Miracle-dz/UniFAR-FTUs huggingface dataset:
The P2X7 Receptor in Inflammatory Diseases: Angel or Demon?

Under physiological conditions, adenosine triphosphate (ATP) is present at low levels in the extracellular milieu, being massively released by stressed or dying cells. Once outside the cells, ATP and related nucleotides/nucleoside generated by ectonucleotidases mediate a high evolutionary conserved signaling system: the purinergic signaling, which is involved in a variety of pathological conditions, including inflammatory diseases. Extracellular ATP has been considered an endogenous adjuvant that can initiate inflammation by acting as a danger signal through the activation of purinergic type 2 receptors—P2 receptors (P2Y G-protein coupled receptors and P2X ligand-gated ion channels). Among the P2 receptors, the P2X7 receptor is the most extensively studied from an immunological perspective, being involved in both innate and adaptive immune responses. P2X7 receptor activation induces large-scale ATP release via its intrinsic ability to form a membrane pore or in association with pannexin hemichannels, boosting purinergic signaling. ATP acting via P2X7 receptor is the second signal to the inflammasome activation, inducing both maturation and release of pro-inflammatory cytokines, such as IL-1β and IL-18, and the production of reactive nitrogen and oxygen species. Furthermore, the P2X7 receptor is involved in caspases activation, as well as in apoptosis induction. During adaptive immune response, P2X7 receptor modulates the balance between the generation of T helper type 17 (Th17) and T regulatory (Treg) lymphocytes. Therefore, this receptor is involved in several inflammatory pathological conditions. In infectious diseases and cancer, P2X7 receptor can have different and contrasting effects, being an angel or a demon depending on its level of activation, cell studied, type of pathogen, and severity of infection. In neuroinflammatory and neurodegenerative diseases, P2X7 upregulation and function appears to contribute to disease progression. In this review, we deeply discuss P2X7 receptor dual function and its pharmacological modulation in the context of different pathologies, and we also highlight the P2X7 receptor as a potential target to treat inflammatory related diseases.
Resource Availability Drives Responses of Soil Microbial Communities to Short-term Precipitation and Nitrogen Addition in a Desert Shrubland

Desert microbes are expected to be substantially sensitive to global environmental changes, such as precipitation changes and elevated nitrogen deposition. However, the effects of precipitation changes and nitrogen enrichment on their diversity and community composition remain poorly understood. We conducted a field experiment over 2 years with multi-level precipitation and nitrogen addition in a desert shrubland of northern China, to examine the responses of soil bacteria and fungi in terms of diversity and community composition and to explore the roles of plant and soil factors in structuring microbial communities. Water addition significantly increased soil bacterial diversity and altered the community composition by increasing the relative abundances of stress-tolerant (dormant) taxa (e.g., Acidobacteria and Planctomycetes); however, nitrogen addition had no substantial effects. Increased precipitation and nitrogen did not impact soil fungal diversity, but significantly shifted the fungal community composition. Specifically, water addition reduced the relative abundances of drought-tolerant taxa (e.g., the orders Pezizales, Verrucariales, and Agaricales), whereas nitrogen enrichment decreased those of oligotrophic taxa (e.g., the orders Agaricales and Sordariales). Shifts in microbial community composition under water and nitrogen addition occurred primarily through changing resource availability rather than plant community. Our results suggest that water and nitrogen addition affected desert microbes in different ways, with watering shifting stress-tolerant traits and fertilization altering copiotrophic/oligotrophic traits of the microbial communities. These findings highlight the importance of resource availability in driving the desert microbial responses to short-term environmental changes.
SilE is an intrinsically disordered periplasmic “molecular sponge” involved in bacterial silver resistance

Ag+ resistance was initially found on the Salmonella enetrica serovar Typhimurium multi‐resistance plasmid pMG101 from burns patients in 1975. The putative model of Ag+ resistance, encoded by the sil operon from pMG101, involves export of Ag+ via an ATPase (SilP), an effluxer complex (SilCFBA) and a periplasmic chaperon of Ag+ (SilE). SilE is predicted to be intrinsically disordered. We tested this hypothesis using structural and biophysical studies and show that SilE is an intrinsically disordered protein in its free apo‐form but folds to a compact structure upon optimal binding to six Ag+ ions in its holo‐form. Sequence analyses and site‐directed mutagenesis established the importance of histidine and methionine containing motifs for Ag+‐binding, and identified a nucleation core that initiates Ag+‐mediated folding of SilE. We conclude that SilE is a molecular sponge for absorbing metal ions.
Mechanics-Based Approach for Detection and Measurement of Particle Contamination in Proximity Nanofabrication Processes

In spite of the great progress made toward addressing the challenge of particle contamination in nanomanufacturing, its deleterious effect on yield is still not negligible. This is particularly true for nanofabrication processes that involve close proximity or contact between two or more surfaces. One such process is Jet-and-Flash Imprint Lithography (J-FIL), which involves the formation of a nanoscale liquid film between a patterned template and a substrate. In this process, the presence of any frontside particle taller than the liquid film thickness, which is typically sub-25 nm, can not only disrupt the continuity of this liquid film but also damage the expensive template upon contact. The detection of these particles has typically relied on the use of subwavelength optical techniques such as scatterometry that can suffer from low throughput for nanoscale particles. In this paper, a novel mechanics-based method has been proposed as an alternative to these techniques. It can provide a nearly 1000 amplification of the particle size, thereby allowing for optical microscopy based detection. This technique has been supported by an experimentally validated multiphysics model which also allows for estimation of the loss in yield and potential contact-related template damage because of the particle encounter. Also, finer inspection of template damage needs to be carried out over a much smaller area, thereby increasing throughput of the overall process. This technique also has the potential for inline integration, thereby circumventing the need for separate tooling for subwavelength optical inspection of substrates. [DOI: 10.1115/1.4033742]
Prevalence of overweight and obesity in Canadian children, 2004 to 2013: Impact of socioeconomic determinants.

Background We recently reported an encouraging decline in the prevalence of overweight (OW) or obesity (OB) in Canadian children from 31% to 27% with stabilization in OB rates at ~13% using national survey data between 2004 and 2013. Although rates were lower for toddlers, girls and those of European (White) race-ethnicity, secular trends persisted after adjustment. In this follow-up study, we explored the ability of socioeconomic status to explain or modify these relationships using the same data set. Methods We analyzed a decade of anthropometric data from 14,014 children aged 3 to 19 years. We explored the influence of income adequacy, education, immigration status, family type (e.g., single-parent) and geographic region by multivariable logistic regression. Data sets included Canadian Community Health Survey cycle 2.2 and Canadian Health Measures Surveys cycles 2 and 3. Results Children from higher-income families fared better than their lower-income counterparts in each survey era and demonstrated a significant decline in OW/OB from 29.1% (95% confidence interval [CI]: 27.3 to 30.8) in 2004 to 2005 to 22.2% (95% CI: 19.8 to 24.6) in 2012 to 2013, P<0.001. Regression models confirmed the effects of time, age, sex, race, income, education, immigration and region. Although single-parent families did less well in univariate analyses, this effect vanished after adjustment for other socioeconomic status variables, such as income and education. Regional variations persisted, with lower rates of OB and OW/OB in British Columbia and higher rates in Atlantic Canada. Conclusions These results confirm that progress is possible against this important public health challenge, underline the need to better understand sociodemographic risk factors and identify groups at higher risk for possible interventions.
Assessing physiotherapists’ communication skills for promoting patient autonomy for self-management: reliability and validity of the communication evaluation in rehabilitation tool

Abstract Purpose: To assess the inter-rater reliability and concurrent validity of the Communication Evaluation in Rehabilitation Tool, which aims to externally assess physiotherapists competency in using Self-Determination Theory-based communication strategies in practice. Materials and methods: Audio recordings of initial consultations between 24 physiotherapists and 24 patients with chronic low back pain in four hospitals in Ireland were obtained as part of a larger randomised controlled trial. Three raters, all of whom had Ph.Ds in psychology and expertise in motivation and physical activity, independently listened to the 24 audio recordings and completed the 18-item Communication Evaluation in Rehabilitation Tool. Inter-rater reliability between all three raters was assessed using intraclass correlation coefficients. Concurrent validity was assessed using Pearson’s r correlations with a reference standard, the Health Care Climate Questionnaire. Results: The total score for the Communication Evaluation in Rehabilitation Tool is an average of all 18 items. Total scores demonstrated good inter-rater reliability (Intraclass Correlation Coefficient (ICC) = 0.8) and concurrent validity with the Health Care Climate Questionnaire total score (range: r = 0.7–0.88). Item-level scores of the Communication Evaluation in Rehabilitation Tool identified five items that need improvement. Conclusion: Results provide preliminary evidence to support future use and testing of the Communication Evaluation in Rehabilitation Tool. Implications for Rehabilitation Promoting patient autonomy is a learned skill and while interventions exist to train clinicians in these skills there are no tools to assess how well clinicians use these skills when interacting with a patient. The lack of robust assessment has severe implications regarding both the fidelity of clinician training packages and resulting outcomes for promoting patient autonomy. This study has developed a novel measurement tool Communication Evaluation in Rehabilitation Tool and a comprehensive user manual to assess how well health care providers use autonomy-supportive communication strategies in real world-clinical settings. This tool has demonstrated good inter-rater reliability and concurrent validity in its initial testing phase. The Communication Evaluation in Rehabilitation Tool can be used in future studies to assess autonomy-supportive communication and undergo further measurement property testing as per our recommendations.
The BIG protein distinguishes the process of CO 2‐induced stomatal closure from the inhibition of stomatal opening by CO 2

Summary We conducted an infrared thermal imaging‐based genetic screen to identify Arabidopsis mutants displaying aberrant stomatal behavior in response to elevated concentrations of CO 2. This approach resulted in the isolation of a novel allele of the Arabidopsis BIG locus (At3g02260) that we have called CO 2 insensitive 1 (cis1). BIG mutants are compromised in elevated CO 2‐induced stomatal closure and bicarbonate activation of S‐type anion channel currents. In contrast with the wild‐type, they fail to exhibit reductions in stomatal density and index when grown in elevated CO 2. However, like the wild‐type, BIG mutants display inhibition of stomatal opening when exposed to elevated CO 2. BIG mutants also display wild‐type stomatal aperture responses to the closure‐inducing stimulus abscisic acid (ABA). Our results indicate that BIG is a signaling component involved in the elevated CO 2‐mediated control of stomatal development. In the control of stomatal aperture by CO 2, BIG is only required in elevated CO 2‐induced closure and not in the inhibition of stomatal opening by this environmental signal. These data show that, at the molecular level, the CO 2‐mediated inhibition of opening and promotion of stomatal closure signaling pathways are separable and BIG represents a distinguishing element in these two CO 2‐mediated responses.
Title Hypertonic saline reduces inflammation and enhances theresolution of oleic acid induced acute lung injury

Background: Hypertonic saline (HTS) reduces the severity of lung injury in ischemia-reperfusion, endotoxin-induced and ventilation-induced lung injury. However, the potential for HTS to modulate the resolution of lung injury is not known. We investigated the potential for hypertonic saline to modulate the evolution and resolution of oleic acid induced lung injury. Methods: Adult male Sprague Dawley rats were used in all experiments. Series 1 examined the potential for HTS to reduce the severity of evolving oleic acid (OA) induced acute lung injury. Following intravenous OA administration, animals were randomized to receive isotonic (Control, n = 12) or hypertonic saline (HTS, n = 12), and the extent of lung injury assessed after 6 hours. Series 2 examined the potential for HTS to enhance the resolution of oleic acid (OA) induced acute lung injury. Following intravenous OA administration, animals were randomized to receive isotonic (Control, n = 6) or hypertonic saline (HTS, n = 6), and the extent of lung injury assessed after 6 hours. Results: In Series I, HTS significantly reduced bronchoalveolar lavage (BAL) neutrophil count compared to Control [61.5 ± 9.08 versus 102.6 ± 11.89 × 103 cells.ml-1]. However, there were no between group differences with regard to: A-a O2 gradient [11.9 ± 0.5 vs. 12.0 ± 0.5 KPa]; arterial PO2; static lung compliance, or histologic injury. In contrast, in Series 2, hypertonic saline significantly reduced histologic injury and reduced BAL neutrophil count [24.5 ± 5.9 versus 46.8 ± 4.4 × 103 cells.ml-1], and interleukin-6 levels [681.9 ± 190.4 versus 1365.7 ± 246.8 pg.ml-1]. Conclusion: These findings demonstrate, for the first time, the potential for HTS to reduce pulmonary inflammation and enhance the resolution of oleic acid induced lung injury. Background Hypertonic saline (7.5% saline, HTS) exhibits considerable potential as a therapeutic agent in diverse injury models. HTS has been demonstrated to inhibit acute lung injury (ALI) induced by systemic ischemia-reperfusion [1], hemorrhagic shock [2], and acute pancreatitis [3,4] in Published: 8 July 2008 BMC Pulmonary Medicine 2008, 8:9 doi:10.1186/1471-2466-8-9 Received: 20 May 2008 Accepted: 8 July 2008 This article is available from: http://www.biomedcentral. com/1471-2466/8/9 © 2008 Kennedy et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BMC Pulmonary Medicine 2008, 8:9 http://www.biomedcentral. com/1471-2466/8/9
Psychological factors influence the overlap syndrome in functional gastrointestinal disorders (FGIDs) among middle-aged women in South Korea

ABSTRACT This study investigated the psychological factors related to the overlap syndrome, i.e., multiple gastrointestinal conditions that are part of functional gastrointestinal disorders (FGIDs) in the same individual and potentially related to quality of life (QOL) among women aged 45–60 years (n = 627) in South Korea. The study was undertaken between July 2014 and March 2015. Depressive and anxiety symptoms were ascertained using the Center for Epidemiologic Studies Depression scale (CES-D) and the Beck Anxiety Inventory (BAI), respectively. Negative cognition and the cognitive triad were identified using the Automatic Thoughts Questionnaire–Negative (ATQ-N) and the Cognitive Triad Inventory (CTI), respectively. Resilience and QOL were assessed using the Connor–Davidson Resilience Scale (CD-RISC) and World Health Organization Quality of Life scale abbreviated version (WHOQOL-BREF). Women with the overlap syndrome had the highest CES-D (mean = 16.66 ± 11.79, p < .001), BAI (mean = 17.46 ± 12.67, p < .001), and ATQ-N scores (mean = 53.61 ± 20.88, p < .001), followed by women with gastrointestinal disorders but without the overlap syndrome and healthy controls. Healthy controls had the highest WHOQOL-BREF score (mean = 77.69 ± 12.53, p < .001). After stepwise selection, the final model explained 61.8 percent of the variance in QOL. Thus, depressive symptoms, anxiety, negative cognition, cognitive triad, and resilience were significantly related to QOL in women with the overlap syndrome.
Residual‐based model diagnosis methods for mixture cure models

Model diagnosis, an important issue in statistical modeling, has not yet been addressed adequately for cure models. We focus on mixture cure models in this work and propose some residual‐based methods to examine the fit of the mixture cure model, particularly the fit of the latency part of the mixture cure model. The new methods extend the classical residual‐based methods to the mixture cure model. Numerical work shows that the proposed methods are capable of detecting lack‐of‐fit of a mixture cure model, particularly in the latency part, such as outliers, improper covariate functional form, or nonproportionality in hazards if the proportional hazards assumption is employed in the latency part. The methods are illustrated with two real data sets that were previously analyzed with mixture cure models.
Introduction to the SP theory of intelligence

This article provides a brief introduction to the "Theory of Intelligence" and its realisation in the "SP Computer Model". The overall goal of the SP programme of research, in accordance with long-established principles in science, has been the simplification and integration of observations and concepts across artificial intelligence, mainstream computing, mathematics, and human learning, perception, and cognition. In broad terms, the SP system is a brain-like system that takes in "New" information through its senses and stores some or all of it as "Old" information. A central idea in the system is the powerful concept of "SP-multiple-alignment", borrowed and adapted from bioinformatics. This the key to the system's versatility in aspects of intelligence, in the representation of diverse kinds of knowledge, and in the seamless integration of diverse aspects of intelligence and diverse kinds of knowledge, in any combination. There are many potential benefits and applications of the SP system. It is envisaged that the system will be developed as the "SP Machine", which will initially be a software virtual machine, hosted on a high-performance computer, a vehicle for further research and a step towards the development of an industrial-strength SP Machine.
Organographs - Multi-faceted Hierarchical Categorization of Web Documents

The data deluge of information in the Web challenges interna uts to organize their references to interesting content in the Web as well as in their private storage space of f-line. Having an automatically managed personal index to content acquired from the Web is useful for everybod , but critical to researchers and scholars. In this paper, we discuss concepts and problems related to organizi ng information through multi-faceted hierarchical categorization. We introduce the organographas a mechanism to specify multiple views of how content is organized. Organographs can help scientists to automatica lly organize their documents along multiple axes, improving sharing and navigation through themes and concep ts according to a particular research objective.
RMPD - A Recursive Mid-Point Displacement Algorithm for Path Planning

Motivated by what is required for real-time path planning, the paper starts out by presenting sRMPD, a new recursive "local" planner founded on the key notion that, unless made necessary by an obstacle, there must be no deviation from the shortest path between any two points, which would normally be a straight line path in the configuration space. Subsequently, we increase the power of sRMPD by using it as a "connect" subroutine call in a higher-level sampling-based algorithm mRMPD that is inspired by multi-RRT. As a consequence, mRMPD spawns a larger number of space exploring trees in regions of the configuration space that are characterized by a higher density of obstacles. The overall effect is a hybrid tree growing strategy with a trade-off between random exploration as made possible by multi-RRT based logic and immediate exploitation of opportunities to connect two states as made possible by sRMPD. The mRMPD planner can be biased with regard to this trade-off for solving different kinds of planning problems efficiently. Based on the test cases we have run, our experiments show that mRMPD can reduce planning time by up to 80% compared to basic RRT.
Towards Matching User Mobility Traces in Large-Scale Datasets

The problem of unicity and reidentifiability of records in large-scale databases has been studied in different contexts and approaches, with focus on preserving privacy or matching records from different data sources. With an increasing number of service providers nowadays routinely collecting location traces of their users on unprecedented scales, there is a pronounced interest in the possibility of matching records and datasets based on spatial trajectories. Extending previous work on reidentifiability of spatial data and trajectory matching, we present the first large-scale analysis of user matchability in real mobility datasets on realistic scales, i.e. among two datasets that consist of several million people's mobility traces, coming from a mobile network operator and transportation smart card usage. We extract the relevant statistical properties which influence the matching process and analyze their impact on the matchability of users. We show that for individuals with typical activity in the transportation system (those making 3-4 trips per day on average), a matching algorithm based on the co-occurrence of their activities is expected to achieve a 16.8 percent success only after a one-week long observation of their mobility traces, and over 55 percent after four weeks. We show that the main determinant of matchability is the expected number of co-occurring records in the two datasets. Finally, we discuss different scenarios in terms of data collection frequency and give estimates of matchability over time. We show that with higher frequency data collection becoming more common, we can expect much higher success rates in even shorter intervals.