Miracle-dz/UniFAR-FTUs huggingface dataset:
The Many Faces of Fear: Comparing the Pathways and Impacts of Nonconsumptive Predator Effects on Prey Populations

Background Most ecological models assume that predator and prey populations interact solely through consumption: predators reduce prey densities by killing and consuming individual prey. However, predators can also reduce prey densities by forcing prey to adopt costly defensive strategies. Methodology/Principal Findings We build on a simple Lotka-Volterra predator-prey model to provide a heuristic tool for distinguishing between the demographic effects of consumption (consumptive effects) and of anti-predator defenses (nonconsumptive effects), and for distinguishing among the multiple mechanisms by which anti-predator defenses might reduce prey population growth rates. We illustrate these alternative pathways for nonconsumptive effects with selected empirical examples, and use a meta-analysis of published literature to estimate the mean effect size of each pathway. Overall, predation risk tends to have a much larger impact on prey foraging behavior than measures of growth, survivorship, or fecundity. Conclusions/Significance While our model provides a concise framework for understanding the many potential NCE pathways and their relationships to each other, our results confirm empirical research showing that prey are able to partially compensate for changes in energy income, mitigating the fitness effects of defensive changes in time budgets. Distinguishing the many facets of nonconsumptive effects raises some novel questions, and will help guide both empirical and theoretical studies of how predation risk affects prey dynamics.
BulPhonC: Bulgarian Speech Corpus for the Development of ASR Technology

In this paper we introduce a Bulgarian speech database, which was created for the purpose of ASR technology development. The paper describes the design and the content of the speech database. We present also an empirical evaluation of the performance of a LVCSR system for Bulgarian trained on the BulPhonC data. The resource is available free for scientific usage.
The roles and regulation of multicellular rosette structures during morphogenesis

Multicellular rosettes have recently been appreciated as important cellular intermediates that are observed during the formation of diverse organ systems. These rosettes are polarized, transient epithelial structures that sometimes recapitulate the form of the adult organ. Rosette formation has been studied in various developmental contexts, such as in the zebrafish lateral line primordium, the vertebrate pancreas, the Drosophila epithelium and retina, as well as in the adult neural stem cell niche. These studies have revealed that the cytoskeletal rearrangements responsible for rosette formation appear to be conserved. By contrast, the extracellular cues that trigger these rearrangements in vivo are less well understood and are more diverse. Here, we review recent studies of the genetic regulation and cellular transitions involved in rosette formation. We discuss and compare specific models for rosette formation and highlight outstanding questions in the field.
Melatonin administration and pituitary hormone secretion

The relationship between the pineal gland and pituitary function remains controversial, while the role of melatonin in the adaptation of the organism to the light‐dark cycle of the environment is becoming increasingly recognized. The aim of this study was to investigate the effect of a manipulation of the melatonin rhythm on pituitary hormone secretion in man.
Interferon Gamma and Sonic Hedgehog Signaling Are Required to Dysregulate Murine Neural Stem/Precursor Cells

Background The pro-inflammatory cytokine interferon gamma (IFNγ), a key player in various neurological diseases, was recently shown to induce a dysregulated phenotype in neural stem/precursor cells (NSPCs) that is characterized by the simultaneous expression of glial and neuronal markers and irregular electrophysiological properties. Thus far, the mechanisms of this phenomenon have remained unclear. Methodology/Principal Findings To determine if binding of the signal transducers and activators of transcription (Stat 1) to the sonic hedgehog (SHH) promoter is important for this phenomenon to occur, chromatin immunoprecipitation and pharmacological inhibition studies were performed. We report here that the activation of both the Stat 1 and SHH pathways is necessary to elicit the dysregulated phenotype. Conclusions/Significance Thus, blocking these pathways might preserve functional differentiation of NSPCs under inflammatory conditions leading to more effective regeneration.
Using cultural metadata for artist recommendations

Our approach to generate recommendations for similar artists follows a recent tradition of authors tackling the problem not with content-based audio analysis. Following this novel procedure we rely on the acquisition, filtering and condensing of unstructured text-based information that can be found in the Web. The beauty of this approach lies in the possibility to access so-called cultural metadata that is the agglomeration of several independent -originally subjective - perspectives about music.
Improved Methods of Carnivore Faecal Sample Preservation, DNA Extraction and Quantification for Accurate Genotyping of Wild Tigers

Background Non-invasively collected samples allow a variety of genetic studies on endangered and elusive species. However due to low amplification success and high genotyping error rates fewer samples can be identified up to the individual level. Number of PCRs needed to obtain reliable genotypes also noticeably increase. Methods We developed a quantitative PCR assay to measure and grade amplifiable nuclear DNA in feline faecal extracts. We determined DNA degradation in experimentally aged faecal samples and tested a suite of pre-PCR protocols to considerably improve DNA retrieval. Results Average DNA concentrations of Grade I, II and III extracts were 982pg/µl, 9.5pg/µl and 0.4pg/µl respectively. Nearly 10% of extracts had no amplifiable DNA. Microsatellite PCR success and allelic dropout rates were 92% and 1.5% in Grade I, 79% and 5% in Grade II, and 54% and 16% in Grade III respectively. Our results on experimentally aged faecal samples showed that ageing has a significant effect on quantity and quality of amplifiable DNA (p<0.001). Maximum DNA degradation occurs within 3 days of exposure to direct sunlight. DNA concentrations of Day 1 samples stored by ethanol and silica methods for a month varied significantly from fresh Day 1 extracts (p<0.1 and p<0.001). This difference was not significant when samples were preserved by two-step method (p>0.05). DNA concentrations of fresh tiger and leopard faecal extracts without addition of carrier RNA were 816.5pg/µl (±115.5) and 690.1pg/µl (±207.1), while concentrations with addition of carrier RNA were 49414.5pg/µl (±9370.6) and 20982.7pg/µl (±6835.8) respectively. Conclusions Our results indicate that carnivore faecal samples should be collected as freshly as possible, are better preserved by two-step method and should be extracted with addition of carrier RNA. We recommend quantification of template DNA as this facilitates several downstream protocols.
Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast

The budding yeast multi-K homology domain RNA-binding protein Scp160p binds to >1000 messenger RNAs (mRNAs) and polyribosomes, and its mammalian homolog vigilin binds transfer RNAs (tRNAs) and translation elongation factor EF1alpha. Despite its implication in translation, studies on Scp160p's molecular function are lacking to date. We applied translational profiling approaches and demonstrate that the association of a specific subset of mRNAs with ribosomes or heavy polysomes depends on Scp160p. Interaction of Scp160p with these mRNAs requires the conserved K homology domains 13 and 14. Transfer RNA pairing index analysis of Scp160p target mRNAs indicates a high degree of consecutive use of iso-decoding codons. As shown for one target mRNA encoding the glycoprotein Pry3p, Scp160p depletion results in translational downregulation but increased association with polysomes, suggesting that it is required for efficient translation elongation. Depletion of Scp160p also decreased the relative abundance of ribosome-associated tRNAs whose codons show low potential for autocorrelation on mRNAs. Conversely, tRNAs with highly autocorrelated codons in mRNAs are less impaired. Our data indicate that Scp160p might increase the efficiency of tRNA recharge, or prevent diffusion of discharged tRNAs, both of which were also proposed to be the likely basis for the translational fitness effect of tRNA pairing.
Directional cell breathing: a module for congestion control and load balancing in WCDMA networks

In this paper, we outline the basis of a novel cooperative module for congestion control and load balancing in WCDMA networks. Through carefully exploiting the capabilities of smart and directional antennas, we propose a controllable directional breathing where a base station's (BS) sectorized coverage is varied reactively in instances of congestion, and proactively in instances of exercising load balancing. This proposal, called Directional Cell Breathing (DCB), overcomes the drawbacks of non-sectorized and non-controllable WCDMA breathing management by optimizing the coverage level within each sector under constraints minding sectoral traffic load and interference bounds. Interference analysis is carried out to determine the eligibility of a cell to be considered in DCB if one of its adjacent cells becomes overloaded. This analysis is then used in a mathematical formulation to facilitate the optimization of the proposed scheme.
DNA methylation and gene activity.

PERSPECTIVES AND SUMMARY 93 BIOCHEMISTRY OF DNA METHYLATION . 95 Occurrence of Modified Bases . 95 Maintenance and de novo Methylations . 96 Methods to Determine Methylated Bases . 99 Distribution of 5-Methylcytosine . 100 DN A Methylatiun and Structural Changes uf DN A 102 THE BIOLOGICAL FUNCTION OF DNA METHYLATION . 103 DNA Methylation--a Regulatory Signal in Eukaryotic Gene Expression . 103 Correlations . 105 The Drosophila Problem . 109 Treatment of Cells with 5-Azacytidine Can Lead to the Activation of Previously Dormant Genes . 110 DNA Methylation at Specific Sites is Causally Related /0 Gene Inactivation . 112 Additional Observations . 115 Overall Conclusions . 116 DNA Methylation and Genetic Recombination . 117 A Model of Herpes Simplex Virus Latency 117 IN SEARCH OF MORE COMPLEX GENETIC CODING SIGNALS . 118 OUTLOOK . 118
Immunological studies of mouse decidual cells. I. Membrane markers of decidual cells in the days after implantation

Mouse decidual cell suspensions from day 6 to day 8 of gestation were prepared by enzymatic treatment with collagenase and trypsin and tested for various membrane markers. (a) Besides H-2 antigens, Thy-1 antigens are present on about 50% of the cells; this may reflect the fibroblastic origin of decidual cells or be a marker expressed on some decidual cells possibly under hormonal control. (b) T or B lymphocytes, as defined by four Lyt antigens or surface immunoglobulins, are not present in significant amounts. (c) A substantial number of cells bearing receptors for the Fc portion of IgG (FcR) is detectable in the decidua, probably closely connected with trophoblast cells; these FcR- bearing cells may act in preventing excessive invasion of uterine tissue by trophoblast or could contribute to the protection of the embryo by interacting with maternal blocking antibodies and trophoblast. No receptors for for complement were detected, even after 16-20 h in culture after trypsin treatment.
A GWAS platform built on iPlant cyber-infrastructure

We demonstrated a flexible Genome-Wide Association Study (GWAS) platform built upon the iPlant Collaborative Cyber-infrastructure. The platform supports big data management, sharing, and large scale study of both genotype and phenotype data on clusters. End users can add their own analysis tools, and create customized analysis workflows through the graphical user interfaces in both iPlant Discovery Environment and BioExtract server.
A Trainable Method of Parametric Shape Description

We have developed a trainable method of shape representation which can automatically capture the invariant properties of a class of shapes and provide a compact parametric description of variability. We have applied the method to a family of flexible ribbons (worms) and to heart shapes in echocardiograms. We show that in both cases a natural parameterisation of shape results.
Cement-based Composites: Materials, Mechanical Properties and Performance

Introduction Composites and Multiphase Materials Concrete-Like Composites Components of Cement Based Composites Reinforcement of Cement-Based Composites Structure of Cement Composites Interfaces Strength and Deformability Under Short-Term Static Load Cracking in Cement Matrices and Propagation of Cracks Fracture and Failure of Material Structures Behaviour of Cement Matrix Composites in Various Service Conditions Design and Optimization of Cement Based Composites High-Strength Concrete and High Performance Concretes Application and Development of Cement-Based Composites
Evaluation of Human Leukocyte Antigen-A (HLA-A), Other Non-HLA Markers on Chromosome 6p21 and Risk of Nasopharyngeal Carcinoma

Background The association between human leukocyte antigen (HLA) genes (located in the Major Histocompatibility Complex [MHC] region of chromosome 6p21) and NPC has been known for some time. Recently, two genome-wide association studies (GWAS) conducted in Taiwan and China confirmed that the strongest evidence for NPC association was mapped to the MHC region. It is still unclear, however, whether these findings reflect direct associations with Human Leukocyte Antigen (HLA) genes and/or to other genes in this gene-rich region. Methods To better understand genetic associations for NPC within the MHC region of chromosome 6, we conducted an evaluation that pooled two previously conducted NPC case-control studies in Taiwan (N = 591 cases and N = 521 controls). PCR-based genotyping was performed for 12 significant SNPs identified within 6p21 in the Taiwan NPC GWAS and for the HLA-A gene (exons 2 and 3). Findings After confirming homogeneity between the two studies, pooled odds ratios (OR) and 95% confidence intervals (CI) were estimated by logistic regression. We found that HLA-A (p-trend = 0.0006) and rs29232 (within the GABBR1 gene; p-trend = 0.005) were independent risk factors for NPC after adjustment for age, gender, study and each other. NPC risk was highest among individuals who were homozygous for the HLA-A*0207 risk allele and carriers of the rs29232 risk allele (A). Conclusion Our study suggests that most of the SNPs significantly associated with NPC from GWAS reflect previously identified HLA-A associations. An independent effect of rs29232 (GABBR1), however, remained, suggesting that additional genes within this region might be associated with NPC risk.
High-resolution transmission electron microscopy and electron energy loss spectroscopy of doped nanocarbons

Graphene, a one-atom thick sheet of carbon, is the thinnest, strongest and most electrically conductive material ever discovered. Alongside carbon nanotubes it is part of the group of nanocarbons whose unique properties have sparked huge interest in possible applications, including electronic devices, solar cells and biosensors. Doping of these materials allows for the modification of their optical and electronic properties,which is crucial to realising these applications. Studying the properties of these doped materials at atomic resolution and finding controllable and industrially scalable routes to doping, such as low energy ion implantation, are thus essential if they are to becomethe materials of the future. In this thesis, highly localised optical enhancements in metal doped graphene are studied using energy-filtered transmission electron microscopy in a monochromated and aberration corrected electron microscope. The ideal conditions for imaging the low energy loss region of graphene using EFTEM are discussed and new methods to compensate for image artifacts when using this technique at high resolution are presented. Density functional theory is used to reveal new visible spectrum plasmon excitations in the electron energy loss spectra of boron and nitrogen doped nanocarbons. Atomic resolution scanning transmission electron microscopy and nanoscale electron energy loss spectroscopy are used to investigate controllable and defect-free substitutional doping of suspended graphene films through low energy ion implantation. Computational methods for filtering high angle annular dark field images are shown and software for the automated processing and spectroscopic analysis of these images is developed.
Implicit Interaction in Collaborative Music Performances

The use of physiological signals in Human Computer Interaction (HCI) is becoming popular and widespread, mostly due to sensors miniaturization and advances in real-time processing. However, most of the studies that use physiologybased interaction focus on single-user paradigms, and its usage in collaborative scenarios is still in its beginning. Our research explores collaborative music performances where interactive sonification of brain and heart signals take place. We hypothesize that the representation of physiological signals through physical objects (physiopucks) in a tabletop interface may enhance motivational and controlling aspects of music collaboration. Here we show a multimodal system, based on electro-physiology sensors (Enobio) and the Reactable, a musical tabletop interface. Performance and motivation variables were assessed in an experiment involving a test “Physio” group (N=22) and a control “Placebo” group (N=22). Participants in Physio Group worked in pairs using two methods for sound creation: implicit interaction through physiological signals, and explicit interaction by means of gestural manipulation. In Placebo Group, no real-time sonification was provided as the system was driven by pre-recorded physiological signals. Users in Placebo Group were unaware of such effect. The results show that pairs in the Physio Group declare less difficulty, higher confidence and more symmetric control compared to the Placebo Group. We also discuss the correlations within pairs for different performance and motivation measures in Physio and Placebo Groups. The results show that our new multimodal system do not impose major difficulties for music collaboration. On the contrary, the similar ratings of distribution of control that were given by the Physio Group (but not Placebo) show that the proposed implicit interaction model encouraged symmetric music collaboration between participants. These results support the feasibility of introducing physiology-based interaction in multimodal tabletop interfaces for collaborative music performance. Together with the creation and control of sounds, brain and body signals may be powerful indicators of performers' emotional and cognitive states during collaboration, guiding music anticipation and interpersonal synchronization.
Implicit and Explicit Learning of a Sequential Postural Weight-Shifting Task in Young and Older Adults

Sequence-specific postural motor learning in a target-directed weight-shifting task in 12 older and 12 young participants was assessed. In the implicit sequence learning condition participants performed a concurrent spatial cognitive task and in the two explicit conditions participants were required to discover the sequence order either with or without the concurrent cognitive task. Participants moved a cursor on the screen from the center location to one of the target locations projected in a semi-circle and back by shifting their center of pressure (CoP) on force plates. During the training the targets appeared in a simple fixed 5-target sequence. Plan-based control (i.e., direction of the CoP displacement in the first part of the target-directed movement) improved by anticipating the sequence order in the implicit condition but not in the explicit dual task condition. Only the young participants were able to use the explicit knowledge of the sequence structure to improve the directional error as indicated by a significant decrease in directional error over practice and an increase in directional error with sequence removal in the explicit single task condition. Time spent in the second part of the movement trajectory to stabilize the cursor on the target location improved over training in both the implicit and explicit sequence learning conditions, for both age groups. These results might indicate that an implicit motor learning method, which holds back explicit awareness of task relevant features, may be desirable for improving plan-based motor control in older adults.
Paroxetine attenuates the development and existing pain in a rat model of neurophatic pain.

BACKGROUND P2X4 receptor (P2X4R), a purinoceptor expressed in activated spinal microglia, plays a key role in the pathogenesis of neuropathic pain. Spinal nerve injury induces up-regulation of P2X4R on activated microglia in the spinal cord, and blockade of this receptor can reduce neuropathic pain. The present study was undertaken to determine whether paroxetine, an inhibitor of P2X4R, could attenuate allodynia and hyperalgesia in chronic constriction injury (CCI) model of neuropathic pain when used preemptively or after the sciatic nerve injury. METHODS Male Wistar rats (150-200 g, n = 6) were divided into 3 different groups: 1- CCI vehicle-treated group, 2- Sham group, and 3- CCI paroxetine-treated group. Paroxetine (10 mg/kg, i.p.) was administered 1 h before surgery and continued daily until day 14. In other part of the study, paroxetine (10 mg/kg, i.p.) was administered at day 7 post injury and continued daily until day 14. von Frey filaments for mechanical allodynia and analgesia meter for thermal hyperalgesia were used to assay pain behavior. RESULTS In a preventive paradigm, paroxetine significantly attenuated both mechanical allodynia and thermal hyperalgesia (P<0.001). A significant decrease in pain behavior was seen with paroxetine on existing allodynia (P<0.001) and hyperalgesia (P<0.01) when initiated at day 7 post injury. CONCLUSION It seems that paroxetine can attenuate pain behavior when administered before and also after sciatic nerve injury in CCI model of neuropathic pain.
Uncoupling the Proinflammatory from the Immunosuppressive Properties of Tumor Necrosis Factor (Tnf) at the P55 TNF Receptor Level

Multiple sclerosis (MS) is a disabling inflammatory demyelinating disease of the central nervous system, considered to result from self-reactivity to myelin antigens. Tumor necrosis factor (TNF) and the p55 TNF receptor (TNFR) have been strongly implicated in MS pathogenesis. We reveal in this study a dual role for TNF in experimental autoimmune encephalomyelitis (EAE), a mouse model for MS. In addition to its well-established proinflammatory effects, TNF exhibits potent immunosuppressive properties, providing one possible explanation for the immune and disease activating effect of anti-TNF treatment of MS. We show that in TNF-deficient mice, myelin-specific T cell reactivity fails to regress and expansion of activated/memory T cells is abnormally prolonged, leading to exacerbated EAE. Strikingly, immnosuppression by TNF and protection against EAE does not require the p55 TNFR, whereas the same receptor is necessary for the detrimental effects of TNF during the acute phase of the disease. Thus, blocking the function of the p55 TNFR in autoimmune demyelination may inhibit the noxious proinflammatory activities of TNF without compromising its immunosuppressive properties.