pinecone/core-2020-05-10-deduplication huggingface dataset:
Challenges in microbial ecology: building predictive understanding of community function and dynamics.

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model-experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved
Does Vascular Calcification Accelerate Inflammation? A Sub-Study of the dal-PLAQUE Trial

Objectives:
We sought to investigate non-coronary vascular calcification and its influence on changes in vascular inflammation.
	
Background:
Atherosclerosis is an inflammatory condition with calcification apparent late in the disease process. The extent and progression of coronary calcification predict cardiovascular events. Relatively little is known about non-coronary vascular calcification. 
	
Methods:
One hundred and thirty participants in the dal-PLAQUE study underwent fluorodeoxyglucose positron emission tomography/computed tomography at entry and at 6 months. Calcification of the ascending aorta, arch, carotid, and coronary arteries was quantified. Cardiovascular risk factors were related to arterial calcification. The influence of baseline calcification and drug therapy (dalcetrapib vs. placebo) on progression of calcification was determined. Finally, baseline calcification was related to changes in vascular inflammation. 
	
Results:
Age >65 years was consistently associated with higher baseline calcium scores. Arch calcification trended to progress more in those with calcification at baseline (p = 0.055). There was no significant difference in progression of vascular calcification with dalcetrapib as compared to placebo. Average carotid target-to-background ratio indices declined over 6 months if carotid calcium was absent (single hottest slice [p = 0.037], mean of maximum target-to-background ratio [p = 0.010], and mean most diseased segment [p = <0.001]), but did not significantly change if calcification was present at baseline. 
	
Conclusions:
Across multiple arterial regions, higher age is consistently associated with higher calcium scores. The presence of vascular calcification at baseline is associated with progressive calcification; in the carotid arteries, calcification appears to influence vascular inflammation. Dalcetrapib therapy did not affect vascular calcification.The study was supported by F. Hoffmann-La Roche Ltd, Basel, Switzerland. Some editorial assistance was provided by Prime Healthcare and was funded by F. Hoffmann-La Roche Ltd, Basel, Switzerland. Partial support is acknowledged from NIH/NHLBI R01 HL071021 (ZAF). We thank Elisabetta Damonte for helping with statistical analyses.This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.jacc.2015.10.05
T-cell brain infiltration and immature antigen-presenting cells in transgenic models of Alzheimer's disease-like cerebral amyloidosis

Cerebral beta-amyloidosis, one of the pathological hallmarks of Alzheimer's disease (AD), elicits a well-characterised, microglia-mediated local innate immune response. In contrast, it is not clear whether cells of the adaptive immune system, in particular T-cells, react to cerebral amyloidosis in AD. Even though parenchymal T-cells have been described in post-mortem brains of AD patients, it is not known whether infiltrating T-cells are specifically recruited to the extracellular deposits of beta-amyloid, and whether they are locally activated into proliferating, effector cells upon interaction with antigen-presenting cells (APCs). To address these issues we have analysed by confocal microscopy and flow-cytometry the localisation and activation status of both T-cells and APCs in transgenic (tg) mice models of AD-like cerebral amyloidosis. Increased numbers of infiltrating T-cells were found in amyloid-burdened brain regions of tg mice, with concomitant up-regulation of endothelial adhesion molecules ICAM-1 and VCAM-1, compared to non-tg littermates. The infiltrating T-cells in tg brains did not co-localise with amyloid plaques, produced less interferon-gamma than those in controls and did not proliferate locally. Bona-fide dendritic cells were virtually absent from the brain parenchyma of both non-tg and tg mice, and APCs from tg brains showed an immature phenotype, with accumulation of MHC-II in intracellular compartments. These results indicate that cerebral amyloidosis promotes T-cell infiltration but interferes with local antigen presentation and T-cell activation. The inability of the brain immune surveillance to orchestrate a protective immune response to amyloid-beta peptide might contribute to the accumulation of amyloid in the progression of the disease
A transformation-driven approach to automate feedback verification results

The integration of formal verification methods in modeling activities is a key issue to ensure the correctness of complex system design models. In this purpose, the most common approach consists in defining a translational semantics mapping the abstract syntax of the designer dedicated Domain-Specific Modeling Language (DSML) to a formal verification dedicated semantic domain in order to reuse the available powerful verification technologies. Formal verification is thus usually achieved using model transformations. However, the verification results are available in the formal domain which significantly impairs their use by the system designer which is usually not an expert of the formal technologies.  In this paper, we introduce a novel approach based on Higher-Order transformations that analyze and instrument the transformation that expresses the semantics in order to produce traceability data to automatize the back propagation of verification results to the DSML end-user
Search for pair-produced long-lived neutral particles decaying to jets in the ATLAS hadronic calorimeter in pp collisions at root s = 8 TeV

The ATLAS detector at the Large Hadron Collider at CERN is used to search for the decay of a scalar boson to a pair of long-lived particles, neutral under the Standard Model gauge group, in 20.3 fb−120.3 fb−1 of data collected in proton–proton collisions at View the MathML sources=8 TeV. This search is sensitive to long-lived particles that decay to Standard Model particles producing jets at the outer edge of the ATLAS electromagnetic calorimeter or inside the hadronic calorimeter. No significant excess of events is observed. Limits are reported on the product of the scalar boson production cross section times branching ratio into long-lived neutral particles as a function of the proper lifetime of the particles. Limits are reported for boson masses from 100 GeV to 900 GeV, and a long-lived neutral particle mass from 10 GeV to 150 GeV.G. Aad … L. Lee … A. Petridis … N. Soni ... M. White ... et al. (The ATLAS Collaboration
Measurement of colour flow with the jet pull angle in tt ¯ events using the ATLAS detector at √s=8  TeV

The distribution and orientation of energy inside jets is predicted to be an experimental handle on colour connections between the hard--scatter quarks and gluons initiating the jets. This Letter presents a measurement of the distribution of one such variable, the jet pull angle. The pull angle is measured for jets produced in tt ¯ events with one W  boson decaying leptonically and the other decaying to jets using 20.3 fb⁻¹ of data recorded with the ATLAS detector at a centre-of-mass energy of √s=8  TeV at the LHC. The jet pull angle distribution is corrected for detector resolution and acceptance effects and is compared to various models
Search for resonances in diphoton events at √s = 13 TeV with the ATLAS detector

Journal of High Energy Physics 2016.9 (2016): 001 reproduced by permission of Scuola Internazionale Superiore di Studi Avanzati (SISSA)Artículo escrito por un elevado número de autores, sólo se referencian el nombre del que aparece en primer lugar, el nombre del grupo de colaboración, si le hubiere y los autores que firman como pertenecientes a la UAMSearches for new resonances decaying into two photons in the ATLAS experiment  at the CERN Large Hadron Collider are described. The analysis is based on protonproton  collision data corresponding to an integrated luminosity of 3.2 fb−1 at √  s = 13 TeV  recorded in 2015. Two searches are performed, one targeted at a spin-2 particle of mass larger than 500 GeV, using Randall-Sundrum graviton states as a benchmark model, and one optimized for a spin-0 particle of mass larger than 200 GeV. Varying both the mass and the decay width, the most significant deviation from the background-only hypothesis is observed at a diphoton invariant mass around 750 GeV with local significances of 3.8 and 3.9
 standard deviations in the searches optimized for a spin-2 and spin-0 particle, respectively. The global significances are estimated to be 2.1 standard deviations for both analyses. The consistency between the data collected at 13 TeV and 8 TeV is also evaluated. Limits on the production cross section times branching ratio to two photons for the two resonance
 types are reportedWe acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia; BMWFW and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF and DNSRC, Denmark; IN2P3-CNRS, CEA-DSM/IRFU, France; GNSF, Georgia; BMBF, HGF, and MPG, Germany; GSRT, Greece; RGC, Hong Kong SAR, China; ISF, I-CORE and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS,Japan; CNRST, Morocco; FOM and NWO, Netherlands; RCN, Norway; MNiSW and NCN, Poland; FCT, Portugal; MNE/IFA, Romania; MES of Russia and NRC KI, Russian Federation; JINR; MESTD, Serbia; MSSR, Slovakia; ARRS and MIZS, Slovenia; DST/NRF, ˇ South Africa; MINECO, Spain; SRC and Wallenberg Foundation, Sweden; SERI, SNSF and Cantons of Bern and Geneva, Switzerland; MOST, Taiwan; TAEK, Turkey; STFC, United Kingdom; DOE and NSF, United States of America. In addition, individual groups and members have received support from BCKDF, the Canada Council, CANARIE, CRC, Compute Canada, FQRNT, and the Ontario Innovation Trust, Canada; EPLANET, ERC, FP7, Horizon 2020 and Marie Sk lodowska-Curie Actions, European Union; Investissements d’Avenir Labex and Idex, ANR, R´egion Auvergne and Fondation Partager le Savoir, France;
DFG and AvH Foundation, Germany; Herakleitos, Thales and Aristeia programmes co-financed by EU-ESF and the Greek NSRF; BSF, GIF and Minerva, Israel; BRF, Norway; Generalitat de Catalunya, Generalitat Valenciana, Spain; the Royal Society and Leverhulme Trust, United Kingdo
Species distribution modelling for Rhipicephalus microplus (Acari : Ixodidae) in Benin, West Africa : comparing datasets and modelling algorithms

Rhipicephalus microplus is one of the most widely distributed and economically important ticks, transmitting Babesia bigemina, B. bovis and Anaplasma marginale. It was recently introduced to West Africa on live animals originating from Brazil. Knowing the precise environmental suitability for the tick would allow veterinary health officials to draft vector control strategies for different regions of the country. To test the performance of modelling algorithms and different sets of environmental explanatory variables, species distribution models for this tick species in Benin were developed using generalized linear models, lin-ear discriminant analysis and random forests. The training data for these models were a dataset containing reported absence or presence in 104 farms, randomly selected across Benin. These farms were sampled at the end of the rainy season, which corresponds with an annual peak in tick abundance. Two environmental datasets for the country of Benin were compared: one based on interpolated climate data (WorldClim) and one based on remotely sensed images (MODIS). The pixel size for both environmental datasets was 1 km. Highly suitable areas occurred mainly along the warmer and humid coast extending northwards to central Benin. The northern hot and drier areas were found to be unsuitable. The models developed and tested on data from the entire country were generally found to perform well, having an AUC value greater than 0.92. Although statistically significant, only small differences in accuracy measures were found between the modelling algorithms, or between the environmental datasets. The resulting risk maps differed nonetheless. Models based on interpolated climate suggested gradual variations in habitat suitability, while those based on remotely sensed data indicated a sharper contrast between suitable and unsuitable areas, and a patchy distribution of the suitable areas. Remotely sensed data yielded more spatial detail in the predictions. When computing accuracy measures on a subset of data along the invasion front, the modelling technique Random Forest outperformed the other modelling approaches, and results with MODIS-derived variables were better than those using WorldClim data.Belgian Science Pol-icy Programs (Belspo, SR/00/144).http://www.elsevier.com/locate/prevetmedhb201
Asymptotic representations and q-oscillator solutions of the graded Yang–Baxter equation related to Baxter Q-operators

AbstractWe consider a class of asymptotic representations of the Borel subalgebra of the quantum affine superalgebra Uq(glˆ(M|N)). This is characterized by Drinfeld rational fractions. In particular, we consider contractions of Uq(gl(M|N)) in the FRT formulation and obtain explicit solutions of the graded Yang–Baxter equation in terms of q-oscillator superalgebras. These solutions correspond to L-operators for Baxter Q-operators. We also discuss an extension of these representations to the ones for contracted algebras of Uq(glˆ(M|N)) by considering the action of renormalized generators of the other side of the Borel subalgebra. We define model independent universal Q-operators as the supertrace of the universal R-matrix and write universal T-operators in terms of these Q-operators based on shift operators on the supercharacters. These include our previous work on Uq(slˆ(2|1)) case [1] in part, and also give a cue for the operator realization of our Wronskian-like formulas on T- and Q-functions in [2,3]
Criticality on the international scene: Quo vadis?

AbstractThis paper brings a discussion on the current state-of-the-art in criticality assessment in an international context. It analyzes the status of resource criticality concepts and their calculation methods. The current practice often exhibits a common two-axis assessment framework but the way the two axes are further operationalized shows heterogeneous approaches. Apart from the two-axis as key element of criticality assessment, the scope of the materials, the role of substitution, the delineation of the supply chain and data, and indicator selection are addressed as key elements. The abovementioned criticality assessment practice is approached in function of the upcoming international debate on criticality. The paper tackles the role of criticality assessment in the context of the sustainability assessment toolbox and it proposes a clear distinction between criticality assessment and resilience to criticality. The insights offered in the paper may feed the international discussion in the identification of elements that may be harmonized and elements that may be better left open in function of the particular application
CtBPs Sense Microenvironmental Oxygen Levels to Regulate Neural Stem Cell State

SummaryBone morphogenetic proteins (BMPs) secreted by the dorsal neural tube and overlying ectoderm are key signals for the specification of the roof plate and dorsal interneuron populations. However, the signals that confer nonneurogenic character to the roof plate region are largely unknown. We report that the roof plate region shows elevated oxygen levels compared to neurogenic regions of the neural tube. These high oxygen levels are required for the expression of the antineuronal transcription factor Hes1 in the roof plate region. The transcriptional corepressor CtBP is a critical mediator of the oxygen-sensing response. High oxygen promotes a decrease in the CtBP occupancy of the promoter of Hes1. Furthermore, under conditions of high oxygen and BMP, CtBP associates with HES1 and represses neurogenesis. We propose that CtBP integrates signals originating from microenvironmental levels of oxygen and BMP to confer nonneurogenic character to the roof plate region
Reduced cortical thickness with increased lifetime burden of PTSD in OEF/OIF Veterans and the impact of comorbid TBI

AbstractPosttraumatic stress disorder (PTSD) and mild traumatic brain injury (mTBI) in military personnel is increasing dramatically following the OEF/OIF conflicts and is associated with alterations to brain structure. The present study examined the relationship between PTSD and cortical thickness, and its possible modification by mTBI, in a 104-subject OEF/OIF veteran cohort ranging in age from 20 to 62years. For each participant, two T1-weighted scans were averaged to create high-resolution images for calculation of regional cortical thickness. PTSD symptoms were assessed using the Clinician Administered PTSD Scale (CAPS) and scores were derived based on the previous month's symptoms (“current”) and a Cumulative Lifetime Burden of PTSD (CLB-P) reflecting the integral of CAPS scores across the lifetime. Mild TBI was diagnosed using the Boston Assessment of TBI-Lifetime (BAT-L). Results demonstrated a clear negative relationship between current PTSD severity and thickness in both postcentral gyri and middle temporal gyri. This relationship was stronger and more extensive when considering lifetime burden (CLB-P), demonstrating the importance of looking at trauma in the context of an individual's lifetime, rather than only at their current symptoms. Finally, interactions with current PTSD only and comorbid current PTSD and mTBI were found in several regions, implying an additive effect of lifetime PTSD and mTBI on cortical thickness
mu+md from isovector pseudoscalar sum rules

AbstractWe revisit the isovector pseudoscalar sum rule determination of mu+md, using families of finite energy sum rules known to be very accurately satisfied in the isovector vector channel. The sum rule constraints are sufficiently strong to allow a determination of both mu+md and the excited resonance decay constants. The corresponding Borel transformed sum rules are also very well satisfied, providing a non-trivial consistency check on the treatment of direct instanton contributions. We obtain [mu+md](2 GeV)=7.8±1.1 MeV (in the MS scheme), only marginally compatible with the most recent sum rule determinations, but in good agreement with recent unquenched lattice extractions
Human skin dendritic cell fate is differentially regulated by the monocyte identity factor Kruppel-like factor 4 during steady state and inflammation

BackgroundLangerhans cell (LC) networks play key roles in immunity and tolerance at body surfaces. LCs are established prenatally and can be replenished from blood monocytes. Unlike skin-resident dermal DCs (dDCs)/interstitial-type DCs and inflammatory dendritic epidermal cells appearing in dermatitis/eczema lesions, LCs lack key monocyte-affiliated markers. Inversely, LCs express various epithelial genes critical for their long-term peripheral tissue residency.ObjectiveDendritic cells (DCs) are functionally involved in inflammatory diseases; however, the mechanisms remained poorly understood.MethodsIn vitro differentiation models of human DCs, gene profiling, gene transduction, and immunohistology were used to identify molecules involved in DC subset specification.ResultsHere we identified the monocyte/macrophage lineage identity transcription factor Kruppel-like factor 4 (KLF4) to be inhibited during LC differentiation from human blood monocytes. Conversely, KLF4 is maintained or induced during dermal DC and monocyte-derived dendritic cell/inflammatory dendritic epidermal cell differentiation. We showed that in monocytic cells KLF4 has to be repressed to allow their differentiation into LCs. Moreover, respective KLF4 levels in DC subsets positively correlate with proinflammatory characteristics. We identified epithelial Notch signaling to repress KLF4 in monocytes undergoing LC commitment. Loss of KLF4 in monocytes transcriptionally derepresses Runt-related transcription factor 3 in response to TGF-β1, thereby allowing LC differentiation marked by a low cytokine expression profile.ConclusionMonocyte differentiation into LCs depends on activation of Notch signaling and the concomitant loss of KLF4
Validation of Occupants’ Behaviour Models for Indoor Quality Parameter and Energy Consumption Prediction

AbstractOccupants’ behaviour related to building control system plays a significant role to achieve thermal comfort and air quality in naturally-ventilated buildings. Generally, the published models of occupant's behavior are not validated, meaning that the predictive power has not yet been tested. For this reason, the validation of occupant's behavioral models is an issue that is gaining importance.In this paper validation was carried out through dynamic Building Energy Performance simulation (BEPS); behavioral models of windows opening and thermostats set-point published in literature were implemented in a dynamic BEPS software and the obtained results in terms of temperature, relative humidity and CO2 concentration were compared to real measurements. Through this comparison it will be possible to verify the accuracy of the implemented behavioral models.The models were able to reproduce the general tendencies in the measured temperatures but the simulation results diverged from the measured CO2 concentrations and relative humidity
Phytochemical characterization of South African bush tea (Athrixia phylicoides DC.)

AbstractA methanolic extract of bush tea (Athrixia phylicoides, Asteraceae) was evaluated sensorially. A High Temperature Liquid Chromatography (HTLC)-coupled sensory-guided analysis was performed on bush tea extract to identify potential taste modulating compounds. One fraction showed bitter enhancing effects on caffeine. Fractionation using Fast Centrifugal Partition Chromatography (FCPC) and preparative HPLC followed by structure elucidation using NMR and LC NMR led to the identification of three polymethoxylated flavones, quercetin-3′-O-glucoside (1), as well as a methoxylated derivative (2). In addition, two dicaffeoyl quinic acids and one coumaric acid ester (3) were isolated. Sensory evaluation of isolated compounds led to the identification of quercetin-3′-O-glucoside as bitterness enhancing principle