Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions among Polycomb Domains Are Guided by Chromosome Architecture

Polycomb group (PcG) proteins bind and regulate hundreds of genes. Previous evidence has suggested that long-range chromatin interactions may contribute to the regulation of PcG target genes. Here, we adapted the Chromosome Conformation Capture on Chip (4C) assay to systematically map chromosomal interactions in Drosophila melanogaster larval brain tissue. Our results demonstrate that PcG target genes interact extensively with each other in nuclear space. These interactions are highly specific for PcG target genes, because non-target genes with either low or high expression show distinct interactions. Notably, interactions are mostly limited to genes on the same chromosome arm, and we demonstrate that a topological rather than a sequence-based mechanism is responsible for this constraint. Our results demonstrate that many interactions among PcG target genes exist and that these interactions are guided by overall chromosome architecture.
Joint WMT 2013 Submission of the QUAERO Project

This paper describes the joint submission of the QUAERO project for the German! English translation task of the ACL 2013 Eighth Workshop on Statistical Machine Translation (WMT 2013). The submission was a system combination of the output of four different translation systems provided by RWTH Aachen University, Karlsruhe Institute of Technology (KIT), LIMSI-CNRS and SYSTRAN Software, Inc. The translations were joined using the RWTH’s system combination approach. Experimental results show improvements of up to 1.2 points in BLEU and 1.2 points in TER compared to the best single translation.
Outcome Evaluation of Surgical and Nonsurgical Management of Lumbar Disc Protrusion Causing Radiculopathy

Study Design. Prospective cohort study. Objective. To assess health-related quality of life (HRQOL) following either lumbar discectomy or nonoperative care for lumbar disc protrusion causing radiculopathy (LDPR). Summary of Background Data. Although LDPR is a prevalent disorder, little progress has been made in defining the optimal treatment strategy. Methods. A total of 497 patients (333 in the lumbar discectomy group and 164 in the nonoperative group) were analyzed. Patients completed baseline as well as 6- and 12-month generic (SF-36) and disease-specific (NASS Lumbar Spine Instrument) HRQOL measures. Demographic comparisons between groups, using standard descriptive statistics, were made. Multivariate analysis was used to obtain a regression coefficient for the primary outcome: the neurogenic symptoms score (NSS) from the NASS instrument. Outcome measures were compared between groups and to published normative data. Results. The mean baseline score was lower in the surgical group (30.9 nonoperative, 25.3 surgical), indicative of greater baseline disability. The scores at follow-up were approximately equivalent (44.6 nonoperative, 43.8 surgical). However, neither group returned to an age-matched normative NSS (51.6) within the timeframe of the study. Using regression analysis, the outcome “change in NSS” was not associated with variable “treatment group. ” Conclusions. HRQOL after LDPR, as measured in this study by NASS NSS, demonstrated similar improvement in both groups and was not meaningfully associated with the treatment received, within the timeframe of this study. At follow-up, all outcome measures remained lower than population normative scores, suggesting that, irrespective of treatment, an element of disability remained.
The distribution of synapsin I and synaptophysin in hippocampal neurons developing in culture

As a first step toward elucidating mechanisms involved in the sorting of synaptic vesicle proteins in neurons, we have used immunofluorescence microscopy to determine the distribution of two synaptic vesicle proteins, synapsin I and synaptophysin, in hippocampal neurons developing in culture. In mature cultures, synapsin I and synaptophysin immunoreactivity was concentrated in puncta that were restricted to sites where axons contacted neuronal cell bodies or dendrites. Electron-microscopic immunocytochemistry demonstrated that these puncta corresponded to vesicle-filled axonal varicosities that were exclusively presynaptic. At early stages of development, before cell-cell contact, both synapsin I and synaptophysin were preferentially localized in axons, where they were particularly concentrated in the distal axon and growth cone. In axons that did not contact other cells, immunostaining for these two proteins had a granular appearance, which persisted for at least 7 d, but focal accumulations of vesicles comparable to those seen at sites of synaptic contact were not observed. When neurons contacted one another, numerous puncta of synapsin I and synaptophysin formed within the first week in culture. Double-label immunofluorescence demonstrated that the two vesicle antigens were closely codistributed throughout these stages of development. These observations demonstrate that synaptic vesicle proteins assume a polarized distribution within nerve cells beginning early in development, as soon as the axon can be identified. In contrast, differences in microtubule polarity orientation that distinguish mature axons and dendrites, and that have been proposed to account for the selective sorting of some materials in nerve cells, first appear at a subsequent stage of development. The selective distribution of synaptic vesicle proteins to the axon occurs in isolated cells, independent of interactions with other cells. In contrast, the formation of large clusters of vesicles typical of presynaptic specializations requires contact with an appropriate postsynaptic target. Thus, in cultured hippocampal neurons, the localization of synaptic vesicles in presynaptic specializations is the result of sorting mechanisms intrinsic to individual neurons as well as to mechanisms mediated by cell-cell contact.
On Discriminative and Semi-Supervised Dimensionality Reduction

We are interested in using the goal of making predictions to influence dimensionality reduction procedures. A number of new methods are emerging aimed at combining attributes of generative and discriminative approaches to data modeling. New approaches to semi-supervised learning have also been emerging. We present and apply some new methods to non-linear and richly structured problems comparing and contrasting models designed for computer vision with those designed for text processing and discuss essential properties that need to be preserved when reducing dimensionality.
Nonlinear observers of tire forces and sideslip angle estimation applied to road safety: Simulation and experimental validation

Extensive research is focus on the stability control in the modern industrial auto-mobile society. Some active safety systems, such as Electronic Stability Program (ESP) and Traction Control System (TCS) have been widely used as safety option in our quotidian cars. These systems are based on the information which contains the motion characteristic of vehicle. Nevertheless, some complex safety system needs more information which can preferable describe the precise motion features, such as sideslip angle and tire forces. This article will principally present two non-linear observers: EKF (Extended Kalman filter) and PF (Particle filter) to estimate these variables, respectively. These observers are designed based on the non-linear double track model. The Dugoff model is used to elaborate the relation between tire forces and sideslip angle. Performances of these observers are tested by using the experimental data in real driving test, using our laboratory vehicle equipped with a real-time sampling and processing system. Particularly, the estimation process with EKF has been developed as a real-time application for the onboard test. Furthermore, a simulator is involved in the critical driving test which is hazardous in real driving condition.
Analyzing the Complexity of a Domain with Respect to an Information Extraction Task

In this paper we describe a method of classifying facts (information) into categories or levels; where each level signi(cid:12)es a di(cid:11)erent degree of syntactic complexity related to a fact. Based on this classi(cid:12)cation mechanism, we also propose a method of evaluating a domain by assigning to it a \domain number" based on the levels of a set of standard facts present in the articles of that domain
Understanding Renal Toxicity of Heavy Metals

The mechanisms by which metals induce renal injury are, in general, poorly understood. Characteristic features of metal nephrotoxicity are lesions that tend to predominate in specific regions of the nephron within specific cell types. This suggests that certain regions of the nephron are selectively sensitive to specific metals. Regional variability in sensitivity could result from the localization of molecular targets in certain cell populations and/or the localization of transport and binding ligands that deliver metals to targets within the nephron. Significant progress has been made in identifying various extracellular, membrane, and intracellular ligands that are important in the expression of the nephrotoxicity of metals. As an example, mercuric chloride induces a nephropathy that, at the lowest effective doses, is restricted primarily to the S3 segment of the proximal tubule, with involvement of the S2 and S1 segments at higher doses. This specificity appears to be derived, at least in part, from the distribution of enzymes and transport proteins important for the uptake of mercury into proximal tubule cells: apical γ-glutamyltranspeptidase and the basolateral organic anion transport system. Regional distributions of transport mechanisms for binding proteins appear to be important in the expression of nephrotoxicity of metals. These and other new research developments are reviewed.
Comparative transcriptome analysis reveals a regulatory network of microRNA-29b during mouse early embryonic development

MicroRNAs are endogenous ~22 nt RNAs that regulate gene expression by translational inhibition and mRNA destabilization. MicroRNA-29b (miR-29b) is essential for progression of mouse embryos past preimplantation development; however, details of the underlying regulatory network remain to be elucidated. Here, we used RNA sequencing to identify changes in the transcriptome of mouse embryos in response to miR-29b inhibition. Morula-stage embryos that had been subject to miR-29b inhibition throughout preimplantation development exhibited significant expression changes in 870 genes compared with controls. Among 405 genes that were downregulated, 30 genes encoded factors with known essential function during early embryonic development, including the pluripotent stem cell factor Nanog. We identified 19 genes encoding putative miR-29b target transcripts. These included Zbtb40, Hbp1, Ccdc117, Ypel2, Klf4, and Tmed9, which are upregulated at the 4-cell state of mouse development concomitant with miR-29b downregulation. Luciferase reporter analysis confirmed that Zbtb40, Hbp1, Ccdc117, Ypel2, and Klf4 transcripts are direct targets of miR-29b. These results suggest that miR-29b decreases the mRNA levels of several target genes during early mouse development, including the gene encoding the reprogramming factor Klf4. We hypothesize that inhibition of miR-29b causes overexpression of its target genes, triggering downstream signaling networks to decrease the expression of genes that are essential for embryonic development. In conclusion, miR-29b controls an extensive regulatory network in early mouse embryos, which comprises reprogramming factors and molecular regulators of post-transcriptional modification processes.
Traumatic cardiac arrest

Traumatic cardiac arrest is known to have a poor outcome, and some authors have stated that attempted resuscitation from traumatic cardiac arrest is futile. However, advances in damage control resuscitation and understanding of the differences in pathophysiology of traumatic cardiac arrest compared to medical cardiac arrest have led to unexpected survivors. Recently published data have suggested that outcome from traumatic cardiac arrest is no worse than that for medical causes of cardiac arrest, and in some groups may be better. This review highlights key areas of difference between traumatic cardiac arrest and medical cardiac arrest, and outlines a strategy for the management of patients in traumatic cardiac arrest. Standard Advanced Life Support algorithms should not be used for patients in traumatic cardiac arrest.
Effects of Inversion and Negation on Social Inferences from Faces

Judgments about personality and other social characteristics based on facial appearance are remarkably consistent across individuals. However, whereas the facial cues that underpin age and sex judgments are already well understood, the physical bases for judgments of characteristics such as intelligence or trustworthiness are still unknown. Inversion and photographic negation are used here to investigate the visual processes underlying social inferences from the face and to explore whether various judgments might rely on different perceptual representations. In experiment 1, the perceptions of age, sex, attractiveness, approachability, intelligence, and trustworthiness, but not distinctiveness, were affected by inversion, and all these characteristics were affected by negation. The effects of inversion and negation were independent, suggesting that they impaired the encoding of different types of information. Moreover, an independent manipulation of hue and luminance in experiment 2 showed that the effects of negation were mainly due to the reversal of luminance values. These results are consistent with the view that information about the configuration of features (the processing of which is impaired by inversion) and information about surface properties (the processing of which is impaired by brightness negation) are both used in the perception of social characteristics from faces. In addition, the fact that there was a similar pattern of impairment across most judgments suggests that there is an initial common perceptual representation of the face, from which most characteristics are inferred.
Towards Automated Large-Scale 3D Phenotyping of Vineyards under Field Conditions

In viticulture, phenotypic data are traditionally collected directly in the field via visual and manual means by an experienced person. This approach is time consuming, subjective and prone to human errors. In recent years, research therefore has focused strongly on developing automated and non-invasive sensor-based methods to increase data acquisition speed, enhance measurement accuracy and objectivity and to reduce labor costs. While many 2D methods based on image processing have been proposed for field phenotyping, only a few 3D solutions are found in the literature. A track-driven vehicle consisting of a camera system, a real-time-kinematic GPS system for positioning, as well as hardware for vehicle control, image storage and acquisition is used to visually capture a whole vine row canopy with georeferenced RGB images. In the first post-processing step, these images were used within a multi-view-stereo software to reconstruct a textured 3D point cloud of the whole grapevine row. A classification algorithm is then used in the second step to automatically classify the raw point cloud data into the semantic plant components, grape bunches and canopy. In the third step, phenotypic data for the semantic objects is gathered using the classification results obtaining the quantity of grape bunches, berries and the berry diameter.
BeppoSAX spectroscopy of the luminous X-ray sources in M33

The nearby galaxy M33 was observed by the imaging X-ray instruments on-board BeppoSAX. Two observations at different phases of the 105.9 day intensity cycle of the luminous central source X-8 failed to reveal the expected modulation, suggesting that it is probably transitory. Similar behavior has been observed from several X-ray binary sources. This strengthens somewhat the idea that M33 X-8 is a black hole accreting from a binary companion. The 0.2-10 keV spectrum of M33 X-8 can best be modeled by an absorbed power-law with a photon index of 1.89 +0.40 -0.79 and a disk-blackbody with a temperature, kT, of 1.10 +/0 0.05 keV and a projected inner-disk radius of 55.4 +6.0 -7.7 km. This spectral shape is in good agreement with earlier ASCA results. The 2-10 keV spectra of M33 X-4, X-5, X-7, X-9 and X-10 are all consistent with power-law or bremsstrahlung models, whilst that of X-6 appears to be significantly more complex and may be reasonably well modeled with a disk-blackbody with kT = 1.7 +/- 0.2 keV and a projected inner-disk radius of 7 +/- 2 km. The spectrum of M33 X-9 is rather hard with a photon index of 1.3. Compared to earlier Einstein and ROSAT observations, M33 X-7 and X-9 varied in intensity, M33 X-4, X-6, and X-10 may have varied and M33 X-5 remained constant.
Stark spectroscopy of mixed-valence systems

Many mixed-valence systems involve two or more states with different electric dipole moments whose magnitudes depend upon the charge transfer distance and the degree of delocalization; these systems can be interconverted by excitation of an intervalence charge transfer transition. Stark spectroscopy involves the interaction between the change in dipole moment of a transition and an electric field, so the Stark spectra of mixed-valence systems are expected to provide quantitative information on the degree of delocalization. In limiting cases, a classical Stark analysis can be used, but in intermediate cases the analysis is much more complex because the field affects not only the band position but also the intrinsic bandshape. Such non-classical Stark effects lead to widely different bandshapes. Several examples of both classes are discussed. Because electric fields are applied to immobilized samples, complications arise from inhomogeneous broadening, along with other effects that limit our ability to extract unique parameters in some cases. In the case of the radical cation of the special pair in photosynthetic reaction centres, where the mixed-valence system is in a very complex but structurally well-defined environment, a detailed analysis can be performed.
Moral reasoning among Nigerian and Northern Irish children : the impact of political conflict

The Moral and Social Action Interdisciplinary Colloquium (MOSAIC) is an international multidisciplinary network of scholars working within the fields of the philosophy, psychology and sociology of moral development, moral education and moral thought. MOSAIC runs an annual conference, traditionally in June or July. This conference attracts an international mix of doctoral students, early career researchers and more established academics. The theme of the 2005 conference, held at the Universität Konstanz in Germany, was the moral and religious challenges facing education in Europe. The programme was diverse, with papers covering topics as varied as values education, religious orientation, morality across cultures, measuring morality, individual differences and moral domains. The inaugural lecture, delivered by Reinhard Hesse of the Pedagogical University of Freiburg, Switzerland, discussed how global changes impact on ethical reasoning and how, in an age of nuclear arsenals, ethics and science are welded together. He concluded that individuals must do all they can to sustain the globe and change destructive human urges. This research review aims to showcase some of the research presented at this MOSAIC conference. A selection of seven abstracts extended and edited to form summaries demonstrates the varied research in the fields of moral development, moral education and moral thought currently being undertaken by MOSAIC members. These provide a resource for those involved in, or who intend to embark on, related work. The first summary, from Mudje Koca of Liverpool Hope University, UK, is concerned with the implicit barriers faced by university students living with a disability. The next two summaries explore the challenges ethno-religious conflict pose for moral development. Marijana Handziska of Ss Cyril & Methodius University, Republic of Macedonia, focused on the impact that living during a period of political instability in the Republic of Macedonia had on the moral competence of Macedonian adolescents, whilst I explored how differences in the intensity of ethno-political conflicts impact on moral maturity. Both studies illustrated the negative and regressive impact political violence has on moral development. Sieglinde Weyringer and Jean-Luc Patry of the University of Salzburg, Austria, presented a values education programme being pioneered in Austria. Georg Lind, from the University of Konstanz, Germany, reflected on the 30th anniversary of the Moral Judgment Test (MJT; Lind & Wakenhut, 1985) by presenting the findings from 17 validation studies. The presentation illustrated the development of Journal of Moral Education Vol. 35, No. 1, March 2006, pp. 129–136
Self-Confirming Price Prediction for Bidding in Simultaneous Ascending Auctions

Simultaneous ascending auctions present agents with the exposure problem: bidding to acquire a bundle risks the possibility of obtaining an undesired subset of the goods. Auction theory provides little guidance for dealing with this problem. We present a new family of decision-theoretic bidding strategies that use probabilistic predictions of final prices. We focus on self-confirming price distribution predictions, which by definition turn out to be correct when all agents bid decision-theoretically based on them. Bidding based on these is provably not optimal in general, but our experimental evidence indicates the strategy can be quite effective compared to other known methods.
Perfusion Fixation of Kidneys and Lungs

GIomerular podocytes are invested with a thick layer of cell surface fuzzy coat, presumably a carbohydrate-rich husk, glycocalyx, of cell periphery (1). The podocyte fuzzy coat is particularly rich in anionic sialoproteins (2, 3), which also fill the interpedicellar slits (4, 5) and may be part of the anionic charge barrier of the glomerular filter. Decrease in the colloidal iron-stainable sialoproteins has been documented in experimental animal (6) as well as human (7) nephrotic syndrome, when glomerular capillary permeability is increased. Interactions of polycations with the fuzzy coat polyanions cause rapid and profound alterations of podocyte structure (8), suggesting that binding of ligands to the cell surface sentinel molecules may modulate the structural as well as functional state of podocytes. Interest in the podocyte fuzzy coat is fur ther heightened by the discovery (9) that antibodies against one of the podocyte cell surface glycoproteins, gp330, may be responsible for in situ immune complex formation (10) and the membranous glomerulopathy seen in experimental Heymann 's nephritis. Recently, Kerjaschki, Sharkey, and Farquhar (11) fur ther identified a major sialoprotein in the podocyte fuzzy coat, a 140 kilodalton (kD) molecule called podocalyxin. In this report, we describe the identification and characterization of another novel podocyte fuzzy coat protein, podoendin, using a monoclonal antibody (mAb) 1 developed in our laboratory. The 62 kD protein is also found on the endothelial cell surface.