Miracle-dz/UniFAR-FTUs huggingface dataset:
Imbalance between endothelial damage and repair capacity in chronic obstructive pulmonary disease

Background Circulating endothelial microparticles (EMPs) and progenitor cells (PCs) are biological markers of endothelial function and endogenous repair capacity. The study was aimed to investigate whether COPD patients have an imbalance between EMPs to PCs compared to controls and to evaluate the effect of cigarette smoke on these circulating markers. Methods Circulating EMPs and PCs were determined by flow cytometry in 27 nonsmokers, 20 smokers and 61 COPD patients with moderate to severe airflow obstruction. We compared total EMPs (CD31+CD42b-), apoptotic if they co-expressed Annexin-V+ or activated if they co-expressed CD62E+, circulating PCs (CD34+CD133+CD45+) and the EMPs/PCs ratio between groups. Results COPD patients presented increased levels of total and apoptotic circulating EMPs, and an increased EMPs/PCs ratio, compared with nonsmokers. Women had less circulating PCs than men through all groups and those with COPD showed lower levels of PCs than both control groups. In smokers, circulating EMPs and PCs did not differ from nonsmokers, being the EMPs/PCs ratio in an intermediate position between COPD and nonsmokers. Conclusions We conclude that COPD patients present an imbalance between endothelial damage and repair capacity that might explain the frequent concurrence of cardiovascular disorders. Factors related to the disease itself and gender, rather than cigarette smoking, may account for this imbalance.
Xome-Blender: A novel cancer genome simulator

The adoption of next generation sequencing based methods in cancer research allowed for the investigation of the complex genetic structure of tumor samples. In the last few years, considerable importance was given to the research of somatic variants and several computational approaches were developed for this purpose. Despite continuous improvements to these programs, the validation of their results it’s a hard challenge due to multiple sources of error. To overcome this drawback different simulation approaches are used to generate synthetic samples but they are often based on the addition of artificial mutations that mimic the complexity of genomic variations. For these reasons, we developed a novel software, Xome-Blender, that generates synthetic cancer genomes with user defined features such as the number of subclones, the number of somatic variants and the presence of copy number alterations (CNAs), without the addition of any synthetic element. The singularity of our method is the “morphological approach” used to generate mutation events. To demonstrate the power of our tool we used it to address the hard challenge of evaluating the performance of nine state-of-the-art somatic variant calling methods for small and large variants (VarScan2, MuTect, Shimmer, BCFtools, Strelka, EXCAVATOR2, Control-FREEC and CopywriteR). Through these analyses we observed that by using Xome-Blender data it is possible to appraise small differences between their performance and we have designated VarScan2 and EXCAVATOR2 as best tool for this kind of applications. Xome-Blender is unix-based, licensed under the GPLv3 and freely available at https://github.com/rsemeraro/XomeBlender.
An efficient point based registration of intra-operative ultrasound images with MR images for computation of brain shift; A phantom study

Intra-operative brain deformation (brain shift) limits the accuracy of image-guided neuro-surgery systems. Ultrasound imaging as a simple, fast and being real time has become an alternative to MR imaging which is an expensive system for brain shift calculation. The main challenges due to speckle noise and artifacts in US images, is to perform an accurate and fast registration of Us images with pre-operative MR images. In this paper an efficient point based registration method based on the alignment of probability density functions called Coherent Point Drift (CPD) is implemented and compared to the conventional ICP method. To perform this, a brain phantom that allows simulating the brain deformation is made. As the results of our phantom study confirm the CPD method clearly outperforms the ICP algorithm for brain shift calculation. Also the result proves that using intra-operative US has led to recover almost 80% of displacement in the region of interest.
Average nearest neighbor degrees in scale-free networks

The average nearest neighbor degree (ANND) of a node of degree $k$ is widely used to measure dependencies between degrees of neighbor nodes in a network. We formally analyze ANND in undirected random graphs when the graph size tends to infinity. The limiting behavior of ANND depends on the variance of the degree distribution. When the variance is finite, the ANND has a deterministic limit. When the variance is infinite, the ANND scales with the size of the graph, and we prove a corresponding central limit theorem in the configuration model (CM, a network with random connections). As ANND proved uninformative in the infinite variance scenario, we propose an alternative measure, the average nearest neighbor rank (ANNR). We prove that ANNR converges to a deterministic function whenever the degree distribution has finite mean. We then consider the erased configuration model (ECM), where self-loops and multiple edges are removed, and investigate the well-known `structural negative correlations', or `finite-size effects', that arise in simple graphs, such as ECM, because large nodes can only have a limited number of large neighbors. Interestingly, we prove that for any fixed $k$, ANNR in ECM converges to the same limit as in CM. However, numerical experiments show that finite-size effects occur when $k$ scales with $n$.
Association of the FBXO11 gene with chronic otitis media with effusion and recurrent otitis media: the Minnesota COME/ROM Family Study.

OBJECTIVE The FBXO11 gene is the human homologue of the gene mutated in the novel deaf mouse mutant jeff (Jf), a single gene model of otitis media. We have evaluated single nucleotide polymorphisms (SNPs) in the FBXO11 gene for association with chronic otitis media with effusion/recurrent otitis media (COME/ROM). DESIGN A total of 13 SNPs were genotyped across the 98.7 kilobases of genomic DNA encompassing FBXO11. Data were analyzed for single SNP association using generalized estimating equations, and haplotypes were evaluated using Pedigree Disequilibrium Test methods. PATIENTS The Minnesota COME/ROM Family Study, a group of 142 families (619 subjects) with multiple affected individuals with COME/ROM. MAIN OUTCOME MEASURES Genetic association of COME/ROM with polymorphisms in FBXO11. RESULTS The FBXO11 SNPs are contained in a single linkage disequilibrium haplotype block. Ten of the 13 SNPs were sufficiently polymorphic in the sample to permit analysis. In univariate genetic analysis, 1 reference SNP (hereinafter rs) (rs2134056) showed nominal evidence of association to COME/ROM (P = .02), and 2 SNPs approached significance (rs2020911, P = .06; rs3136367, P = .09). In multivariable analyses, including known risk factors for COME/ROM (sex, exposure to smoking, attending day care centers, no prior breastfeeding, and having allergies), the evidence of independent association was reduced for each SNP (eg, rs2134056, from P = .02 to P = .08). In subsequent analyses using the Pedigree Disequilibrium Test, the association of FBXO11 SNP rs2134056 (P = .06) with COME/ROM was confirmed. Incorporating multiple SNPs in 2- and 3-locus SNP haplotypes, those haplotypes containing rs2134056 also exhibited evidence of association of FBXO11 and COME/ROM (P values ranging from .03 to .10). CONCLUSION We have observed evidence consistent with an association between polymorphisms in FBXO11, the human homologue of the Jeff mouse model gene, and COME/ROM.
Influence of surface coverage on the formation of 4,4′-bipyridinium (viologen) single molecular junctions

Single-molecule conductance experiments using the STM-based I(s) method and samples of N,N′-di(4-(trimethylsilylethynyl)benzyl)-4,4′-bipyridinium bis(tetrafluoroborate) ([1](BF4)2) prepared on gold substrates with low-surface coverage of [1](BF4)2 (Γ = 1.25 × 10−11 mol cm−2) give rise to molecular junctions with two distinct conductance values. From the associated break-off distances and comparison experiments with related compounds, the higher conductance junctions are attributed to molecular contacts between the molecule and the electrodes via the N,N′-dibenzyl-4,4′-bipyridinium (viologen) moiety and one trimethylsilylethynyl (TMSE) group (G = (5.4 ± 0.95) × 10−5 G0, break-off distance (1.56 ± 0.09) nm). The second, lower conductance junction (G = (0.84 ± 0.09) × 10−5 G0) is consistent with an extended molecular conformation between the substrate and tip contacted through the two TMSE groups giving rise to a break-off distance (1.95 ± 0.12) nm that compares well with the Si⋯Si distance (2.0 nm) in the extended molecule. Langmuir monolayers of [1](BF4)2 formed at the air–water interface can be transferred onto a gold-on-glass substrate by the Langmuir–Blodgett (LB) technique to give well-ordered, compact films with surface coverage Γ = 2.0 × 10−10 mol cm−2. Single-molecule conductance experiments using the STM-based I(s) method reveal only the higher conductance junctions (G = (5.4 ± 0.95) × 10−5 G0, break-off distance (1.56 ± 0.09) nm) due to the restricted range of molecular conformations in the tightly packed, well-ordered LB films.
Residual stress and its role in failure

Our safety, comfort and peace of mind are heavily dependent upon our capability to prevent, predict or postpone the failure of components and structures on the basis of sound physical principles. While the external loadings acting on a material or component are clearly important, There are other contributory factors including unfavourable materials microstructure, pre-existing defects and residual stresses. Residual stresses can add to, or subtract from, the applied stresses and so when unexpected failure occurs it is often because residual stresses have combined critically with the applied stresses, or because together with the presence of undetected defects they have dangerously lowered the applied stress at which failure will occur. Consequently it is important that the origins of residual stress are understood, opportunities for removing harmful or introducing beneficial residual stresses recognized, their evolution in-service predicted, their influence on failure processes understood and safe structural integrity assessments made, so as to either remove the part prior to failure, or to take corrective action to extend life. This paper reviews the progress in these aspects in the light of the basic failure mechanisms.
Cross transfer acute effects of foam rolling with vibration on ankle dorsiflexion range of motion

Introduction: Foam roller is a device used as a massage intervention for rehabilitation and fitness performance. Objective: To examine the effects on the ankle dorsiflexion mobility of the foam roller as well as the combination of foam roller and vibration applied to the ankle plantarflexors muscles, and to observe the possible cross-effect. Methods: Thirty-eight undergraduate students participated in the study (19 males and 19 females). This study investigated. Three conditions (3 sets of 20 s) were performed in a randomized order (independent variables): 1) foam roller (Roller), 2) foam roller and vibration (Roller+VIB), and 3) no foam roller or vibration (Control). to determine whether of foam roller with or without vibration would benefit ankle dorsiflexion mobility. Ankle dorsiflexion ROM and plantar flexor were measured in both legs before and immediately after the treatment. Results: A cross-effect was found in the non-stimulated leg. There was a significant effect on ankle mobility of Roller and Roller+VIB conditions (6% and 7%, p<0.001). Conclusion: Foam roller massage and vibration stimulus’ foam roller massage increase ankle mobility producing a cross-effect.
Weighted objective function selector algorithm for parameter estimation of SVAT models with remote sensing data

The objective function of the inverse problem in Soil‐Vegetation‐Atmosphere‐Transfer (SVAT) models can be expressed as the aggregation of two criteria, accounting for the uncertainties of surface soil moisture (θ) and evapotranspiration (ET), retrieved from remote sensing (RS). In this context, we formulate a Weighted‐Objective‐Function (WOF) with respect to model effective soil hydraulic parameters, comprising of two components for θ and ET, respectively, and a dimensionless coefficient w. Given that the sensitivity of θ is increased by omitting the periods when soil moisture decoupling occurs, we also introduce within the WOF a threshold, θd, which outlines the decoupling of the surface and root‐zone moisture. The optimal values of w and θd are determined by using a novel framework, weighted objective function selector algorithm (WOFSA). This performs numerical experiments, assuming known reference conditions. In particular, it solves the inverse problem for different sets of θ and ET, considering the uncertainties of retrieving them from RS, and then runs the hydrological model to obtain the simulated water fluxes and their residuals, ΔWF, against the reference responses. It estimates the two unknown variables, w and θd, by maximizing the linear correlation between the WOF and maximum ΔWF. The framework is tested using a modified Soil‐Water‐Atmosphere‐Plant (SWAP) model, under 22 contrasting hydroclimatic scenarios. It is shown that for each texture class, w can be expressed as function of the average θ and ET‐fraction, while that for all scenarios θd can be modeled as function of the average θ, average ET, and standard deviation of ET. Based on the outcomes of this study, we also provide recommendations on the most suitable time period for soil moisture measurements for capturing its dynamics and thresholds. Finally, we propose the implementation of WOFSA within multiobjective calibration, as a generalized tool for recognizing robust solutions from the Pareto front.
Towards Reconciling SPARQL and Certain Answers

SPARQL entailment regimes are strongly influenced by the big body of works on ontology-based query answering, notably in the area of Description Logics (DLs). However, the semantics of query answering under SPARQL entailment regimes is defined in a more naive and much less expressive way than the certain answer semantics usually adopted in DLs. The goal of this work is to introduce an intuitive certain answer semantics also for SPARQL and to show the feasibility of this approach. For OWL 2 QL entailment, we present algorithms for the evaluation of an interesting fragment of SPARQL (the so-called well-designed SPARQL). Moreover, we show that the complexity of the most fundamental query analysis tasks (such as query containment and equivalence testing) is not negatively affected by the presence of OWL 2 QL entailment under the proposed semantics.
Prevalence of thromboembolic events among 8,860 patients with thalassaemia major and intermedia in the Mediterranean area and Iran

Summary Beta-thalassaemia isa congenital haemolytic anaemia characterized by partial (intermedia, TI) or complete (major, TM) deficiency in the production of β-globin chains.The primary aim of this study was to determine the prevalence of thromboembolic events in patients with β-thalassaemia.To achieve this,a multiple-choice questionnaire was sent to 56 tertiary referral centres in eight countries (Lebanon, Italy, Israel, Greece, Egypt, Jordan, Saudi Arabia and Iran), requesting specific information on patients who had experienced a thromboembolic event.The study demonstrated that thromboembolic events occurred ina clinically relevant proportion (1.65%) of 8,860 thalassaemia patients (TI – 24.7% or TM – 75.3%) from the Mediterranean and Iran. Thromboembolism occurred 4.38 times more frequently in TI thanTM (p<0.001), with more venous events occurring inTI and more arterial events occurring in TM.Thrombosis in thalassaemia was also more common in females, splenectomized patients and those with profound anaemia (haemoglobin <9 g/dl). Due to the increased risk of thromboembolic events, the rationale for splenectomy should perhaps be re-assessed and the role of transfusion therapy for the prophylaxis of thrombosis, among other complications, be evaluated prospectively.
The effects of martensite morphology on mechanical properties, corrosion behavior and hydrogen assisted cracking in A516 grade steel

A low carbon A516 steel (0.2% C) having 0.9% Mn content has been annealed at 760 °C with predominantly austenite and martensite input structure. This treatment lead to a dual phase (DP) ferrite–martensite microstructures with 50% martensite volume fraction in two morphologies, i.e. bulk martensite (BM) and fibrous martensite (FM) respectively. The ferrite–martensite DP steels exhibits much higher strength (∼2 times) than ferrite–pearlite (FP) steel albeit with lower elongation (50%). The martensite morphology does not affect the uniform elongation but FM morphology exhibits higher strain to fracture. However, the corrosion rate is effected by the fraction of interfaces rather than the type of constituent phase. The BM condition with minimum interfaces has the least corrosion rate in weak acidic solution. The DP steels are more disposed to hydrogen embrittlement than FP steel. This phenomena causes a lowering of flow stress and strain fracture, the former is more progressive with rise in temperature than the latter. The crack nucleation is directly related to the corrosion rate, however despite twofold higher corrosion rate in BM condition, the extent of hydrogen embrittlement in both morphologies is similar because of the connected ferrite–martensite boundaries in BM morphology.
The Interleukin-17 Receptor B Subunit Is Essential for the Th2 Response to Helicobacter pylori, but Not for Control of Bacterial Burden

Helicobacter pylori infection leads to an inflammatory response in 100% of infected individuals. The inflammatory cells which are recruited to the gastric mucosa during infection produce several pro- and anti-inflammatory cytokines including several cytokines in the interleukin-17 family. The anti-inflammatory cytokine, interleukin 25 (IL-25, also known as IL-17E), signals through a receptor, which is a heterotrimeric receptor comprised of two IL-17 receptor A subunits and an IL-17 receptor B subunit. Previous studies in our laboratory demonstrated that IL-17RA is required to control infection with Helicobacter pylori in the mouse model. Moreover, the absence of IL-17 receptor A leads to a significant B cell infiltrate and a remarkable increase in lymphoid follicle formation in response to infection compared to infection in wild-type mice. We hypothesized that IL-25, which requires both IL-17 receptor A and IL-17 receptor B for signaling, may play a role in control of inflammation in the mouse model of Helicobacter pylori infection. IL-17 receptor B deficient mice, IL-17 receptor A deficient mice and wild-type mice were infected with Helicobacter pylori (strains SS1 and PMSS1). At several time points H. pylori- infected mice were sacrificed to investigate their ability to control infection and inflammation. Moreover, the effects of IL-17 receptor B deficiency on T helper cytokine expression and H. pylori- specific serum antibody responses were measured. IL-17 receptor B−/− mice (unlike IL-17 receptor A−/− mice) exhibited similar or modest changes in gastric colonization, inflammation, and Th1 and Th17 helper cytokine responses to wild-type mice infected with Helicobacter pylori. However, H. pylori-infected IL-17 receptor B−/− mice have reduced expression of IL-4 and lower serum IgG1 and IgG2a levels compared to infected IL-17 receptor A−/− and wild-type mice. These data indicate that signaling through the IL-17 receptor B subunit is not necessary for control of Helicobacter pylori in our model.
Raman Characterization of Nitrogen Doped Multiwalled Carbon Nanotubes

N-type multi-walled nanotubes were synthesized by nitrogen doping using pyridine and pyridine-melamine mixtures in chemical vapor deposition, and their donor states were verified by Scanning Tunneling Spectroscopy. Tunneling Electron Microscopy reveals small amounts of residual catalyst and Scanning Electron Microscopy show well aligned mats of the Nitrogen doped nanotubes. Nitrogen is present in the lattice of these MWNTs as pyridine structures and CNx structures. Raman scattering measurements were performed as a function of increasing growth temperature and the results compared to previously studied boron doped multiwalled nanotubes.
The prevalence of obesity and the level of adherence to the Korean Dietary Action Guides in Korean preschool children

The objective of this study was to investigate the associations between the prevalence of overweight and obesity and the degree of adherence to the Korean Dietary Action Guides for Children (KDAGC). In a cross-sectional study based on a child care center-based survey in Seoul, Korea, we collected parental-reported questionnaires (n = 2,038) on children's weight and height, frequency of fruit and vegetable consumption, and the quality of dietary and activity behaviors based on the 2009 KDAGC Adherence Index (KDAGCAI) which was developed as a composite measure of adherence to the KDAGC. Overweight and obesity were determined according to age- and sex-specific BMI percentile from the 2007 Korean national growth chart. Associations were assessed with generalized linear models and polytomous logistic regression models. Approximately 17.6% of Korean preschool children were classified as overweight or obese. Obese preschoolers had lower adherence to the KDAGCAI compared to those with lean/normal weight. Preschoolers with a high quality of dietary and activity behaviors had a 51% decreased odds ratio (OR) of being obese (highest vs. lowest tertile of KDAGCAI-score, 95% CI 0.31, 0.78; P = 0.001); the associations were more pronounced among those who were older (P = 0.048) and lived in lower income households (P = 0.014). A greater frequency of vegetable consumption, but not fruit, was associated with a borderline significant reduction in the prevalence of obesity. Our findings support the association between obesity prevention and high compliance with the Korean national dietary and activity guideline among preschool children.
Current practice of ototoxicity management across the United Kingdom (UK)

Abstract Objective: Effective management of patients diagnosed with ototoxicity is needed to reduce hearing and balance damage which affects communication and life quality. Despite widespread recommendations to monitor and manage ototoxicity in an early and effective manner, there is limited evidence to support the actual implementation of these recommendations for affected patient groups in healthcare services across the UK with limited publications available. In this study, an online questionnaire analysed the current practice of ototoxicity management and patient pathways across the UK once the diagnosis of ototoxicity was confirmed, targeting Audiologists, ENTs/AVPs and GPs. Design: Qualitative Survey Study. Study sample: A randomised sample of hearing services in the UK, including audiology departments; GP practices and local health settings were targeted with a total of 134 completed surveys. Results: About 72% reported the absence of ototoxicity management protocols within their centre. Results depicted great inconsistency and variation across the UK in ototoxicity management services provided, treatment modification, monitoring and referral pathways. Conclusion: Developing and advocating national guidelines are intended not only to inform clinical decision making but to provide minimum standards of care in ototoxicity management and offer greater awareness and education to improve patients’ quality of life.