Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidating Genetic and Environmental Influences on Alcohol-Related Phenotypes

Background: Twin studies demonstrate that measures of alcohol consumption show evidence of genetic influence, suggesting they may be useful in gene identification efforts. The extent to which these phenotypes will be informative in identifying susceptibility genes involved in alcohol dependence depends on the extent to which genetic influences are shared across measures of alcohol consumption and alcohol problems. Previous studies have demonstrated that alcohol consumption reported for the period of heaviest lifetime drinking shows a large degree of genetic overlap with alcohol dependence; however, many studies with genetic material assess current alcohol consumption. Further, there are many different aspects of alcohol consumption that can be assessed (e.g., frequency of use, quantity of use, frequency of intoxication,
RelTextRank: An Open Source Framework for Building Relational Syntactic-Semantic Text Pair Representations

We present a highly-ﬂexible UIMA-based pipeline for developing structural kernel-based systems for relational learning from text, i.e., for generating training and test data for ranking, classifying short text pairs or measuring similarity between pieces of text. For example, the proposed pipeline can represent an input question and answer sentence pairs as syntactic-semantic structures, enriching them with relational information, e.g., links between question class, focus and named entities, and serializes them as training and test ﬁles for the tree kernel-based reranking framework. The pipeline generates a number of dependency and shallow chunk-based representations shown to achieve competitive results in previous work. It also enables easy evaluation of the models thanks to cross-validation facilities.
Equilibrium Computation of the Hart and Mas-Colell Bargaining Model

The 8-th problem raised by [Hart, S. , Mas-Colell, A. , 2010. Bargaining and cooperation in strategic form games. Journal of the European Economics Association 8 (1), 7–33], is solved. To be specific, I show that the set of SP equilibria can be determined by a finite number of systems of linear inequalities, which are efficiently solvable when there are two players. This is more or less surprising because the Hart and Mas-Colell bargaining model and the SP equilibrium both seem to be rather complicated, and it is well known that an arbitrary Nash equilibrium is hard to compute, even when there are only two players. Using this algorithm, it is shown that players of Prisoners’ Dilemma can cooperate to some extent in the Hart and Mas-Colell bargaining, and full cooperation is attainable as ρ, a parameter of this model, approaches to 1. Quantitative efficiency, i.e. price of anarchy, is also analyzed.
A new approach of image inpainting based on PSO algorithm

In this paper, an efficient approach is developed to incorporate the exemplar-based image of inpainting method and the minimum error boundary of cut technique, that is proposed to improve the image inpainting in a more nature quality with high performance. The approach is based on the particle swarm optimization. Several advantages are addressed as follow. First, the image inpainting in texture with the linear structure is exploited to reasonably inpaint the damaged image in a high priority. Due to set the first priority to inpaint in the linear structure, such a method guarantees the integrality of the linear structure. In addition, the minimum error boundary of cut technique can effectively decrease the unnatural phenomena through inpainting the gap of damaged image. Owing to the damaged one will be dawdling extraordinarily if searching the similar block while inpainting. In this case, the method is proposed by joined the particle swarm optimization algorithm, and the outcome indeed improves the efficiency of image inpainting.
Structural requirements for enhancement of T-cell responsiveness by the lymphocyte-specific tyrosine protein kinase p56lck

To understand the mechanism(s) by which p56lck participates in T-cell receptor (TCR) signalling, we have examined the effects of mutations in known regulatory domains of p56lck on the ability of F505 p56lck to enhance the responsiveness of an antigen-specific murine T-cell hybridoma. A mutation of the amino-terminal site of myristylation (glycine 2), which prevents stable association of p56lck with the plasma membrane, completely abolished the ability of F505 p56lck to enhance TCR-induced tyrosine protein phosphorylation. Alteration of the major site of in vitro autophosphorylation, tyrosine 394, to phenylalanine diminished the enhancement of TCR-induced tyrosine protein phosphorylation by F505 p56lck. Such a finding is consistent with the previous demonstration that this site is required for full activation of p56lck by mutation of tyrosine 505. Strikingly, deletion of the noncatalytic Src homology domain 2, but not of the Src homology domain 3, markedly reduced the improvement of TCR-induced tyrosine protein phosphorylation by F505 Lck. Additional studies revealed that all the mutations tested, including deletion of the Src homology 3 region, abrogated the enhancement of antigen-triggered interleukin-2 production by F505 p56lck, thus implying more stringent requirements for augmentation of antigen responsiveness by F505 Lck. Finally, it was also observed that expression of F505 p56lck greatly increased TCR-induced tyrosine phosphorylation of phospholipase C-gamma 1, raising the possibility that phospholipase C-gamma 1 may be a substrate for p56lck in T lymphocytes. Our results indicate that p56lck regulates T-cell antigen receptor signalling through a complex process requiring multiple distinct structural domains of the protein.
Geo-localized messages irradiation using smartphones: An energy consumption analysis

The widespread availability of smartphones with wireless communication and geo-positioning capabilities has open new opportunities to services for casual passersby, e.g. the delivery of advertising when they visit a certain area. Typically such messages are delivered to cellular phones, consuming thus part of the energy of these devices. Since these devices are constrained in battery-energy, disseminating messages using little energy represents a challenge for designers of this type of solutions. This paper presents a study based on simulations that intends to identify good strategies to irradiate messages collaboratively, minimizing the energy consumption in the devices involved in the information exchange. The simulation results show that the best irradiation strategy will depend on the number of devices in the area to be irradiated. Moreover, such a strategy will have more influence if the devices are dispersed. These findings should help designers of mobile collaborative applications based on messages irradiation, to identify the best dissemination strategy depending on the current network context.
Need, demand and missed opportunities for integrated reproductive health–HIV care in Kenya and Swaziland: evidence from household surveys

Objective:Little is known about the need and demand for integrated reproductive health and HIV services at the population level. Design:Descriptive data analysis of household surveys collected by the Integra Initiative. Methods:Household surveys were conducted among 18–49-year-olds in Kenya (N = 1752) and Swaziland (N = 779) in 2009. Data on fertility intentions, contraceptive use, sexual behaviours and HIV testing were used to determine unmet needs. Demand for integrated services was defined as wanting reproductive health services with HIV/sexually transmitted infection (STI) services within one visit. Results:At the population level, family planning needs (90%) were higher than HIV/STI prevention needs: 53% (women) and 75% (men). Fewer had unmet family planning needs through non-use of contraceptives: 17% (women) and 27% (men); versus unmet HIV/STI prevention needs through inconsistent condom use: 48 and 26% of women; 51 and 32% of men in Kenya and Swaziland, respectively. Dual need was higher for men: 64% (Kenya) and 73% (Swaziland) versus women (48%) with more unmet in Kenya (43%) compared to Swaziland (25%). Missed opportunities for integrated service provision were high among women: 49 and 57% with unmet family planning needs; and 55 and 32% with unmet HIV/STI prevention needs in Kenya and Swaziland, respectively, used services, but did not receive the needed service. Most men with unmet needs were non-service users. Approximately a quarter of women wanted and received integrated reproductive health–HIV/STI services in both countries. Conclusions:Demand creation at the community level and provider-initiated integrated service provision are needed, using different strategies for men and women, to address substantial family planning and HIV/STI prevention needs.
Design and evaluation of an adaptive sampling strategy for a wireless air pollution sensor network

We present the design of a novel adaptive sampling technique called Exponential Double Smoothing-based Adaptive Sampling (EDSAS), in which the temporal data correlations provide an indication of the prevailing environmental conditions and are used to adapt the sensing rate of a sensor node. EDSAS uses irregular data series prediction to reduce sampling rate in combination with change detection to maintain data fidelity. The prediction method employs Wright's extension to Holt's method of Exponential Double Sampling (EDS) coupled with a change detection mechanism based on exponentially weighted moving averages (EWMA). The main advantages of EDSAS are that it does not require heavy computation, incurs low memory and communication overhead and the prediction model can be implemented with ease on resource constrained sensor nodes. EDSAS has been evaluated by using real urban road traffic Carbon Monoxide (CO) pollution datasets and has been compared and shown to give better results for performance metrics like sampling fraction and miss ratio. We have also undertaken analysis of the pollution data based on the information received and shown that EDSAS scores over other published technique called e-Sense in capturing the underlying characteristics of the real data.
Fully automatic feature localization for medical images using a global vector concentration approach

In this paper, we propose a novel feature localization method based on a global vector concentration approach. Our approach does not rely on the detection of local salient features around feature points. Instead, we exploit global structural information of the object extracted by calculating the concentration of directional vectors from sampling points. Those vectors are combined with local pattern descriptors of a query image and selected from preliminarily trained extended templates by nearest neighbor search. Due to the insensitivity of local changes, our method can handle partially occluded and noisy objects. We apply the proposed method to fully automatic feature localization of the left ventricular in echocardiograms. The results show the effectiveness of our method in comparison with a conventional edge-based method in terms of accuracy and robustness.
Geometric optimization via composite majorization

Many algorithms on meshes require the minimization of composite objectives, i.e., energies that are compositions of simpler parts. Canonical examples include mesh parameterization and deformation. We propose a second order optimization approach that exploits this composite structure to efficiently converge to a local minimum. Our main observation is that a convex-concave decomposition of the energy constituents is simple and readily available in many cases of practical relevance in graphics. We utilize such convex-concave decompositions to define a tight convex majorizer of the energy, which we employ as a convex second order approximation of the objective function. In contrast to existing approaches that largely use only local convexification, our method is able to take advantage of a more global view on the energy landscape. Our experiments on triangular meshes demonstrate that our approach outperforms the state of the art on standard problems in geometry processing, and potentially provide a unified framework for developing efficient geometric optimization algorithms.
Inflammation and disease duration have a cumulative effect on the risk of dysplasia and carcinoma in IBD: A case–control observational study based on registry data

Patients with long‐standing inflammatory bowel disease (IBD) have an increased risk for colorectal carcinoma (CRC). Earlier studies suggest that the severity of inflammation is an independent risk factor for CRC in ulcerative colitis (UC). We investigated the role of histological inflammation as a risk factor for colorectal dysplasia or CRC to better target dysplasia surveillance in IBD. By combining our hospital patient registry and pathology database between 1996 and 2008, we identified 183 IBD patients with dysplasia or CRC. The control group was collected from our registry of IBD patients. Histological severe inflammation was present in 41.4% of patients with dysplasia and in 24.1% of patients with CRC, but in only 4.3% of controls. Severe inflammation had an odds ratio (OR) of 31.8 [95% confidence interval (CI): 15.6–64.9] for dysplasia or carcinoma compared to patients with no inflammation. Among patients with mild to moderate inflammation, the OR was 2.6 (95% CI: 1.6–4.1). Disease duration increased the annual risk for dysplasia or CRC by 4.5%. Coexisting primary sclerosing cholangitis (PSC) did not elevate the risk, whereas use of thiopurines (OR = 0.09, 95% CI: 0.02–0.33) and also 5‐aminosalicylic acid (OR 0.17, 95% CI: 0.017–1.01) protected against CRC. As conclusion, degree of inflammation and duration of disease cumulatively increase the risk for dysplasia and CRC. PSC was not identified as a risk factor. We demonstrated that use of thiopurines strongly protects against CRC. These results can be applied to better target dysplasia surveillance in IBD patients.
LT3: Sentiment Classification in User-Generated Content Using a Rich Feature Set

This paper describes our contribution to the SemEval-2014 Task 9 on sentiment analysis in Twitter. We participated in both strands of the task, viz. classification at message-level (subtask B), and polarity disambiguation of particular text spans within a message (subtask A). Our experiments with a variety of lexical and syntactic features show that our systems benefit from rich feature sets for sentiment analysis on user-generated content. Our systems ranked ninth among 27 and sixteenth among 50 submissions for task A and B respectively.
Hybridization between Cottus gobio and Cottus poecilopus in the Odra River drainage basin (Czech Republic)

Comparisons of morphology, nuclear gene sequencing and microsatellites were used to identify 19 hybrids between the related species Cottus poecilopus and Cottus gobio in three rivers of the Odra River drainage basin. All hybrids were the results of backcrossing and no F1 generation hybrid was found. The resulting progeny are fertile and continue in backcrossing with parental conspecifics. A high representation of backcrosses appears to indicate a lack of reproduction barriers within the hybridization process. It was impossible to differentiate individual back-cross categories on the sole basis of six loci. Mitochondrial haplotypes indicate that this is not a one-way process. In our study, hybridization was asymmetrical in favour of Cottus poecilopus.
Expression and function of Xenopus laevis p75(NTR) suggest evolution of developmental regulatory mechanisms.

Neurotrophins signal through two different classes of receptors, members of the trk family of receptor tyrosine kinases, and p75 neurotrophin receptor (p75(NTR)), a member of the tumor necrosis factor receptor family. While neurotrophin binding to trks results in, among other things, increased cell survival, p75(NTR) has enigmatically been implicated in promoting both survival and cell death. Which of these two signals p75(NTR) imparts depends on the specific cellular context. Xenopus laevis is an excellent system in which to study p75(NTR) function in vivo because of its amenability to experimental manipulation. We therefore cloned partial cDNAs of two p75(NTR) genes from Xenopus, which we have termed p75(NTR)a and p75(NTR)b. We then cloned two different cDNAs, both of which encompass the full coding region of p75(NTR)a. Early in development both p75(NTR)a and p75(NTR)b are expressed in developing cranial ganglia and presumptive spinal sensory neurons, similar to what is observed in other species. Later, p75(NTR)a expression largely continues to parallel p75(NTR) expression in other species. However, Xenopus p75(NTR)a is additionally expressed in the neuroepithelium of the anterior telencephalon, all layers of the retina including the photoreceptor layer, and functioning axial skeletal muscle. Finally, misexpression of full length p75(NTR) and each of two truncated mutants in developing retina reveal that p75(NTR) probably signals for cell survival in this system. This result contrasts with the reported role of p75(NTR) in developing retinae of other species, and the possible implications of this difference are discussed.
Programming agents as a means of capturing self-strategy

In this paper we report results of an extensive evaluation of people's ability to reproduce the strategies they use in simple real-life settings. Having the ability to reliably capture people's strategies in different environments is highly desirable in Multi-Agent Systems (MAS). However, as trivial and daily as these strategies are, the process is not straightforward and people often have a different belief of how they act. We describe our experiments in this area, based on the participation of a pool of subjects in four different games with variable complexity and characteristics. The main measure used for determining the closeness between the two types of strategies used is the level of similarity between the actions taken by the participants and those taken by agents they programmed in identical world states. Our results indicate that generally people have the ability to reproduce their game strategies for the class of games we consider. However, this process should be handled carefully as some individuals tend to exhibit a behavior different from the one they program into their agents. The paper evaluates one possible method for enhancing the process of strategy reproduction.
Multi-Robot Systems Formation Control with Obstacle Avoidance

Abstract This paper deals with the problem of active target tracking with obstacle avoidance for multi-robot systems. A nonlinear model predictive formation control is presented which uses potential functions as terms of the cost function. These terms penalize the proximity with mates and obstacles, splitting the problem of obstacle avoidance into two repulse functions. Experimental results with real robots are presented to demonstrate the performance of the approach.
jfipa - an Architecture for Agent-based Grid Computing

With the increasing focus on grid development, there is a need for proper abstractions for modelling grid applications. Viewed from a distributed AI perspective the most suitable abstraction is the concept of agents. In this paper an agent-based architecture for grid computing is considered. The architecture enables routing and handling of FIPA ACL messages.
Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae

Microarray studies are capable of providing data for temporal gene expression patterns of thousands of genes simultaneously, comprising rich but cryptic information about transcriptional control. However available methods are still not adequate in extraction of useful information about transcriptional regulation from these data. This study presents a dynamic model of gene expression which allows for identification of transcriptional regulators using time series of gene expression. The algorithm was applied for identification of transcriptional regulators controlling 40 cell cycle regulated genes of Saccharomyces cerevisiae. The presented algorithm uses a dynamic model of time continuous gene expression with the assumption that the target gene expression profile results from the action of the upstream regulator. The goal is to apply the model to putative regulators to estimate the transcription pattern of a target gene using a least squares minimization procedure. The procedure iteratively tests all possible transcription factors and selects those that best approximate the target gene expression profile. Results were compared with independently published data and good agreement between the published and identified transcriptional regulators was found.
SUMOylation of Myc-Family Proteins

Myc-family proteins are key controllers of the metabolic and proliferative status of the cell, and are subjected to a complex network of regulatory events that guarantee their efficient and fast modulation by extracellular stimuli. Hence, unbalances in regulatory mechanisms leading to altered Myc levels or activities are often reported in cancer cells. Here we show that c- and N-Myc are conjugated to SUMO proteins at conserved lysines in their C-terminal domain. No obvious effects of SUMOylation were detected on bulk N-Myc stability or activities, including the regulation of transcription, proliferation or apoptosis. N-Myc SUMOylation could be induced by cellular stresses, such as heat shock and proteasome inhibition, and in all instances concerned a small fraction of the N-Myc protein. We surmise that, as shown for other substrates, SUMOylation may be part of a quality-control mechanism acting on misfolded Myc proteins.
Reconstruction and Regeneration of Corneal Endothelium: A Review on Current Methods and Future Aspects

Corneal transplantation is a popular choice of treatment for many corneal disorders. However, the shortage in availability of donor tissues limits the amount of corneal transplantations around the globe. Continuous increase in the number of patients has boosted the need for clinical grade tissues or a reasonable substitute to overcome this issue. Alternatives include cell, tissue or bio-engineering, cell culture in vitro, the potential use of stem cells or other related therapies. There is a very rapid advancement in the field of endothelial keratoplasty as it has advantages being a less-sutured surgery with quicker rehabilitation and better post operative visual outcomes. Thus, to overcome the necessity of donor tissues for selective keratoplasty, the endothelial reconstruction or regeneration is currently studied. This review highlights recent advances in the isolation, culture, expansion of the corneal endothelium and the use of scaffolds or matrices to facilitate endothelial transplantation.