Miracle-dz/UniFAR-FTUs huggingface dataset:
p53 balances between tissue hierarchy and anarchy

Abstract Normal tissues are organized in a hierarchical model, whereas at the apex of these hierarchies reside stem cells (SCs) capable of self-renewal and of producing differentiated cellular progenies, leading to normal development and homeostasis. Alike, tumors are organized in a hierarchical manner, with cancer SCs residing at the apex, contributing to the development and nourishment of tumors. p53, the well-known ‘guardian of the genome’, possesses various roles in embryonic development as well as in adult SC life and serves as the ‘guardian of tissue hierarchy’. Moreover, p53 serves as a barrier for dedifferentiation and reprogramming by constraining the cells to a somatic state and preventing their conversion to SCs. On the contrary, the mutant forms of p53 that lost their tumor suppressor activity and gain oncogenic functions serve as ‘inducers of tissue anarchy’ and promote cancer development. In this review, we discuss these two sides of the p53 token that sentence a tissue either to an ordered hierarchy and life or to anarchy and death. A better understanding of these processes may open new horizons for the development of new cancer therapies.
Topolet: From Atomic Hand Posture Structures to a Comprehensive Gesture Set

We propose a type of time-series model for hierarchical hand posture database which can be viewed as a Markovian temporal structure. The model employs the topology of the points’ cloud, existing in each layer of the database, and exploits a novel type of atomic structure, we refer to as Topolet. Moreover, our temporal structure utilizes a modified version of another atomic gesture structure, known as Poselet. That modification considers Poselets from the vector-based generative perspective (instead of the pixel-based discriminative one). The results suggest a considerable improvement in the accuracy and time-complexity. Furthermore, in contrast to other approaches, our Topolet is capable of considering random gestures, thus introduces a comprehensive set of gestures (suitable for context-free application domain) within the shape-based approach. We prove that the Topolet could be enhanced to different resolutions of gestures’ set which provide the system with the potential to be adapted to different application requirements.
Ingestion of resistant starch by mice markedly increases microbiome‐derived metabolites

Recent research has shown significant health benefits deriving from high‐dietary fiber or microbiome‐accessible carbohydrate consumption. Compared with native starch (NS), dietary resistant starch (RS) is a high microbiome‐accessible carbohydrate that significantly alters the gut microbiome. The aim of this study was to determine the systemic metabolic effects of high microbiome‐accessible carbohydrate. Male C57BL/6 mice were divided into 2 groups and fed either NS or RS for 18 wk (n = 20/group). Metabolomic analyses revealed that plasma levels of numerous metabolites were significantly different between the RS‐fed and NS‐fed mice, many of which are microbiome‐derived. Most strikingly, we observed a 22‐fold increase in gut microbiome‐derived tryptophan metabolite indole‐3‐propionate (IPA), which was positively correlated with several gut microbiota, including Allobaculum, Bifidobacterium, and Lachnospiraceae, with Allobaculum having the most consistently increased abundance of all the IPA‐associated taxa across all RS‐fed mice. In addition, major changes were observed for metabolites solely or primarily metabolized in the gut (e.g., trimethylamine‐N‐oxide), metabolites that have a significant entero‐hepatic circulation (i.e., bile acids), lipid metabolites (e.g., cholesterol sulfate), metabolites indicating increased energy turnover (e.g., tricarboxylic acid cycle intermediates and ketone bodies), and increased antioxidants such as reduced glutathione. Our findings reveal potentially novel mediators of high microbiome‐accessible carbohydrate‐derived health benefits. —Koay,Y. C. , Wali. J. A. , Luk, A. W. S. , Macia, L. , Cogger, V. C. , Pulpitel, T. J., Wahl, D. , Solon‐Biet, S. M. , Holmes, A. , Simpson, S. J., O'Sullivan, J. F. Ingestion of resistant starch by mice markedly increases microbiome‐derived metabolites. FASEB J. 33, 8033–8042 (2019). www.fasebj. org
Gene Expression in Developmental Stages of Schistosoma japonicum Provides Further Insight into the Importance of the Schistosome Insulin-Like Peptide

We showed previously that the Schistosoma japonicum insulin-like peptide (SjILP) binds the worm insulin receptors, thereby, activating the parasite’s insulin pathway and emphasizing its important role in regulating uptake of glucose, a nutrient essential for parasite survival. Here we show that SjILP is differentially expressed in the schistosome life cycle and is especially highly transcribed in eggs, miracidia, and adult female worms. RNA inference was employed to knockdown SjILP in adults in vitro, with suppression confirmed by significantly reduced protein production, declined adenosine diphosphate levels, and reduction in glucose consumption. Immunolocalization showed that SjILP is located to lateral gland cells of mature intra-ovular miracidia in the schistosome egg, and is distributed on the ciliated epithelium and internal cell masses of newly transformed miracidia. In schistosomula, SjILP is present on the tegument in two antero-lateral points, indicating highly polarized expression during cercarial transformation. Analysis of serum from S. japonicum-infected mice by ELISA using a recombinant form of SjILP as an antigen revealed IgG immunoreactivity to this molecule at 7 weeks post-infection indicating it is likely secreted from mature eggs into the host circulation. These findings provide further insights on ILP function in schistosomes and its essential roles in parasite survival and growth in different development stages.
Prediction of Digital Terrestrial Television Coverage Using Machine Learning Regression

Appropriate coverage prediction is a fundamental task for an operator during the dimensioning process and planning of a digital terrestrial television (DTT) system because it allows offering a satisfactory quality of service to end users. Accordingly, several prediction methods based on propagation path loss estimation and traditional statistical models have been proposed. However, the choice of model depends on many factors, such as the presence of obstacles (buildings, trees, and so on) and propagation paths. This fact leads to increasing the error gap between the predicted and real value, which varies from one propagation model to the next. Therefore, novel techniques are required to achieve a high accuracy in the prediction of the signal strength based on few local measurements over the zone of interest. A machine learning regression algorithm is a novel approach that improves the accuracy of DTT coverage prediction regardless of the aforementioned constraints. To this end, we propose an approach based on clustering and machine regression algorithms, such as random forest regression, AdaBoost regression, and ${K}$ -nearest neighbors regression, where we choose the best algorithm for our approach. We use real measurements in terms of electric field strength corresponding to eight DTT channels operating in the city of Quito, Ecuador. Furthermore, we display the coverage results in Google Maps. We perform extensively simulation analysis based on the tenfold cross validation method to evaluate the performance of the machine learning regressor algorithms and compare the results in three error metrics with support vector regression, lasso regression, multilayer perceptron regression, and ordinary kriging technique. Satisfactorily, the results using random forest regression depict a considerable improvement in the accuracy of coverage prediction under a low computational load.
Agent-Based Modelling for Simulation-Based Design of Sustainable Faecal Sludge Management Systems

Re-using faecal sludge (FS) to generate value has the potential to contribute towards solving the issue of long term sanitation solutions in growing urban areas across sub-Saharan Africa; however, hitherto, no design tools have been available that are capable of simulating a system involving economic factors, complex social issues and environmental circumstances. We hypothesized that Agent-Based Modelling (ABM), when deployed with appropriate rigour, can provide such a tool. Extensive field work was carried out in a Malawian city, investigating the adoption of Skyloo above-ground composting toilets by households, and the operation of the municipal FS site. 65 semi-structured interviews and 148 household interviews, together with observations, were carried out to characterize these processes, with the data acquired being used to construct two separate ABMs. The Skyloo ABM was run for various scenarios of start-up capital for business and payback of loans against the toilet cost to households. The municipal FS Site ABM was run for different patterns of dumping fee and enforcement structure. The field work demonstrated that there is potential for further expansion of FS reuse, with a market for agricultural application. The Skyloo ABM identified the significance of start-up capital for a business installing the toilet technology; the municipal FS Site ABM showed that existing fees, fines and regulatory structure were insufficient to reduce illegal dumping of FS to any useful degree, but that a monthly permit system would provide enhanced revenue to the city council compared with per-visit charging of disposal companies at the municipal FS site. Whilst each ABM ideally requires some additional data before full application, we have, for the first time, shown that ABM provides a basis for the simulation-based design of FS management systems, including complex social, economic and environmental factors.
An analysis of general practitioners' perspectives on patient safety incidents using critical incident technique interviews.

BACKGROUND General practitioners report difficulty in knowing how to improve patient safety. OBJECTIVES To analyse general practitioners' perspectives of contributing factors to patient safety incidents by collecting accounts of incidents, identifying the contributory factors to these incidents, assessing the impact and likelihood of occurrence of these incidents and examining whether certain categories of contributory factors were associated with the occurrence of high-risk incidents. METHODS Critical incident technique interviews were carried out with 30 general practitioners in Ireland about a patient safety incident they had experienced. The Yorkshire Contributory Factors Framework was used to classify the contributory factors to incidents. Seven subject matter experts rated the impact and likelihood of occurrence of each incident. RESULTS A total of 26 interviews were analysed. Almost two-thirds of the patient safety incidents were rated as having a major-to-extreme impact on the patient, and over a third were judged as having at least a bimonthly likelihood of occurrence. The most commonly described active failures were 'Medication Error' (34.6%) and 'Diagnostic Error' (30.8%). 'Situational Domain' was identified as a contributory domain in all patient safety incidents. 'Communication' breakdown at both practice and other healthcare-provider interfaces (69.2%) was also a commonly cited contributory factor. There were no significant differences in the levels of risk associated with the contributory factors. CONCLUSIONS Critical incident technique interviews support the identification of contributory factors to patient safety incidents. There is a need to explore the use of the resulting data for quality and safety improvement in general practice.
School tracking and its role in social reproduction: reinforcing educational inheritance and the direct effects of social origin1

Abstract The degree of social reproduction varies considerably between industrialized countries, raising the question of which institutional regulations promote or restrict this process. Education is considered the main mediator of social reproduction. Because school tracking – the sorting of children according to ability and interest at different ages – is known to affect educational attainment and the degree of tracking varies strongly across countries, it may thus account for differences in social reproduction. However, empirical studies are scarce, and the total impact of tracking on social reproduction remains ambiguous. Using the European Social Survey (ESS) 2012 and 2014 from 24 countries, we demonstrate that school tracking is strongly associated with higher degrees of social reproduction. Decomposing the process of social reproduction into educational inheritance, educational returns and direct effects of social origin, we find that although all channels contribute to social reproduction, the impact of tracking seems to be exerted through educational inheritance and to a similar degree through direct effects of social origin, whereas educational returns do not seem to be affected. Even net of educational attainment, social origin thus has a stronger effect on social status in tracked systems. We ascribe this effect to differences in qualitative choices within educational tracks, such as fields of study.
Delay discounting and reward sensitivity in a 2 × 2 study of bipolar disorder and alcohol dependence.

BACKGROUND AND AIMS Separate studies have shown increased delay discounting in people with bipolar disorder (BD) and people with alcohol dependence (AD) relative to people without mental health problems. Delay discounting was compared in people with no mental health problems, AD, BD and AD plus BD. Associations of delay discounting with self-reported impulsivity and reward sensitivity were also assessed. DESIGN The study was a two-by-two factorial comparative observational design. SETTING Data were collected at baseline diagnostic visits as part of a neuroimaging study at a medical university in South Carolina, USA. PARTICIPANTS Twenty-two BD + AD, 33 BD, 28 AD and 27 people without mental health problems participated. MEASUREMENTS Diagnostic and clinician-rated symptom measures, self-report questionnaires and a computerized delay discounting task were administered. Two-by-two general linear univariate models were tested to examine between-group differences on discounting rates, and bivariate correlations and hierarchical regression analyses were performed to examine associations between discounting rates and self-reported reward sensitivity and impulsivity. FINDINGS There was a significant main effect of AD (P = 0.006, η2 = 0.068). The main effect of BD and the BD × AD interaction terms were non-significant (P ≥ 0.293, η2 ≤ 0.010). Reward sensitivity and impulsivity were not significantly associated with discounting rates after adjustment for the other (P ≥ 0.089). CONCLUSIONS People with alcohol dependence appear to have higher delay discounting, while previously found associations between bipolar disorder and delay discounting may be secondary to alcohol use disorder.
C677T Methylenetetrahydrofolate Reductase Homozygosis and Vitamin Supplement in Migraineur Children

Purpose: Methylenetetrahydrofolate reductase (MTHFR) variant C677T has been associated with an increased genetic risk in migraine susceptibility. Individuals with the homozygous genotype show higher levels of plasma homocysteine (Hcy) [1,2,3]. Methods: Open-label study evaluating clinical trial was performed on 148 children migraineurs among 236 children suffering from headache, admitted to the Headache Regional Centre in l’Aquila (Italy)-Neuropsychiatric clinic, recruited and observed sequentially during the years 2015-2017. 31 patients (16,6% of all the sample) MTHFR homozygous were selected and underwent clinical evaluation of migraine characteristics (frequency, severity of pain and use of acute treatment) at baseline and after a 12 month-period of daily supplement of vitamins B9(2 mg), B6(25 mg), B12(400 mcg). In 20 patients with hyper Hcy (>95° percentile for age) the second collection of blood sample was obtained for Hcy assessment. Diagnosis of headache according to ICHD-III criteria. Statistical analysis is made by Wilcoxon test. Results: 20 children suffer from Migraine without aura (MwoA) and 11 from Migraine with aura (MA). 86% of children aged >10 years had significantly higher Hcy values compared with controls (p<0.0001). 21 patients (70%), 14 F and 7 M (13 MwoA and 8 MA), have Hcy values > 95°percentile. In all the sample the vitamin supplementation was effective in producing significant reduction in Hcy levels (p=0.0001) and a significant improvement of migraine disability of frequency (p<0.0001), severity of pain (p<0.0003) and use of acute treatment (p<0.0001). Conclusions: The study results are encouraging and emphasize the importance of a comprehensive therapy in paediatric migraines.
Transforming the University Library One Step at a Time: A Ten Year LibQUAL + Review

Abstract University libraries are going through a period of enormous transformation and have been for some time. This study considers ten years of both incremental and transformational change at the University of Limerick (UL) Library in Ireland. In the last decade library services, staffing, collections, and spaces underwent great changes, in line with international trends. Retrospective analysis of LibQUAL + survey data from 2007 to 2016 was conducted to explore how users responded to these changes and to their gradually transforming library. This study outlines the many changes that occurred in the library over the course of ten years and found that satisfaction levels steadily increased in tandem through a systematic step-by-step approach to driving continuous improvement and managing change. The data tells a compelling story of a library where staffing, services, collections, and spaces transformed and where readers’ perceptions of the quality of library services significantly improved.
A Comprehensive Study of the Parameters in the Creation and Comparison of Feature Vectors in Distributional Semantic Models

ABSTRACT Measuring the semantic similarity and relatedness of words can play a vital role in many natural language processing tasks. Distributional semantic models computing these measures can have many different parameters, such as different weighting schemes, vector similarity measures, feature transformation functions and dimensionality reduction techniques. Despite their importance there is no truly comprehensive study simultaneously evaluating the numerous parameters of such models, while also considering the interaction of these parameters with each other. We would like to address this gap with our systematic study. Taking the necessary distributional information extracted from the chosen dataset as already granted, we evaluate all important aspects of the creation and comparison of feature vectors in distributional semantic models. Testing altogether 10 parameters simultaneously, we try to find the best combination of parameter settings, with a large number of settings examined in case of some of the parameters. Beside evaluating the conventionally used settings for the parameters, we also propose numerous novel variants, as well as novel combinations of parameter settings, some of which significantly outperform the combinations of settings in general use, thus achieving state-of-the-art results.
Least Squares Estimation of Weakly Convex Functions

Function estimation under shape restrictions, such as convexity, has many practical applications and has drawn a lot of recent interests. In this work we argue that convexity, as a global property, is too strict and prone to outliers. Instead, we propose to use weakly convex functions as a simple alternative to quantify ``approximate convexity''---a notion that is perhaps more relevant in practice. We prove that, unlike convex functions, weakly convex functions can exactly interpolate any finite dataset and they are universal approximators. Through regularizing the modulus of convexity, we show that weakly convex functions can be efficiently estimated both statistically and algorithmically, requiring minimal modifications to existing algorithms and theory for estimating convex functions. Our numerical experiments confirm the class of weakly convex functions as another competitive alternative for nonparametric estimation.
Effects of Aromatic Hydrocarbons and Marine Water from Niger Delta on the β-Galactosidase Activity of Mutant Escherichia coli

Aims: To determine effects of aromatic hydrocarbons and marine water from Niger Delta on the β-Galactosidase activity mutant Escherichia coli. Study Design: Fifteen treatments and the control designs were set up in triplicates in microtitre plates containing 200 µL of the 100% concentration of samples (three marine waters and distilled water spiked each with xylene, anthracene and pyrene). The fifteen treatments and control (HgCl2) set ups designated as A, B, C, D, E, F and G were used to determine their median effective concentration (EC50) for the inhibition of β-Galactosidase activity of mutant Escherichia coli. Place and Duration of Study: Department of Microbiology, Chukwuemeka Odumegwu Ojukwu University, Uli Nigeria between February, 2017 to July, 2017. Methodology: A laboratory scale study was carried on the water samples from the three studied areas using physicochemical analyses and bacterial Toxi-chromo test. Results: The findings revealed that the three sampling sites contain higher quantities of aromatic hydrocarbons, heavy metals and other physico-chemical parameters in the sediment samples than water samples. Xylene distilled water had the highest EC50 of 3.417 ± 0.094 mg/l while pyrene Onne water had the least EC50 of 0.015 ± 0.002 mg /L. Also, pyrene and anthracene are significantly (P = .05) highly toxic aromatic hydrocarbons (EC50 < 1 mg /L) while xylene is a significantly (P = .05) toxic aromatic hydrocarbon (1 mg /L < EC50 ≤ 10 mg /L) compare to the positive control (HgCl2) (EC50 < 1 mg /L) indicating that enzyme inhibition among test samples were much different from the positive control. Conclusion: Thus, the toxicity results (< 0.1 mg /L < EC50 ≤ 10 mg /L) in this study indicate that the potential eco-toxicity and environmental health effects of these toxicants should be given attention in order to get rid of their dangerous outcomes.
Retrograde perfusion in isolated perfused mouse lungs—Feasibility and effects on cytokine levels and pulmonary oedema formation

Retrograde lung vascular perfusion can appear in high‐risk surgeries. The present report is the first to study long‐term retrograde perfusion of isolated perfused mouse lungs (IPLs) and to use the tyrosine kinase ephB4 and its ligand ephrinB2 as potential markers for acute lung injury. Mouse lungs were subjected to anterograde or retrograde perfusion with normal‐pressure ventilation (NV) or high‐pressure ventilation (=overventilation, OV) for 4 hours. Outcome parameters were cytokine, ephrinB2 and ephB4 levels in perfusate samples and bronchoalveolar lavage (BAL), and the wet‐to‐dry ratio. Anterograde perfusion was feasible for 4 hours, while lungs receiving retrograde perfusion presented considerable collapse rates. Retrograde perfusion resulted in an increased wet‐to‐dry ratio when combined with high‐pressure ventilation; other physiological parameters were not affected. Cytokine levels in BAL and perfusate, as well as levels of soluble ephB4 in BAL were increased in OV, while soluble ephrinB2 BAL levels were increased in retrograde perfusion. BAL levels of ephrinB2 and ephB4 were also determined in vivo, including mice ventilated for 7 hours with normal‐volume ventilation (NVV) or high‐volume ventilation (HVV) with increased levels of ephB4 in HVV BAL compared to NVV. Retrograde perfusion in IPL is limited as a routine method to investigate effects due to collapse for yet unclear reasons. If successful, retrograde perfusion has an influence on pulmonary oedema formation. In BAL, ephrinB2 seems to be up‐regulated by flow reversal, while ephB4 is a marker for acute lung injury.