Miracle-dz/UniFAR-FTUs huggingface dataset:
A TNF-Regulated Recombinatorial Macrophage Immune Receptor Implicated in Granuloma Formation in Tuberculosis

Macrophages play a central role in host defense against mycobacterial infection and anti- TNF therapy is associated with granuloma disorganization and reactivation of tuberculosis in humans. Here, we provide evidence for the presence of a T cell receptor (TCR) αβ based recombinatorial immune receptor in subpopulations of human and mouse monocytes and macrophages. In vitro, we find that the macrophage-TCRαβ induces the release of CCL2 and modulates phagocytosis. TNF blockade suppresses macrophage-TCRαβ expression. Infection of macrophages from healthy individuals with mycobacteria triggers formation of clusters that express restricted TCR Vβ repertoires. In vivo, TCRαβ bearing macrophages abundantly accumulate at the inner host-pathogen contact zone of caseous granulomas from patients with lung tuberculosis. In chimeric mouse models, deletion of the variable macrophage-TCRαβ or TNF is associated with structurally compromised granulomas of pulmonary tuberculosis even in the presence of intact T cells. These results uncover a TNF-regulated recombinatorial immune receptor in monocytes/macrophages and demonstrate its implication in granuloma formation in tuberculosis.
Cannabis Roots: A Traditional Therapy with Future Potential for Treating Inflammation and Pain

Abstract Introduction: The roots of the cannabis plant have a long history of medical use stretching back millennia. However, the therapeutic potential of cannabis roots has been largely ignored in modern times. Discussion: In the first century, Pliny the Elder described in Natural Histories that a decoction of the root in water could be used to relieve stiffness in the joints, gout, and related conditions. By the 17th century, various herbalists were recommending cannabis root to treat inflammation, joint pain, gout, and other conditions. There has been a subsequent paucity of research in this area, with only a few studies examining the composition of cannabis root and its medical potential. Active compounds identified and measured in cannabis roots include triterpenoids, friedelin (12.8 mg/kg) and epifriedelanol (21.3 mg/kg); alkaloids, cannabisativine (2.5 mg/kg) and anhydrocannabisativine (0.3 mg/kg); carvone and dihydrocarvone; N-(p-hydroxy-β-phenylethyl)-p-hydroxy-trans-cinnamamide (1.6 mg/kg); various sterols such as sitosterol (1.5%), campesterol (0.78%), and stigmasterol (0.56%); and other minor compounds, including choline. Of note, cannabis roots are not a significant source of Δ9-tetrahydrocannabinol (THC), cannabidiol, or other known phytocannabinoids. Conclusion: The current available data on the pharmacology of cannabis root components provide significant support to the historical and ethnobotanical claims of clinical efficacy. Certainly, this suggests the need for reexamination of whole root preparations on inflammatory and malignant conditions employing modern scientific techniques.
Frontiers in Cellular Neuroscience Cellular Neuroscience

By providing a coincidence between pre-and postsynaptic neurons, GDPs are thought to be involved in activity-dependent spike timing dependent plasticity (Kasyanov et al., 2004; Mohajerani and Cherubini, 2006), which is particularly robust during the early developmental period (Isaac et al., 1995; Durand et al., 1996). However, factors determining spatio-temporal characteristics of GPDs and spike timing during GDPs are not completely understood. While excitatory actions of GABA on immature neurons have been well documented in virtually all brain structures using variety of electrophysiological and imaging techniques, an important question of postsynaptic action potential (AP) time coding at the GABAergic synapse has not been addressed. AP temporal coding is a major characteristic of excitatory synapse, which implies a delay of APs and its variability in the postsynaptic cell receiving an excitatory input. AP temporal coding is determined by kinet-ics of transmitter release, kinetics of postsynaptic receptor mediated excitatory currents, and postsynaptic membrane properties including voltage-gated conductances which shape and amplify or inhibit postsynaptic potentials (PSPs) (Fricker and Miles, 2000). In
Deltamethrin Treated Bednets for Control of Malaria Transmitted by Anopheles culicifacies (Diptera: Culicidae) in India

Abstract In a malaria endemic area in Orissa state in eastern India baseline (November 1989 to October 1990) malaria incidence ranged from 215 to 328 cases/1,000 population/yr in different groups of villages. In November 1990, nylon bednets treated with deltamethrin at 25 mg/m2 were given out in two villages (population 1062), untreated bednets were given out in five villages (population 1,226) and in one village (population 786) nets were not given. Nets were retreated in October 1991 and June 1992 in treated-net villages. The trial continued until October 1992. The treated nets caused significant reduction in indoor resting density, biting (landing), light trap catches, human engorgement rate, and parous rate of malaria vector Anopheles culicifacies Giles as compared with untreated nets or no nets. Untreated nets also caused reductions in biting and indoor density. Treated nets retained insecticidal action well over 6 mo. In the final year, malaria incidence was reduced 8.9% in the no-net village, 34.9% in the villages with untreated nets, and 59.1% in villages with treated nets. The relative risk of malaria and parasite rates declined significantly in villages with treated nets. Pediatric splenomegaly rate did not change in the no-net village, increased significantly in villages with untreated nets, but decreased significantly in those with treated nets. Treated nets also reduced pediatric anemia rates, but Hb concentration increased in all villages. Considering the benefits of treated bednets and development of resistance among vectors to DDT and malathion, bednets treated with deltamethrin could be an effective alternative strategy to control malaria in forested areas in India.
Eye tracking the user experience - An evaluation of ontology visualization techniques

Various ontology visualization techniques have been developed over the years, offering essential interfaces to users for browsing and interacting with ontologies, in an effort to assist with ontology understanding. Yet few studies have focused on evaluating the usability of existing ontology visualization techniques. This paper presents an eye-tracking user study that evaluates two commonly used ontology visualization techniques, namely, indented list and graph. The eye-tracking experiment and analysis presented in this paper complements the set of existing evaluation protocols for ontology visualization. In addition, the results found from this study contribute to a greater understanding of the strengths and weaknesses of the two visualization techniques, and in particular, how and why one is more effective than the other. Based on approximately 500MB of eye movement data containing around 30 million rows of gaze data generated by a Tobii eye tracker, we found evidence suggesting indented lists are more efficient at supporting information searches and graphs are more efficient at supporting information processing. Keywords: eye tracking, ontology visualization evaluation, usability study, gaze data processing, statistical analysis * Corresponding author. E-mail: bofu@uvic.ca. † Current affiliation: Google Inc.
Differences in Visual Signal Design and Detectability between Allopatric Populations of Anolis Lizards

We tested the prediction of the sensory drive hypothesis using four allopatric populations of the lizard Anolis cristatellus from two distinct environments (i.e., mesic and xeric conditions). For each population, we measured habitat light characteristics and quantified signal design by measuring the spectral and total reflectance and transmittance of the dewlap. We used these data to calculate dewlap detectability using an empirically based model of signal detection probability. We found that populations from mesic and xeric conditions occupy two distinct habitats with respect to light intensity and spectral quality and that dewlap design has diverged between populations in a way that increases signal detectability in each habitat. The major difference in dewlap design was in total reflectance and transmittance, making dewlaps from xeric habitats darker and dewlaps from mesic habitats brighter. Furthermore, dewlap detection decreased significantly when a dewlap from a xeric habitat is detected under the spectral conditions of a mesic habitat. The converse is true for a dewlap from a mesic habitat. We propose that sensory drive has promoted divergence in dewlap design in distinct habitat light conditions, and we discuss the possibility that selection might promote early stages of reproductive isolation as a by‐product of selection on dewlap design to distinct habitat light conditions.
Channel selection by class separability measures for automatic transcriptions on distant microphones

Channel selection is important for automatic speech recognition as the signal quality of one channel might be significantly better than those of the other channels and therefore, microphone array or blind source separation techniques might not lead to improvements over the best single microphone. The mayor challenge, however, is to find this particular channel who is leading to the most accurate classification. In this paper we present a novel channel selection method, based on class separability, to improve multi-source far distance speech-totext transcriptions. Class separability measures have the advantage, compared to other methods such as the signal to noise ratio (SNR), that they are able to evaluate the channel quality on the actual features of the recognition system. We have evaluated on NISTs RT-07 development set and observe significant improvements in word accuracy over SNR based channel selection methods. We have also used this technique in NISTs RT-07 evaluation.
Adolescent and Early Adulthood Dietary Carbohydrate Quantity and Quality in Relation to Breast Cancer Risk

Background: We investigated quantity and quality of dietary carbohydrate as well as insulin load and insulin index during adolescence and also early adulthood in relation to risk of breast cancer in the Nurses' Health Study II. Methods: During 20 years of follow-up of 90,534 premenopausal women who completed a diet questionnaire in 1991, 2,833 invasive breast cancer cases were documented. In 1998, 44,263 of these women also completed a questionnaire about their diet during high school; among these women, we documented 1,118 cases of breast cancer. Multivariable-adjusted Cox proportional hazards regression was used to model relative risks (RR) and 95% confidence intervals (95% CI) for breast cancer across categories of dietary carbohydrate, glycemic index (GI), glycemic load (GL), as well as insulin load and insulin index scores. Results: Adolescent or early adult intakes of GI or GL were not associated with risk of breast cancer. Comparing women in the highest versus lowest quintile, the multivariable-adjusted RRs were 1.14 (0.95–1.38) for adolescent GI scores and 1.03 (0.91–1.16) for early adulthood GI scores. We also did not observe associations with insulin index and insulin load scores in adolescence or early adulthood and breast cancer risk. Conclusions: We found that diets high in GI, GL, insulin index, and insulin load during adolescence or early adulthood were not associated with an increased risk of breast cancer in this cohort study. Impact: Diets with a high glucose or insulin response in adolescence or early adulthood were not significant predictors of breast cancer incidence. Cancer Epidemiol Biomarkers Prev; 24(7); 1111–20. ©2015 AACR.
Corporate Directions in Supply Chain Management: Implications for SME Competences and Inter-Organisational Relations

The Business School of the Manchester Metropolitan University is one of the largest business schools in the UK comprising more than 150 academic staff organised into eleven thematic research groups. The Working Paper Series brings together research in progress from across the Business School for publication to a wider audience and to facilitate discussion. Working Papers are subject to a peer review process.
Antibiotic Choice Is Independently Associated With Risk of Surgical Site Infection After Colectomy: A Population-Based Cohort Study

Objective: To determine which perioperative care practices are associated with decreased risk of surgical site infection (SSI) after colectomy surgery. Background: Optimization of perioperative care has been a common strategy for improving surgical safety, but the relationship between process measure compliance and surgical complication rates is controversial. Methods: This is a retrospective cohort study performed within the Michigan Surgical Quality Collaborative (MSQC), an organization of hospitals that prospectively collects patient data, processes of care, and 30-day outcomes. Patients undergoing colectomy surgery (n = 4331) were studied. Factors potentially associated with SSI were tested using univariate statistical tests, and a hierarchical generalized linear model was created to test for independent associations between processes of care and SSI, while adjusting for patient risk factors and clustering of patients within hospitals. Results: Several perioperative care practices were independently associated with lower risk of SSI after adjustment for patient risk, procedure type/duration, and clustering of patients by hospital site. Best practices include selection of a Surgical Care Improvement Project (SCIP-2)-compliant prophylactic intravenous antibiotic, postoperative normothermia, postoperative day 1 glucose control, and oral antibiotics given when bowel prep used (SCIP-1 was not significant). Further, several specific prophylactic antibiotic choices were independently associated with lower SSI rates, including cefazolin/metronidazole, ciprofloxacin/metronidazole, and ertapenem. Conclusions: In Michigan, several perioperative care practices are independently associated with decreased risk of SSI after colectomy, including SCIP-2-compliant prophylactic antibiotics, postoperative normothermia, glucose control, and oral antibiotics. Furthermore, specific prophylactic antibiotic choices are associated with lower risk of SSI. These results account for patient factors and unmeasured hospital effects, suggesting that dissemination of these perioperative care practices may decrease SSI rates.
Do we expect most AGN to live in discs

Recent observations have indicated that a large fraction of the low- to intermediate-luminosity AGN population lives in disc-dominated hosts, while the more luminous quasars live in bulge-dominated hosts (that may or may not be major merger remnants), in conflict with some previous model predictions. We therefore build and compare a semi-empirical model for AGN fuelling which accounts for both merger and non-merger ‘triggering’. In particular, we show that the ‘stochastic accretion’ model – in which fuelling in disc galaxies is essentially a random process arising whenever dense gas clouds reach the nucleus – provides a good match to the present observations at low/intermediate luminosities. However, it falls short of the high-luminosity population. We combine this with models for major merger-induced AGN fueling, which lead to rarer but more luminous events, and predict the resulting abundance of disc-dominated and bulge-dominated AGN host galaxies as a function of luminosity and redshift. We compile and compare observational constraints from z ∼ 0 to 2. The models and observations generically show a transition from disc to bulge dominance in hosts near the Seyfert-quasar transition, at all redshifts. ‘Stochastic’ fuelling dominates AGN by number (dominant at low luminosity), and dominates black hole (BH) growth below the ‘knee’ in the present-day BH mass function ( ≲ 10^7 M_⊙). However, it accounts for just ∼10 per cent of BH mass growth at masses ≳ 10^8 M_⊙. In total, fuelling in discy hosts accounts for ∼30 per cent of the total AGN luminosity density/BH mass density. The combined model also accurately predicts the AGN luminosity function and clustering/bias as a function of luminosity and redshift; however, we argue that these are not sensitive probes of BH fuelling mechanisms.
The electronic properties of graphene

This article reviews the basic theoretical aspects of graphene, a one-atom-thick allotrope of carbon, with unusual two-dimensional Dirac-like electronic excitations. The Dirac electrons can be controlled by application of external electric and magnetic fields, or by altering sample geometry and/or topology. The Dirac electrons behave in unusual ways in tunneling, confinement, and the integer quantum Hall effect. The electronic properties of graphene stacks are discussed and vary with stacking order and number of layers. Edge (surface) states in graphene depend on the edge termination (zigzag or armchair) and affect the physical properties of nanoribbons. Different types of disorder modify the Dirac equation leading to unusual spectroscopic and transport properties. The effects of electron-electron and electron-phonon interactions in single layer and multilayer graphene are also presented.
Residue formulae, vector partition functions and lattice points in rational polytopes

We obtain residue formulae for certain functions of several vari- ables. As an application, we obtain closed formulae for vector partition func- tions and for their continuous analogs. They imply an Euler-MacLaurin sum- mation formula for vector partition functions, and for rational convex poly- topes as well: we express the sum of values of a polynomial function at all lattice points of a rational convex polytope in terms of the variation of the integral of the function over the deformed polytope. Institut Fourier, B.P. 74, 38402 Saint-Martin d’Heres Cedex, France E-mail address: mbrion@fourier.ujf-grenoble.fr Ecole Normale Superieure, 45 rue d’Ulm, 75005 Paris Cedex 05, France E-mail address: vergne@dmi.ens. fr
Efficient evaluation of n-ary conjunctive queries over trees and graphs

N-ary conjunctive queries, i.e., queries with any number of answer variables, are the formal core of many Web query languages including XSLT, XQuery, SPARQL, and Xcerpt. Despite a considerable body of research on the optimization of such queries over tree-shaped XML data, little attention has been paid so far to efficient access to graph-shaped XML, RDF, or Topic Maps. We propose the first evaluation technique for n-ary conjunctive queries that applies to both tree- and graph-shaped data and retains the same complexity as the best known approaches that are restricted to tree-shaped data only. Furthermore, the approach treats tree and graph-shaped queries uniformly without sacrificing evaluation complexity on the restricted query class. The core of the evaluation technique is based on dynamic programming using a memoization data structure, called "memoization matrix". It can be populated and consumed in different ways. For each of population and consumption, we propose two resp. three algorithms each having their own advantages. The complexity of the algorithms is compared analytically and experimentally.
2016 Ieee International Conference on Big Data (big Data) Quantifying Moral Foundations from Various Topics on Twitter Conversations

—Moral foundations theory explains variations in moral behavior using innate moral foundations: Care, Fairness , Ingroup, Authority, and Purity, along with experimental supports. However, little is known about the roles of and relationships between those foundations in everyday moral situations. To address these, we quantify moral foundations from a large amount of online conversations (tweets) about moral topics on the social media site Twitter. We measure moral loadings using latent semantic analysis of tweets related to topics on abortion, homosexuality, immigration, religion, and immorality in general, showing how the five moral foundations function in spontaneous conversations about moral violating situations. The results indicate that although the five foundations are mutually related, Purity is the most distinctive foundation and Care is the most dominant foundation in everyday conversations on immorality. Our study shows a new possibility of natural language processing and social big data for moral psychology.
Interconnection and Damping Assignment Passivity-Based Control: A Survey

Interconnection and damping assignment passivitybased control is a technique that regulates the behavior of nonlinear systems assigning a desired (portcontrolled Hamiltonian) structure to the closed-loop. Since the introduction of this controller design methodology five years ago, many theoretical extensions and practical applications have been reported in the literature. The theoretical developments include some variations and shortcuts that are useful when dealing with particular classes of systems, and the incorporation of additional features to handle control scenarios other than just stabilization.On the application side the method has provided solutions to a wide variety of physical problems. The purpose of this paper is to review the fundamental theory, main new results and practical applications of this control system design approach as well as to discuss the current open problems and future directions.
Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi

Delineating ancestral gene relations among a large set of sequenced eukaryotic genomes allowed us to rigorously examine links between evolutionary and functional traits. We classified 86% of over 1.36 million protein-coding genes from 40 vertebrates, 23 arthropods, and 32 fungi into orthologous groups and linked over 90% of them to Gene Ontology or InterPro annotations. Quantifying properties of ortholog phyletic retention, copy-number variation, and sequence conservation, we examined correlations with gene essentiality and functional traits. More than half of vertebrate, arthropod, and fungal orthologs are universally present across each lineage. These universal orthologs are preferentially distributed in groups with almost all single-copy or all multicopy genes, and sequence evolution of the predominantly single-copy orthologous groups is markedly more constrained. Essential genes from representative model organisms, Mus musculus, Drosophila melanogaster, and Saccharomyces cerevisiae, are significantly enriched in universal orthologs within each lineage, and essential-gene-containing groups consistently exhibit greater sequence conservation than those without. This study of eukaryotic gene repertoire evolution identifies shared fundamental principles and highlights lineage-specific features, it also confirms that essential genes are highly retained and conclusively supports the “knockout-rate prediction” of stronger constraints on essential gene sequence evolution. However, the distinction between sequence conservation of single- versus multicopy orthologs is quantitatively more prominent than between orthologous groups with and without essential genes. The previously underappreciated difference in the tolerance of gene duplications and contrasting evolutionary modes of “single-copy control” versus “multicopy license” may reflect a major evolutionary mechanism that allows extended exploration of gene sequence space.