Miracle-dz/UniFAR-FTUs huggingface dataset:
A Subfamily of Dr Adhesins of Escherichia coli Bind Independently to Decay-accelerating Factor and the N-domain of Carcinoembryonic Antigen*

Escherichia coli expressing the Dr family of adhesins adheres to epithelial cells by binding to decay-accelerating factor (DAF) and carcinoembryonic antigen (CEA)-related cell surface proteins. The attachment of bacteria expressing Dr adhesins to DAF induces clustering of DAF around bacterial cells and also recruitment of CEA-related cell adhesion molecules. CEA, CEACAM1, and CEACAM6 have been shown to serve as receptors for some Dr adhesins (AfaE-I, AfaE-III, DraE, and DaaE). We demonstrate that AfaE-I, AfaE-V, DraE, and DaaE adhesins bind to the N-domain of CEA. To identify the residues involved in the N-CEA/DraE interaction, we performed SPR binding analyses of naturally occurring variants and a number of randomly generated mutants in DraE and N-CEA. Additionally, we used chemical shift mapping by NMR to determine the surface of DraE involved in N-CEA binding. These results show a distinct CEA binding site located primarily in the A, B, E, and D strands of the Dr adhesin. Interestingly, this site is located opposite to the β-sheet encompassing the previously determined binding site for DAF, which implies that the adhesin can bind simultaneously to both receptors on the epithelial cell surface. The recognition of CEACAMs from a highly diverse DrCEA subfamily of Dr adhesins indicates that interaction with these receptors plays an important role in niche adaptation of E. coli strains expressing Dr adhesins.
March of the Froblins: simulation and rendering massive crowds of intelligent and detailed creatures on GPU

Artificial intelligence (AI) is generally considered to be one of the key components of a computer game. Sometimes when we play a game, we may wish that the computer opponents were written better. At those times while playing against the computer, we feel that the game is unbalanced. Perhaps the computer player has been given different set of rules, or uses the same rules, but has more resources (health, weapons, etc.). The complexity of underlying AI systems, along with game design, belies the resulting feeling we have when playing any game. As the CPU and GPU speed and power continues to grow, along with increasing memory amounts and bandwidth, game developers are constantly improving the graphics of their games. In the last five years the production quality of games has been increasing (along with the corresponding budgets). Recent games woo players with incredible breakthroughs in real- time 3D graphics, complexity of the worlds and characters, as well as various post-processing effects. And while there had been tremendous improvements for parallelizing rendering through the evolution of consumer GPU pipelines, artificial intelligence computations are treading behind. To date, there had been rather few attempts at parallelizing AI computations.
Persian part of speech tagger based on Hidden Markov Model

This paper introduces the Persian Part of Speech (POS) tagger, based on the Hidden Markov Models (HMM). This POS tagger is part of the Persian Text-to-Speech (TTS) system called ParsGooyan. The tagger supports some properties of TTS systems, such as Break Phrase Detection, Homograph words Disambiguation, and Lexical Stress Search. A POS lexicon with 61,521 entries and 64,003 trigrams is used as the language model. It is implemented in Festival software and makes use of the Viterbi Decoder provided by Edinburgh Speech Tools. The average overall accuracy for this tagger is 95.11%. The accuracy of the known and unknown words is 96.136% and 60.25%, respectively.
Long‐term hospitalisation rates among 5‐year survivors of Hodgkin lymphoma in adolescence or young adulthood: A nationwide cohort study

In the present study, we report on the full range of physical diseases acquired by survivors of Hodgkin lymphoma diagnosed in adolescence or young adulthood. In a Danish nationwide population‐based cohort study, 1,768 five‐year survivors of Hodgkin lymphoma diagnosed at ages 15–39 years during 1943–2004 and 228,447 comparison subjects matched to survivors on age and year of birth were included. Hospital discharge diagnoses and bed‐days during 1977–2010 were obtained from the Danish Patient Register for 145 specific disease categories gathered in 14 main diagnostic groups. The analysis was conducted separately on three subcohorts of survivors, that is, survivors diagnosed 1943–1976 for whom we had no information on rehospitalisation for Hodgkin lymphoma and survivors diagnosed 1977–2004, split into a subcohort with no expected relapses and a subcohort for whom a rehospitalisation for Hodgkin lymphoma indicated a relapse. The overall standardised hospitalisation rate ratios (RRs) were 2.0 [95% confidence interval (CI), 1.9–2.1], 1.5 (1.4–1.6) and 2.9 (2.6–3.1) respectively, and the corresponding RRs for bed‐days were 3.5 (3.4–3.5), 1.8 (1.8–1.9) and 10.4 (10.3–10.6). Highest RRs were seen for nonmalignant haematological conditions (RR: 2.6; 3.1 and 9.7), malignant neoplasms (RR: 3.2; 2.5 and 4.7) and all infections combined (RR: 2.5; 2.2 and 5.3). Survivors of Hodgkin lymphoma in adolescence or young adulthood are at increased risk for a wide range of diseases that require hospitalisation. The risk depends on calendar period of treatment and on whether the survivors were rehospitalised for Hodgkin lymphoma, and thus likely had a relapse.
Attributed Relational Graph Based Feature Extraction of Body Poses In Indian Classical Dance Bharathanatyam

Articulated body pose estimation in computer vision is an important problem because of convolution of the models. It is useful in real time applications such as surveillance camera, computer games, human computer interaction etc. Feature extraction is the main part in pose estimation which helps for a successful classification. In this paper, we propose a system for extracting the features from the relational graph of articulated upper body poses of basic Bharatanatyam steps, each performed by different persons of different experiences and size. Our method has the ability to extract features from an attributed relational graph from challenging images with background clutters, clothing diversity, illumination etc. The system starts with skeletonization process which determines the human pose and increases the smoothness using B-Spline approach. Attributed relational graph is generated and the geometrical features are extracted for the correct discrimination between shapes that can be useful for classification and annotation of dance poses. We evaluate our approach experimentally on 2D images of basic Bharatanatyam poses.
Neural Induction in Xenopus: Requirement for Ectodermal and Endomesodermal Signals via Chordin, Noggin, β-Catenin, and Cerberus

The origin of the signals that induce the differentiation of the central nervous system (CNS) is a long-standing question in vertebrate embryology. Here we show that Xenopus neural induction starts earlier than previously thought, at the blastula stage, and requires the combined activity of two distinct signaling centers. One is the well-known Nieuwkoop center, located in dorsal-vegetal cells, which expresses Nodal-related endomesodermal inducers. The other is a blastula Chordin- and Noggin-expressing (BCNE) center located in dorsal animal cells that contains both prospective neuroectoderm and Spemann organizer precursor cells. Both centers are downstream of the early β-Catenin signal. Molecular analyses demonstrated that the BCNE center was distinct from the Nieuwkoop center, and that the Nieuwkoop center expressed the secreted protein Cerberus (Cer). We found that explanted blastula dorsal animal cap cells that have not yet contacted a mesodermal substratum can, when cultured in saline solution, express definitive neural markers and differentiate histologically into CNS tissue. Transplantation experiments showed that the BCNE region was required for brain formation, even though it lacked CNS-inducing activity when transplanted ventrally. Cell-lineage studies demonstrated that BCNE cells give rise to a large part of the brain and retina and, in more posterior regions of the embryo, to floor plate and notochord. Loss-of-function experiments with antisense morpholino oligos (MO) showed that the CNS that forms in mesoderm-less Xenopus embryos (generated by injection with Cerberus-Short [CerS] mRNA) required Chordin (Chd), Noggin (Nog), and their upstream regulator β-Catenin. When mesoderm involution was prevented in dorsal marginal-zone explants, the anterior neural tissue formed in ectoderm was derived from BCNE cells and had a complete requirement for Chd. By injecting Chd morpholino oligos (Chd-MO) into prospective neuroectoderm and Cerberus morpholino oligos (Cer-MO) into prospective endomesoderm at the 8-cell stage, we showed that both layers cooperate in CNS formation. The results suggest a model for neural induction in Xenopus in which an early blastula β-Catenin signal predisposes the prospective neuroectoderm to neural induction by endomesodermal signals emanating from Spemann's organizer.
Entity relation discovery from web tables and links

The World-Wide Web consists not only of a huge number of unstructured texts, but also a vast amount of valuable structured data. Web tables [2] are a typical type of structured information that are pervasive on the web, and Web-scale methods that automatically extract web tables have been studied extensively [1]. Many powerful systems (e.g.OCTOPUS [4], Mesa [3]) use extracted web tables as a fundamental component. In the database vernacular, a table is defined as a set of tuples which have the same attributes. Similarly, a web table is defined as a set of rows (corresponding to database tuples) which have the same column headers (corresponding to database attributes). Therefore, to extract a web table is to extract a relation on the web. In databases, tables often contain foreign keys which refer to other tables. Therefore, it follows that hyperlinks inside a web table sometimes function as foreign keys to other relations whose tuples are contained in the hyperlink's target pages. In this paper, we explore this idea by asking: can we discover new attributes for web tables by exploring hyperlinks inside web tables? This poster proposes a solution that takes a web table as input. Frequent patterns are generated as new candidate relations by following hyperlinks in the web table. The confidence of candidates are evaluated, and trustworthy candidates are selected to become new attributes for the table. Finally, we show the usefulness of our method by performing experiments on a variety of web domains.
Virtual Sculptor FP : A Feature Preserving Multiresolution Volumetric Sculpting System

Volumetric sculpting has been developed for years, but real application still lacks of accuracy and suffers from tremendous space consumption. To avoid these drawbacks, a multiresolution volumetric sculpting system with feature preserving is proposed. Manipulating with extended Marching Cube algorithm (EMC), features of 3D mesh model are well preserved on multiresolution isosurface. To apply EMC to volumetric sculpting without defects, a feature refinement strategy is proposed to prevent out-of-range feature and undetected feature. Moreover, in order to represent the details of intersecting graver via curvature threshold, surface is refined to the level of detail (LOD) based on the curvature of the graver shape. Above all, our refinement strategy results in uniform and elegant representations for both carving and filling operations under multiresolution. Besides basic Constructive Solid Geometry (CSG) operations and color painting, we also integrate a force feedback device, the PHANToM, into our system to provide realistic force simulation based on the tangent-plane force model.
Capacity and Utilization of Blood Culture in Two Referral Hospitals in Indonesia and Thailand

Abstract. It is generally recommended that sepsis patients should have at least two blood cultures obtained before antimicrobial therapy. From 1995 to 2015, the number of blood cultures taken each year in a 1,100-bed public referral hospital in Ubon Ratchathani northeast Thailand rose from 5,235 to 56,719, whereas the number received in an 840-bed referral public hospital in South Sulawesi, Indonesia, in 2015 was 2,779. The proportion of patients sampled for blood cultures out of all inpatients in South Sulawesi in 2015 (9%; 2,779/30,593) was lower than that in Ubon Ratchathani in 2003 (13%; 8,707/66,515), at a time when health expenditure per capita in the two countries was comparable. Under-use of bacterial cultures may lead to an underestimate and underreporting of the incidence of antimicrobial-resistant infections. Raising capacity and utilization of clinical microbiology laboratories in developing countries, at least at sentinel hospitals, to monitor the antimicrobial resistance situation should be prioritized.
The self-feeding process: a unifying model for communication dynamics in the web

How often do individuals perform a given communication activity in the Web, such as posting comments on blogs or news? Could we have a generative model to create communication events with realistic inter-event time distributions (IEDs)? Which properties should we strive to match? Current literature has seemingly contradictory results for IED: some studies claim good fits with power laws; others with non-homogeneous Poisson processes. Given these two approaches, we ask: which is the correct one? Can we reconcile them all? We show here that, surprisingly, both approaches are correct, being corner cases of the proposed Self-Feeding Process (SFP). We show that the SFP (a) exhibits a unifying power, which generates power law tails (including the so-called "top-concavity" that real data exhibits), as well as short-term Poisson behavior; (b) avoids the "i.i. d. fallacy", which none of the prevailing models have studied before; and (c) is extremely parsimonious, requiring usually only one, and in general, at most two parameters. Experiments conducted on eight large, diverse real datasets (e.g., Youtube and blog comments, e-mails, SMSs, etc) reveal that the SFP mimics their properties very well.
Numerical approach for separation and movement of the fingers of the HUGO model for analysis of SAR distribution

The aim of this paper is to describe a numerical approach for separation and movement of the fingers of the human body model HUGO, which is implemented as an enhancement of the “BodyFlex” application. The algorithm allows the generation of a proper posture of the HUGO model's hand for evaluation of the electromagnetic effects from mobile phones through the analysis and comparison of the SAR values. Non-axis aligned control lattices aligned with the position of the fingers were introduced, in order to optimally treat the movement of the fingers, which are bent over the lower part of the abdomen in the original model.
Ensemble: A Hybrid Human-Machine System for Generating Melody Scores from Audio

Music transcription is a highly complex task that is difﬁ-cult for automated algorithms, and equally challenging to people, even those with many years of musical training. Furthermore, there is a shortage of high-quality datasets for training automated transcription algorithms. In this research, we explore a semi-automated, crowdsourced approach to generate music transcriptions, by ﬁrst running an automatic melody transcription algorithm on a (poly-phonic) song to produce a series of discrete notes representing the melody, and then soliciting the crowd to correct this melody. We present a novel web-based interface that enables the crowd to correct transcriptions, report re-sults from an experiment to understand the capabilities of non-experts to perform this challenging task, and characterize the characteristics and actions of workers and how they correlate with transcription performance.
Rigid-body Ligand Recognition Drives Cytotoxic T-lymphocyte Antigen 4 (CTLA-4) Receptor Triggering

The inhibitory T-cell surface-expressed receptor, cytotoxic T lymphocyte-associated antigen-4 (CTLA-4), which belongs to the class of cell surface proteins phosphorylated by extrinsic tyrosine kinases that also includes antigen receptors, binds the related ligands, B7-1 and B7-2, expressed on antigen-presenting cells. Conformational changes are commonly invoked to explain ligand-induced “triggering” of this class of receptors. Crystal structures of ligand-bound CTLA-4 have been reported, but not the apo form, precluding analysis of the structural changes accompanying ligand binding. The 1.8-Å resolution structure of an apo human CTLA-4 homodimer emphasizes the shared evolutionary history of the CTLA-4/CD28 subgroup of the immunoglobulin superfamily and the antigen receptors. The ligand-bound and unbound forms of both CTLA-4 and B7-1 are remarkably similar, in marked contrast to B7-2, whose binding to CTLA-4 has elements of induced fit. Isothermal titration calorimetry reveals that ligand binding by CTLA-4 is enthalpically driven and accompanied by unfavorable entropic changes. The similarity of the thermodynamic parameters determined for the interactions of CTLA-4 with B7-1 and B7-2 suggests that the binding is not highly specific, but the conformational changes observed for B7-2 binding suggest some level of selectivity. The new structure establishes that rigid-body ligand interactions are capable of triggering CTLA-4 phosphorylation by extrinsic kinase(s).
Effects of homeostatic constraints on associative memory storage and synaptic connectivity of cortical circuits

The impact of learning and long-term memory storage on synaptic connectivity is not completely understood. In this study, we examine the effects of associative learning on synaptic connectivity in adult cortical circuits by hypothesizing that these circuits function in a steady-state, in which the memory capacity of a circuit is maximal and learning must be accompanied by forgetting. Steady-state circuits should be characterized by unique connectivity features. To uncover such features we developed a biologically constrained, exactly solvable model of associative memory storage. The model is applicable to networks of multiple excitatory and inhibitory neuron classes and can account for homeostatic constraints on the number and the overall weight of functional connections received by each neuron. The results show that in spite of a large number of neuron classes, functional connections between potentially connected cells are realized with less than 50% probability if the presynaptic cell is excitatory and generally a much greater probability if it is inhibitory. We also find that constraining the overall weight of presynaptic connections leads to Gaussian connection weight distributions that are truncated at zero. In contrast, constraining the total number of functional presynaptic connections leads to non-Gaussian distributions, in which weak connections are absent. These theoretical predictions are compared with a large dataset of published experimental studies reporting amplitudes of unitary postsynaptic potentials and probabilities of connections between various classes of excitatory and inhibitory neurons in the cerebellum, neocortex, and hippocampus.
On the Polyhedral Decision Problem

Computational problems sometimes can be cast in the following form: Given a point ${\bf x}$ in $R^n $, determine if ${\bf x}$ lies in some fixed polyhedron. In this paper we give a general lower bound to the complexity of such problems, showing that $\frac{1}{2}\log _2 f_s $ linear comparisons are needed in the worst case, for any polyhedron with $f_s$s-dimensional faces. For polyhedra with abundant faces, this leads to lower bounds nonlinear in n, the number of variables.
Apixaban pharmacodynamic activity in umbilical cord, paediatric, and adult plasma

Summary The objective was to characterise apixaban pharmacodynamic (PD) activity in umbilical cord (UC), paediatric, and adult plasma. Plasma was obtained from blood samples from six UC donors, 70 paediatric (neonates [birth–≤1 month], infants [>1–≤6 months], toddlers [>6 months–≤2 years], young children [>2–≤6 years], children [>6–≤12 years], adolescents [>12–≤18 years]), and six adult (19–45 years) subjects. Plasma spiked with apixaban 0 (baseline), 30, or 110 ng/ml was analysed for anti-factor Xa activity, factor X levels, prothrombin time (PT), and modified PT (mPT). Apixaban had similar concentration-related effects on anti-factor Xa activity across groups (30 ng/ml: 0.223–0.295 IU/ml; 110 ng/ml: 1.212–1.474 IU/ml). Endogenous baseline factor X levels were 43%–68% lower in plasma from UC and subjects ≤6 months versus adults. Factor Xa inhibition (percentage change from baseline in apparent factor X levels) was similar for both apixaban concentrations across groups, except UC, neonate, and infant groups, which showed greater inhibition vs adults for apixaban 110 ng/ml. Baseline PT and mPT were similar across groups. Apixaban had no effect on PT at the concentrations tested. Apixaban 110 ng/ml prolonged mPT similarly across groups (44.4–53.2 s to 64.5–70.0 s); no prolongation was found with apixaban 30 ng/ml. Apixaban demonstrated consistent concentration-related effects on other PD endpoints in plasma samples from all age groups, except factor Xa inhibition. Supplementary Material to this article is available at www.thrombosis-online.com.
Mean body temperature does not modulate eccrine sweat rate during upright tilt.

Conflicting reports exist about the role of baroreflexes in efferent control of eccrine sweat rate. These conflicting reports may be due to differing mean body temperatures between studies. The purpose of this project was to test the hypothesis that mean body temperature modulates the effect of head-up tilt on sweat rate and skin sympathetic nerve activity (SSNA). To address this question, mean body temperature (0.9.internal temperature + 0.1.mean skin temperature), SSNA (microneurography of peroneal nerve, n = 8), and sweat rate (from an area innervated by the peroneal nerve and from two forearm sites, one perfused with neostigmine to augment sweating at lower mean body temperatures and the second with the vehicle, n = 12) were measured in 13 subjects during multiple 30 degrees head-up tilts during whole body heating. At the end of the heat stress, mean body temperature (36.8 +/- 0.1 to 38.0 +/- 0.1 degrees C) and sweat rate at all sites were significantly elevated. No significant correlations were observed between mean body temperature and the change in SSNA during head-up tilt (r = 0.07; P = 0.62), sweating within the innervated area (r = 0.06; P = 0.56), sweating at the neostigmine treated site (r = 0.04; P = 0.69), or sweating at the control site (r = 0.01; P = 0.94). Also, for each tilt throughout the heat stress, there were no significant differences in sweat rate (final tilt sweat rates were 0.69 +/- 0.11 and 0.68 +/- 0.11 mg.cm(-2). min(-1) within the innervated area; 1.04 +/- 0.16 and 1.06 +/- 0.16 mg.cm(-2). min(-1) at the neostigmine-treated site; and 0.85 +/- 0.15 and 0.85 +/- 0.15 mg.cm(-2). min(-1) at the control site, for supine and tilt, respectively). Hence, these data indicate that mean body temperature does not modulate eccrine sweat rate during baroreceptor unloading induced via 30 degrees head-up tilt.