Miracle-dz/UniFAR-FTUs huggingface dataset:
Secreted single-stranded DNA is involved in the initial phase of biofilm formation by Neisseria gonorrhoeae.

Neisseria gonorrhoeae is an obligate human pathogen that colonizes the genital tract and causes gonorrhoea. Neisseria gonorrhoeae can form biofilms during natural cervical infections, on glass and in continuous flow-chamber systems. These biofilms contain large amounts of extracellular DNA, which plays an important role in biofilm formation. Many clinical isolates contain a gonococcal genetic island that encodes a type IV secretion system (T4SS). The T4SS of N. gonorrhoeae strain MS11 secretes ssDNA directly into the medium. Biofilm formation, studied in continuous flow-chamber systems by confocal laser scanning microscopy (CLSM), was strongly reduced, especially in the initial phases of biofilm formation, in the presence of Exonuclease I, which specifically degrades ssDNA or in a ΔtraB strain that does not secrete ssDNA. To specifically detect ssDNA in biofilms using CLSM, a novel method was developed in which thermostable fluorescently labelled ssDNA- and ss/dsDNA-binding proteins were used to visualize ssDNA and total DNA in biofilms and planktonic cultures. Remarkably, mainly dsDNA was detected in biofilms of the ssDNA secreting strain. We conclude that the secreted ssDNA facilitates initial biofilm formation, but that the secreted ssDNA is not retained in mature biofilms.
Utility blindness: Why do we fall for deals?

MAGGIE WENJING LIU*School of Economics and Management, Tsinghua University, Beijing 100084, ChinaABSTRACTUtility blindness occurs under limited information processing when consumers base their purchase decisions solely on transaction utility(gains from the deal) rather than on total utility. When the deal is attractive enough, consumers will buy a product even though the totalutility is little or negative; on the other hand, an unattractive deal might decrease consumers’ purchase likelihood even when the total utilityis unaffected by the promotion. In this paper, three experiments provide evidence for the existence of utility blindness and demonstrate thatinformation processing limitation is the underlying process. Transaction utility salience and cognitive load are identiﬁed as the moderatingfactors. Theoreticalcontributions, managerialimplications, limitations, andfuture areasofthecurrent research arealso discussed.Copyright© 2013 John Wiley & Sons, Ltd.
Consequences of Sharp Military Assistance Increases for International Conflict and Cooperation

Effects of sharp increases in military assistance on international conflict and cooperation on the part of recipient nations are investigated. Since traditional bivariate and multivariate statistical techniques are often conceptually inapplicable to this subject matter, a quasi-experimental design is used which relies on autoregressive moving average models and exponential smoothing forecasting mechanisms. Twenty-five annual observations, from 1946 through 1970, of 15 Asian nations serve as the data base. Key findings are: (1) sharp increases in military assistance tend to change decidedly the recipient nation's international conflict and cooperative behavior; (2) in a substantial majority of cases examined, the direction of that behavior change is toward increased conflict and decreased cooperation; and (3) a two-year lag between military assistance and behavior change of recipient nations is statistically supported. The effects of increased capabilities as well as bureaucratic politics, habit, expectation, and prior deals are offered as possible reasons for these results. The findings seem to refute the argument that giving military aid to a nation not involved in a war will help strengthen that nation and thereby avoid future conflict.
Molecular control of mitochondrial function in preimplantation mouse embryos

Mitochondria play a key role in a number of physiological events during all stages of life, including the very first stages following fertilization. It is, therefore, important to understand the mechanisms controlling mitochondrial activity during early embryogenesis to determine their role in development outcome. The objective of this study was to investigate the molecular control of mitochondrial transcription and mitochondrial DNA (mtDNA) replication in mouse preimplantation embryos. We estimated the mtDNA copy number and characterized the expression patterns of two mitochondrial genes and several nuclear genes that encode mitochondrial transcription and replication factors throughout preimplantation development. Mitochondrial gene transcripts were present in larger quantities in morula and blastocyst stage embryos relative to other stages. A significant increase in the amount of mRNA for nuclear genes encoding mtDNA transcription factors was observed in eight‐cell stage embryos. Although a similar increase in the mRNA levels of nuclear genes encoding mtDNA replication factors was observed in morula and blastocyst stage embryos, the number of mtDNA molecules remained stable during preimplantation stages, suggesting that nuclear‐encoded mitochondrial transcription factors are involved in the regulation of mtDNA transcription during early development. Although transcripts of replication factors are abundant at the morula and blastocyst stage, mtDNA replication did not occur until the blastocyst stage, suggesting that the inhibition of mtDNA replication is controlled at the post‐transcriptional level during early embryogenesis. Mol. Reprod. Dev. © 2005 Wiley‐Liss, Inc.
Poetics, Power, Possibilities, and Playfulness: Zombies, Performance, and Making Meaning in Young People's Lives

This article considers drama/theater education as a form of constructivism where popular culture is both accessed and employed to engage young people and animate education. Using the familiar cultural trope of zombies, and in reference to three separate performance projects, attention is drawn to why projects such as these matter and why they work—and those who might be touched by them. The article further considers how knowledge might be transformed when young people work as artists and how participatory arts experiences reference questions relating to the nature of knowledge, our relationship to knowledge, and what this relationship might mean. Finally, the article considers how policy might delimit these generative possibilities.
L'organització de l'activitat conjunta i el pensament del professorat sobre l'acció docent en educació física escolar

Teacher thinking and teaching action of a PE teacher in organising joint activities is studied. The theoretical and methodological bases are founded on principles of the ecological paradigm, the perspective of the reflective practitioner, the perspective of the situated action and the sociocultural-orientated constructivism. The “constructivist conception of school teaching and learning” is adopted to analyse the relationships in the interactive triangle on which thinking is analysed. To study the organization of joint activities, analysing the interactivity process has been adopted. To find out and analyse teacher’s thinking, self-confrontation interviews have been carried out and discourse analysis has been adopted. Is revealed that: the organisation of joint activity represents a suitable scenario for the study of teacher thinking, thinking about these actions enables to identify conditions that govern teaching actions, this is determined and governed by both the immediate, unpredictable and uncertain nature of the interactivity situations and the teacher’s implicit theories, and that thinking in action and thinking on action are very often different.
On Tropical Compactifications

We give an affirmative answer to a conjecture proposed by Tevelev in characteristic 0 case: any variety contains a sch\"on very affine open subvariety. Also we show that any fan supported on the tropicalization of a sch\"on very affine variety produces a sch\"on compactification. Using toric schemes over a discrete valuation ring, we extend tropical compatifications to the non-constant coefficient case.
Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

An integrated Feynman path integral‐free energy perturbation and umbrella sampling (PI‐FEP/UM) method has been used to investigate the kinetic isotope effects (KIEs) in the proton transfer reaction between nitroethane and acetate ion in water. In the present study, both nuclear and electronic quantum effects are explicitly treated for the reacting system. The nuclear quantum effects are represented by bisection sampling centroid path integral simulations, while the potential energy surface is described by a combined quantum mechanical and molecular mechanical (QM/MM) potential. The accuracy essential for computing KIEs is achieved by a FEP technique that transforms the mass of a light isotope into a heavy one, which is equivalent to the perturbation of the coordinates for the path integral quasiparticle in the bisection sampling scheme. The PI‐FEP/UM method is applied to the proton abstraction of nitroethane by acetate ion in water through molecular dynamics simulations. The rule of the geometric mean and the Swain–Schaad exponents for various isotopic substitutions at the primary and secondary sites have been examined. The computed total deuterium KIEs are in accord with experiments. It is found that the mixed isotopic Swain–Schaad exponents are very close to the semiclassical limits, suggesting that tunneling effects do not significantly affect this property for the reaction between nitroethane and acetate ion in aqueous solution. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Professional education as a structural barrier to lifelong learning in the NHS

The concept of the learning society is analysed in relation to the healthcare sector and various occupations within it. It is maintained that although traditional boundaries have been blurred or eroded in the workplace in recent years, there remains strong opposition to this erosion on the part of many healthcare professions. This professional demarcation is particularly illustrated by the educational arrangements for various healthcare occupations, where it has prevented recognition of any overlap in the initial education and training of these groups. The resulting educational boundaries are argued to be incompatible with the concept of a learning society, as well as holding negative consequences for the provision of health care. Suggestions are made for a new approach to health care education.
Dialog Act Annotation for Twitter Conversations

We present a dialog act annotation for German Twitter conversations. In this paper, we describe our annotation effort of a corpus of German Twitter conversations using a full schema of 57 dialog acts, with a moderate inter-annotator agreement of multi- = 0.56 for three untrained annotators. This translates to an agreement of 0.76 for a minimal set of 10 broad dialog acts, comparable to previous work. Based on multiple annotations, we construct a merged gold standard, backing off to broader categories when needed. We draw conclusions wrt. the structure of Twitter conversations and the problems they pose for dialog act characterization.
Species Composition and Fire: Non-Additive Mixture Effects on Ground Fuel Flammability

Diversity effects on many aspects of ecosystem function have been well documented. However, fire is an exception: fire experiments have mainly included single species, bulk litter, or vegetation, and, as such, the role of diversity as a determinant of flammability, a crucial aspect of ecosystem function, is poorly understood. This study is the first to experimentally test whether flammability characteristics of two-species mixtures are non-additive, i.e., differ from expected flammability based on the component species in monospecific fuel. In standardized fire experiments on ground fuels, including monospecific fuels and mixtures of five contrasting subarctic plant fuel types in a controlled laboratory environment, we measured flame speed, flame duration, and maximum temperature. Broadly half of the mixture combinations showed non-additive effects for these flammability indicators; these were mainly enhanced dominance effects for temporal dynamics – fire speed and duration. Fuel types with the more flammable value for a characteristic determined the rate of fire speed and duration of the whole mixture; in contrast, maximum temperature of the fire was determined by the biomass-weighted mean of the mixture. These results suggest that ecological invasions by highly flammable species may have effects on ground-fire dynamics well out of proportion to their biomass.
Integration of exteroceptive and interoceptive cues in spatial localization

s and posTers Van Barneveld D.C.P.B. M. , Van Wanrooij M.M. and Van Opstal A.J. (2011) The reference frame of the ventriloquist effect TU/e Dag van de Perceptie 2011 Van Opstal A.J. and Van Barneveld D.C.P.B. M. (2011) Audio-vestibular interactions in human orienting, Vergadering Werkgemeenschap Auditief Systeem Van Barneveld D.C.P.B. M. , Kiemeneij A.C. M. and Van Opstal (2010) Free-field sound localization during passive whole-body rotation Association for Research in Otolaryngology Midwinter Meeting 2010, 174 Kiemeneij A.C. M. , Van Barneveld D.C.P.B. M. and Van Opstal A.J. (2010) Saccades to brief visual flashes presented during passive vestibular whole-body rotation FENS abstract, vol. 5, 084.8 Van Barneveld D.C.P.B. M. , Binkhorst F. and Van Opstal A.J. (2010) Failure to compensate for vestibularly-evoked passive head rotations in human sound localization FENS abstract, vol. 5, 083.11 Van Barneveld D.C.P.B. M. and Van Opstal A.J. (2008) Influence of eye position on audiovestibular interaction during whole-body rotation Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 367.11 Van Barneveld D.C.P.B. M. , Meijerink, E. and Van Opstal A.J. (2008) Influence of eye position on audio-vestibular interactions during whole-body rotation TNO Soesterberg Dag van de Perceptie 2008 Cpter 11 Eplogue CurriCulum ViTae Denise van Barneveld werd op 1 juli 1983 geboren in Geleen. Hier ging zij naar basisschool De Driesprong en vervolgens naar de Albert Schweitzer Scholengemeenschap (later gefuseerd tot het Graaf Huijn College), waar ze in 2001 cum laude haar VWO diploma behaalde. Hierna verhuisde zij naar Nijmegen om daar de opleiding Natuurwetenschappen te volgen aan de Radboud Universiteit. Als snel werd duidelijk dat haar hart lag bij de biofysica, met name de werking van de hersenen. Een logisch vervolg op de bachelor Natuurwetenschappen was dan ook de research master Cognitive Neuroscience, waaraan zij in 2004 begon. Tegelijkertijd heeft zij de master Natuurwetenschappen afgerond. Na het beëindigen van deze twee opleidingen, is zij in 2007 als promovenda aan de slag gegaan bij de afdeling Biofysica aan de Radboud Universiteit, onder begeleiding van Prof. Dr. A. John van Opstal. Deze afdeling is in 2008 opgegaan in het Donders Institute for Brain, Cognition and Behaviour. De resultaten van het onderzoek dat zij daar gedaan heeft, staan beschreven in dit proefschrift. Sinds 1 november 2011 werkt zij aan het Leids Universitair Medisch Centrum, waar ze bij de afdeling KNO onderzoek doet naar de verbetering van spraakverstaaan in een ruizige omgeving van patiënten met een cochleair implantaat.
Identification of a sequence element immediately upstream of the polypurine tract that is essential for replication of simian immunodeficiency virus

A short stretch of T‐rich sequences immediately upstream of the polypurine tract (PPT) is highly conserved in the proviral genomes of human and simian immunodeficiency viruses (HIV and SIV). To investigate whether this ‘U‐box’ influences SIVmac239 replication, we analyzed the properties of mutants with changes in this region of the viral genome. All mutants were either retarded in their growth (up to one month delay) or did not replicate detectably in CEMx174 cells. When U‐box mutants did replicate detectably, compensatory changes were consistently observed in the viral genome. The most common compensatory change was the acquisition of thymidines immediately upstream of the PPT, but marked expansion in the length of the PPT was also observed. U‐box mutants produced transiently by transfection were severely impaired in their ability to produce reverse transcripts in infectivity assays. Analysis of transiently produced mutant virus revealed no defect in RNA packaging or virus assembly. These results identify a new structural element important for an early step in the viral life cycle that includes reverse transcription.
Increased Levels of Extracellular Microvesicle Markers and Decreased Levels of Endocytic/Exocytic Proteins in the Alzheimer's Disease Brain.

BACKGROUND Alzheimer's disease (AD) is a chronic neurodegenerative disorder accounting for more than 50% of all dementia cases. AD neuropathology is characterized by the formation of extracellular plaques and intracellular neurofibrillary tangles consisting of aggregated amyloid-β and tau, respectively. The disease mechanism has only been partially elucidated and is believed to also involve many other proteins. OBJECTIVE This study intended to perform a proteomic profiling of post mortem AD brains and compare it with control brains as well as brains from other neurological diseases to gain insight into the disease pathology. METHODS Here we used label-free shotgun mass spectrometry to analyze temporal neocortex samples from AD, other neurological disorders, and non-demented controls, in order to identify additional proteins that are altered in AD. The mass spectrometry results were verified by antibody suspension bead arrays. RESULTS We found 50 proteins with altered levels between AD and control brains. The majority of these proteins were found at lower levels in AD. Pathway analyses revealed that several of the decreased proteins play a role in exocytic and endocytic pathways, whereas several of the increased proteins are related to extracellular vesicles. Using antibody-based analysis, we verified the mass spectrometry results for five representative proteins from this group of proteins (CD9, HSP72, PI42A, TALDO, and VAMP2) and GFAP, a marker for neuroinflammation. CONCLUSIONS Several proteins involved in exo-endocytic pathways and extracellular vesicle functions display altered levels in the AD brain. We hypothesize that such changes may result in disturbed cellular clearance and a perturbed cell-to-cell communication that may contribute to neuronal dysfunction and cell death in AD.
High-throughput functional testing of ENCODE segmentation predictions

The histone modification state of genomic regions is hypothesized to reflect the regulatory activity of the underlying genomic DNA. Based on this hypothesis, the ENCODE Project Consortium measured the status of multiple histone modifications across the genome in several cell types and used these data to segment the genome into regions with different predicted regulatory activities. We measured the cis-regulatory activity of more than 2000 of these predictions in the K562 leukemia cell line. We tested genomic segments predicted to be Enhancers, Weak Enhancers, or Repressed elements in K562 cells, along with other sequences predicted to be Enhancers specific to the H1 human embryonic stem cell line (H1-hESC). Both Enhancer and Weak Enhancer sequences in K562 cells were more active than negative controls, although surprisingly, Weak Enhancer segmentations drove expression higher than did Enhancer segmentations. Lower levels of the covalent histone modifications H3K36me3 and H3K27ac, thought to mark active enhancers and transcribed gene bodies, associate with higher expression and partly explain the higher activity of Weak Enhancers over Enhancer predictions. While DNase I hypersensitivity (HS) is a good predictor of active sequences in our assay, transcription factor (TF) binding models need to be included in order to accurately identify highly expressed sequences. Overall, our results show that a significant fraction (∼26%) of the ENCODE enhancer predictions have regulatory activity, suggesting that histone modification states can reflect the cis-regulatory activity of sequences in the genome, but that specific sequence preferences, such as TF-binding sites, are the causal determinants of cis-regulatory activity.
On the spectrum of a bent chain graph

We study Schrödinger operators on an infinite quantum graph of a chain form which consists of identical rings connected at the touching points by δ-couplings with a parameter . If the graph is ‘straight’, i.e. periodic with respect to ring shifts, its Hamiltonian has a band spectrum with all the gaps open whenever α ≠ 0. We consider a ‘bending’ deformation of the chain consisting of changing one position at a single ring and show that it gives rise to eigenvalues in the open spectral gaps. We analyze dependence of these eigenvalues on the coupling α and the ‘bending angle’ as well as resonances of the system coming from the bending. We also discuss the behaviour of the eigenvalues and resonances at the edges of the spectral bands.
Disruption of the Bcl6 Gene Results in an Impaired Germinal Center Formation

The Bcl6 gene has been identified from the chromosomal translocation breakpoint in B cell lymphomas, and its products are expressed highly in germinal center (GC) B cells. To investigate the function of Bcl6 in lymphocytes, we have generated RAG1-deficient mice reconstituted with bone marrow cells from Bcl6-deficient mice (Bcl6−/−RM). Lymphogenesis in primary lymphoid tissues of Bcl6−/−RM is normal, and Bcl6−/−RM produced control levels of primary IgG1 antibodies specific to T cell–dependent antigens. However, GCs were not found in these mice. This defect was mainly due to the abnormalities of B cells. Therefore, Bcl6 is essential for the differentiation of GC B cells.
Quality of extracurricular activities - considering developmental changes in the impact on school attachment and achievement

According to the stage-environment fit approach, the development of motivation is influenced by the fit between learning context and basic needs (i.e., the needs for autonomy, competence, and social relatedness). It is supposed that school-based extracurricular activities are especially suitable for fostering motivation and, thus, achievement by providing developmentally appropriate learning contexts. Until now, the influence of need fulfillment in extracurricular activities on school attachment and achievement has not been investigated. The aim of this study is to examine these relationships in German all-day schools and to explore the specific impact of each need across age. The longitudinal research sample consists of more than 3,000 students in Grades 5, 7 and 9. The students’ perceptions of autonomy, competence (challenge) and social relatedness (student-staff-relationship) are analyzed as predictors of school attachment and achievement (i.e., grades). A conditional growth curve model reveals that the three quality features influence school attachment across age, but barely relate to achievement. Student-staff-relationship proves to be the most infl uential predictor in all age groups. However, the development of school attachment significantly influences achievement. Thus, promoting school attachment by means of high quality extracurricular activities should lead to the positive development of academic achievement.