Miracle-dz/UniFAR-FTUs huggingface dataset:
Visual exploration of relationships between document clusters

The visualization of networks with additional attributes attached to the network elements is one of the ongoing challenges in the information visualization domain. Such so-called multivariate networks regularly appear in various application fields, for instance, in data sets which describe friendship networks or co-authorship networks. Here, we focus on networks that are based on text documents, i.e., the network nodes represent documents and the edges show relationships between them. Those relationships can be derived from common topics or common co-authors. Attached attributes may be specific keywords (topics), keyword frequencies, etc. The analysis of such multivariate networks is challenging, because a deeper understanding of the data provided depends on effective visualization and interaction techniques that are able to bring all types of information together. In addition, automatic analysis methods should be used to support the analysis process of potentially large amounts of data. In this paper, we present a visualization approach that tackles those analysis problems. Our implementation provides a combination of new techniques that shows intra-cluster and inter-cluster relations while giving insight into the content of the cluster attributes. Hence, it facilitates the interactive exploration of the networks under consideration by showing the relationships between node clusters in context of network topology and multivariate attributes.
Entry, Exit and Productivity: Empirical Results for German Manufacturing Industries

Abstract From a model by Hopenhayn, three hypotheses can be derived: (H1) Firms that exit in year t were less productive in t -1 than firms that continue to produce in t. (H2) Firms that enter in year t are less productive than incumbent firms in year t. (H3) Surviving firms from an entry cohort were more productive than nonsurviving firms from this cohort in the start year. This paper uses unique newly available panel datasets for all manufacturing plants from Germany (1995-2002) to test these hypotheses. All three hypotheses are supported empirically for West and East Germany.
Modular Small Diameter Vascular Grafts with Bioactive Functionalities

We report the fabrication of a novel type of artificial small diameter blood vessels, termed biomimetic tissue-engineered blood vessels (bTEBV), with a modular composition. They are composed of a hydrogel scaffold consisting of two negatively charged natural polymers, alginate and a modified chitosan, N,O-carboxymethyl chitosan (N,O-CMC). Into this biologically inert scaffold two biofunctionally active biopolymers are embedded, inorganic polyphosphate (polyP) and silica, as well as gelatin which exposes the cell recognition signal, Arg-Gly-Asp (RGD). These materials can be hardened by exposure to Ca2+ through formation of Ca2+ bridges between the polyanions, alginate, N,O-CMC, and polyP (alginate-Ca2+-N,O-CMC-polyP). The bTEBV are formed by pressing the hydrogel through an extruder into a hardening solution, containing Ca2+. In this universal scaffold of the bTEBV biomaterial, polycations such as poly(l-Lys), poly(d-Lys) or a His/Gly-tagged RGD peptide (three RGD units) were incorporated, which promote the adhesion of endothelial cells to the vessel surface. The mechanical properties of the biopolymer material (alginate-Ca2+-N,O-CMC-polyP-silica) revealed a hardness (elastic modulus) of 475 kPa even after a short incubation period in CaCl2 solution. The material of the artificial vascular grafts (bTEBVs with an outer size 6 mm and 1.8 mm, and an inner diameter 4 mm and 0.8 mm, respectively) turned out to be durable in 4-week pulsatile flow experiments at an alternating pressure between 25 and 100 mbar (18.7 and 75.0 mm Hg). The burst pressure of the larger (smaller) vessels was 850 mbar (145 mbar). Incorporation of polycationic poly(l-Lys), poly(d-Lys), and especially the His/Gly-tagged RGD peptide, markedly increased the adhesion of human, umbilical vein/vascular endothelial cells, EA.HY926 cells, to the surface of the hydrogel. No significant effect of the polyP samples on the clotting of human plasma is measured. We propose that the metabolically degradable polymeric scaffold bTEBV is a promising biomaterial for future prosthetic vascular grafts.
Identification of an alternative polyadenylation site in the human C3b/C4b receptor (complement receptor type 1) transcriptional unit and prediction of a secreted form of complement receptor type 1

The human C3b/C4b receptor or complement receptor type one (CR1) is an approximately 200-kD single chain membrane glycoprotein of human peripheral blood cells that mediates the binding, processing, and transport of C3b-bearing immune complexes and regulates the activity of the complement cascade. Analysis of partial cDNA clones has shown that the COOH terminus is composed predominantly of three tandemly repeated regions of 450 amino acids each (15). In this report, we present a cDNA sequence that encodes the NH2 terminus of CR1. It appears to have been derived from an alternatively processed transcript, caused by polyadenylation occurring at a site within an intron in the CR1 transcriptional unit. The resulting truncated messenger carries an open reading frame that would produce a short, secreted CR1 form. We present genomic sequences and Northern blots which support this hypothesis and we propose that the NH2-terminal end of CR1 is a likely location for active sites. In addition, we report evidence for a CR1-like sequence in the human genome and we present a model for the organization of CR1.
Coflex: Navigating the fairness-efficiency tradeoff for coflow scheduling

Fair and efficient coflow scheduling improves application-level networking performance in today's datacenters. Ideally, a coflow scheduler should provide isolation guarantees on the minimum coflow progress to achieve predictable networking performance. Network operators, on the other hand, strive to decrease the average coflow completion time (CCT). Unfortunately, optimal isolation guarantees and minimum average CCT are conflicting objectives and cannot be achieved at the same time. Existing coflow schedulers either optimize isolation guarantees at the expense of long CCTs (e.g., HUG [1]), or decrease the average CCT without performance isolation (e.g., Varys and Aalo [2], [3]). The lack of a smooth tradeoff in between poses a dilemma between low efficiency and no performance isolation. To bridge this gap, we develop a new coflow scheduler, Coflex, to navigate this tradeoff. Coflex allows network operators to specify the desired level of isolation guarantee using a tunable fairness knob, while at the same time decreasing the average CCT. Both our real-world deployments and trace-driven simulations have shown that Coflex offers a smooth tradeoff between fairness and efficiency. At an appropriate tradeoff level, Coflex outperforms fair schedulers by 2 χ in minimizing the average CCT.
Large scale genomic analysis shows no evidence for repeated pathogen adaptation during the invasive phase of bacterial meningitis in humans

Recent studies have provided evidence for rapid pathogen genome variation, some of which could potentially affect the course of disease. We have previously detected such variation by comparing isolates infecting the blood and cerebrospinal fluid (CSF) of a single patient during a case of bacterial meningitis. To determine whether the observed variation repeatedly occurs in cases of disease, we performed whole genome sequencing of paired isolates from blood and CSF of 938 meningitis patients. We also applied the same techniques to 54 paired isolates from the nasopharynx and CSF. Using a combination of reference-free variant calling approaches we show that no genetic adaptation occurs in the invasive phase of bacterial meningitis for four major pathogen species: Streptococcus pneumoniae, Neisseria meningitidis, Listeria monocytogenes and Haemophilus influenzae. From nasopharynx to CSF, no adaptation was seen in S. pneumoniae, but in N. meningitidis mutations potentially mediating adaptation to the invasive niche were occasionally observed in the dca gene. This study therefore shows that the bacteria capable of causing meningitis are already able to do this upon entering the blood, and no further sequence change is necessary to cross the blood-brain barrier. The variation discovered from nasopharyngeal isolates suggest that larger studies comparing carriage and invasion may help determine the likely mechanisms of invasiveness. Author Summary We have analysed the entire DNA sequence from bacterial pathogen isolates from cases of meningitis in 938 Dutch adults, focusing on comparing pairs of isolates from the patient’s blood and their cerebrospinal fluid. Previous research has been on only a single patient, but showed possible signs of adaptation to treatment within the host over the course of a single case of disease. By sequencing many more such paired samples, and including four different bacterial species, we were able to determine that adaptation of the pathogen does not occur after bloodstream invasion during bacterial meningitis. We also analysed 54 pairs of isolates from pre- and post-invasive niches from the same patient. In N. meningitidis we found variation in the sequence of one gene which appears to provide bacteria with an advantage after invasion of the bloodstream. Overall, our findings indicate that evolution after invasion in bacterial meningitis is not a major contribution to disease pathogenesis. Future studies should involve more extensive sampling between the carriage and disease niches, or on variation of the host.
Generating Diverse Spinal Motor Neuron Subtypes from Human Pluripotent Stem Cells

Resolving the mechanisms underlying human neuronal diversification remains a major challenge in developmental and applied neurobiology. Motor neurons (MNs) represent a diverse pool of neuronal subtypes exhibiting differential vulnerability in different human neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). The ability to predictably manipulate MN subtype lineage restriction from human pluripotent stem cells (PSCs) will form the essential basis to establishing accurate, clinically relevant in vitro disease models. I first overview motor neuron developmental biology to provide some context for reviewing recent studies interrogating pathways that influence the generation of MN diversity. I conclude that motor neurogenesis from PSCs provides a powerful reductionist model system to gain insight into the developmental logic of MN subtype diversification and serves more broadly as a leading exemplar of potential strategies to resolve the molecular basis of neuronal subclass differentiation within the nervous system. These studies will in turn permit greater mechanistic understanding of differential MN subtype vulnerability using in vitro human disease models.
FAST CONVERGENCE OF INERTIAL DYNAMICS AND ALGORITHMS WITH ASYMPTOTIC VANISHING DAMPING

In a Hilbert space setting H, we study the fast convergence properties as t → +∞ of the trajectories of the second-order differential equation ẍ(t) + α t ẋ(t) +∇Φ(x(t)) = g(t), where ∇Φ is the gradient of a convex continuously differentiable function Φ : H → R, α is a positive parameter, and g : [t0,+∞[→ H is a small perturbation term. In this inertial system, the viscous damping coefficient αt vanishes asymptotically, but not too rapidly. For α ≥ 3, and ∫+∞ t0 t∥g(t)∥dt < +∞, just assuming that argminΦ ̸= ∅, we show that any trajectory of the above system satisfies the fast convergence property Φ(x(t))−min H Φ ≤ C t2 . Moreover, for α > 3, we show that any trajectory converges weakly to a minimizer of Φ. The strong convergence is established in various practical situations. These results complement the O(t−2) rate of convergence for the values obtained by Su, Boyd and Candès in the unperturbed case g = 0. Time discretization of this system, and some of its variants, provides new fast converging algorithms, expanding the field of rapid methods for structured convex minimization introduced by Nesterov, and further developed by Beck and Teboulle with FISTA. This study also complements recent advances due to Chambolle and Dossal.
Registered report: Intestinal inflammation targets cancer-inducing activity of the microbiota

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of 50 papers in the field of cancer biology published between 2010 and 2012. This Registered report describes the proposed replication plan of key experiments from ‘Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota’ by Arthur et al. (2012), published in Science in 2012. Arthur and colleagues identified a genotoxic island in Escherichia coli NC101 that appeared to be responsible for causing neoplastic lesions in inflammation-induced IL10−/− mice treated with azoxymethane. The experiments that will be replicated are those reported in Figure 4 (Arthur et al., 2012). Arthur and colleagues inoculated IL10−/− mice with a mutated strain of E. coli NC101 lacking the genotoxic island, and showed that those mice suffered from fewer neoplastic lesions than mice inoculated with the wild type form of E. coli NC101 (Figure 4). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife. DOI: http://dx.doi. org/10.7554/eLife.04186. 001
Development and Validation of a Real-Time PCR for Detection of Pathogenic Leptospira Species in Clinical Materials

Available serological diagnostics do not allow the confirmation of clinically suspected leptospirosis at the early acute phase of illness. Several conventional and real-time PCRs for the early diagnosis of leptospirosis have been described but these have been incompletely evaluated. We developed a SYBR Green-based real-time PCR targeting secY and validated it according to international guidelines. To determine the analytical specificity, DNA from 56 Leptospira strains belonging to pathogenic, non-pathogenic and intermediate Leptospira spp. as well as 46 other micro-organisms was included in this study. All the pathogenic Leptospira gave a positive reaction. We found no cross-reaction with saprophytic Leptospira and other micro-organisms, implying a high analytical specificity. The analytical sensitivity of the PCR was one copy per reaction from cultured homologous strain M 20 and 1.2 and 1.5 copy for heterologous strains 1342 K and Sarmin, respectively. In spiked serum & blood and kidney tissue the sensitivity was 10 and 20 copies for M 20, 15 and 30 copies for 1342 K and 30 and 50 copies for Sarmin. To determine the diagnostic sensitivity (DSe) and specificity (DSp), clinical blood samples from 26 laboratory-confirmed and 107 negative patients suspected of leptospirosis were enrolled as a prospective consecutive cohort. Based on culture as the gold standard, we found a DSe and DSp of 100% and 93%, respectively. All eight PCR positive samples that had a negative culture seroconverted later on, implying a higher actual DSp. When using culture and serology as the gold standard, the DSe was lower (89%) while the DSp was higher (100%). DSe was 100% in samples collected within the first – for treatment important - 4 days after onset of the illness. Reproducibility and repeatability of the assay, determined by blind testing kidney samples from 20 confirmed positive and 20 negative rodents both appeared 100%. In conclusion we have described for the first time the development of a robust SYBR Green real-time PCR for the detection of pathogenic Leptospira combined with a detailed assessment of its clinical accuracy, thus providing a method for the early diagnosis of leptospirosis with a well-defined satisfactory performance.
Excesso de peso e baixa estatura em crianças de comunidades urbana, rural e indígena

Changes in lifestyle have led to an increase of overweight in the juvenile population. However, there are limited studies about this topic in relation to an indigenous population. The aim of this study is to verify the overweight and height defi cit in children aged 8 and 9 years, of both sexes, from urban, rural and indigenous communities of the city of Nova Laranjeiras in the State of Paraná. The 277 (148 boys) students were divided into three groups: rural (n = 100), urban (n = 99) and Indian communities (n = 78). The measurements taken were body mass (kg), height (m) and body mass index. The statistics method was an analysis of covariance and chi-square test (P <.05). Among the 277 schoolchildren, the prevalence of overweight was 14.6% in the rural area, 27.1% in urban area and 30.3% in the indigenous area in boys, and 15.7% in rural areas, 17.6% in urban and 20% in Indian girls. There was no difference in the frequency of overweight among groups for both sexes. The prevalence of height defi cit was different between the groups; it was higher in indigenous children than urban and rural children. Among the Indians, 42.4% of boys and 51.1% girls had low stature. Only indigenous children were overweight and of low height, while being prevalent in 15.1% of boys and 11.1% girls. Low stature is frequent in indigenous populations, and it would be ideal to have more research to identify its causes and consequences. Children showed high rates of overweight in all regions, demonstrating that poor eating habits and a sedentary lifestyle are not only characteristics of urban centres.
Weak Glycolipid Binding of a Microdomain-Tracer Peptide Correlates with Aggregation and Slow Diffusion on Cell Membranes

Organized assembly or aggregation of sphingolipid-binding ligands, such as certain toxins and pathogens, has been suggested to increase binding affinity of the ligand to the cell membrane and cause membrane reorganization or distortion. Here we show that the diffusion behavior of the fluorescently tagged sphingolipid-interacting peptide probe SBD (Sphingolipid Binding Domain) is altered by modifications in the construction of the peptide sequence that both result in a reduction in binding to ganglioside-containing supported lipid membranes, and at the same time increase aggregation on the cell plasma membrane, but that do not change relative amounts of secondary structural features. We tested the effects of modifying the overall charge and construction of the SBD probe on its binding and diffusion behavior, by Surface Plasmon Resonance (SPR; Biacore) analysis on lipid surfaces, and by Fluorescence Correlation Spectroscopy (FCS) on live cells, respectively. SBD binds preferentially to membranes containing the highly sialylated gangliosides GT1b and GD1a. However, simple charge interactions of the peptide with the negative ganglioside do not appear to be a critical determinant of binding. Rather, an aggregation-suppressing amino acid composition and linker between the fluorophore and the peptide are required for optimum binding of the SBD to ganglioside-containing supported lipid bilayer surfaces, as well as for interaction with the membrane. Interestingly, the strength of interactions with ganglioside-containing artificial membranes is mirrored in the diffusion behavior by FCS on cell membranes, with stronger binders displaying similar characteristic diffusion profiles. Our findings indicate that for aggregation-prone peptides, aggregation occurs upon contact with the cell membrane, and rather than giving a stronger interaction with the membrane, aggregation is accompanied by weaker binding and complex diffusion profiles indicative of heterogeneous diffusion behavior in the probe population.
Exploring the use of soft X-ray microscopy for imaging subcellular structures of the inner ear

* Biomedical and X-ray Physics, Department of Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden † Department of Otolaryngology/Head and Neck Surgery, Columbia University, New York, NY 10032, U.S.A. ‡ Center for X-ray Optics, Lawrence Berkeley Laboratory, University of California, Berkley, CA 94720, U.S.A. § Center for Hearing and Communication Research, and Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
Apprehension or motivation to defend attitudes? Exploring the underlying threat mechanism in inoculation-induced resistance to persuasion

ABSTRACT This study questions the traditional conceptualization of the threat component of inoculation and compares it to an alternative operationalization that was hypothesized to better capture the psychological function of threat according to inoculation theory, focusing less on an apprehensive response in favor of how inoculation treatments cognitively function to motivate resistance. Two measures of threat were contrasted by examining resistance to 9/11 Truth conspiracy propaganda. The results revealed motivational threat was conceptually distinct from the traditional threat measure, better predicted by inoculation treatments, less related to fear, more predictive of resistance to attitude change, and more supportive of inoculation theory when mediating the relationship between inoculation and resistance.
Application of single agent Q-learning for light exploration

Machine learning refers to systematic design and development of algorithms that allows computers to evolve behaviors based on some realistic data (online or offline). Q-learning, a sub-part of the reinforcement learning is being used world wide for easy learning of mobile robots. Light exploration is one of the important issues for developing green robots. This paper describes the work carried out for light exploration by a robot using single-agent based Q-learning. Here a single agent is taking care of all the tasks for learning. ARBIB III, an indigenous behaviour-based robot has been used to implement the Q-learning algorithm for light exploration. The system uses one light sensor and two touch (press) sensors for exploration. It has been found that the algorithm has good applicability for robot learning.
An algorithm for planning collision-free paths among polyhedral obstacles

This paper describes a collision avoidance algorithm for planning a safe path for a polyhedral object moving among known polyhedral objects. The algorithm transforms the obstacles so that they represent the locus of forbidden positions for an arbitrary reference point on the moving object. A trajectory of this reference point which avoids all forbidden regions is free of collisions. Trajectories are found by searching a network which indicates, for each vertex in the transformed obstacles, which other vertices can be reached safely.