Miracle-dz/UniFAR-FTUs huggingface dataset:
IL-36R signalling activates intestinal epithelial cells and fibroblasts and promotes mucosal healing in vivo

Objective Interleukin (IL)-36R signalling plays a proinflammatory role in different organs including the skin, but the expression of IL-36R ligands and their molecular function in intestinal inflammation are largely unknown. Design We studied the characteristics of IL-36R ligand expression in IBDs and experimental colitis. The functional role of IL-36R signalling in the intestine was addressed in experimental colitis and wound healing models in vivo by using mice with defective IL-36R signalling (IL-36R−/−) or Myd88, neutralising anti-IL-36R antibodies, recombinant IL-36R ligands and RNA-seq genome expression analysis. Results Expression of IL-36α and IL-36γ was significantly elevated in active human IBD and experimental colitis. While IL-36γ was predominantly detected in nuclei of the intestinal epithelium, IL-36α was mainly found in the cytoplasm of CD14+ inflammatory macrophages. Functional studies showed that defective IL-36R signalling causes high susceptibility to acute dextran sodium sulfate colitis and impairs wound healing. Mechanistically, IL-36R ligands released upon mucosal damage activated IL-36R+ colonic fibroblasts via Myd88 thereby inducing expression of chemokines, granulocyte-macrophage colony-stimulating factor (GM-CSF) and IL-6. Moreover, they induced proliferation of intestinal epithelial cells (IECs) and expression of the antimicrobial protein lipocalin 2. Finally, treatment of experimental intestinal wounds with IL-36R ligands significantly accelerated mucosal healing in vivo. Conclusions IL-36R signalling is activated upon intestinal damage, stimulates IECs and fibroblasts and drives mucosal healing. Modulation of the IL-36R pathway emerges as a potential therapeutic strategy for induction of mucosal healing in IBD.
Hitchhiker's Guide to Voltammetry: Acute and Chronic Electrodes for in Vivo Fast-Scan Cyclic Voltammetry

Fast-scan cyclic voltammetry (FSCV) has been used for over 20 years to study rapid neurotransmission in awake and behaving animals. These experiments were first carried out with carbon-fiber microelectrodes (CFMs) encased in borosilicate glass, which can be inserted into the brain through micromanipulators and guide cannulas. More recently, chronically implantable CFMs constructed with small diameter fused-silica have been introduced. These electrodes can be affixed in the brain with minimal tissue response, which permits longitudinal measurements of neurotransmission in single recording locations during behavior. Both electrode designs have been used to make novel discoveries in the fields of neurobiology, behavioral neuroscience, and psychopharmacology. The purpose of this Review is to address important considerations for the use of FSCV to study neurotransmitters in awake and behaving animals, with a focus on measurements of striatal dopamine. Common issues concerning experimental design, data collection, and calibration are addressed. When necessary, differences between the two methodologies (acute vs chronic recordings) are discussed. The topics raised in this Review are particularly important as the field moves beyond dopamine toward new neurochemicals and brain regions.
Non‐genetic polymorphisms in rotifers: environmental and endogenous controls, development, and features for predictable or unpredictable environments

Pronounced non‐genetic polymorphisms, or polyphenisms, occur in some monogonont rotifers reproducing by diploid, female parthenogenesis. In many brachionids, there is great variation in spine length. In trimorphic species of Asplanchna, females can vary in size and shape, from a small saccate morph to giant cruciform and campanulate morphs. In species that also reproduce sexually, diploid eggs can develop into two types of females. Amictic females produce diploid eggs that develop parthenogenetically into females; mictic females produce haploid eggs that develop parthenogenetically into males or, if fertilized, into resting eggs. In a species of Synchaeta, amictic females produce diploid eggs that can be either thin‐shelled and subitaneous or thicker‐shelled and diapausing. In all cases, morph determination occurs during the oogenesis or embryological development of diploid eggs in the maternal body cavity. For the first time, these polymorphisms are reviewed together and compared regarding a number of features associated with transitions from default to induced morphs: (i) type of variation (morphological, physiological, or both; continuous or discrete); (ii) inducing signal (environmental, endogenous, or both); (iii) universality of response to that signal (all or only some individuals); (iv) fitness cost; (v) reversibility; and (vi) ecological significance. Most of the polymorphisms fall into two major categories regarding these features. Transitions suitable for predictable environments involve: universal responses to environmental signals; continuous morphological variation; low reproductive cost; rapid reversibility; and adaptations for defence, hydrodynamics or prey ingestion. Transitions suitable for unpredictable environments are bet‐hedging strategies and usually involve: partial (stochastic) responses to environmental or endogenous signals; discontinuous physiological variation; initiation of diapause, and thus high reproductive cost and slow reversibility. Two cases of morphological variation also involve the simultaneous production of different morphs and likely are adaptations for an uncertain future: continuous spine‐length variation due to maternal age in Brachionus calyciflorus, and production of discrete cruciform and campanulate females in Asplanchna spp.
An 8-gene signature for prediction of prognosis and chemoresponse in non-small cell lung cancer

Identification of a potential gene signature for improved diagnosis in non-small cell lung cancer (NSCLC) patient is necessary. Here, we aim to establish and validate the prognostic efficacy of a gene set that can predict prognosis and benefits of adjuvant chemotherapy (ACT) in NSCLC patients from various ethnicities. An 8-gene signature was calculated from the gene expression of 181 patients using univariate Cox proportional hazard regression analysis. The prognostic value of the signature was robustly validated in 1,477 patients from five microarray independent data sets and one RNA-seq data set. The 8-gene signature was identified as an independent predictor of patient survival in the presence of clinical parameters in univariate and multivariate analyses [hazard ratio (HR): 2.84, 95% confidence interval CI (1.74-4.65), p=3.06e-05, [HR] 2.62, 95% CI (1.51-4.53), p=0.001], respectively. Subset analysis demonstrated that the 8-gene signature could identify high-risk patients in stage II-III with improved survival from ACT [(HR) 1.47, 95% CI (1.01-2.14), p=0.044]. The 8-gene signature also stratified risk groups in EGFR-mutated and wild-type patients. In conclusion, the 8-gene signature is a strong and independent predictor that can significantly stratify patients into low- and high-risk groups. Our gene signature also has the potential to predict patients in stage II-III that are likely to benefit from ACT.
North Atlantic Intermediate to Deep Water circulation and chemical stratification during the past 1 Myr

Benthic foraminiferal carbon isotope records from a suite of drill sites in the North Atlantic are used to trace variations in the relative strengths of Lower North Atlantic Deep Water (LNADW), Upper North Atlantic Deep Water (UNADW), and Southern Ocean Water (SOW) over the past 1 Myr. During glacial intervals, significant increases in intermediate-to-deep δ13C gradients (commonly reaching >1.2‰) are consistent with changes in deep water circulation and associated chemical stratification. Bathymetric δ13C gradients covary with benthic foraminiferal δ18O and covary inversely with Vostok CO2, in agreement with chemical stratification as a driver of atmospheric CO2 changes. Three deep circulation indices based on δ13C show a phasing similar to North Atlantic sea surface temperatures, consistent with a Northern Hemisphere control of NADW/SOW variations. However, lags in the precession band indicate that factors other than deep water circulation control ice volume variations at least in this band.
Low Prevalence of Human Pathogens on Fresh Produce on Farms and in Packing Facilities: A Systematic Review

Foodborne illness burdens individuals around the world and may be caused by consuming fresh produce contaminated with bacterial, parasite, and viral pathogens. Pathogen contamination on produce may originate at the farm and packing facility. This research aimed to determine the prevalence of human pathogens (bacteria, parasites, and viruses) on fresh produce (fruits, herbs, and vegetables) on farms and in packing facilities worldwide through a systematic review of 38 peer-reviewed articles. The median and range of the prevalence was calculated, and Kruskal–Wallis tests and logistic regression were performed to compare prevalence among pooled samples of produce groups, pathogen types, and sampling locations. Results indicated a low median percentage of fresh produce contaminated with pathogens (0%). Both viruses (p-value = 0.017) and parasites (p-value = 0.033), on fresh produce, exhibited higher prevalence than bacteria. No significant differences between fresh produce types or between farm and packing facility were observed. These results may help to better quantify produce contamination in the production environment and inform strategies to prevent future foodborne illness.
Ex Vivo Evaluation of Cementless Acetabular Cup Stability Using Impact Analyses with a Hammer Instrumented with Strain Sensors

The acetabular cup (AC) implant stability is determinant for the success of cementless hip arthroplasty. A method based on the analysis of the impact force applied during the press-fit insertion of the AC implant using a hammer instrumented with a force sensor was developed to assess the AC implant stability. The aim of the present study was to investigate the performance of a method using a hammer equipped with strain sensors to retrieve the AC implant stability. Different AC implants were inserted in five bovine samples with different stability conditions leading to 57 configurations. The AC implant was impacted 16 times by the two hammers consecutively. For each impact; an indicator IS (respectively IF) determined by analyzing the time variation of the signal corresponding to the averaged strain (respectively force) obtained with the stress (respectively strain) hammer was calculated. The pull-out force F was measured for each configuration. F was significantly correlated with IS (R2 = 0.79) and IF (R2 = 0.80). The present method has the advantage of not modifying the shape of the hammer that can be sterilized easily. This study opens new paths towards the development of a decision support system to assess the AC implant stability.
Length Expansion and Cracking of Plain and Reinforced Concrete Prisms Due to Alkali-Silica Reaction

Measurements of length expansion and observations of cracking of plain and reinforced concrete prisms with varying sizes and amount of reinforcement caused by alkali-silica reaction (ASR) are presented. Ends of the prisms were sealed to make the data relatable to existing structural members. The specimens were made with either reactive or nonreactive aggregates and immersed in an alkali solution for one year to accelerate ASR. Visible cracks appeared on reactive specimens after 4 months of conditioning, when length expansion caused by ASR was about 400 microstrain. Expansion of the prisms that contained longitudinal bars was greatly reduced by the reinforcement, and the dominant cracking was oriented in the direction parallel to the reinforcement. Strain of bars caused by ASR was close to yield. The effect of expansion and cracking from ASR on structural behavior of reinforced beams and on mechanical properties of companion cylinders that accompanied these prism tests is reported separately.
Estimation of pure qubits on circles

Gisin and Popescu (Gisin N and Popescu S 1999 Phys. Rev. Lett. 83 432) have shown that more information about their direction can be obtained from a pair of anti-parallel spins compared to a pair of parallel spins, where the first member of the pair (which we call the pointer member) can point equally along any direction in the Bloch sphere. They argued that this was due to the difference in dimensionality spanned by these two alphabets of states. Here we consider similar alphabets, but with the first spin restricted to a fixed small circle of the Bloch sphere. In this case, the dimensionality spanned by the anti-parallel versus parallel alphabet is now equal. However, the anti-parallel alphabet is found to still contain more information in general. We generalize this to having N parallel spins and M anti-parallel spins. When the pointer member is restricted to a small circle these alphabets again span spaces of equal dimension, yet in general, more directional information can be found for sets with smaller |N − M| for any fixed total number of spins. We find that the optimal POVMs for extracting directional information in these cases can always be expressed in terms of the Fourier basis. Our results show that dimensionality alone cannot explain the greater information content in anti-parallel combinations of spins compared to parallel combinations. In addition, we describe an LOCC protocol which extracts optimal directional information when the pointer member is restricted to a small circle and a pair of parallel spins are supplied.
Edinburgh Research Explorer Identification of Immune Traits Correlated with Dairy Cow Health, Reproduction and Productivity

Detailed biological analyses (e.g. epidemiological, genetic) of animal health and fitness in the field are limited by the lack of large-scale recording of individual animals. An alternative approach is to identify immune traits that are associated with these important functions and can be subsequently used in more detailed studies. We have used an experimental dairy herd with uniquely dense phenotypic data to identify a range of potentially useful immune traits correlated with enhanced (or depressed) health and fitness. Blood samples from 248 dairy cows were collected at two-monthly intervals over a 10- month period and analysed for a number of immune traits, including levels of serum proteins associated with the innate immune response and circulating leukocyte populations. Immune measures were matched to individual cow records related to productivity, fertility and disease. Correlations between traits were calculated using bivariate analyses based on animal repeatability and random regression models with a Bonferroni correction to account for multiple testing. A number of significant correlations were found between immune traits and other recorded traits including: CD4 + :CD8 + T lymphocyte ratio and subclinical mastitis; % CD8 + lymphocytes and fertility; % CD335 + natural killer cells and lameness episodes; and serum haptoglobin levels and clinical mastitis. Importantly these traits were not associated with reduced productivity and, in the case of cellular immune traits, were highly repeatable. Moreover these immune traits displayed significant between-animal variation suggesting that they may be altered by genetic selection. This study represents the largest simultaneous analysis of multiple immune traits in dairy cattle to-date and demonstrates that a number of immune traits are associated with health events. These traits represent useful selection markers for future programmes aimed at improving animal health and fitness.
Superplasticity in a 5024 Aluminium Alloy Processed by Severe Plastic Deformation

The superplastic behaviour of an Al-4.6%Mg-0.35%Mn-0.2%Sc-0.09%Zr alloy was studied in the temperature range 250-500°C at strain rates ranging from 10-4 to 10-1 s-1. The AA5024 was subjected to equal channel angular pressing (ECAP) at 300°C up to ~12. The highest elongation-to-failure of ∼3300% was attained at a temperature of 450°C and an initial strain rate of 5.6×10-1 s-1. Regularities of superplastic behaviour of the 5024 aluminium alloy are discussed.
From Competition to Complementarity: Comparative Influence Diffusion and Maximization

Influence maximization is a well-studied problem that asks for a small set of influential users from a social network, such that by targeting them as early adopters, the expected total adoption through influence cascades over the network is maximized. However, almost all prior work focuses on cascades of a single propagating entity or purely-competitive entities. In this work, we propose the Comparative Independent Cascade (Com-IC) model that covers the full spectrum of entity interactions from competition to complementarity. In Com-IC, users' adoption decisions depend not only on edge-level information propagation, but also on a node-level automaton whose behavior is governed by a set of model parameters, enabling our model to capture not only competition, but also complementarity, to any possible degree. We study two natural optimization problems, Self Influence Maximization and Complementary Influence Maximization, in a novel setting with complementary entities. Both problems are NP-hard, and we devise efficient and effective approximation algorithms via non-trivial techniques based on reverse-reachable sets and a novel "sandwich approximation" strategy. The applicability of both techniques extends beyond our model and problems. Our experiments show that the proposed algorithms consistently outperform intuitive baselines on four real-world social networks, often by a significant margin. In addition, we learn model parameters from real user action logs.
Out of Place: Racial Stereotypes and the Ecology of Frisks and Out of Place: Racial Stereotypes and the Ecology of Frisks and Searches Following Traffic Stops Searches Following Traffic Stops

Objectives : Test hypotheses drawn from Smith and Alpert's social conditioning theory that explains biased policing as the result of implicit racial stereotypes. Distinguishing between frisks, external pat-downs, and probable cause searches, we hypothesize that (1) black drivers are more likely than white drivers to be frisked and searched; (2) racial disparity is greater in frisks than searches; (3) racial disparity in frisks, but not searches, is conditional upon the racial composition of the community; and (4) that drivers' race is not related to the productivity of searches. Methods : Data are all traffic stops made by the Rhode Island State Police in 2006, exclusive of those in which a search was mandatory. Multinomial and binary logistic regression is employed to estimate models of frisks, searches, search productivity and to test the conditional effect of community context. Result s: Each of the four hypotheses is supported. Conclusion : Biased policing is largely the product of implicit stereotypes that are activated in contexts in which black drivers appear out of place and in police actions that require quick decisions providing little time to monitor cognitions. This insight has important implications for police training. Because of limitations in this study, additional research that distinguishes frisks and searches is needed
Evolution of Circumstellar Disks Around Normal Stars: Placing Our Solar System in Context

Over the past 10 years abundant evidence has emerged that many (if not all) stars are born with circumstellar disks. Understanding the evolution of post-accretion disks can provide strong constraints on theories of planet formation and evolution. In this review, we focus on developments in understanding: a) the evolution of the gas and dust content of circumstellar disks based on observational surveys, highlighting new results from the Spitzer Space Telescope; b) the physical properties of specific systems as a means to interpret the survey results; c) theoretical models used to explain the observations; d) an evolutionary model of our own solar system for comparison to the observations of debris disks around other stars; and e) how these new results impact our assessment of whether systems like our own are common or rare compared to the ensemble of normal stars in the disk of the Milky Way.
Structural and Mechanistic Basis for Extended-Spectrum Drug-Resistance Mutations in Altering the Specificity of TEM, CTX-M, and KPC β-lactamases

The most common mechanism of resistance to β-lactam antibiotics in Gram-negative bacteria is the production of β-lactamases that hydrolyze the drugs. Class A β-lactamases are serine active-site hydrolases that include the common TEM, CTX-M, and KPC enzymes. The TEM enzymes readily hydrolyze penicillins and older cephalosporins. Oxyimino-cephalosporins, such as cefotaxime and ceftazidime, however, are poor substrates for TEM-1 and were introduced, in part, to circumvent β-lactamase-mediated resistance. Nevertheless, the use of these antibiotics has lead to evolution of numerous variants of TEM with mutations that significantly increase the hydrolysis of the newer cephalosporins. The CTX-M enzymes emerged in the late 1980s and hydrolyze penicillins and older cephalosporins and derive their name from the ability to also hydrolyze cefotaxime. The CTX-M enzymes, however, do not efficiently hydrolyze ceftazidime. Variants of CTX-M enzymes, however, have evolved that exhibit increased hydrolysis of ceftazidime. Finally, the KPC enzyme emerged in the 1990s and is characterized by its broad specificity that includes penicillins, most cephalosporins, and carbapenems. The KPC enzyme, however, does not efficiently hydrolyze ceftazidime. As with the TEM and CTX-M enzymes, variants have recently evolved that extend the spectrum of KPC β-lactamase to include ceftazidime. This review discusses the structural and mechanistic basis for the expanded substrate specificity of each of these enzymes that result from natural mutations that confer oxyimino-cephalosporin resistance. For the TEM enzyme, extended-spectrum mutations act by establishing new interactions with the cephalosporin. These mutations increase the conformational heterogeneity of the active site to create sub-states that better accommodate the larger drugs. The mutations expanding the spectrum of CTX-M enzymes also affect the flexibility and conformation of the active site to accommodate ceftazidime. Although structural data are limited, extended-spectrum mutations in KPC may act by mediating new, direct interactions with substrate and/or altering conformations of the active site. In many cases, mutations that expand the substrate profile of these enzymes simultaneously decrease the thermodynamic stability. This leads to the emergence of additional global suppressor mutations that help correct the stability defects leading to increased protein expression and increased antibiotic resistance.
Aspects of alkali treatment of sponge gourd (Luffa cylindrica) fibers on the flexural properties of polyester matrix composites

Sponge gourd (Luffa cylindrica) forms a natural mat that deviates the crack path in brittle thermoset resin matrix composites, leading to a controlled fracture mode and increasing the toughness of the composite. The use of luffa as reinforcement is, however, restricted by a very weak fiber–matrix interface. In this work, luffa fibers were alkali-treated at two temperatures, with varying alkali concentrations. Although the surface analysis shows that the treatments promote a clear removal of the outer surface layer of the fibers with the exposition of the inner fibrillar structure and the consequent increase of the fiber surface area, only a secondary increase on the mechanical properties was obtained. The slight increase observed was attributed only to mechanical interlock. Long pullout lengths and neat fiber beads were the main features observed at the fracture surface of the treated and untreated fiber composites. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 87: 1927–1932, 2003