Miracle-dz/UniFAR-FTUs huggingface dataset:
Subspecialization of Cxcr5+ T Cells

The T helper (Th) cell pool is composed of specialized cells with heterogeneous effector functions. Apart from Th1 and 2 cells, CXCR5+ T cells have been suggested to be another type of effector T cell specialized for B cell help. We show here that CXCR5+ T cells are heterogeneous, and we identify subsets of CXCR5+ CD4 T cells that differ in function and microenvironmental localization in secondary lymphoid tissues. CD57+CXCR5 T cells, hereafter termed germinal center Th (GC-Th) cells, are localized only in GCs, lack CCR7, and are highly responsive to the follicular chemokine B lymphocyte chemoattractant but not to the T cell zone EBI1-ligand chemokine. Importantly, GC-Th cells are much more efficient than CD57−CXCR5+ T cells or CXCR5− T cells in inducing antibody production from B cells. Consistent with their function, GC-Th cells produce elevated levels of interleukin 10 upon stimulation which, with other cytokines and costimulatory molecules, may help confer their B cell helper activity. Our results demonstrate that CXCR5+ T cells are functionally heterogeneous and that the GC-Th cells, a small subset of CXCR5+ T cells, are the key helpers for B cell differentiation and antibody production in lymphoid tissues.
Molecular Characterization of the Epstein-Barr Virus BGLF2 Gene, its Expression, and Subcellular Localization

Background Epstein–Barr virus (EBV) is a universal herpes virus which can cause a life-long and largely asymptomatic infection in the human population. However, the exact pathogenesis of the EBV infection is not well known. Objective A comprehensive bioinformatics prediction was carried out for investigating the molecular properties of the BGLF2 and to afford a foundation for future research of the role and instrument of BGLF2 in the course of EBV infection. Materials and Methods A 1011-base-pair sequence of BGLF2 gene from the Epstein-Barr virus (EBV) Akata strain genome was amplified using polymerase chain reaction and was further characterized by cloning, sequencing, and subcellular localization in the COS-7 cells. Results The bioinformatics analysis demonstrated that EBV BGLF2 gene encodes a putative BGLF2 polypeptide which contains a conservative Herpes_UL16 domain. It was established that the polypeptide shows a close relationship with the Herpes UL16 tegument protein family and is extremely conserved among its homologues proteins encoded by UL16 genes. Multiple sequence alignments of the nucleic acid and amino acid sequence showed that the gene product of EBV BGLF2 contains a comparatively higher homology with the BGLF2-like proteins of the subfamily Gammaherpesvirinae than that of other subfamilies of the herpes virus. Moreover, the phylogenetic analyses suggested that EBV BGLF2 has a close genetic relationship with the member of Gammaherpesvirinae; in particular with the members of Cercopithecine herpesvirus 15 and Callitrichine herpesvirus 3. An antigen epitope analysis indicated that BGLF2 contains several potential B-cell epitopes. In addition, the secondary structure, as well as the three dimensional structure prediction suggests that BGLF2 consists of the both α-helix and β-strand. Besides, the subcellular localization prediction revealed that BGLF2 localizes in both nucleus and cytoplasm. Conclusions Illustrating the relevance of the molecular properties and genetic evolution of EBV, BGLF2 will offer the perspectives for further study on the role and mechanism of the BGLF2 in course of EBV infection. These works will also conduct our understanding of the EBV at the molecular level as well as enriching the herpesvirus database.
Factorial Design Analysis for Quality of Video on MANET

The quality of video transmitted by mobile ad hoc networks (MANETs) can be influenced by several factors, including protocol layers; parameter settings of each protocol. In this paper, we are concerned with understanding the functional relationship between these influential factors and objective video quality in MANETs. We illustrate a systematic statistical design of experiments (DOE) strategy can be used to analyze MANET parameters and performance. Using a factorial design, we quantify the main and interactive effects of 7 factors on a response metric (i.e., mean opinion score (MOS) calculated by PSNR with Evalvid package) we then develop a first-order linear regression model between the influential factors and the performance metric. Keywords—Evalvid, full factorial design, mobile ad hoc networks, ns-2.
Xe irradiation of graphene on Ir(111): From trapping to blistering

Using x-ray photoelectron spectroscopy, thermal desorption spectroscopy, and scanning tunneling microscopy, we show that upon keV Xe+ irradiation of graphene on Ir(111), Xe atoms are trapped under the graphene. Upon annealing, aggregation of Xe leads to graphene bulges and blisters. The efficient trapping is an unexpected and remarkable phenomenon given the absence of chemical binding of Xe to Ir and to graphene, the weak interaction of a perfect graphene layer with Ir(111), as well as the substantial damage to graphene due to irradiation. By combining molecular dynamics simulations and density functional theory calculations with our experiments, we uncover the mechanism of trapping. We describe ways to avoid blister formation during graphene growth, and also demonstrate how ion implantation can be used to intentionally create blisters without introducing damage to the graphene layer. Our approach may provide a pathway to synthesize new materials at a substrate-2D material interface or to enable confined reactions at high pressures and temperatures. (Less)
A Low-Overhead Non-Block Check Pointing and Recovery Approach for Mobile Computing Environment

Check pointing/rollback-recovery strategy is used for providing fault-tolerance to distributed applications (Y.M. Wang, 1997; M. Singhal & N. G. Shivaratri, 1994; R. E. Strom and S. Yemini 1985; R. Koo & S. Toueg, 1987; S. Venkatesan et al.,1997; G. Cao & M. Singhal, 1998; D. Manivannan & M. Singhal, 1999). A checkpoint is a snapshot of the local state of a process, saved on local nonvolatile storage to survive process failures. A global checkpoint of an n-process distributed system consists of n checkpoints (local) such that each of these n checkpoints corresponds uniquely to one of the n processes. A global checkpoint M is defined as a consistent global checkpoint if no message is sent after a checkpoint of M and received before another checkpoint of M (Y.M. Wang, 1997). The checkpoints belonging to a consistent global checkpoint are called globally consistent checkpoints (GCCs). The set of such checkpoints is also known as recovery line.
Convergence analysis of the vortex blob method for the $b$-equation

In this paper, we prove the convergence of the vortex blob method for a family of nonlinear evolutionary partial differential equations (PDEs), the so-called b-equation. This kind of PDEs, including the Camassa-Holm equation and the Degasperis-Procesi equation, has many applications in diverse scientific fields. Our convergence analysis also provides a proof for the existence of the global weak solution to the b-equation when the initial data is a nonnegative Radon measure with compact support.
Cancer and Oxidative Stress

Oxidative stress is closely related to all aspects of cancer, from carcino- genesis to the tumor-bearing state, from treatment to prevention. The human body is constantly under oxidative stress arising from exogenous origins (e.g., ultraviolet rays) and endogenous origins (at the cellular level where mitochondria are involved). When such oxidative stress exceeds the capacity of the oxidation-reduction system of the body, gene mutations may result or intracellular signal transduction and transcription factors may be affected directly or via antioxidants, leading to carcino- genesis. The tumor-bearing state is also said to be under oxidative stress associ- ated with active oxygen production by tumor cells and abnormal oxidation-reduction control. One of the mechanisms by which anticancer agents and radiation therapy exert their effects is through apoptosis of cancer cells. Oxidative stress is also involved in the problem of resistance to these treatments. The efficacy of anti- oxidants in the prevention of carcinogenesis is currently under investigation. Issues to be addressed in the future include the establishment of easy, accurate methods of measurement and evaluation of the extent of oxidative stress in the body as well as the clinical application of experimentally obtained knowledge to the prevention and treatment of cancer.
Cortisol and testosterone in association with history of sexual abuse within incarcerated adolescent youth

Adolescence is a challenging developmental transition in the lives of young adults, yet despite these challenges youth must normatively transition through adolescence and take on adult roles and responsibilities. Research on the topic of adolescence has addressed many of the biological, psychological, and social changes that occur during this time and this evidence converges on the notion that this normative transition can be a period of vulnerabilities or opportunities. Exposure to many forms of early adversity can exacerbate the biopsychosocial challenges of adolescence, with emerging research illustrating that child abuse and maltreatment exert particularly deleterious consequences on adolescent physiology and development. What is under-studied is whether specific forms of maltreatment in early life have immediate and long lasting effects on physiological health and wellbeing of developing youth. The present study examined cortisol and testosterone, two hormones that play important roles in adolescence and pubertal development. In addition to being acutely responsive to context, the two hormones follow a diurnal rhythm, which is highly associated with health outcomes. The present study examined effects of sexual abuse on diurnal testosterone and cortisol of incarcerated adolescent girls and boys (N=101, 49.5% female, 53% Non-White), ages 13-18 (M=16.17). The present study examined whether sexual abuse had a unique effect on cortisol and testosterone diurnal slopes for males and females. Gender was explored as a potential moderator of the relationship between sexual abuse and hormones. Race, BMI, and puberty were controlled for in examining the effects of sexual abuse on waking hormones and diurnal slope. Sexually abused youth had steeper cortisol slopes (p<.005). Girls had flatter cortisol slopes (B=.088, p<.05) and lower waking testosterone (p<.001). No significant effect of sexual abuse on testosterone was found after
Supporting Environmental Information Systems and Services Realization with the Geo-Spatial and Streaming Dimensions of the Semantic Web

Environmental Information Systems and Services require ex- ible discovery and chaining of distributed environmental services to sup- port a large number of concurrent decision processes. The ability to cope with geo-spatial features of the environment and to process in real time huge and possibly noisy data streams are two critical factors in supporting such decision processes. Solution to separately cope with the two aspects are available. The geo-spatial aspect has been studied for decades in the Geographic Information System (GIS) community. Data Stream Management Systems (DSMS) are the result of a decade of investigation on data stream processing by the database community. However, seamless integrated usage of GIS and DSMS is still a di- cult task. Recent developments of the Semantic Web community have been trying to overcome the barriers between these two technologies by proposing to extend the Semantic Web with both a Geo-Spatial and a Streaming dimension. In this paper, these two dimensions of Semantic Web are show-cased for environmental monitoring and management in oil and gas operations.
Characterization of Oil Contaminated Soil Kuwait Oil Lakes

During the Gulf War (1991) more than 600 oil wells were set on fire. The gushed oil from Kuwait wells created what is known as oil lakes by filling natural depressions in the topography and artillery trenches which even contain live ammunition. Since the liberation of Kuwait, individual efforts tried to decontaminate the soil with only partial successes. Recently, a joint project between the United Nation Compensation Commission (UNCC), Kuwait National Focal Point (KNFP), and Kuwait University (KU) has been initiated to conduct a comprehensive work to eliminate the contaminated soil and its environmental impacts. The objective of this study is to characterize oil contaminated soil by the assessment of its physical, chemical, and geotechnical properties. The results estimate the contaminated volume to be between 16.5×10 m and 22.7 ×10 m, and show that its physical properties were heavily deteriorated and chemical characteristics were highly affected as well as the geotechnical properties due to the presence of oil. Keywords-Kuwait, oil lakes; oil contaminated soil charactaristics
The Role of Function Words and Prosody for Phrasal Parsing in Preverbal Infants

We examined whether infants use function words for phrasal parsing and how functors and prosody interact for parsing. In a preferential looking procedure Frenchlearning 8and 11-month-olds were familiarized with sentences with the subject-NP+VP structure. The VP began with a functor (va, “will”) in half of the sentences (e.g., [Le niveau imposant] va gâcher l’enquête des jeunes. – “The imposing level will waste the survey of the young ones.”) and a nonsense-functor (ko) in the other half of the sentences ([Un produit imposant] ko cibler l’usage du client. – “The imposing product ko target the use of the client.”). In Experiment 1, the subject-NPs contained phrase-final prosodic cues. Infants were tested with the subject-NP spliced from the va versus the subject-NP from the ko sentences. In Experiment 2 we re-created the familiarization sentences by removing all phrase-final prosodic cues of the subject-NPs using cross-splicing, i.e., the subject-NPs ended with phrase-internal prosody. Infants were tested with the subject-NPs spliced from the va versus ko sentences of this experiment. Results showed that infants were able to use the functor to assist their parsing of the subject-NP by 11 months of age. Furthermore, 11-month-olds’ use of the functor for phrasal parsing was more efficient when phrase-final prosodic cues were also present than when the prosodic cues were absent. The findings demonstrate that functors and prosody are both useful for bootstrapping initial syntactic learning in preverbal infants. * Mireille Babineau, Rushen Shi and Andréane Melançon, Université du Québec à Montréal. Corresponding author: babineau.mireille@courrier.uqam. ca. This research is supported by SSHRC, NSERC and CFI grants to the second author.
ON DOMAIN MONOTONICITY FOR THE PRINCIPAL EIGENVALUE OF THE LAPLACIAN WITH A MIXED DIRICHLET-NEUMANN BOUNDARY CONDITION

Let Ω ⊂ Rd be a bounded domain with smooth boundary and let A ⊂⊂ Ω be a smooth, compactly embedded subdomain. Consider the operator − 1 2 ∆ in Ω − Ā with the Dirichlet boundary condition at ∂A and the Neumann boundary condition at ∂Ω, and let λ0(Ω, A) > 0 denote its principal eigenvalue. We discuss the question of monotonicity of λ0(Ω, A) in its dependence on the domain Ω. The main point of this note is to suggest an open problem that is in the spirit of Chavel’s question concerning domain monotonicity for the Neumann heat kernal. Let Ω ⊂ R be a bounded domain with smooth boundary and let A ⊂⊂ Ω be a smooth, compactly embedded subdomain. Consider the operator − 12∆ in Ω − Ā with the Dirichlet boundary condition at ∂A and the Neumann boundary condition at ∂Ω, and let λ0(Ω, A) > 0 denote its principal eigenvalue. If instead of the Neumann boundary condition, one imposes the Dirichlet boundary condition at ∂Ω, then it’s easy to see that λ0(Ω, A) is monotone decreasing in Ω and increasing in A. Similarly, in the case at hand, it is clear that λ0(Ω, A) is monotone increasing in A; however, the question of monotonicity in Ω is not easily resolved. The impetus for studying this question arose in part from a recent paper [5] in which one can find the asymptotic behavior of λ0(Ω, A) when A is a ball that shrinks to a point, 1991 Mathematics Subject Classification. 60C05, 60F05.
Petri Nets for Game Plot

We have developed a technique for authoring a nonlinear plot and for managing a story according to the plot in an interactive story-based virtual reality application. The technique exploits Petri Nets that alter reactive plans controlling individual actors. Its main advantage is that it allows for iterative design and copes with large virtual worlds inhabited with tens of actors. In this paper, we describe the technique and a prototype application.
Explaining migration as a process of cumulative causation in the life course

Despite manifold studies in the field of migration, the process of migration decision-making and succeeding migration behaviour is still not fully understood. In this paper a more elaborated theoretical framework for the explanation of migration decision-making and behaviour is proposed by including a life-course perspective on goal formation into a psychological model of action phases. Hypotheses derived from this framework in regard to the influence of all relevant groups of predictors on certain stages of the migration process are empirically tested. The results support an explanation of the migration process within a threestage model, in that perceived opportunity differentials between the place of living and alternative places, the influences of "significant others", life-course events, and resources are prominent. Varieties in the importance of those factors in different phases of the life course are analyzed and interpreted referring to the changing importance of instrumental goals within the theoretical framework. The data come from a tailormade panel study with initially 2,400 respondents in Germany.
Shear Thickening in Dense Suspensions

The rheological properties of two types of dense suspensions are explored. Repulsive suspensions of cornstarch in solution of water in glycerol are found to be shear thickening. The measured flow curves present features compatible with the recent theoretical idea of sigmoidal flow curves to explain shear thickening, which would implies the formation of vorticity bands and stress localisation. Attractive suspensions of cornstarch in oil shows interesting dynamic behaviour in Large Amplitude Oscillatory Shear experiments, with the mean viscosity increasing with the strain amplitude above 0.5. This increase is interpreted in terms of shear reversal and structures forming in the compression direction.
Scalable Local Community Detection with Mapreduce for Large Networks

Community detection from complex information networks draws much attention from both academia and industry since it has many real-world applications. However, scalability of community detection algorithms over very large networks has been a major challenge. Real-world graph structures are often complicated accompanied with extremely large sizes. In this paper, we propose a MapReduce version called 3MA that parallelizes a local community identification method which uses the $M$ metric. Then we adopt an iterative expansion approach to find all the communities in the graph. Empirical results show that for large networks in the order of millions of nodes, the parallel version of the algorithm outperforms the traditional sequential approach to detect communities using the M-measure. The result shows that for local community detection, when the data is too big for the original M metric-based sequential iterative expension approach to handle, our MapReduce version 3MA can finish in a reasonable time.
FaceGANs: Stable Generative Adversarial Networks with High-Quality Images

Generative Adversarial Networks (GANs) have shown impressive performance in producing images highly similar to original dataset under unsupervised learning. However, the losses of discriminator and generator are highly fluctuated, which affects the quality of fake images produced by the generator. In this work, we propose Face Generative Adversarial Networks (FaceGANs). Compared to the conventional GANs, our new structure can stabilize the loss fluctuation of discriminator and generator. It also improves the capabilities of generator and discriminator. In order to fully investigate FaceGANs, we compare the performance of FaceGANs with Deep Convolution Generative Adversarial Network (DCGANs) on the Celeba dataset. Experimental results show that our FaceGANs structure can fast generate images with better quality than DCGANs in a facial reconstruction.
Lowrie, Fiona M. and Behnke, Jerzy M. and Barnard, Christopher J. (2004) Density-dependent effects on the survival and growth of the rodent stomach worm

The spirurid nematode, Protospirura muricola, is of intrinsic interest as a rodent model of gastric nematode infections. Since worm burdens can be very heavy in nature, density dependent processes may constrain parasite growth. Laboratory mice (BKW) were exposed to varying doses of infective larvae of P. muricola in the range 5 to 40 third-stage larvae (L3), in four separate experiments in which progressively higher doses were utilized. All mice were culled 60 days after infection and a total of 518 worms (226 male and 292 female worms) was recovered, measured and weighed. Overall survival was 58.9%, but survival declined significantly with increasing dose by approximately 21% (from 66% at 5 L3 per mouse to 52% at 40 L3 per mouse). The length and weight of worms correlated positively in both sexes. Total worm biomass increased linearly with increasing numbers of worms. However, whilst the length and weight of male worms declined with increasing worm burden (8.4 and 24.6% respectively), female worms were less affected, only length showing a significant reduction with increasing parasite burden (16.0%). Therefore, increasing worm burdens impeded growth of P. muricola, but reduction in length and weight were relatively small in relation to the overall size of this nematode. Increasing worm burdens were associated with loss of host weight and reduction in stomach weight and worm burdens in excess of 20 exerted a measurable cost to the host, which in the field, may be associated with loss of overall host fitness.
Highlights from the Tenth International Society for Computational Biology (ISCB) Student Council Symposium 2014

A1 Highlights from the tenth ISCB Student Council Symposium 2014 Farzana Rahman, Katie Wilkins, Annika Jacobsen, Alexander Junge, Esmeralda Vicedo, Dan DeBlasio, Anupama Jigisha, Tomás Di Domenico Genomics and Computational Biology Research Group, University of South Wales, UK; Computational Biology Department, Cornell University, USA; Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Netherlands; Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark; Department of Bioinformatics and Computational Biology, Fakultät für Informatik, Germany; Department of Computer Science, University of Arizona, USA; University of Geneva, Switzerland; Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, UK E-mail: tdido@tdido.com. ar BMC Bioinformatics 2015, 16(Suppl 2):A1
A RANDOM SUBSYNCHRONOUS RESONANCE IN A TURBINE GENERATOR SET

The electrical arc furnace (EAF) load is the largest load in power systems. Since electromechanical interactions between electrical loads and turbine-generator are seldom discussed, this paper investigates the torsional vibrations in turbine-generator shafts and blades subject to real and reactive power variations from a large-scale EAF plant. The transient power fluctuation of the load is randomly dramatic; nevertheless, most of the frequencies of the induced voltage flicker, generator delivering power and even electromagnetic torque are subsynchronous. Therefore such a continued stochastic disturbance can impose random subsynchronous resonant stresses on turbine mechanisms.