Miracle-dz/UniFAR-FTUs huggingface dataset:
Logarithmic-Time Updates and Queries in Probabilistic Networks

In this paper we propose a dynamic data structure that supports efficient algorithms for updating and querying singly connected Bayesian networks (causal trees and polytrees). In the conventional algorithm, new evidence is absorbed in time O(1) and queries are processed in time O(N), where N is the size of the network. We propose a practical algorithm which, after a preprocessing phase, allows us to answer queries in time O(log N) at the expense of O(log N) time per evidence absorption. The usefulness of sub-linear processing time manifests itself in applications requiring (near) real-time response over large probabilistic databases.
The Mediterranean subsurface phytoplankton dynamics and their impact on Mediterranean bioregions

Abstract. Ocean bioregions are generally defined using remotely-sensed sea surface chlorophyll fields, based on the assumption that surface chlorophyll is representative of euphotic layer phytoplankton biomass. Here we investigate the impact of subsurface phytoplankton dynamics on the characterisation of ocean bioregions. The Mediterranean Sea is known for its contrasting bioregimes despite its limited area, and represents an appropriate case for this study. We modelled this area using a high resolution regional dynamical model, NEMO-MED12, coupled to a biogeochemical model, PISCES, and focused our analysis on the bioregions derived from lower trophic levels. Validated by satellite and Biogeochemical-Argo float observations, our model shows that chlorophyll phenology can be significantly different when estimated from surface concentrations or integrated over the first 300 m deep layer. This was found in both low chlorophyll, oligotrophic bioregions as well as in high chlorophyll, bloom bioregions. The underlying reason for this difference is the importance of subsurface phytoplankton dynamics, in particular those associated with the Deep Chlorophyll Maximum (DCM) at the base of the upper mixed layer. Subsurface phytoplankton are found to significantly impact the bloom bioregions, while in oligotrophic regions, surface and subsurface chlorophyll are of similar importance. Consequently, our results show that surface chlorophyll is not representative of total phytoplankton biomass. Analysis of the DCM finds that its dynamics are extremely homogeneous throughout the Mediterranean Sea, and that it follows the annual cycle of solar radiation. In the most oligotrophic bioregion, the total phytoplankton biomass is almost constant along the year, implying that the summertime DCM biomass increase is not due to DCM photoacclimation, nor an increase of DCM production, but instead of the migration – with photoacclimation – of surface phytoplankton into the DCM.
Gate-Sizing-Based Single $V_{\rm dd}$ Test for Bridge Defects in Multivoltage Designs

The use of multiple voltage settings for dynamic power management is an effective design technique. Recent research has shown that testing for resistive bridging faults in such designs requires more than one voltage setting for 100% fault coverage; however, switching between several supply voltage settings has a detrimental impact on the overall cost of test. This paper proposes an effective gate sizing technique for reducing test cost of multi-Vdd designs with bridge defects. Using synthesized ISCAS and ITC benchmarks and a parametric fault model, experimental results show that for all the circuits, the proposed technique achieves single Vdd test, without affecting the fault coverage of the original test. In addition, the proposed technique performs better in terms of timing, area, and power than the recently proposed test point insertion technique. This is the first reported work that achieves single Vdd test for resistive bridge defects, without compromising fault coverage in multi-Vdd designs.
Influence of Mediterranean Diet on Asthma Symptoms, Lung Function, and Systemic Inflammation: A Randomized Controlled Trial

Objective. The rapidly increasing prevalence of asthma in developed countries suggests an environmental cause. The benefits of Mediterranean diet (MD) in cardiovascular disease have been tentatively attributed to its anti-inflammatory properties. Asthma is an inflammatory disease and MD is associated with reduced asthma risk in epidemiological studies, but there are no reported interventional studies of MD in asthma. Methods. In this 12-week open-label randomized trial, 38 adults with symptomatic asthma were allocated to high-intervention (HI), low-intervention (LI), and control groups. The first two groups were encouraged to adopt an MD and received multiple consultation sessions with a nutritionist, written advice, and vouchers for the purchase of appropriate foods. Food frequency questionnaires, asthma control questionnaires, asthma-related quality of life questionnaires (AQLQs), and spirometry were completed at the beginning and at the end of the study. Results: The MDt score increased in the HI group (p < .001), indicating successful alteration of dietary behavior. Statistically, nonsignificant improvements were seen in spirometry and several AQLQ subdomains in the two intervention groups. No changes were seen in the asthma control or in inflammatory markers. Conclusions: The trial intervention has successfully altered the dietary behavior among adults with asthma. Small but consistent improvements were seen in quality of life and spirometry among the intervention group. The use of the MD to treat asthma is feasible and warrants evaluation in a larger study, powered to examine clinical endpoints.
Analysis of Unannotated Equine Transcripts Identified by mRNA Sequencing

Sequencing of equine mRNA (RNA-seq) identified 428 putative transcripts which do not map to any previously annotated or predicted horse genes. Most of these encode the equine homologs of known protein-coding genes described in other species, yet the potential exists to identify novel and perhaps equine-specific gene structures. A set of 36 transcripts were prioritized for further study by filtering for levels of expression (depth of RNA-seq read coverage), distance from annotated features in the equine genome, the number of putative exons, and patterns of gene expression between tissues. From these, four were selected for further investigation based on predicted open reading frames of greater than or equal to 50 amino acids and lack of detectable homology to known genes across species. Sanger sequencing of RT-PCR amplicons from additional equine samples confirmed expression and structural annotation of each transcript. Functional predictions were made by conserved domain searches. A single transcript, expressed in the cerebellum, contains a putative kruppel-associated box (KRAB) domain, suggesting a potential function associated with zinc finger proteins and transcriptional regulation. Overall levels of conserved synteny and sequence conservation across a 1MB region surrounding each transcript were approximately 73% compared to the human, canine, and bovine genomes; however, the four loci display some areas of low conservation and sequence inversion in regions that immediately flank these previously unannotated equine transcripts. Taken together, the evidence suggests that these four transcripts are likely to be equine-specific.
A Simulation Software Tool for Cell-like Spiking Neural P Systems

Spiking neural P systems (SN P systems, for short) constitute a class of computing models in the research field of membrane computing. Inspired by the interactions among neurons in the brain, they have attracted much attention since their appearance in 2006. Many variants have emerged, presenting a graph-based structure, and several software simulators were developed for them. Recently, a different approach was proposed by introducing cell-like spiking neural P systems. Unlike previous SN P systems, this new model includes a tree-based structure, taking elements from traditional rewriting rules in the original P systems. In this work, a software tool within the framework of P-Lingua and MeCoSim is presented. This software may play an important role assisting in tasks of design, simulation and experimental validation. Key-words: Bio-inspired computing, Membrane computing, Spiking neural P system, Cell-like P system, P-Lingua
Temperature Compensation in Determining of Remazol Black B Concentrations Using Plastic Optical Fiber Based Sensor

In this study, the construction and test of tapered plastic optical fiber (POF) sensors, based on an intensity modulation approach are described. Tapered fiber sensors with different diameters of 0.65 mm, 0.45 mm, and 0.35 mm, were used to measure various concentrations of Remazol black B (RBB) dye aqueous solutions at room temperature. The concentrations of the RBB solutions were varied from 0 ppm to 70 ppm. In addition, the effect of varying the temperature of the RBB solution was also investigated. In this case, the output of the sensor was measured at four different temperatures of 27 °C, 30 °C, 35 °C, and 40 °C, while its concentration was fixed at 50 ppm and 100 ppm. The experimental results show that the tapered POF with d = 0.45 mm achieves the best performance with a reasonably good sensitivity of 61 × 10−4 and a linearity of more than 99%. It also maintains a sufficient and stable signal when heat was applied to the solution with a linearity of more than 97%. Since the transmitted intensity is dependent on both the concentration and temperature of the analyte, multiple linear regression analysis was performed to combine the two independent variables into a single equation. The resulting equation was then validated experimentally and the best agreement between the calculated and experimental results was achieved by the sensor with d = 0.45 mm, where the minimum discrepancy is less than 5%. The authors conclude that POF-based sensors are suitable for RBB dye concentration sensing and, with refinement in fabrication, better results could be achieved. Their low fabrication cost, simple configuration, accuracy, and high sensitivity would attract many potential applications in chemical and biological sensing.
Persistent Pure Ground-Glass Nodules Larger Than 5 mm: Differentiation of Invasive Pulmonary Adenocarcinomas From Preinvasive Lesions or Minimally Invasive Adenocarcinomas Using Texture Analysis

ObjectiveTo evaluate the differentiating potentials of computed tomography texture analysis for invasive pulmonary adenocarcinomas (IPAs) from their preinvasive lesions or minimally invasive adenocarcinomas (MIAs) manifesting as persistent pure ground-glass nodules (PGGNs) larger than 5 mm. Materials and MethodsThis institutional review board–approved retrospective study included 63 patients (23 men and 40 women) with 66 PGGNs larger than 5 mm on unenhanced computed tomography from 2005 to 2013. All PGGNs were pathologically confirmed and categorized into 2 groups [IPAs (n = 11) vs preinvasive lesions (n = 41)/MIAs (n = 14)]. Each PGGN was segmented manually, and their texture features were quantitatively extracted. To identify significant differentiating factors of IPAs from preinvasive lesions/MIAs, multivariate logistic regression and C-statistic analyses were performed. ResultsBetween IPAs and preinvasive lesions/MIAs, nodule size, volume, mass, entropy, effective diameter, and surface area were significantly different (P < 0.05), and homogeneity and gray level co-occurrence matrix inverse difference moment showed marginal significance (P < 0.10). Subsequent multivariate analysis revealed larger nodule mass [adjusted odds ratio (OR), 11.92], higher entropy (adjusted OR, 35.12), and lower homogeneity (adjusted OR, 0.278 × 10−3) as independent differentiating factors of IPAs. Subgroup analysis showed that larger nodule mass, higher entropy, and lower homogeneity were also significant differentiating variables of IPAs in nodules of diameter 10 mm or larger. A multiple logistic regression model using these features showed excellent [area under the curve (AUC), 0.962] and significantly higher differentiating performance compared to nodule size (AUC, 0.712) or mass (AUC, 0.788) alone. ConclusionComputed tomography texture features such as higher entropy and lower homogeneity were significant differentiating factors of IPAs presenting as PGGNs larger than 5 mm and have potentials to enhance the differentiating performance.
An electrophysiological and anatomical study of afferents reaching the cerebellar uvula in the rabbit

Stimulation of a medial region of the cerebellar uvula cortex produces sympathetically mediated cardiovascular effects in the decerebrate rabbit. In the present study the afferents to this cerebellar area have been determined using electrophysiological and neuroanatomical methods. Field potentials of prevalent mossy origin evoked by single‐shock stimulation of different peripheral nerves have been recorded from sublobules IXa and IXb. No response to vagus and aortic nerves stimulation has been found. A modulation of Purkinje cell discharge following natural vestibular stimulation has been found. A modulation of Purkinje cell discharge following natural vestibular stimulation has been recorded from sublobules IXb and IXc. The retrograde transport of horseradish peroxidase from the uvula cortex has revealed a widespread afferent input to this cerebellar region arising from brain stem reticular and sensory nuclei. On the basis of the results obtained, together with the results of experiments performed in conscious rabbits, contained in the following paper (Bradley, Ghelarducci, La Noce & Spyer, 1990), it is suggested that the uvula participates in co‐ordination of the visceral and somatic components of the alerting reaction in the rabbit.
Common Sense Data Acquisition for Indoor Mobile Robots

Common sense knowledge can be efficiently collected from non-experts over the web in a similar fashion to the Open Mind family of distributed knowledge capture projects. We describe the collection of common sense data through the Open Mind Indoor Common Sense (OMICS) website. We restrict the domain to indoor home and office environments to obtain dense knowledge. The knowledge was collected through sentence templates that were generated dynamically based on previous user input. Entries were converted into relations and saved into a database. We discuss the results of this online collaborative effort and describe two applications of the collected data to indoor mobile robots. We discuss active desire selection based on current beliefs and commands and a room-labeling application based on probability estimates from the common sense knowledge base.
On the Formalization of the Modal µ-Calculus in the Calculus of Inductive Constructions

We present a natural deduction proof system for the propositional modal ? -calculus and its formalization in the calculus of inductive constructions. We address several problematic issues, such as the use of higher-order abstract syntax in inductive sets in the presence of recursive constructors, and the formalization of modal (sequent-style) rules and of context sensitive grammars. The formalization can be used in the system Coq, providing an experimental computer-aided proof environment for the interactive development of error-free proofs in the modal ? -calculus. The techniques we adopt can be readily ported to other languages and proof systems featuring similar problematic issues.
Desarrollo Turístico versus Calidad y Sustentabilidad Percibidas: Barrancas del Cobre, México

The study of perceptions about tourism development at the Copper Canyon Park in Chihuahua, Mexico, is presented in order to assess the perceived quality and sustainability of the current model of territorial tourism development. A qualitative methodology by means of an explanatory and deductive approach was used, through which valid qualitative data were obtained, such as words and texts based on personal opinions of the hosts and visitors, which were obtained through surveys, interviews and online opinion. The sample was composed of residents from Creel, Divisadero, Urique and Otero, as well as tourists who have visited the destination. As result, the characterization of the tourist development of Copper Canyon Park is presented, as well as the study of local opinion regarding the tourism development model, and the analysis of visitors' perceptions. It is concluded that the projection of tourism development using the opinions of hosts and visitors is a necessary tool for the participatory management of quality and territorial sustainability of tourism.
NUCB2 gene polymorphism and its relationship with nesfatin-1 levels in polycystic ovary syndrome

Abstract Nesfatin-1, encoded by the nucleobindin-2 (NUCB2) gene, is an anorexigenic protein related to energy metabolism, obesity, and insulin resistance. The aim of this study was to evaluate NUCB2 gene polymorphism (rs757081) and its association with serum levels of nesfatin-1 in obese and non-obese women with polycystic ovary syndrome (PCOS). In the study population, we analyzed 60 patients with PCOS and 26 age-matched healthy women as controls. The patients with PCOS were divided into two groups based on body mass index (BMI): obese group (n = 28) or non-obese group (n = 32). NUCB2 was genotyped using the polymerase chain reaction-restriction (PCR) technique. Serum nesfatin-1 level was measured by enzyme-linked immunosorbent assay (ELISA). Nesfatin-1 levels in the obese PCOS group were significantly lower than those in the non-obese PCOS and control groups (p < 0.001). There was no statistically significant difference in the distribution of NUCB2 genotypes among the groups (p > 0.05), whereas nesfatin-1 levels in the CC and CG genotypes were lower than those in the GG genotype. Nesfatin-1 decreases in PCOS, especially in obese women, and is negatively correlated with cardiometabolic risk factors. Although genotype disturbances of NUCB2 were similar among the groups, CC and CG genotypes accompanied lower nesfatin-1 levels. C allele of NUCB2 gene polymorphism and nesfatin-1 may play a role in the pathophysiology of PCOS.
Effect of extracorporeal membrane oxygenation flow on pulmonary capillary blood flow.

OBJECTIVE To validate a new application of the modified acetylene rebreathing method for pulmonary capillary blood flow in a swine extracorporeal membrane oxygenation (ECMO) model. DESIGN Prospective, sequential measurements of pulmonary capillary blood flow, using a rebreathing technique, as affected by different flows through the ECMO circuit. SETTING A cardiovascular hemodynamic research laboratory at a university medical center. SUBJECTS Fifteen young mature farm swine (48 to 52 kg). INTERVENTIONS Pulmonary capillary blood flow was measured using a modified rebreathing technique, and this measurement repeated at different flow rates through the extracorporeal membrane oxygenation circuit. Pulmonary artery flow rates were measured using both thermodilution and echo-Doppler techniques for comparison purposes. MEASUREMENTS AND MAIN RESULTS Pulmonary capillary blood flow measurements, as assessed by modified acetylene rebreathing, compared well with both the thermodilution cardiac output measurement during normal circulation and the pulmonary artery flow probe measurement while the subjects received ECMO. Mean pulmonary capillary blood flow measured by acetylene rebreathing decreased from 89.72 +/- 6.97 (baseline) to 43.59 +/- 5.66 mL/kg/min as ECMO flow was maximized to 56.22 +/- 3.62 mL/kg/min. Decreasing the ECMO flow rate by half (to 28.23 +/- 3.45 mL/kg/min) caused an increase in mean pulmonary capillary blood flow to 53.79 +/- 6.16 mL/kg/min. When ECMO flow was discontinued, pulmonary capillary blood flow returned to a near baseline value of 71.68 +/- 7.05 mL/kg/min (mean values of pooled data for both closed- and open-chest animals [n = 15]). These measurements correlated well with both thermodilution cardiac output and pulmonary artery ultrasonic flow probe measurements. CONCLUSIONS The modified acetylene rebreathing method is a valid and accurate method for the measurement of pulmonary capillary blood flow in the presence of ECMO flows. Pulmonary blood flow decreases as ECMO flow is increased, and the extent of decrease is directly proportional to the amount of flow through the extracorporeal circulation.
Immunomodulatory Effects of Four Leishmania infantum Potentially Excreted/Secreted Proteins on Human Dendritic Cells Differentiation and Maturation

Leishmania parasites and some molecules they secrete are known to modulate innate immune responses through effects on dendritic cells (DCs) and macrophages. Here, we characterized four Leishmania infantum potentially excreted/secreted recombinant proteins (LipESP) identified in our laboratory: Elongation Factor 1 alpha (LiEF-1α), a proteasome regulatory ATPase (LiAAA-ATPase) and two novel proteins with unknown functions, which we termed LiP15 and LiP23, by investigating their effect on in vitro differentiation and maturation of human DCs and on cytokine production by DCs and monocytes. During DCs differentiation, LipESP led to a significant decrease in CD1a. LiP23 and LiEF-1α, induced a decrease of HLA-DR and an increase of CD86 surface expression, respectively. During maturation, an up-regulation of HLA-DR and CD80 was found in response to LiP15, LiP23 and LiAAA-ATPase, while an increase of CD40 expression was only observed in response to LiP15. All LipESP induced an over-expression of CD86 with significant differences between proteins. These proteins also induced significant IL-12p70 levels in immature DCs but not in monocytes. The LipESP-induced IL-12p70 production was significantly enhanced by a co-treatment with IFN-γ in both cell populations. TNF-α and IL-10 were induced in DCs and monocytes with higher levels observed for LiP15 and LiAAA-ATPase. However, LPS-induced cytokine production during DC maturation or in monocyte cultures was significantly down regulated by LipESP co-treatment. Our findings suggest that LipESP strongly interfere with DCs differentiation suggesting a possible involvement in mechanisms established by the parasite for its survival. These proteins also induce DCs maturation by up-regulating several costimulatory molecules and by inducing the production of proinflammatory cytokines, which is a prerequisite for T cell activation. However, the reduced ability of LipESP-stimulated DCs and monocytes to respond to lipopolysaccharide (LPS) that can be observed during human leishmaniasis, suggests that under certain circumstances LipESP may play a role in disease progression.
Inflammatory Bowel Disease Associated Colorectal Neoplasia

Patients with ulcerative colitis (UC) or Crohn’s colitis have a greater risk for developing colorectal cancer (CRC). Many studies have described the evolving epidemiology and risk factors for CRC in patients with inflammatory bowel disease (IBD). Recent evidence indicates that the incidence has been decreasing with the advancement of medical and surgical therapies, and surveillance has emerged as the foundation of prevention. Chemoprophylaxis is another area of research; however, given the limited efficacy of these agents, they are only being used in conjunction with endoscopic surveillance. Our ability to formulate effective strategies for the prevention of this dreaded complication expands as more is discovered of the molecular events underlying IBD carcinogenesis. Management strategies are constantly updated as new evidence and endoscopic techniques emerge. In this paper, we review the literature regarding epidemiology, pathogenesis, risk factors and chemoprophylaxis as well as the latest consensus guidelines for management of dysplasia and neoplasia in IBD patients.