caller-specific variants. We further examined several parameters to improve the validation rate, and found that strand bias (SB) was a key parameter. SB in NGS data showed a strong difference between the variants passing validation and those that failed validation, showing a validation rate of more than 92% (filtering cutoff value: alternate allele forward [AF]≥20 and AF<80 in SAMtools, SB<–10 in GATK). Moreover, the validation rate increased significantly (up to 97–99%) when the variant was filtered together with the suggested values of mapping quality (MQ), SNPQ and SB. This detailed and systematic study provides comprehensive recommendations for improving validation rates, saving time and lowering cost in NGS analyses.
A bare bone attentive semantics for might ∗

This paper introduces a semantic framework in which the meaning of a sentence embodies both its informative and its attentive content. This framework allows for an improved implementation of the analysis of might proposed in Ciardelli, Groenendijk, and Roelofsen (2009), which in turn builds on an idea from Groenendijk, Stokhof, and Veltman (1996). The analysis sheds new light on the way in which might interacts with conjunction, dis-junction, and negation, which is puzzling for the standard modal account of might, as well as its treatment in update semantics. occasion of their upcoming retirement, with deepest respect and gratitude.
The Intelligent Home Testbed

Intelligent environments are an interesting development and research application problem for multi-agent systems. The functional and spatial distribution of tasks naturally lends itself to a multi-agent model and the existence of shared resources creates interactions over which the agents must coordinate. In the UMASS Intelligent Home project we have designed and implemented a set of distributed autonomous home control agents and deployed them in a simulated home environment. Our focus is primarily on resource coordination, though this project has multiple goals and areas of exploration ranging from the intellectual evaluation of the application as a general MAS testbed to the practical evaluation of our agent building and simulation tools.
Does Affirmative Action Reduce Effort Incentives? – A Contest Game Analysis

This paper analyzes the incentive effects of affirmative action in competitive environments modeled as contest games. Competition is between heterogeneous players where heterogeneity might be due to past discrimination. Two policy options are analyzed that tackle the underlying asymmetry: Either it is ignored and the contestants are treated equally, or affirmative action is implemented which compensates discriminated players. It is shown in a simple two-player contest game that a trade-off between affirmative action and high effort exertion does not exist. Instead, the implementation of affirmative action fosters effort incentives. Similar results hold in the n-player contest as well as under imperfect information if the heterogeneity between contestants is moderate.
Molecular Properties, Biology, and Clinical Implications of TT Virus, a Recently Identified Widespread Infectious Agent of Humans

SUMMARY TT virus (TTV) was first described in 1997 by representational difference analysis of sera from non-A to non-G posttransfusion hepatitis patients and hence intensively investigated as a possible addition to the list of hepatitis-inducing viruses. The TTV genome is a covalently closed single-stranded DNA of approximately 3.8 kb with a number of characteristics typical of animal circoviruses, especially the chicken anemia virus. TTV is genetically highly heterogeneous, which has led investigators to group isolates into numerous genotypes and subtypes and has limited the sensitivity of many PCR assays used for virus detection. The most remarkable feature of TTV is the extraordinarily high prevalence of chronic viremia in apparently healthy people, up to nearly 100% in some countries. The original hypothesis that it might be an important cause of cryptogenic hepatitis has not been borne out, although the possibility that it may produce liver damage under specific circumstances has not been excluded. The virus has not yet been etiologically linked to any other human disease. Thus, TTV should be considered an orphan virus.
4-Hydroxyisoleucine improves insulin resistance in HepG2 cells by decreasing TNF-α and regulating the expression of insulin signal transduction proteins

Previous studies have indicated that 4-hydroxy-isoleucine (4-HIL) improves insulin resistance, however, the underlying mechanisms remain to be elucidated. In the present study, the molecular mechanisms underlying how 4-HIL improves insulin resistance in hepatocytes were examined. HepG2 cells were co-cultured with insulin and a high glucose concentration to obtain insulin-resistant (IR) HepG2 cells. Insulin sensitivity was determined by measuring the glucose uptake rate. The IR HepG2 cells were treated with different concentrations of 4-HIL to determine its effect on IR Hep2 cells. The levels of tumor necrosis factor-α (TNF-α) were measured by an enzyme-linked immunosorbent assay and protein levels of TNF-α converting enzyme (TACE)/tissue inhibitor of metalloproteinase 3 (TIMP3), insulin receptor substrate (IRS)-1, IRS-2, phosphorylated (p)-IRS-1 (Ser307) and glucose transporter type 4 (GLUT4) were measured by western blot analysis. The results of the present study demonstrated that insulin-induced glucose uptake was reduced in IR HepG2 cells; however, this reduction was reversed by 4-HIL in a dose-dependent manner. 4-HIL achieved this effect by downregulating the expression of TNF-α and TACE, and upregulating the expression of TIMP3 in IR HepG2 cells. In addition, 4-HIL increased the expression of the insulin transduction regulators IRS-1 and GLUT4, and decreased the expression of p-IRS-1 (Ser307), without affecting the expression of IRS-2. The present study suggests that 4-HIL improved insulin resistance in HepG2 cells by the following mechanisms: 4-HIL reduced TNF-α levels by affecting the protein expression of the TACE/TIMP3 system and 4-HIL stimulated the expression of IRS-1 and GLUT4, but inhibited the expression of p-IRS-1 (Ser307).
Aneuploidy Predicts Outcome in Patients with Endometrial Carcinoma and Is Related to Lack of CDH13 Hypermethylation

Purpose: Many investigators have reported that aneuploidy detected by flow cytometry is a useful prognostic marker in patients with endometrial cancer. Laser scanning cytometry (LSC) is a technology similar to flow cytometry but is more feasible for clinical laboratory use. We evaluated the usefulness of DNA ploidy detected by LSC as a prognostic marker in patients with endometrial cancer and investigated genetic and epigenetic factors related to aneuploidy. Experimental Design: Endometrial cancer specimens from 106 patients were evaluated. The methylation status of CDH13, Rassf1, SFRP1, SFRP2, SFRP4, SFRP5, p16, hMLH1, MGMT, APC, ATM, and WIF1 and mutations in the p53 and CDC4 genes were investigated. LSC was carried out to determine DNA ploidy. Fluorescence in situ hybridization was done with chromosome-specific centromeric probes to assess chromosomal instability. Results: Univariate and multivariate analyses revealed that p53 mutation and lack of CDH13 hypermethylation associated positively with aneuploidy. Univariate analysis showed that aneuploidy, chromosomal instability, and lack of CDH13 hypermethylation as well as surgical stage were significantly predictive of death from endometrial cancer. Furthermore, multivariate analysis revealed that stage in combination with either DNA aneuploidy or lack of CDH13 hypermethylation was an independent prognostic factor. Conclusion: These results suggest that analysis of DNA ploidy and methylation status of CDH13 may help predict clinical outcome in patients with endometrial cancer. Prospective randomized trials are needed to confirm the validity of an individualized approach, including determination of tumor ploidy and methylation status of CDH13, to management of endometrial cancer patients.
Effects of Unpaid Overtime : Evidence for West Germany Discussion Papers

Opinions expressed in this paper are those of the author and do not necessarily reflect views of the Institute. Why do people work unpaid overtime? We show that remarkable long-term labor earnings gains are associated with unpaid overtime in West Germany. A descriptive analysis suggests that over a 10-year period workers with unpaid overtime experience on average at least a 10 percentage points higher increase in real labor earnings than their co-workers. Applying panel data models this result generally holds. Furthermore, we find evidence for gender specific differences with respect to the effects of cumulative average unpaid overtime work. Our results point to the importance of investment in current working hours beyond the standard work week to enhance real earnings prospects.