Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical constraints and functional characteristics of transcription factor–DNA interaction

We study theoretical “design principles” for transcription factor (TF)–DNA interaction in bacteria, focusing particularly on the statistical interaction of the TFs with the genomic background (i.e., the genome without the target sites). We introduce and motivate the concept of programmability, i.e., the ability to set the threshold concentration for TF binding over a wide range merely by mutating the binding sequence of a target site. This functional demand, together with physical constraints arising from the thermodynamics and kinetics of TF–DNA interaction, leads us to a narrow range of “optimal” interaction parameters. We find that this parameter set agrees well with experimental data for the interaction parameters of a few exemplary prokaryotic TFs, which indicates that TF–DNA interaction is indeed programmable. We suggest further experiments to test whether this is a general feature for a large class of TFs.
Altered Gray Matter Volume and White Matter Integrity in College Students with Mobile Phone Dependence

Mobile phone dependence (MPD) is a behavioral addiction that has become an increasing public mental health issue. While previous research has explored some of the factors that may predict MPD, the underlying neural mechanisms of MPD have not been investigated yet. The current study aimed to explore the microstructural variations associated with MPD as measured with functional Magnetic Resonance Imaging (fMRI). Gray matter volume (GMV) and white matter (WM) integrity [four indices: fractional anisotropy (FA); mean diffusivity (MD); axial diffusivity (AD); and radial diffusivity (RD)] were calculated via voxel-based morphometry (VBM) and tract-based spatial statistics (TBSS) analysis, respectively. Sixty-eight college students (42 female) were enrolled and separated into two groups [MPD group, N = 34; control group (CG), N = 34] based on Mobile Phone Addiction Index (MPAI) scale score. Trait impulsivity was also measured using the Barratt Impulsiveness Scale (BIS-11). In light of underlying trait impulsivity, results revealed decreased GMV in the MPD group relative to controls in regions such as the right superior frontal gyrus (sFG), right inferior frontal gyrus (iFG), and bilateral thalamus (Thal). In the MPD group, GMV in the above mentioned regions was negatively correlated with scores on the MPAI. Results also showed significantly less FA and AD measures of WM integrity in the MPD group relative to controls in bilateral hippocampal cingulum bundle fibers (CgH). Additionally, in the MPD group, FA of the CgH was also negatively correlated with scores on the MPAI. These findings provide the first morphological evidence of altered brain structure with mobile phone overuse, and may help to better understand the neural mechanisms of MPD in relation to other behavioral and substance addiction disorders.
A transcriptional network underlies susceptibility to kidney disease progression

The molecular networks that control the progression of chronic kidney diseases (CKD) are poorly defined. We have recently shown that the susceptibility to development of renal lesions after nephron reduction is controlled by a locus on mouse chromosome 6 and requires epidermal growth factor receptor (EGFR) activation. Here, we identified microphthalmia‐associated transcription factor A (MITF‐A), a bHLH‐Zip transcription factor, as a modifier of CKD progression. Sequence analysis revealed a strain‐specific mutation in the 5′ UTR that decreases MITF‐A protein synthesis in lesion‐prone friend virus B NIH (FVB/N) mice. More importantly, we dissected the molecular pathway by which MITF‐A modulates CKD progression. MITF‐A interacts with histone deacetylases to repress the transcription of TGF‐α, a ligand of EGFR, and antagonizes transactivation by its related partner, transcription factor E3 (TFE3). Consistent with the key role of this network in CKD, Tgfa gene inactivation protected FVB/N mice from renal deterioration after nephron reduction. These data are relevant to human CKD, as we found that the TFE3/MITF‐A ratio was increased in patients with damaged kidneys. Our study uncovers a novel transcriptional network and unveils novel potential prognostic and therapeutic targets for preventing human CKD progression.
Entamoeba dispar: infrastructure, Surface Properties and Cytopathic Effect

The cytological features of Entamoeba dispar, recently recognized by biochemical and molecular biology criteria as a distinct species, were compared to those of Entamoeba histolytica. When cultured under axenic conditions, living trophozoites of E. dispar strain SAW 760RR clone A were more elongated in form, had a single frontal pseudopodium, and showed a noticeable uroid. In sections of E. dispar trophozoites stained with Toluidine blue, characteristic areas of cytoplasmic metachromasia were seen due to the presence of large deposits of glycogen, seldom found in E. histolytica strain HM1:IMSS. Under the light microscope the periphery of the nucleus in E. dispar was lined by finer, more regularly distributed dense granules. With transmission electron microscopy the surface coat of E. dispar was noticeable thinner. In addition, E. dispar had a lower sensitivity to agglutinate with concanavalin A and a higher negative surface charge, measured by cellular microelectrophoresis. The cytopathic effect of E. dispar was much slower, analyzed by the gradual loss of transmural electrical resistance of MDCK epithelial cell monolayers mounted in Ussing chambers. Whereas in E. histolytica phagocytosis of epithelial cells plays an important role in its cytopathic effect, E. dispar trophozoites placed in contact with MDCK cells showed only rare evidence of phagocytosis. The results demonstrate that the morphology of E. dispar is different to that of E. histolytica, both at the light microscopical and the ultrastructural levels. In addition, they show that E. dispar in axenic culture has a moderate cytopathic effect on epithelial cell monolayers. However, when compared to E. histolytica, the in vitro lytic capacity of E. dispar is much slower and less intense.
The Use of Communication to Motivate College Sales Teams

This study explored how sales managers and sales people construct and perform motivational communication. Sullivan's (1988) Motivational Language Theory (MLT) was used as a starting point. This theory is critiqued and reinterpreted within a framework emphasizing multiple communication goals and multiple levels of communication competence. Participants included 24 sales managers and sales representatives from University Directories, a major publishing company of campus telephone directories. A thematic analysis was conducted on interview notes and transcripts, from which three major and four minor themes emerged. The experiences of three sales teams are explored to contextualize the themes, to illustrate deficiencies in MLT, and to highlight the potential of the alternative theoretical framework for explaining motivational communication. Findings demonstrate that motivational communication acts often address multiple communication goals and are open to multiple interpretations. Motiva tional communication considered competent by employees typically addresses multiple goals (instrumental, identity, and relational) by strategies of integra tion or separation and fits employees' beliefs about what constitutes competent communication. Managers therefore must pay attention to the multiple implica tions and interpretations of their motivational attempts and must adapt their communication strategically to employees' beliefs and values.
The Relation Between Self-Beliefs and Academic Achievement: A Meta-Analytic Review

There has been extensive debate among scholars and practitioners concerning whether self-beliefs influence academic achievement. To address this question, findings of longitudinal studies investigating the relation between self-beliefs and achievement were synthesized using meta-analysis. Estimated effects are consistent with a small, favorable influence of positive self-beliefs on academic achievement, with an average standardized path or regression coefficient of . 08 for self-beliefs as a predictor of later achievement, controlling for initial levels of achievement. Stronger effects of self-beliefs are evident when assessing self-beliefs specific to the academic domain and when measures of self-beliefs and achievement are matched by domain (e.g., same subject area). Under these conditions, the relation of self-beliefs to later achievement meets or exceeds Cohen's (1988) definition of a small effect size.
Is the soft excess in AGN real

We systematically analyse all publicly available XMM-Newton spectra of radio-quiet PG quasars. The soft X-ray excess in these objects is well modelled by an additional, cool, Compton scattering region. However, the remarkably constant temperature derived for this component over the whole sample requires a puzzling ﬁne tuning of the parameters. Instead, we propose that the soft excess is an artifact of strong, relativistically smeared, partially ionized absorption. The strong jump in opacity at ∼ 0.7 keV from o vii , o viii and iron can lead to an apparent soft excess below this energy, which is trivially constant since it depends on atomic processes. This can have a dramatic eﬀect on the derived spectrum, which has implications for ﬁtting the relativistic smearing of the reﬂected iron line emission from the disc.
Teaching consecutive interpreting

The authors provide two perspectives on the teaching of consecutive interpreting: The pragmatic approach and the cognitive justification. Consecutive interpreting is described as requiring outstanding skills in language comprehension and production; the article provides relevant exercises to enhance these skills and features an overview of CI practice and teaching. It concludes with a list of references of published and non-published sources dealing with the wider aspects of the CI process.
Mother-to-Child HIV-1 Transmission Events Are Differentially Impacted by Breast Milk and Its Components from HIV-1-Infected Women

Breast milk is a vehicle of infection and source of protection in post-natal mother-to-child HIV-1 transmission (MTCT). Understanding the mechanism by which breast milk limits vertical transmission will provide critical insight into the design of preventive and therapeutic approaches to interrupt HIV-1 mucosal transmission. However, characterization of the inhibitory activity of breast milk in human intestinal mucosa, the portal of entry in postnatal MTCT, has been constrained by the limited availability of primary mucosal target cells and tissues to recapitulate mucosal transmission ex vivo. Here, we characterized the impact of skimmed breast milk, breast milk antibodies (Igs) and non-Ig components from HIV-1-infected Ugandan women on the major events of HIV-1 mucosal transmission using primary human intestinal cells and tissues. HIV-1-specific IgG antibodies and non-Ig components in breast milk inhibited the uptake of Ugandan HIV-1 isolates by primary human intestinal epithelial cells, viral replication in and transport of HIV-1- bearing dendritic cells through the human intestinal mucosa. Breast milk HIV-1-specific IgG and IgA, as well as innate factors, blocked the uptake and transport of HIV-1 through intestinal mucosa. Thus, breast milk components have distinct and complementary effects in reducing HIV-1 uptake, transport through and replication in the intestinal mucosa and, therefore, likely contribute to preventing postnatal HIV-1 transmission. Our data suggests that a successful preventive or therapeutic approach would require multiple immune factors acting at multiple steps in the HIV-1 mucosal transmission process.
Child Protection Conferences: A Framework for Chairperson Preparation

The transition to becoming a chairperson of child protection conferences can be a scary and lonely experience. This is alarming since we know that the chairperson is crucial to good outcomes for children. The roles and responsibilities of the chairperson are many and onerous, yet there is no agreed or 'correct' way to chair a child protection conference. Neither is there a correct formula or checklist. What is known, however, is that chairing any meeting involves a number of interpersonal skills and complex group dynamics, and each chairperson will develop a personal approach to the task. If they are forced to repeat a script prepared by someone else, a chairperson will feel awkward and constrained and an uneasy atmosphere can quickly inhibit the contributions of other members of the conference. There are, however, some useful 'tricks of the trade' that can be passed on to alert chairpersons to some of the important and common issues that allow them to consider how you may deal with them before being faced with difficulties in the middle of an emotionally charged child protection conference. This paper provides an overview on some of the steps needed to help chairpersons address their tasks effectively.
Improved inversion for seismic structure using transformed, S‐wavevector receiver functions: Removing the effect of the free surface

The determination of structure from the inversion of teleseismic receiver functions may be improved by removing the contribution of the free surface. The free surface interaction gives rise to the highest amplitude signal on standard receiver functions and yet this initial pulse tells us little about the receiver structure below the surface layer. We apply a transformation to P, S and Horizontal wavevector components, which removes the free surface response and hence the initial P‐pulse. A “pure” receiver function is calculated by deconvolving the S‐wavevector component with the P‐wavevector. In general, converted phase amplitudes within the receiver function waveform are better matched by the inverse algorithm, resulting in an improved estimation of seismic structure. In particular, low amplitude receiver function waveforms, often associated with poorly constrained structure, now yield a successful inverse.
Developing a Sociological Model for Researching Women’s Self and Social Identities

This paper presents an empirical model for researching women’s self and social identities. The model was devised as a theoretical and methodological framework to assist the author to recognize self-identity and social identity in single women’s narratives of their lives. Self-identity is understood as our own sense of ourselves as persons while social identity is categorizations of us by others. For those interested in researching the consequences of strong ideologies (such as familism) on women’s identities, or for recognizing resistance and understanding the development of new conceptions of womanhood, an empirical model which focuses our research attention on the self-identity of individual women is helpful.
Working Paper / Document de travail 2013-10 A New Linear Estimator for Gaussian Dynamic Term Structure Models

Bank of Canada working papers are theoretical or empirical works-in-progress on subjects in economics and finance. The views expressed in this paper are those of the author. No responsibility for them should be attributed to the Bank of Canada. and seminar participants at the Bank of Canada, CEMFI, and European Central Bank for their suggestions. Any remaining errors are my own. Abstract This paper proposes a novel regression-based approach to the estimation of Gaussian dynamic term structure models that avoids numerical optimization. This new estimator is an asymptotic least squares estimator defined by the no-arbitrage conditions upon which these models are built. We discuss some efficiency considerations of this estimator, and show that it is asymptotically equivalent to maximum likelihood estimation. Further, we note that our estimator remains easy-to-compute and asymptotically efficient in a variety of situations in which other recently proposed approaches lose their tractability. We provide an empirical application in the context of the Canadian bond market. Résumé Un cadre de régression novateur permettant d'éviter l'optimisation numérique est proposé pour l'estimation de modèles dynamiques gaussiens de la structure par terme des taux d'intérêt. Ce nouvel estimateur est un estimateur des moindres carrés asymptotiques et est défini par les conditions d'absence d'arbitrage à la base de ces modèles. L'auteur analyse les caractéristiques d'efficience de son estimateur et montre que celui-ci est asymptotiquement équivalent à un estimateur du maximum de vraisemblance. De plus, il reste simple à calculer et asymptotiquement efficient dans un éventail de situations où d'autres approches récentes deviennent très difficiles à utiliser. L'auteur présente une application empirique de son cadre au cas du marché obligataire canadien.
z ∼ 7–10 GALAXIES BEHIND LENSING CLUSTERS: CONTRAST WITH FIELD SEARCH RESULTS

We conduct a search for z ≳ 7 dropout galaxies behind 11 massive lensing clusters using 21 arcmin2 of deep Hubble Space Telescope NICMOS, ACS, and WFPC2 image data. In total, over this entire area, we find only one robust z ∼ 7 z-dropout candidate (previously reported around Abell 1689). Four less robust z-dropout and J-dropout candidates are also found. The nature of the four weaker candidates could not be precisely determined due to the limited depth of the available optical data, but detailed simulations suggest that all four are likely to be low-redshift interlopers. By contrast, we estimate that our robust candidate A1689-zD1 has <0.2% probability of being a low-redshift interloper. We compare these numbers with what we might expect using the z ∼ 7 UV luminosity function (LF) determined from field searches. We predict 2.7 z ∼ 7 z-dropouts and 0.3 z ∼ 9 J-dropouts over our cluster search area, in reasonable agreement with our observational results, given the small numbers. The number of z ≳ 7 candidates we find in the present search is much lower than that which has been reported in several previous studies of the prevalence of z ≳ 7 galaxies behind lensing clusters. To understand these differences, we examined z ≳ 7 candidates in other studies and conclude that only a small fraction are likely to be z ≳ 7 galaxies. Our findings support models that show that gravitational lensing from clusters is of the most value for detecting galaxies at magnitudes brighter than L* (H ≲ 27) where the LF is expected to be very steep. Use of these clusters to constrain the faint-end slope or determine the full LF is likely of less value due to the shallower effective slope measured for the LF at fainter magnitudes, as well as significant uncertainties introduced from modeling both the gravitational lensing and incompleteness.
Derived categories of coherent sheaves on rational homogeneous manifolds

Starting point of the present work is a conjecture of F. Catanese which says that in the derived category of coherent sheaves on any rational homogeneous manifold G/P there should exist a complete strong exceptional poset and a bijection of the elements of the poset with the Schubert varieties in G/P such that the partial order on the poset is the order induced by the Bruhat-Chevalley order. The goal of this work is to provide further evidence for Catanese's conjecture, clarify some aspects of it and supply new techniques. In particular we prove a theorem on the derived categories of quadric bundles, and show how one can find "small" generating sets for D^b(X) on symplectic or orthogonal isotropic Grassmannians by fibrational techniques. - The last section discusses a different approach based on a theorem of M. Brion and cellular resolutions of monomial ideals.
Reflection in teacher education: how can it be supported?

Abstract The main aim of this article is to explore the ways in which teacher educators can improve levels of reflection in postgraduate student teachers. The author argues that postgraduate student teachers are able to reflect on their practice in schools, and that the insights gained are useful in clarifying their own beliefs about teaching and learning. The outcome of such reflection at an early stage of their career may have implications for their ability to engage with the development opportunities made available to them as they move through their teaching careers. Using a qualitative approach, data from the learning journals and reflective writing assignments of student teachers, and a focus group interview, are examined in order to evaluate students' ability to engage in reflective writing at various stages over a 1 year course. The support given to students over the course of the year is examined with a view to evaluating its impact on students' abilities to reflect on their practice and their own learning. A number of recommendations are made for possible improvements to supporting student teachers in this important area of work.
The Rare Decay K + → π + νν̄ at the Next-to-Next-to-Leading Order in QCD

We calculate the complete next-to-next-to-leading order QCD correction of the charm quark contribution to the branching ratio for the rare decay K + → π + ν ¯ ν in the standard model. The inclusion of these O(αs) contributions leads to a significant reduction of the theoretical uncertainty from ±10.1% down to ±2.4% in the relevant parameter Pc, implying the left over scale uncertainties in B(K + → π + ν ¯ ν) and in the determination of |V td |, sin 2β and γ from the K → πν ¯ ν system to be ±1.3%, ±1.0%, ±0.006 and ±1.2 • , respectively. For the charm quark MS mass mc(mc) = (1.30 ± 0.05) GeV and |Vus| = 0.2248 the next-to-leading order value Pc = 0.37 ± 0.06 is modified to Pc = 0.37 ± 0.04 at the next-to-next-to-leading order level with the latter error fully dominated by the uncertainty in mc(mc). Adding the recently calculated long-distance contributions we find B(K + → π + ν ¯ ν) = (8.0 ± 1.1) × 10 −11 with the quoted error almost entirely due to the present uncertainties in mc(mc) and the Cabibbo-Kobayashi-Maskawa elements. The rare process K + → π + ν ¯ ν belongs to the theoretically cleanest decays in the field of K-and B-mesons. As it offers in conjunction with K L → π 0 ν ¯ ν a very clean determination of the standard unitarity triangle (UT) [1], a comparison of the information obtained from the K → πν ¯ ν system with the one from B-decays provides a critical and truly unique test of the Cabibbo-Kobayashi-Maskawa (CKM) mechanism in the standard model (SM) [2, 3]. Even if these K-and B-physics predictions agree, K + → π + ν ¯ ν will allow to discriminate between different extensions of the SM [2, 3], by probing effective scales of new physics operators of up to a several TeV or even higher [4]. In the SM the decay K + → π + ν ¯ ν proceeds through Z-penguin and electroweak box diagrams, that are sensitive to short-distance dynamics. As the required hadronic matrix elements can be extracted, including isospin breaking corrections [5], from the accurately measured leading semileptonic decay K + → π 0 e + ν, and the remaining long-distance contributions turn out to be small [6], and in principle calculable by means of lattice QCD [7], theoretical …