Miracle-dz/UniFAR-FTUs huggingface dataset:
Methemoglobin levels in umbilical cord blood of women with intrauterine growth restriction and preeclampsia

Abstract Objective: To measure nitric oxide (NO) levels, as assessed by methemoglobin (MetHb), in the umbilical cord arterial blood of women with preeclampsia (PE), normotensive pregnancies with intrauterine growth restriction (IUGR, <10th percentile for birth weight) and normotensive pregnancies with appropriate for gestational age (AGA) infants. Design/Methods: Prospective analysis of MetHb levels in umbilical arterial blood of pregnancies with PE, normotensive IUGR and normotensive AGA infants using spectrophotometry. Exclusion criteria included cigarette smoke exposure, hemolytic disorders, chronic hypertension, any significant medical illness and medications affecting NO or MetHb levels. Results: There were 42 women in the PE, 42 in the AGA and 37 in the IUGR group. Maternal age, mode of delivery, gravidity, parity and infant gender were similar in the three groups. MetHb levels were significantly lower in the IUGR group compared to the AGA group (p < 0.01). MetHb levels, while higher in the PE group compared to the AGA group, did not reach statistical significance. Conclusion: Our data suggests that NO may play a key role in the pathogenesis of IUGR. We also, for the first time, provide information on umbilical arterial MetHb levels in PE, normotensive IUGR and normotensive AGA pregnancies.
Cortical-inspired image reconstruction via sub-Riemannian geometry and hypoelliptic diffusion

In this paper we review several algorithms for image inpainting based on the hypoelliptic diffusion naturally associated with a mathematical model of the primary visual cortex. In particular, we present one algorithm that does not exploit the information of where the image is corrupted, and others that do it. While the first algorithm is able to reconstruct only images that our visual system is still capable of recognize, we show that those of the second type completely transcend such limitation providing reconstructions at the state-of-the-art in image inpainting. This can be interpreted as a validation of the fact that our visual cortex actually encodes the first type of algorithm.
Queues and artificial potential trenches for multirobot formations

In this paper, we present a novel approach for representing formation structures in terms of queues and formation vertices, rather than with nodes, as well as the introduction of the new concept of artificial potential trenches, for effectively controlling the formation of a group of robots. The scheme improves the scalability and flexibility of robot formations when the team size changes, and at the same time, allows formations to adapt to obstacles. Furthermore, for multirobot teams to operate successfully in real and unstructured environments, the instant goal method is used to effectively solve the local minima problem.
Influence of the TSH receptor gene on susceptibility to Graves' disease and Graves' ophthalmopathy.

BACKGROUND A large gene region, called GD-1, was first described by this laboratory as linked to Graves' disease (GD) and included the gene for the thyroid-stimulating hormone receptor (TSHR). Recent studies have now suggested an association of TSHR intronic polymorphisms with GD. We have taken the opportunity to examine a population of well-characterized patients with autoimmune thyroid disease (AITD) typed for an additional thyroid susceptibility gene, the immunoregulatory gene for cytotoxic T-lymphocyte antigen 4 (CTLA-4), to examine its relationship with the susceptibility to GD endowed by TSHR gene polymorphisms. METHODS We used TSHR-SNP-rs2268458, located in intron 1 of the TSHR gene, measured using standard PCR-RFLP procedures, as our marker for the TSHR gene association. We genotyped 200 patients with GD, 83 patients with Hashimoto's thyroiditis (HT), and 118 healthy controls (all female Caucasians). RESULTS The allele and genotype frequencies from GD patients, but not HT patients, were significantly different from controls. The frequency of the combined genotype (allele) CC + TC was significantly higher in GD patients versus controls, suggesting that the C-containing genotype increased the risk for GD in a dominant manner (p = 0.018, odds ratio [OR] = 1.8). When compared with CTLA-4 (A/G)(49) single-nucleotide polymorphism (SNP), we were unable to demonstrate additive risk in patients with established AITD. Further, subsetting the patients (n = 120) into those with clinically significant Graves' ophthalmopathy (GO) showed no association with the TSHR SNP. CONCLUSIONS These results demonstrated that the intronic TSHR-SNP-rs2268458 was associated with GD, but not with HT, thus indicating that the TSHR gene has the potential to increase susceptibility to GD. However, we were not able to demonstrate any additive risk with the CTLA-4 (A/G)(49) SNP, which is, therefore, an independent risk factor for AITD. This suggested that, within the limits of the study population, each of these two genes provided a small contribution to GD susceptibility and that neither was essential. In addition, there was no evidence for the TSHR gene association adding to the risk of developing GO. Direct functional analyses are now needed to help explain the mechanisms of this TSHR gene susceptibility to GD.
What’s in a Preposition? Dimensions of Sense Disambiguation for an Interesting Word Class

Choosing the right parameters for a word sense disambiguation task is critical to the success of the experiments. We explore this idea for prepositions, an often overlooked word class. We examine the parameters that must be considered in preposition disambiguation, namely context, features, and granularity. Doing so delivers an increased performance that significantly improves over two state-of-the-art systems, and shows potential for improving other word sense disambiguation tasks. We report accuracies of 91.8% and 84.8% for coarse and fine-grained preposition sense disambiguation, respectively.
QUESEM: Towards building a Meta Search Service utilizing Query Semantics

Current Web Search Engines are built to serve needs of all users, independent of the special needs of any individual. The documents are returned by matching their queries with available documents, with no emphasis on the semantics of query. As a result, the generated information is often very large and inaccurate that results in increased user perceived latency. In this paper, a
Nutritional Manipulation of One-Carbon Metabolism: Effects on Arsenic Methylation and Toxicity

Exposure to arsenic (As) through drinking water is a substantial problem worldwide. The methylation of As, a reactive metalloid, generates monomethyl- (MMA) and dimethyl-arsenical (DMA) species. The biochemical pathway that catalyzes these reactions, one-carbon metabolism, is regulated by folate and other micronutrients. Arsenic methylation exerts a critical influence on both its urinary elimination and chemical reactivity. Mice having the As methyltransferase null genotype show reduced urinary As excretion, increased As retention, and severe systemic toxicity. The most toxic As metabolite in vitro is MMAIII, an intermediate in the generation of DMAV, a much less toxic metabolite. These findings have raised the question of whether As methylation is a detoxification or bioactivation pathway. Results of population-based studies suggest that complete methylation of inorganic As to DMA is associated with reduced risk for As-induced health outcomes, and that nutrients involved in one-carbon metabolism, such as folate, can facilitate As methylation and elimination.
Detecting telecommunications fraud based on signature clustering analysis

In the telecommunications services, fraud situations have a significant business impact. Due to the massive amounts of data handled, fraud detection stands as a very difficult and challenging task. In this paper, we propose the application of dynamic clustering over signatures to support this task. Traditional static clustering is applied to determine clusters characteristics, and dynamic clustering analysis is provided to identify changes on cluster membership over time. This approach eliminates the bias caused by special situations like market campaigns or holidays. In order to overcome scalability issues with respect to the huge volume of data involved, a partition-clustering approach is also proposed. Experimental evaluation demonstrates the scalability of the method and its ability to detect previous fraud cases as well as new potential fraud situations.
Computational Estimation and Experimental Verification of Off-Target Silencing during Posttranscriptional Gene Silencing in Plants1[W][OA]

Successful application of posttranscriptional gene silencing (PTGS) for gene function study in both plants and animals depends on high target specificity and silencing efficiency. By computational analysis with genome and/or transcriptome sequences of 25 plant species, we predicted that about 50% to 70% of gene transcripts in plants have potential off-targets when used for PTGS that could obscure experimental results. We have developed a publicly available Web-based computational tool called siRNA Scan to identify potential off-targets during PTGS. Some of the potential off-targets obtained from this tool were tested by measuring the amount of off-target transcripts using quantitative reverse transcription-PCR. Up to 50% of the predicted off-target genes tested in plants were actually silenced when tested experimentally. Our results suggest that a high risk of off-target gene silencing exists during PTGS in plants. Our siRNA Scan tool is useful to design better constructs for PTGS by minimizing off-target gene silencing in both plants and animals.
Metformin and the Incidence of Prostate Cancer in Patients with Type 2 Diabetes

Background: Several in vitro studies have indicated that metformin may reduce the risk of prostate cancer; however, epidemiologic studies have been inconclusive. The objective of this study was to determine whether metformin decreases the risk of prostate cancer in patients with type 2 diabetes. Methods: A nested case–control analysis was conducted within a population-based cohort from the UK General Practice Research Database. The cohort included patients over the age of 40 who were prescribed a first oral hypoglycemic agent (OHA) between 1988 and 2009. Cases of prostate cancer were matched up to ten controls on year of birth, date of cohort entry, and duration of follow-up. Adjusted rate ratios (RR) were estimated using conditional logistic regression. Results: The cohort included 63,049 incident users of OHAs, in which 739 cases of prostate cancer were matched to 7,359 controls. Metformin use did not decrease the risk of prostate cancer (RR: 1.23, 95% CI: 0.99–1.52). In secondary analyses, prostate cancer risk was found to increase as a function of the number of metformin prescriptions received (one to seven prescriptions: RR: 1.05, 95% CI: 0.80–1.37; seven to eighteen prescriptions: RR: 1.29, 95% CI: 0.99–1.69; eighteen to thirty-six prescriptions: RR: 1.37, 95% CI: 1.04–1.81; more than thirty-six prescriptions: RR: 1.40, 95% CI: 1.03–1.89). Conclusion: The results of this study indicate that metformin does not reduce the risk of prostate cancer in patients with type 2 diabetes. Impact: The secondary analyses need to be interpreted with caution given the inverse association between type 2 diabetes and prostate cancer. Cancer Epidemiol Biomarkers Prev; 20(2); 337–44. ©2010 AACR.
Role of the Sodium-Dependent Phosphate Cotransporter, Pit-1, in Vascular Smooth Muscle Cell Calcification

Vascular calcification is associated with cardiovascular morbidity and mortality. Hyperphosphatemia is an important contributor to vascular calcification. Our previous studies demonstrated that elevated phosphate induces calcification of smooth muscle cells (SMC) in vitro. Inhibition of phosphate transport by phosphonoformic acid blocked phosphate-induced calcification, implicating sodium-dependent phosphate cotransporters in this process. In the present study, we have investigated the role of the type III sodium-dependent phosphate cotransporter, Pit-1, in SMC calcification in vitro. Human SMC stably expressing Pit-1 small interfering double-stranded RNA (SMC-iRNA) were established using a retroviral system. SMC-iRNA had decreased Pit-1 mRNA and protein levels and sodium-dependent phosphate transport activity compared with the control transduced cells (SMC-CT) (2.9 versus 9.78 nmol/mg protein per 30 minutes, respectively). Furthermore, phosphate-induced SMC calcification was significantly inhibited in SMC-iRNA compared with SMC-CT at all time points examined. Overexpression of Pit-1 restored phosphate uptake and phosphate-induced calcification in Pit-1 deficient cells. Mechanistically, although Pit-1–mediated SMC calcification was not associated with apoptosis or cell-derived vesicles, inhibition of phosphate uptake in Pit-1 knockdown cells blocked the induction of the osteogenic markers Cbfa-1 and osteopontin. Our results indicate that phosphate uptake through Pit-1 is essential for SMC calcification and phenotypic modulation in response to elevated phosphate.
Agroecology and Ecological Intensification. A Discussion from a Metabolic Point of View

This paper documents the origin and conceptual ambiguity of the terms Sustainable, Ecological and Agroecological Intensification. It defines the concept of Ecological Intensification from an agroecological perspective, and examines in energy terms whether it may be sustainable. To illustrate the theory, we apply Land Cost of Sustainable Agriculture (LACAS) methodology to Spanish agriculture, which is representative of Mediterranean agroclimatic conditions. As a result, we demonstrate the impossibility of generalizing an extensive Organic Farming (OF) scenario under the techniques currently used by organic farmers. This is due to the fact that it would bring about a reduction of 13% in agricultural production. Which necessarily means that OF has to be intensified under agroecological criteria. This option is also explored in two scenarios. As a result, we show that it is possible to compensate the yield gap between OF and conventional agriculture by implementing low-entropy internal loop strategies which reduce the land cost of generating the necessary nitrogen flows. However, these cannot exceed the limits established by the structure of Spanish territory. That is, agroecological intensification cannot be prolonged indefinitely over time since it is limited by the land available.
CR-Tractors and the Fefferman Space

We develop the natural tractor calculi associated to conformal and CR structures as a fundamental tool for the study of Fefferman's construction of a canonical conformal class on the total space of a circle bundle over a non--degenerate CR manifold of hypersurface type. In particular we construct and treat the basic objects that relate the natural bundles and natural operators on the two spaces. This is illustrated with several applications: We prove that a number of conformally invariant overdetermined systems admit non--trivial solutions on any Fefferman space. We show that the space of conformal Killing fields on a Fefferman space naturally decomposes into a direct sum of subspaces, which admit an interpretaion as solutions of certain CR invariant PDE's. Finally we explicitly analyze the relation between tractor calculus on a CR manifold and the complexified conformal tractor calculus on its Fefferman space, thus obtaining a powerful computational tool for working with the Fefferman construction.
Inhibition of SREBP1 sensitizes cells to death ligands

Evasion of death receptor ligand-induced apoptosis contributs to cancer development and progression. To better understand mechanisms conferring resistance to death ligands, we screened an siRNA library to identify sequences that sensitize resistant cells to fas activating antibody (CH-11). From this screen, we identified the Sterol-Regulatory Element-Binding Protein 1 (SREBP1), a transcription factor, which regulates genes involved in cholesterol and fatty acid synthesis including fatty acid synthase. Inhibition of SREBP1 sensitized PPC-1 and HeLa to the death receptor ligands CH-11 and TRAIL. In contrast, DU145 prostate cancer cells that are resistant to death ligands despite expressing the receptors on their cell surface remained resistant to CH-11 and TRAIL after knockdown of SREBP1. Consistent with the effects on cell viability, the addition of CH-11 activated caspases 3 and 8 in HeLa but not DU145 cells with silenced SREBP1. We demonstrated that knockdown of SREBP1 produced a marked decrease in fatty acid synthase expression. Furthermore, genetic or chemical inhibition of fatty acid synthase with shRNA or orlistat, respectively, recapitulated the effects of SREBP1 inhibition and sensitized HeLa but not DU145 cells to CH-11 and TRAIL. Sensitization to death receptor ligands by inhibition of fatty acid synthase was associated with activation of caspase 8 prior to caspase 9. Neither silencing of SREBP1 or fatty acid synthase changed basal expression of the core death receptor components Fas, caspase 8, FADD, caspase 3 or FLIP. Thus, inhibition of SREBP1 or its downstream target fatty acid synthase sensitizes resistant cells to death ligands.
Towards a Learning Companion that Recognizes Affect

This paper reports work in progress to build a Learning Companion, a computerized system sensitive to the affective aspects of learning, which facilitates the child’s own efforts at learning. Learning related to science, math, engineering, and technology naturally involves failure and a host of associated affective responses. This article describes techniques and tools being developed to recognize affective states important in the interplay between emotions and learning.
Characterization of the grappa Gene, the Drosophila Histone H3 Lysine 79 Methyltransferase

We have identified a novel gene named grappa (gpp) that is the Drosophila ortholog of the Saccharomyces cerevisiae gene Dot1, a histone methyltransferase that modifies the lysine (K)79 residue of histone H3. gpp is an essential gene identified in a genetic screen for dominant suppressors of pairing-dependent silencing, a Polycomb-group (Pc-G)-mediated silencing mechanism necessary for the maintenance phase of Bithorax complex (BX-C) expression. Surprisingly, gpp mutants not only exhibit Pc-G phenotypes, but also display phenotypes characteristic of trithorax-group mutants. Mutations in gpp also disrupt telomeric silencing but do not affect centric heterochromatin. These apparent contradictory phenotypes may result from loss of gpp activity in mutants at sites of both active and inactive chromatin domains. Unlike the early histone H3 K4 and K9 methylation patterns, the appearance of methylated K79 during embryogenesis coincides with the maintenance phase of BX-C expression, suggesting that there is a unique role for this chromatin modification in development.
Integral localized approximation description of ordinary Bessel beams and application to optical trapping forces

Ordinary Bessel beams are described in terms of the generalized Lorenz-Mie theory (GLMT) by adopting, for what is to our knowledge the first time in the literature, the integral localized approximation for computing their beam shape coefficients (BSCs) in the expansion of the electromagnetic fields. Numerical results reveal that the beam shape coefficients calculated in this way can adequately describe a zero-order Bessel beam with insignificant difference when compared to other relative time-consuming methods involving numerical integration over the spherical coordinates of the GLMT coordinate system, or quadratures. We show that this fast and efficient new numerical description of zero-order Bessel beams can be used with advantage, for example, in the analysis of optical forces in optical trapping systems for arbitrary optical regimes.
The HadCM3 contribution to PlioMIP Phase 2 Part 1: Core and Tier 1 experiments

Abstract. We present the UK's input into the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) using the HadCM3 climate model. We outline the process of setting up HadCM3 with the enhanced PRISM4 boundary conditions and discuss in detail the assumptions and choices made. We then present the HadCM3 spin-up process from an initial arbitrary atmosphere, zero-momentum ocean state through to a well-equilibriated climatic state. We present data from the spin-up and final climatological mean state of the pre-industrial and Pliocene experiments. We focus on large-scale climatic and oceanic features. Comparing the control Pliocene experiment to pre-industrial the change in palaeogeography and CO2 combined account for a warming in globally integrated air temperature (sea surface temperature) of 1.4 °C (0.8 °C) and 1.5 °C (1.0 °C). For the pre-industrial and Pliocene we see climate sensitivities (for 2 × CO2) of 3.5 °C and 2.9 °C. We derive an approximation of Earth System Sensitivity of ~ 5.5 °C leading to an ESS / CS ratio ~ 1.90. Precipitation change is more complex, with geographic and land surface changes primarily modifying the geographical extent, and increasing CO2 leading to a general wet-get-wetter response. We see a reduction in summer and winter sea ice extent driven by both geographical – land surface changes and CO2 increase. In our model, the Atlantic Meridional overturning is relatively insensitive to CO2 but is strengthened in the Pliocene (from 15.7 to 19.6 Sv) due to the change in palaeogeography. Understanding the change in Antarctic Circumglobal Current within the Pliocene is problematic given an overly intense modern ACC and palaeogeography-driven changes in barotropic model set-up within the Pliocene. We confirm that the modern orbit used throughout PlioMIP2, is a satisfactory substitute for the Pliocene 3.205 Myr KM5c orbit in terms of large-scale climate and a number of important climatic indices. We also quantify the impact of the total solar irradiance choice (1361 versus 1365 W m−2) on the Pliocene – pre-industrial anomaly and absolute climatic state and highlight climatic systems which may present non-linear responses.
Learning Where You Are Going and from Whence You Came: h- and g-Cost Learning in Real-Time Heuristic Search

Real-time agent-centric algorithms have been used for learning and solving problems since the introduction of the LRTA* algorithm in 1990. In this time period, numerous variants have been produced, however, they have generally followed the same approach in varying parameters to learn a heuristic which estimates the remaining cost to arrive at a goal state. Recently, a different approach, RIBS, was suggested which, instead of learning costs to the goal, learns costs from the start state. RIBS can solve some problems faster, but in other problems has poor performance. We present a new algorithm, f-cost Learning Real-Time A* (f-LRTA*), which combines both approaches, simultaneously learning distances from the start and heuristics to the goal. An empirical evaluation demonstrates that f-LRTA* outperforms both RIBS and LRTA*-style approaches in a range of scenarios.