Miracle-dz/UniFAR-FTUs huggingface dataset:
Miscommunication in an investment game with one-way messages

This paper aims to study the effects of free-form messages (cheap talk) in an investment game as Berg et al. (1995). We guess that messages matter, but they may not affect the outcomes on average because different outcomes of communication can be systematically misunderstood generating different effects that offset each other. Considering a non-binary choice game, where misunderstandings are more likely to be observed, we test our intuition in two steps. First, we classify messages by their contents and then we verify their impact on participants’ behavior accordingly to their kind.
Spatial dynamics and genetics of infectious diseases on heterogeneous landscapes

Explicit spatial analysis of infectious disease processes recognizes that host–pathogen interactions occur in specific locations at specific times and that often the nature, direction, intensity and outcome of these interactions depend upon the particular location and identity of both host and pathogen. Spatial context and geographical landscape contribute to the probability of initial disease establishment, direction and velocity of disease spread, the genetic organization of resistance and susceptibility, and the design of appropriate control and management strategies. In this paper, we review the manner in which the physical organization of the landscape has been shown to influence the population dynamics and spatial genetic structure of host–pathogen interactions, and how we might incorporate landscape architecture into spatially explicit population models of the infectious disease process to increase our ability to predict patterns of disease occurrence and optimally design vaccination and control policies.
Incommensurate antiferromagnetic order in the manifoldly-frustrated SrTb2O4 with transition temperature up to 4.28 K

The Neel temperature of the new frustrated family of SrRE2O4 (RE = rare earth) compounds is yet limited to 0.9 K, which more or less hampers a complete understanding of the magnetic frustrations and spin interactions. Here we report on a new frustrated member to the family, SrTb2O4 with a record TN = 4.28(2) K, and an experimental study of the magnetic interacting and frustrating mechanisms by polarized and unpolarized neutron scattering. The compound of SrTb2O4 displays an incommensurate antiferromagnetic (AFM) order with a transverse wave vector Q = (0.5924(1), 0.0059(1), 0) albeit with partially-ordered moments, 1.92(6) uB at 0.5 K, stemming from only one of the two inequivalent Tb sites by virtue of their different octahedral distortions. The localized moments are confined to the bc plane, 11.9(66) degree away from the b axis by single-ion anisotropy. We reveal that this AFM order is dominated mainly by dipole-dipole interactions and disclose that the octahedral distortion, nearest-neighbour (NN) ferromagnetic (FM) arrangement, different next NN FM and AFM configurations, and in-plane anisotropic spin correlations are vital to the magnetic structure and associated multiple frustrations. The discovery of the thus far highest AFM transition temperature renders SrTb2O4 a new friendly frustrated platform in the family for exploring the nature of magnetic interactions and frustrations.
How does presentation method and measurement protocol affect distance estimation in real and virtual environments?

We conducted two experiments that compared distance perception in real and virtual environments in six visual presentation methods using either timed imagined walking or direct blindfolded walking, while controlling for several other factors that could potentially impact distance perception. Our presentation conditions included unencumbered real world, real world seen through an HMD, virtual world seen through an HMD, augmented reality seen through an HMD, virtual world seen on multiple, large immersive screens, and photo-based presentation of the real world seen on multiple, large immersive screens. We found that there was a similar degree of underestimation of distance in the HMD and large-screen presentations of virtual environments. We also found that while wearing the HMD can cause some degree of distance underestimation, this effect depends on the measurement protocol used. Finally, we found that photo-based presentation did not help to improve distance perception in a large-screen immersive display system. The discussion focuses on points of similarity and difference with previous work on distance estimation in real and virtual environments.
Highly Pathogenic Avian Influenza Virus H5N1 Infects Alveolar Macrophages without Virus Production or Excessive TNF-Alpha Induction

Highly pathogenic avian influenza virus (HPAIV) of the subtype H5N1 causes severe, often fatal pneumonia in humans. The pathogenesis of HPAIV H5N1 infection is not completely understood, although the alveolar macrophage (AM) is thought to play an important role. HPAIV H5N1 infection of macrophages cultured from monocytes leads to high percentages of infection accompanied by virus production and an excessive pro-inflammatory immune response. However, macrophages cultured from monocytes are different from AM, both in phenotype and in response to seasonal influenza virus infection. Consequently, it remains unclear whether the results of studies with macrophages cultured from monocytes are valid for AM. Therefore we infected AM and for comparison macrophages cultured from monocytes with seasonal H3N2 virus, HPAIV H5N1 or pandemic H1N1 virus, and determined the percentage of cells infected, virus production and induction of TNF-alpha, a pro-inflammatory cytokine. In vitro HPAIV H5N1 infection of AM compared to that of macrophages cultured from monocytes resulted in a lower percentage of infected cells (up to 25% vs up to 84%), lower virus production and lower TNF-alpha induction. In vitro infection of AM with H3N2 or H1N1 virus resulted in even lower percentages of infected cells (up to 7%) than with HPAIV H5N1, while virus production and TNF-alpha induction were comparable. In conclusion, this study reveals that macrophages cultured from monocytes are not a good model to study the interaction between AM and these influenza virus strains. Furthermore, the interaction between HPAIV H5N1 and AM could contribute to the pathogenicity of this virus in humans, due to the relative high percentage of infected cells rather than virus production or an excessive TNF-alpha induction.
Classical and Novel Prognostic Markers for Breast Cancer and their Clinical Significance

The use of biomarkers ensures breast cancer patients receive optimal treatment. Established biomarkers such as estrogen receptor (ER) and progesterone receptor (PR) have been playing significant roles in the selection and management of patients for endocrine therapy. HER2 is a strong predictor of response to trastuzumab. Recently, the roles of ER as a negative and HER2 as a positive indicator for chemotherapy have been established. Ki67 has traditionally been recognized as a poor prognostic factor, but recent studies suggest that measurement of Ki67-positive cells during treatment will more effectively predict treatment efficacy for both anti-hormonal and chemotherapy. p53 mutations are found in 20–35% of human breast cancers and are associated with aggressive disease with poor clinical outcome when the DNA-binding domain is mutated. The utility of cyclin D1 as a predictor of breast cancer prognosis is controversial, but cyclin D1b overexpression is associated with poor prognosis. Likewise, overexpression of the low molecular weight form of cyclin E1 protein predicts poor prognosis. Breast cancers from BRCA1/2 carriers often show high nuclear grades, negativity to ER/PR/HER2, and p53 mutations, and thus, are associated with poor prognosis. The prognostic values of other molecular markers, such as p14ARF, TBX2/3, VEGF in breast cancer are also discussed. Careful evaluation of these biomarkers with current treatment modality is required to determine whether their measurement or monitoring offer significant clinical benefits.
Cholinergic regulation of neurite outgrowth from isolated chick sympathetic neurons in culture

Neurotransmitters have been reported to regulate neurite outgrowth in several vertebrate and nonvertebrate species. In this study, cultures of isolated embryonic day 12 (E12) chick sympathetic neurons were grown in the presence of cholinergic receptor agonists or antagonists. Both ACh and the nonhydrolyzable cholinergic agonist carbamylcholine (CCh) inhibited neurite outgrowth. ACh (0.1–1.0 mM) decreased the percentage of neurons bearing neurites, but had no significant effect on cell survival. The effect of ACh was increased in the presence of the cholinesterase inhibitors BW284C51 (1 microM), Tacrine (20 microM), and edrophonium (200 microM). Neurite outgrowth was strongly inhibited by the muscarinic receptor agonist oxotremorine (5–100 microM) and weakly inhibited by nicotine (50 nM to 10 microM). The inhibitory effect of CCh was decreased by the muscarinic receptor antagonist atropine (10 microM), demonstrating that the effect of CCh on neurite outgrowth was mediated, at least in part, through a muscarinic receptor. The possibility that AChE can influence neurite outgrowth directly, through a noncatalytic mechanism, was also examined. When dissociated chick brain or sympathetic neurons were grown on plates precoated with purified AChE, neurite outgrowth was strongly stimulated. However, the neurite outgrowth-promoting effect of AChE was strictly dependent upon the presence of substratum-bound heparan sulfate proteoglycans (HSPG). Pretreatment of AChE with diisopropylfluorophosphate to inhibit the esterase activity did not abolish this effect, suggesting that the neurite outgrowth-promoting effect of AChE was associated with a noncatalytic mechanism, a view supported by the observation that soluble AChE had no effect on neurite outgrowth. (ABSTRACT TRUNCATED AT 250 WORDS)
Tractable Nonlinear Capacity Models for Production Planning Part I : Modelling and Formulations

A fundamental problem in developing effective production planning models has been their inability to accurately reflect the nonlinear dependency between workload and lead times. In the first part of this two-part paper we focus on the relationship between capacity, which we interpret as expected throughput, and workload at an aggregate level using nonlinear Clearing Functions to capture the leadtime dynamics accurately in a mathematical programming model for production planning. A partitioning scheme is introduced to allocate capacity across products, capturing the effects of varying product mix. We then present a linear programming formulation based on outer linearization of the nonlinear clearing functions that is able to capture the nonlinear dynamics observed between capacity, lead-time and workload in a tractable manner. The second part of this paper (Asmundsson et al. 2004) provides extensive computational experiments validating the approach and comparing its results to more conventional mod-
The Relationship between Physical Activity and Sleep

The current study aimed to examine the naturalistic relationship between physical activity and sleep by exploring frequency, type, and timing of exercise and their association with a variety of sleep variables (e.g., sleep onset latency, wake after sleep onset, sleep efficiency). Young adults (n = 1003) completed a variety of self-report questionnaires, including a week-long sleep diary and a survey of typical frequency, type, and timing of exercise completed in the past week. Increased frequency of physical activity was related to increased sleep efficiency (total sleep time/time in bed), decreased time in bed, and decreased time spent awake in bed in the morning. Greater amounts of exercise energy expenditure (i.e., metabolic equivalents) per week was related to increased sleep efficiency, and decreased time in bed and time spent awake in bed in the morning. After controlling for other factors, this relationship remained true only for time spent awake in bed in the morning. Early morning exercisers reported shorter total sleep time and time in bed than those who typically exercised at other times. No exercise differences were found between those who met the research diagnostic criteria for insomnia and those who did not. This study provides valuable information to help guide future experimental and intervention studies.
The Influence of Negative Emotions in an Online Brand Community on Customer Innovation Activities

With Web 2.0 increased user participation in diverse e-communities results in prevalence of information, including emotional information. We examined the influence of negative emotion in an online brand community, MyStarbuckIdea.com developed to collect diverse customer ideas for firm's innovation, with the purpose to investigate how such emotion affects customer innovation activities in the community. We first established several hypotheses on the relationships between discrete negative emotions and innovation activities. Then, having collected 84,918 customer ideas, we conducted POS tagging and term-based matching to calculate the inclusion and intensity of negative emotion, using negative emotion lexicon which we developed. As a result of testing hypotheses with regression models, we show that 1) negative emotion significantly affects innovation activities in the brand community and frustration is the most influential among the discrete negative emotions; 2) as the intensity level of negative emotions increases, so does their influence.
A Pilot Study of Parent Mentors for Early Childhood Obesity

Objective. To assess the feasibility of a parent mentor model of intervention for early childhood obesity using positive deviance-based methods to inform the intervention. Methods. In this pilot, randomized clinical trial, parent-child dyads (age: 2–5) with children whose body mass index (BMI) was ≥95th percentile were randomized to parent mentor intervention or community health worker comparison. The child's height and weight were measured at baseline, after the six-month intervention, and six months after the intervention. Feasibility outcomes were recruitment, participation, and retention. The primary clinical outcome was BMI z-score change. Results. Sixty participants were enrolled, and forty-eight completed the six-month intervention. At baseline, the BMI z-score in the parent mentor group was 2.63 (SD = 0.65) and in the community health worker group it was 2.61 (SD = 0.89). For change in BMI z-score over time, there was no difference by randomization group at the end of the intervention: −0.02 (95% CI: −0.26, 0.22). At the end of the intervention, the BMI z-score for the parent mentor group was 2.48 (SD = 0.58) and for the community health worker group it was 2.45 (SD = 0.91), both reduced from baseline, p < 0.001. Conclusion. The model of a parent mentor clinical trial is feasible, and both randomized groups experienced small, sustained effects on adiposity in an obese, Hispanic population.
An acoustic analysis of the vowel space in young and old cochlear-implant speakers

The main purpose of this study was to compare acoustically the vowel spaces of two groups of cochlear implantees (CI) with two age-matched normal hearing groups. Five young test persons (15–25 years) and five older test persons (55–70 years) with CI and two control groups of the same age with normal hearing were recorded. The speech material consisted of five German vowels V = /aː, eː, iː, oː, uː/ in bilabial and alveolar contexts. The results showed no differences between the two groups on Euclidean distances for the first formant frequency. In contrast, Euclidean distances for F2 of the CI group were shorter than those of the control group, causing their overall vowel space to be compressed. The main differences between the groups are interpreted in terms of the extent to which the formants are associated with visual cues to the vowels. Further results were partially longer vowel durations for the CI speakers.
Adaptive Dunnett tests for treatment selection

Clinical trials incorporating treatment selection at pre‐specified interim analyses allow to integrate two clinical studies into a single, confirmatory study. In an adaptive interim analysis, treatment arms are selected based on interim data as well as external information. The specific selection rule does not need to be pre‐specified in advance in order to control the multiple type I error rate. We propose an adaptive Dunnett test procedure based on the conditional error rate of the single‐stage Dunnett test. The adaptive procedure uniformly improves the classical Dunnett test, which is shown to be strictly conservative if treatments are dropped at interim. The adaptive Dunnett test is compared in a simulation with the classical Dunnett test as well as with adaptive combination tests based on the closure principle. The method is illustrated with a real‐data example. Copyright © 2007 John Wiley & Sons, Ltd.
Juru at TREC 2005: Query Prediction in the Terabyte and the Robust Tracks

Our experiments focus this year on the ad-hock tasks of the Terabyte and the Robust tracks. In both tracks we experimented with the query prediction technology we developed recently. In the Terabyte track, we investigated how query prediction can be used to improve federation of search results extracted from several indices. We show that federated search based on query prediction can achieve comparable results to single-index search. In the Robust track we trained a predictor over one collection (TREC-8) for predicting query diculty over another collection (AQUAINT). The experimental results show that dicult
CrossCheck: A Holistic Approach for Tolerating Crash-Faults and Arbitrary Failures

High availability is no longer optional since more and more Internet-based services provide economical or otherwise critical offerings. Traditionally, crash faults are addressed using state-machine replication (SMR) and critical data is selectively protected by checksums. Both techniques can be efficiently combined, however, large parts of a service remain susceptible to transient errors such as bit-flips or more severe state corruptions. To address this weakness and also to reduce the labouring and non-trivial effort of identifying and selectively hardening a complex service, we propose CrossCheck - a holistic approach. CrossCheck extends the crash-fault protection of SMR to also provide tolerance against arbitrary state corruptions, thereby especially addressing multithreaded applications. This is achieved by a fine-grained state comparison and a precise recovery mechanism using fault-free replicas. The implementation utilizes aspectoriented programming and therefore requires only minimal manual changes to the underlying software. In our evaluation, we show that a multithreaded key-value store can be made resilient to crashes and hardened against arbitrary state corruptions with moderate overhead.
Fast Mode Decision Algorithm for Intra prediction in H.264/AVC Video Coding

Summary The new video coding standard, H.264/MPEG-4 AV C, uses an intra prediction mode with 4x4 blocks and 16x16 blocks sizes for luma component and 8x8 blocks size for chroma component. This new feature of H.264/AVC offers a considerably higher improvement in coding efficiency compared to other compression standards. In order to achieve this, a robust Rate-distortion optimization (RDO) technique is employed to select the best coding mode for each block sizes. However, the computational complexity of H.264 encoder is drastically increased due to the various intra prediction modes. In this paper, we propose a fast mode decision algorithm for intra prediction to reduce the complexity of H.264 video coding. The proposed algorithm based the fact that the dominating direction of a smaller block is similar to that of bigger block, the directional correlation of each block is consistent with directions of the edges, and the prediction modes of each block are also correlated with those of neighboring modes. The experimental results show that the fast intra mode decision algorithm is able to reduce on the average 84.68% encoding time, with a negligible peak signal-to noise ratio loss of 0.19dB or, equivalently, a bit rate increment of 1.88%.
The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain‐like thiol protease fold

A Rho GTPase inactivation domain (RID) has been discovered in the multifunctional, autoprocessing RTX toxin RtxA from Vibrio cholerae. The RID domain causes actin depolymerization and rounding of host cells through inactivation of the small Rho GTPases Rho, Rac, and Cdc42. With only a few toxin proteins containing RID domains in the current sequence database, the structure and molecular mechanisms of this domain are unknown. Using comparative sequence and structural analyses, we report homology inference, fold recognition, and active site prediction for RID domains. Remote homologs of RID domains were identified in two other experimentally characterized bacterial virulence factors: IcsB of Shigella flexneri and BopA of Burkholderia pseudomallei, as well as in a group of uncharacterized bacterial membrane proteins. IcsB plays an important role in helping Shigella to evade the host autophagy defense system. RID domain homologs share a conserved diad of cysteine and histidine residues, and are predicted to adopt a circularly permuted papain‐like thiol protease fold. RID domains from MARTX toxins and virulence factors IcsB and BopA thus could function as proteases or acyltransferases acting on host molecules. Our results provide structural and mechanistic insights into several important proteins functioning in bacterial pathogenesis. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Identification of XMRV Infection-Associated microRNAs in Four Cell Types in Culture

Introduction XMRV is a gammaretrovirus that was thought to be associated with prostate cancer (PC) and chronic fatigue syndrome (CFS) in humans until recently. The virus is culturable in various cells of human origin like the lymphocytes, NK cells, neuronal cells, and prostate cell lines. MicroRNAs (miRNA), which regulate gene expression, were so far not identified in cells infected with XMRV in culture. Methods Two prostate cell lines (LNCaP and DU145) and two primary cells, Peripheral Blood Lymphocytes [PBL] and Monocyte-derived Macrophages [MDM] were infected with XMRV. Total mRNA was extracted from mock- and virus-infected cells at 6, 24 and 48 hours post infection and evaluated for microRNA profile in a microarray. Results MicroRNA expression profiles of XMRV-infected continuous prostate cancer cell lines differ from that of virus-infected primary cells (PBL and MDMs). miR-193a-3p and miRPlus-E1245 observed to be specific to XMRV infection in all 4 cell types. While miR-193a-3p levels were down regulated miRPlus-E1245 on the other hand exhibited varied expression profile between the 4 cell types. Discussion The present study clearly demonstrates that cellular microRNAs are expressed during XMRV infection of human cells and this is the first report demonstrating the regulation of miR193a-3p and miRPlus-E1245 during XMRV infection in four different human cell types.