Miracle-dz/UniFAR-FTUs huggingface dataset:
Disorganized Microtubules Underlie the Formation of Retraction Bulbs and the Failure of Axonal Regeneration

Axons in the CNS do not regrow after injury, whereas lesioned axons in the peripheral nervous system (PNS) regenerate. Lesioned CNS axons form characteristic swellings at their tips known as retraction bulbs, which are the nongrowing counterparts of growth cones. Although much progress has been made in identifying intracellular and molecular mechanisms that regulate growth cone locomotion and axonal elongation, a comprehensive understanding of how retraction bulbs form and why they are unable to grow is still elusive. Here we report the analysis of the morphological and intracellular responses of injured axons in the CNS compared with those in the PNS. We show that retraction bulbs of injured CNS axons increase in size over time, whereas growth cones of injured PNS axons remain constant. Retraction bulbs contain a disorganized microtubule network, whereas growth cones possess the typical bundling of microtubules. Using in vivo imaging, we find that pharmacological disruption of microtubules in growth cones transforms them into retraction bulb-like structures whose growth is inhibited. Correspondingly, microtubule destabilization of sensory neurons in cell culture induces retraction bulb formation. Conversely, microtubule stabilization prevents the formation of retraction bulbs and decreases axonal degeneration in vivo. Finally, microtubule stabilization enhances the growth capacity of CNS neurons cultured on myelin. Thus, the stability and organization of microtubules define the fate of lesioned axonal stumps to become either advancing growth cones or nongrowing retraction bulbs. Our data pinpoint microtubules as a key regulatory target for axonal regeneration.
Biomineralization Patterns of Intracellular Carbonatogenesis in Cyanobacteria: Molecular Hypotheses

The recent discovery of intracellular carbonatogenesis in several cyanobacteria species has challenged the traditional view that this process was extracellular and not controlled. However, a detailed analysis of the size distribution, chemical composition and 3-D-arrangement of carbonates in these cyanobacteria is lacking. Here, we characterized these features in Candidatus Gloeomargarita lithophora C7 and Candidatus Synechococcus calcipolaris G9 by conventional transmission electron microscopy, tomography, ultramicrotomy, and scanning transmission X-ray microscopy (STXM). Both Ca. G. lithophora C7 and Ca. S. calcipolaris G9 formed numerous polyphosphate granules adjacent or engulfing Ca-carbonate inclusions when grown in phosphate-rich solutions. Ca-carbonates were scattered within Ca. G. lithophora C7 cells under these conditions, but sometimes arranged in one or several chains. In contrast, Ca-carbonates formed at cell septa in Ca. S. calcipolaris G9 and were segregated equally between daughter cells after cell division, arranging as distorted disks at cell poles. The size distribution of carbonates evolved from a positively to a negatively skewed distribution as particles grew. Conventional ultramicrotomy did not preserve Ca-carbonates explaining partly why intracellular calcification has been overlooked in the past. All these new observations allow discussing with unprecedented insight some nucleation and growth processes occurring in intracellularly calcifying cyanobacteria with a particular emphasis on the possible involvement of intracellular compartments and cytoskeleton.
Natural Language Query System for RDF Repositories

We report insights gained from a project of enabling natural language question answering using information stored in RDF repositories targeted to mobile phones users. We present ways of improving portability of natural language interfaces across different data domains based on the Natural Query (NQ) system. NQ enables portable NLI to RDF repositories, can effectively rank different semantic interpretations of a natural language questions with respect to information in RDF repository. NQ can retrieve information that answers the question and can be used for additional explanation, disambiguation or guiding the dialog. We have successfully applied NQ to creating natural language access capability for mobile device data and for two externally hosted repositories – a corporate personnel directory and a job search database.
Heuristic learning of rules for information extraction from web documents

The efficacy of an information extraction system is mostly determined by the quality of the extraction rules. Building these extraction rules is time-consuming and difficult to implement by hand. Hence, we propose a Heuristic Rule Learning (HRL) algorithm which can automatically and efficiently acquire high-quality extraction rules from a user labeled training corpus. Moreover, these extraction rules are maintained at the most suitable generalization level to enhance information extraction efficacy. In HRL, we use a Dynamic tErm eXtraction Technique (DEXT) to construct terms and extraction rules at different generalization levels. The conditional entropy model is used to evaluate the suitability of these different generalization levels of the extraction rules so as to maintain them at a high-quality level. Experimental results show the algorithm's efficacy of acquiring extraction rules at different generalization levels and the efficacy of these extraction rules in the information extraction tasks.
MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database

The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the effects of environmental chemicals on human health. CTD biocurators manually curate a triad of chemical–gene, chemical–disease and gene–disease relationships from the scientific literature. The CTD curation paradigm uses controlled vocabularies for chemicals, genes and diseases. To curate disease information, CTD first had to identify a source of controlled terms. Two resources seemed to be good candidates: the Online Mendelian Inheritance in Man (OMIM) and the ‘Diseases’ branch of the National Library of Medicine's Medical Subject Headers (MeSH). To maximize the advantages of both, CTD biocurators undertook a novel initiative to map the flat list of OMIM disease terms into the hierarchical nature of the MeSH vocabulary. The result is CTD’s ‘merged disease vocabulary’ (MEDIC), a unique resource that integrates OMIM terms, synonyms and identifiers with MeSH terms, synonyms, definitions, identifiers and hierarchical relationships. MEDIC is both a deep and broad vocabulary, composed of 9700 unique diseases described by more than 67 000 terms (including synonyms). It is freely available to download in various formats from CTD. While neither a true ontology nor a perfect solution, this vocabulary has nonetheless proved to be extremely successful and practical for our biocurators in generating over 2.5 million disease-associated toxicogenomic relationships in CTD. Other external databases have also begun to adopt MEDIC for their disease vocabulary. Here, we describe the construction, implementation, maintenance and use of MEDIC to raise awareness of this resource and to offer it as a putative scaffold in the formal construction of an official disease ontology. Database URL: http://ctd.mdibl. org/voc.go? type=disease
Position control of SMA actuator for 3D tactile display

The purpose of this study is to design and fabricate an actuator system for a 3D tactile display. Small size actuator or portable actuator has many possible applications in medicine and industry. In the past, motors have been widely used to create motion in large-area tactile displays. Thus, the device discussed in this paper uses shape memory alloy (SMA) which allows us to create a small, lightweight and high-resolution tactile display. However, there are also challenges using SMA as actuator. The nonlinear hysteresis properties of the SMA cause difficulties during the control of the display. Our design is an 8x8 display consists of 64 SMA springs to create motion for 64 pin display. Each of the pin display takes approximately 0.4 seconds to response to the input. The pin displacement can travel up to 25mm.
Role of polysaccharide and lipid in lipopolysaccharide induced prion protein conversion

ABSTRACT Conversion of native cellular prion protein (PrPc) from an α-helical structure to a toxic and infectious β-sheet structure (PrPSc) is a critical step in the development of prion disease. There are some indications that the formation of PrPSc is preceded by a β-sheet rich PrP (PrPβ) form which is non-infectious, but is an intermediate in the formation of infectious PrPSc. Furthermore the presence of lipid cofactors is thought to be critical in the formation of both intermediate-PrPβ and lethal, infectious PrPSc. We previously discovered that the endotoxin, lipopolysaccharide (LPS), interacts with recombinant PrPc and induces rapid conformational change to a β-sheet rich structure. This LPS induced PrPβ structure exhibits PrPSc-like features including proteinase K (PK) resistance and the capacity to form large oligomers and rod-like fibrils. LPS is a large, complex molecule with lipid, polysaccharide, 2-keto-3-deoxyoctonate (Kdo) and glucosamine components. To learn more about which LPS chemical constituents are critical for binding PrPc and inducing β-sheet conversion we systematically investigated which chemical components of LPS either bind or induce PrP conversion to PrPβ. We analyzed this PrP conversion using resolution enhanced native acidic gel electrophoresis (RENAGE), tryptophan fluorescence, circular dichroism, electron microscopy and PK resistance. Our results indicate that a minimal version of LPS (called detoxified and partially de-acylated LPS or dLPS) containing a portion of the polysaccharide and a portion of the lipid component is sufficient for PrP conversion. Lipid components, alone, and saccharide components, alone, are insufficient for conversion.
Robotics education: A case study in soft-bodied locomotion

Locomotion has been one of the frequently used case studies in hands-on curricula in robotics education. Students are usually instructed to construct their own wheeled or legged robots from modular robot kits. In the development process of a robot students tend to emphasize on the programming part and consequently, neglect the design of the robot's body. However, the morphology of a robot (i.e. its body shape and material properties) plays an important role especially in dynamic tasks such as locomotion. In this paper we introduce a case study of a tutorial on soft-robotics where students were encouraged to focus solely on the morphology of a robot to achieve stable and fast locomotion. The students should experience the influence material properties exert on the performance of a robot and consequently, extract design principles. This tutorial was held in the context of the 2012 Summer School on Soft Robotics at ETH Zurich, which was one of the world's first courses specialized in the emerging field. We describe the tutorial set-up, the used hardware and software, the students assessment criteria as well as the results. Based on the high creativity and diversity of the robots built by the students, we conclude that the concept of this tutorial has great potentials for both education and research.
Thrombospondin-1 Contributes to Mortality in Murine Sepsis through Effects on Innate Immunity

Background Thrombospondin-1 (TSP-1) is involved in many biological processes, including immune and tissue injury response, but its role in sepsis is unknown. Cell surface expression of TSP-1 on platelets is increased in sepsis and could activate the anti-inflammatory cytokine transforming growth factor beta (TGFβ1) affecting outcome. Because of these observations we sought to determine the importance of TSP-1 in sepsis. Methodology/Principal Findings We performed studies on TSP-1 null and wild type (WT) C57BL/6J mice to determine the importance of TSP-1 in sepsis. We utilized the cecal ligation puncture (CLP) and intraperitoneal E.coli injection (IP E.coli) models of peritoneal sepsis. Additionally, bone-marrow-derived macrophages (BMMs) were used to determine phagocytic activity. TSP-1−/− animals experienced lower mortality than WT mice after CLP. Tissue and peritoneal lavage TGFβ1 levels were unchanged between animals of each genotype. In addition, there is no difference between the levels of major innate cytokines between the two groups of animals. PLF from WT mice contained a greater bacterial load than TSP-1−/− mice after CLP. The survival advantage for TSP-1−/− animals persisted when IP E.coli injections were performed. TSP-1−/− BMMs had increased phagocytic capacity compared to WT. Conclusions TSP-1 deficiency was protective in two murine models of peritoneal sepsis, independent of TGFβ1 activation. Our studies suggest TSP-1 expression is associated with decreased phagocytosis and possibly bacterial clearance, leading to increased peritoneal inflammation and mortality in WT mice. These data support the contention that TSP-1 should be more fully explored in the human condition.
Innovation in vocational education and training in England, Germany, and Austria : implications of practitioners’ perspectives for policy development and college leadership

This research project conducted an in-depth, qualitative assessment of vocational education and training (VET) teachers’ perceptions of pedagogic innovation, with an emphasis on obstacles and supporting factors. The main research question was: “How do teachers’ roles and perspectives shape innovation processes in VET and what does this imply for the development of teaching and learning practices? ” Three clusters of subsidiary questions were derived around thematic foci: ‘perceptions and concepts’, ‘documentation of practice’, and ‘dynamics, limitations, and lessons for innovation’. Based on analytical strategies derived from grounded theory, two phases of interviews – the first with ten experts and the second with 62 VET practitioners at 20 colleges – were conducted in England, Germany, and Austria, with a focus on full-time VET (Further Education Colleges, Berufskollegs, and Berufsbildende Mittlere und Hohere Schulen) in the 16-19 age range. Classroom observation preceded semi-structured, 30 to 60 minute interviews with teachers. The study builds on previous research and existing frameworks such as Lipsky’s concept of ‘street-level bureaucracy’ and Flyvbjerg’s ‘critical cases’. However, it fills a gap in the literature by focusing on practitioner perceptions, motivations, professionalism, autonomy, work contexts, and own learning in relation to pedagogic innovation, whilst tracing relevant connections to educational policy, college management, and societal influences. Teachers are shown in multiple roles as inventors, designers, and implementers of innovation, facing nine categories of obstacles. Those include limited time and budgets, bureaucracy and lack of autonomy, problems with project planning and execution, and issues related to lack of support. In addition, this study provides a comparative investigation of practitioners’ interpretations of key terms (‘pedagogy’, ‘didactics’, ‘innovation’), revealing differences between England on the one hand, and Germany and Austria on the other, based on different degrees of autonomy and innovative focus. Based on such findings, the study details recommendations for college leaders and policy makers for facilitating pedagogic innovation, placing each in their respective national contexts.
Factors Determining Long-term Success of a Measurement Program: An Industrial Case Study

Introducing measurement programs into organizations is a lengthy process aected by organizational and technical constraints. There exist several aspects that determine whether a measurement program has the chances of succeeding, like management commitment or existence of proper tool support. The establishing of a program, however, is only a part of the success. As organizations are dynamic entities, the measurement programs should constantly be maintained and adapted in order to cope with changing needs of the organizations. In this paper we study one of the measurement programs at Ericsson AB in Sweden and as a result we identify factors determining successful adoption and use of the measurement program. The results of our research in this paper are intended to support quality managers and project managers in establishing and maintaining successful metrics programs.
State Income Taxes and Homeownership: A Test of the Tax Arbitrage Theory

Abstract Since states have different income taxes, the marginal tax rate in the top tax bracket varies across states. According to the tax arbitrage theory of homeownership, the frequency of homeownership in any given tax bracket ought to be lower in states with higher top tax rates. To test this hypothesis, we estimated a probit model of homeownership using data on over 16,000 families from 38 different states. As hypothesized, we found that a family was less likely to own its home if it lived in a state with a high top tax rate. We also found that it was more likely to own its home if it had a high marginal tax rate.
Cross-Sectional and Longitudinal Associations between Body Mass Index and Cardiometabolic Risk Factors in Adolescents in a Country of the African Region

We assessed the association between several cardiometabolic risk factors (CRFs) (blood pressure, LDL-cholesterol, HDL-cholesterol, triglycerides, uric acid, and glucose) in 390 young adults aged 19-20 years in Seychelles (Indian Ocean, Africa) and body mass index (BMI) measured either at the same time (cross-sectional analysis) or at the age of 12–15 years (longitudinal analysis). BMI tracked markedly between age of 12–15 and age of 19-20. BMI was strongly associated with all considered CRFs in both cross-sectional and longitudinal analyses, with some exceptions. Comparing overweight participants with those having a BMI below the age-specific median, the odds ratios for high blood pressure were 5.4/4.7 (male/female) cross-sectionally and 2.5/3.9 longitudinally (P < 0.05). Significant associations were also found for most other CRFs, with some exceptions. In linear regression analysis including both BMI at age of 12–15 and BMI at age of 19-20, only BMI at age of 19-20 remained significantly associated with most CRFs. We conclude that CRFs are predicted strongly by either current or past BMI levels in adolescents and young adults in this population. The observation that only current BMI remained associated with CRFs when including past and current levels together suggests that weight control at a later age may be effective in reducing CRFs in overweight children irrespective of past weight status.
Passivity and Passive Feedback Stabilization for a Class of Mixed Potential Systems

Abstract This paper studies the input-output properties of a class of control affine systems where the drift dynamics is generated by a metriplectic structure. Those systems, related to generalized (or dissipative) Hamiltonian systems, are generated by a conserved component and a dissipative component and appear, for example, in non-equilibrium thermodynamics. In non-equilibrium thermodynamics, the two potentials generating the dynamics are interpreted as generalized energy and generalized entropy, respectively. In this note, passivity and passive feedback stabilization of this class of systems are studied, with the output function taken as the gradient of the conserved component of the dynamics, and the proposed storage function is computed using the dissipative (metric) component of the dynamics.
ReLISH: Reliable Label Inference via Smoothness Hypothesis

The smoothness hypothesis is critical for graph-based semi-supervised learning. This paper defines local smoothness, based on which a new algorithm, Reliable Label Inference via Smoothness Hypothesis (ReLISH), is proposed. ReLISH has produced smoother labels than some existing methods for both labeled and unlabeled examples. Theoretical analyses demonstrate good stability and generalizability of ReLISH. Using real-world datasets, our empirical analyses reveal that ReLISH is promising for both transductive and inductive tasks, when compared with representative algorithms, including Harmonic Functions, Local and Global Consistency, Constraint Metric Learning, Linear Neighborhood Propagation, and Manifold Regularization.
Effect of anticoagulants and cell separation media as preanalytical determinants on zymographic analysis of plasma matrix metalloproteinases.

Matrix metalloproteinases (MMPs) are calcium/zinc-dependent endoproteinases involved in physiologic and pathologic processes, modulating extracellular matrix degradation (1). MMP-2 (EC 3.4.24.24) and MMP-9 (EC 3.4.24.35) circulating in the peripheral blood (PB) of patients with neoplasia showed contrasting results, revealing the preanalytical issue of whether the method of PB sampling influences MMP concentrations (2) and their zymographic profiles (3). We therefore analyzed the effects of anticoagulants and cell separation media on PB gelatinolytic profiles. PB samples from 30 healthy volunteers were collected into Vacutainer™ Tubes with clot activator (SST), lithium heparin (LH), dipotassium EDTA (K2E), sodium fluoride/potassium oxalate (NaF/KOx), and buffered/acidic citrate [natrium citrate (9NC), acid-citrate-dextrose (ACD), and citrate-phosphate-dextrose-adenine (CPDA); Becton Dickinson]. After centrifugation at 500 g for 15 min at 4 °C, the supernatants and buffy coats were collected and analyzed. Leukocyte subpopulations were obtained after Lympholyte® gradient (5.64% Nycograde™ Polysucrose 400, 9.65% sodium diatrizoate; Cedarlane), and their subset recovery was tested through cytometric analysis (4). Gelatinases from leukocytes and plasma samples were analyzed by gelatin zymography, with 150 μg of total protein loaded on the gel (3). Calibrators were prepared from capillary PB (5). MMP-2 and MMP-9 were measured by ELISA (5). Differences …
ClpX Contributes to Innate Defense Peptide Resistance and Virulence Phenotypes of Bacillus anthracis

Bacillus anthracis is a National Institute of Allergy and Infectious Diseases Category A priority pathogen and the causative agent of the deadly disease anthrax. We applied a transposon mutagenesis system to screen for novel chromosomally encoded B. anthracis virulence factors. This approach identified ClpX, the regulatory ATPase subunit of the ClpXP protease, as essential for both the hemolytic and proteolytic phenotypes surrounding colonies of B. anthracis grown on blood or casein agar media, respectively. Deletion of clpX attenuated lethality of B. anthracis Sterne in murine subcutaneous and inhalation infection models, and markedly reduced in vivo survival of the fully virulent B. anthracis Ames upon intraperitoneal challenge in guinea pigs. The extracellular proteolytic activity dependent upon ClpX function was linked to degradation of cathelicidin antimicrobial peptides, a front-line effector of innate host defense. B. anthracis lacking ClpX were rapidly killed by cathelicidin and α-defensin antimicrobial peptides and lysozyme in vitro. In turn, mice lacking cathelicidin proved hyper-susceptible to lethal infection with wild-type B. anthracis Sterne, confirming cathelicidin to be a critical element of innate defense against the pathogen. We conclude that ClpX is an important factor allowing B. anthracis to subvert host immune clearance mechanisms, and thus represents a novel therapeutic target for prevention or therapy of anthrax, a foremost biodefense concern.