Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating Microarray-based Classifiers: An Overview

For the last eight years, microarray-based class prediction has been the subject of numerous publications in medicine, bioinformatics and statistics journals. However, in many articles, the assessment of classification accuracy is carried out using suboptimal procedures and is not paid much attention. In this paper, we carefully review various statistical aspects of classifier evaluation and validation from a practical point of view. The main topics addressed are accuracy measures, error rate estimation procedures, variable selection, choice of classifiers and validation strategy.
High-Reliability Trigate Poly-Si Channel Flash Memory Cell With Si-Nanocrystal Embedded Charge-Trapping Layer

This letter introduces a polycrystalline-silicon nanowire (NW) thin-film nonvolatile memory (NVM) with a self-assembled silicon-nanocrystal (Si-NC) embedded charge-trapping (CT) layer. This process is simple and compatible with conventional CMOS processes. Experimental results indicate that this NW NVM exhibits high reliability due to a deep-quantum-well structure and immunity of enhanced electric field underneath a disk-shaped Si-NC. After 10 000 P/E cycles, the memory window loss of the NVM with a Si-NC embedded CT layer is less than 12% until 104 s at 150 °C. Accordingly, a poly-Si thin-film transistor with a Si-NC embedded CT layer is highly promising for NVM applications.
D and E region incoherent scatter radar density measurements over Jicamarca

[1] We present the first daytime E and D region incoherent scatter radar (ISR) measurements of electron densities at equatorial latitudes, using the Jicamarca ISR. Both measurements have been obtained using a high-resolution ISR mode with a relatively short interpulse period. Usually, E region ISR measurements are not feasible due to the clutter caused by strong echoes from equatorial electrojet irregularities (EEJ). Our E region ISR measurements were possible during an event when EEJ echoes were absent and show an excellent agreement with an empirical model based on rockets measurements (FIRI). In addition, we show that the employed high resolution mode also works to get densities between 130 and 200 km even during strong EEJ events, a region that is poorly known. In the case of D region densities, normally they are difficult to obtain due to the presence of strong coherent echoes caused by mesospheric turbulent layers. Fortunately, these layers are usually organized in narrow regions; therefore using a high range resolution, we have been able to get weak signals from the regions in between the layers causing coherent echoes. Our preliminary results show that our D region density estimates are in reasonable agreement with empirical models, in some cases providing slightly larger values. These new D region estimates contain important geophysical information that we plan to explore in the future.
Metabolic control, self-management and psychosocial adjustment in women with type 2 diabetes.

AIMS To examine factors associated with metabolic control, self-management (diet and exercise behaviour), and psychosocial adjustment (diabetes-related distress) in women with type 2 diabetes. DESIGN Cross-sectional design using baseline data of women with type 2 diabetes enrolled to participate in a pilot study of a nurse coaching intervention (n = 53). ETHICAL ISSUES Appropriate ethical review and approval was completed. Informed consent from participants was obtained. OUTCOME MEASURES Physiological measures included body mass index and glycosylated haemoglobin (HbA1c). Self-management measures included the Dietary Subscale of the Summary of Diabetes Self-Care Activities Questionnaire and a modified Paffenbarger Physical Activity Questionnaire. Psychosocial measures included the Problem Areas in Diabetes Survey (diabetes-related distress), the Diabetes Questionnaire, the Diabetes Self-Management Assessment Tool Support and Confidence Subscale, and the Social Functioning Scale. Descriptive, bivariate, and multivariate analyses were completed. RESULTS The most consistent predictor of metabolic control, dietary self-management, and diabetes-related distress was support and confidence in living with diabetes. Additionally, women had difficulty meeting optimal goals for exercise, yet reported higher levels of other physical activity. LIMITATIONS This study was an exploratory analysis with a homogeneous sample of women with type 2 diabetes enrolled in an intervention study and measurements included multiple self-report instruments. CONCLUSIONS Interventions to increase women's perceived self-confidence and support may contribute to positive health outcomes in women with type 2 diabetes. RELEVANCE TO CLINICAL PRACTICE Assessment of social support and self-confidence in diabetes self-management in women with type 2 diabetes may assist in determining individualized goals and strategies. Enhanced social support and self-confidence in diabetes self-management may subsequently improve metabolic control, self-management and psychosocial adjustment to diabetes.
Long-Term Effects of Nitrogen Fertilization on Plant Community Structure on a Coastal Barrier Island Dune Chronosequence

Abstract Nitrogen limitation typically has considerable influence on plant community composition and structure on coastal barrier island dune ecosystems. The purpose of this study was to quantify plant community responses of different age dunes on a coastal barrier island in Virginia, USA to nitrogen addition. We hypothesized that nitrogen addition would increase density and cover, but with differential effects among species as a result of increased interspecific competition, and decrease species diversity. Density, cover and species diversity were monitored along a dune chronosequence on Hog Island (Virginia Coast Reserve Long-Term Ecological Research Site) over a seven year period. There were few significant changes in species dominance in control plots between 1992 and 1998; however, in fertilized plots, Ammophila breviligulata cover increased (except on the oldest dune) and Spartina patens cover decreased (except on the youngest dune). After seven growing seasons, results suggested more intense negative effects of competition in nitrogen-fertilized plots. Greater cover of Ammophila in fertilized plots suggests Ammophila is in a better position to compete for light with enhanced aboveground dominance. Diversity was lower in fertilized plots on all but the dune formed in 1967 and diversity decreased most dramatically in fertilized plots on the oldest dune. The increase in total density with fertilization as diversity decreased, coupled with the shifting composition of Ammophila and other dominants, appears to support the interspecific competitive exclusion hypothesis. Changes in the positions of free surfaces (groundwater level in particular) appear to influence plant community composition. The decline in Spartina density may be at least partially attributed to development of drier conditions on the older dunes.
Fast document-at-a-time query processing using two-tier indexes

In this paper we present two new algorithms designed to reduce the overall time required to process top-k queries. These algorithms are based on the document-at-a-time approach and modify the best baseline we found in the literature, Blockmax WAND (BMW), to take advantage of a two-tiered index, in which the first tier is a small index containing only the higher impact entries of each inverted list. This small index is used to pre-process the query before accessing a larger index in the second tier, resulting in considerable speeding up the whole process. The first algorithm we propose, named BMW-CS, achieves higher performance, but may result in small changes in the top results provided in the final ranking. The second algorithm, named BMW-t, preserves the top results and, while slower than BMW-CS, it is faster than BMW. In our experiments, BMW-CS was more than 40 times faster than BMW when computing top 10 results, and, while it does not guarantee preserving the top results, it preserved all ranking results evaluated at this level.
Stock Selection for Portfolios Using Expected Utility-Entropy Decision Model

Yang and Qiu proposed and then recently improved an expected utility-entropy (EU-E) measure of risk and decision model. When segregation holds, Luce et al. derived an expected utility term, plus a constant multiplies the Shannon entropy as the representation of risky choices, further demonstrating the reasonability of the EU-E decision model. In this paper, we apply the EU-E decision model to selecting the set of stocks to be included in the portfolios. We first select 7 and 10 stocks from the 30 component stocks of Dow Jones Industrial Average index, and then derive and compare the efficient portfolios in the mean-variance framework. The conclusions imply that efficient portfolios composed of 7(10) stocks selected using the EU-E model with intermediate intervals of the tradeoff coefficients are more efficient than that composed of the sets of stocks selected using the expected utility model. Furthermore, the efficient portfolio of 7(10) stocks selected by the EU-E decision model have almost the same efficient frontier as that of the sample of all stocks. This suggests the necessity of incorporating both the expected utility and Shannon entropy together when taking risky decisions, further demonstrating the importance of Shannon entropy as the measure of uncertainty, as well as the applicability of the EU-E model as a decision-making model.
Measurement of antibody release from single cells. I.

Studies of rates of release of IgM were performed in vitro and in vivo. Short term in vivo studies in which 4.98 × 106 tumor cells/mouse were given i.v. in order to quantitate cellular synthetic function showed that the synthetic rate decreased progressively. Samples taken within 1 hr of injection gave rates of release similar to those in the in vitro studies. Nine in vivo samples taken at 30 min gave a rate of 74.03 ± 18.37 and thirteen in vivo samples taken at 1 hr gave 89.98 ± 9.97 molecules/cell/sec. Seventeen separate in vitro measurements gave 76.30 ± 7.44 molecules/cell/sec. The low rate of release of MOPC tumor IgM as compared to the primary response IgM hemolysin to sheep red blood cells is discussed.
In Vitro Activities of Five Oral Cephalosporins Against Aerobic Pathogenic Bacteria

Cefaclor (Lilly 99638) and cefatrizine (BL-S640, SK&F 70771) are orally absorbed, broad-spectrum semisynthetic cephalosporins. They were compared in vitro with cephalexin, cephaloglycin, and cepharadine against a variety of aerobic pathogenic bacteria by an agar dilution procedure. Cefaclor and cefatrizine were found to be similar or superior to cephalexin, cephaloglycin, and cephradine in terms of activity against gram-positive cocci other than enterococci. Only cefatrizine demonstrated any potentially useful activity against some susceptible isolates of enterococci. Cefaclor and cefatrizine also were highly active, equally or more so than the other oral cephalosporins, against several gram-negative species including Escherichia coli, Enterobacter aerogenes, and Klebsiella pneumoniae. None of the cephalosporins were particularly active against Enterobacter cloacae. Both cefaclor and cefatrizine were active against Proteus mirabilis; cefatrizine was uniquely active against indolepositive Proteus species.
Impacts of Priming with Silicon on the Growth and Tolerance of Maize Plants to Alkaline Stress

Silicon (Si) has been known to augment plant defense against biotic and abiotic pressures. Maize (Zea maize L.) is classified as a Si accumulator and is relatively susceptible to alkaline stress. In this study, seeds of maize were grown in pots and exposed to various concentrations of Na2CO3 (0, 25, 50, and 75 mM) with or without 1.5 mM Si in the form of sodium metasilicate Na2O3Si.5H2O for 25 days. Alkaline-stressed plants showed a decrease in growth parameters, leaf relative water content (LRWC), and the contents of photosynthetic pigments, soluble sugars, total phenols and potassium ion (K+), as well as potassium/sodium ion (K+/Na+) ratio. By contrast, alkaline stress increased the contents of soluble proteins, total free amino acids, proline, Na+ and malondialdehyde (MDA), as well as the activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) in stressed plants. On the other hand, application of Si by seed-priming improved growth of stressed plants, which was accompanied by the enhancement in LRWC, and levels of photosynthetic pigments, soluble sugars, soluble proteins, total free amino acids and K+, as well as activities of SOD, CAT, and POD enzymes. Furthermore, Si supplement resulted in a decrease in the contents of proline, MDA and Na+, which together with enhanced K+ level led to a favorable adjustment of K+/Na+ ratio, in stressed plants relative to plants treated with alkaline stress alone. Taken together, these results indicate that Si plays a pivotal role in alleviating the negative effects of alkaline stress on maize growth by improving water status, enhancing photosynthetic pigments, accumulating osmoprotectants rather than proline, activating the antioxidant machinery, and maintaining the balance of K+/Na+ ratio. Thus, our findings demonstrate that seed-priming with Si is an efficient strategy that can be used to boost tolerance of maize plants to alkaline stress.
Improved Molecular Detection of Dengue Virus Serotype 1 Variants

ABSTRACT The dengue virus molecular typing method described by Lanciotti and coworkers (R. S. Lanciotti, C. H. Calisher, D. J. Gubler, G. J. Chang, and A. Vance-Vorndam, J. Clin. Microbiol. 30:545-551, 1992) is used worldwide for diagnosis and surveillance. However, it failed to detect DENV-1 variants in Cambodia due to a point mutation. We describe an improvement of the method that allows the detection of additional DENV-1 strains, including potential variants.
Visual response latencies of magnocellular and parvocellular LGN neurons in macaque monkeys

Signals relayed through the magnocellular layers of the LGN travel on axons with faster conduction speeds than those relayed through the parvocellular layers. As a result, magnocellular signals might reach cerebral cortex appreciably before parvocellular signals. The relative speed of these two channels cannot be accurately predicted based solely on axon conduction speeds, however. Other factors, such as different degrees of convergence in the magnocellular and parvocellular channels and the retinal circuits that feed them, can affect the time it takes for magnocellular and parvocellular signals to activate cortical neurons. We have investigated the relative timing of visual responses mediated by the magnocellular and parvocellular channels. We recorded individually from 78 magnocellular and 80 parvocellular neurons in the LGN of two anesthetized monkeys. Visual response latencies were measured for small spots of light of various intensities. Over a wide range of stimulus intensities the fastest magnocellular response latencies preceded the fastest parvocellular response latencies by about 10 ms. Because parvocellular neurons are far more numerous than magnocellular neurons, convergence in cortex could reduce the magnocellular advantage by allowing parvocellular signals to generate detectable responses sooner than expected based on the responses of individual parvocellular neurons. An analysis based on a simple model using neurophysiological data collected from the LGN shows that convergence in cortex could eliminate or reverse the magnocellular advantage. This observation calls into question inferences that have been made about ordinal relationships of neurons based on timing of responses.
ENSO diversity in the NCAR CCSM4 climate model

[1] In this study we examine ENSO diversity in a 500 year control simulation of the National Center for Atmospheric Research (NCAR) Community Climate System Model version 4 (CCSM4), focusing on warm events. Standard and modified Nino3 and Nino4 indices are used to identify different event types. CCSM4 shows a rich diversity of El Nino flavors with characteristics that are comparable to what was found in observations, the SODA 2.0. 2/3 ocean reanalysis, and the GFDL CM2.1 model, a climate model whose ENSO characteristics have been extensively analyzed. In agreement with previous studies available in the literature, warm events peaking in the central/western Pacific are characterized by wind stress and precipitation fields confined to the western side of the basin, and show weak or absent recharge/discharge thermocline processes. A heat budget analysis of four different El Nino flavors, peaking at different longitudes, confirms the leading role of the thermocline and zonal advective feedbacks in the Nino3 and Nino4 regions, respectively. However, the growth of events centered further west appears to be controlled by nonlinear zonal advection, a result that differs from what was found in the GFDL CM2.1 model, but that is consistent with some observational evidence.
Sensitivity analysis for predicting continuous fields of tree-cover and fractional land-cover distributions in cloud-prone areas

The use of multi-temporal datasets, such as vegetation index time series or phenological metrics, for improved classification and regression performance is well established in the remote-sensing science community. However, the usefulness of such information is less apparent for areas with distinct wet season periods and heavily concentrated cloud cover. In view of this, this study examines the potential of multi-temporal datasets for the estimation of sub-pixel land-cover fractions and percentage tree cover in an area having distinct wet and dry seasons. Prediction is based on a regression tree algorithm in combination with linear least-squares regression planes, which relate multi-spectral and multi-temporal satellite data from the Moderate-Resolution Imaging Spectroradiometer (MODIS) sensor to sub-pixel land-cover proportions and percentage tree cover, derived from high-resolution land-cover maps. Furthermore, several versions of the latter were produced using different classification approaches to evaluate the sensitivity of the response variable on overall prediction accuracy. The results were evaluated according to absolute accuracy levels and according to their long-term inter-annual robustness by applying the regression models to MODIS data over a period of 11 years. The best regression model based on dry season information only estimated continuous fields of percentage tree cover with a prediction error of less than 7% and an inter-annual variability of less than 4% over a time period of 11 years. The inclusion of intra-annual information did not contribute to any improvements in model accuracy compared to information from the dry season alone, and furthermore, deteriorated inter-annual robustness of model predictions. In addition, it has been shown that the quality of the response variable in the training data had significant effects on overall accuracy.
Probiotic Escherichia coli Nissle 1917 Inhibits Leaky Gut by Enhancing Mucosal Integrity

BACKGROUND Probiotics are proposed to positively modulate the intestinal epithelial barrier formed by intestinal epithelial cells (IECs) and intercellular junctions. Disruption of this border alters paracellular permeability and is a key mechanism for the development of enteric infections and inflammatory bowel diseases (IBDs). METHODOLOGY AND PRINCIPAL FINDINGS To study the in vivo effect of probiotic Escherichia coli Nissle 1917 (EcN) on the stabilization of the intestinal barrier under healthy conditions, germfree mice were colonized with EcN or K12 E. coli strain MG1655. IECs were isolated and analyzed for gene and protein expression of the tight junction molecules ZO-1 and ZO-2. Then, in order to analyze beneficial effects of EcN under inflammatory conditions, the probiotic was orally administered to BALB/c mice with acute dextran sodium sulfate (DSS) induced colitis. Colonization of gnotobiotic mice with EcN resulted in an up-regulation of ZO-1 in IECs at both mRNA and protein levels. EcN administration to DSS-treated mice reduced the loss of body weight and colon shortening. In addition, infiltration of the colon with leukocytes was ameliorated in EcN inoculated mice. Acute DSS colitis did not result in an anion secretory defect, but abrogated the sodium absorptive function of the mucosa. Additionally, intestinal barrier function was severely affected as evidenced by a strong increase in the mucosal uptake of Evans blue in vivo. Concomitant administration of EcN to DSS treated animals resulted in a significant protection against intestinal barrier dysfunction and IECs isolated from these mice exhibited a more pronounced expression of ZO-1. CONCLUSION AND SIGNIFICANCE This study convincingly demonstrates that probiotic EcN is able to mediate up-regulation of ZO-1 expression in murine IECs and confer protection from the DSS colitis-associated increase in mucosal permeability to luminal substances.
High Infection Rate of Trichophyton verrucosum in Calves from Central Italy

Recent epidemiological features of the zoonotic dermatophyte Trichophyton verrucosum were investigated in 294 calves from 20 farms located in Central Italy. By the combination of microscopic examinations and fungal cultures, the total prevalence rate of T. verrucosum infection was found to be high, with 87.7% of samples yielding positive results and 100% of farms being infected. Farm to farm prevalence of infection varied from 25% to 100% of the examined calves. Prevalence rates were higher in females than males (91.6% versus 84%), in >3–≤6 than >6–≤9 month old calves (89.8% versus 85.7%), in purebred than in crossbred (88.5% versus 81.8%), and in symptomatic than asymptomatic ones (95.7% versus 80.4%). T. verrucosum was as prevalent in semi‐intensive as in intensive breeding system (88.2% versus 87.6%) but more prevalent in calves raised for meat rather than milk production (91.1% versus 84.9%), and reared under conventional than organic production management system (89.3% versus 82.6%). Prevalence rates were also higher when the cattle present in the farm were of mixed origin, rather than when the whole stock was purchased or was born in the farm (92% versus 88.2% and 85.7%), when other cattle in the farm were showing skin signs (90% versus 84.2%), and at least one case of human ringworm was recorded in the farm (90.9% versus 86.1%). No statistically significant association was found. Therefore, T. verrucosum infection may be more widespread in calves from Central Italy than it was previously thought to be. Calves of any sex, breed, age, and of any of the farm condition considered, are highly exposed to the risk of infection. As calves may play a considerable role as reservoirs of the infection, our results highlight the need to determine the incidence and the importance of T. verrucosum ringworm in personnel involved with cattle care in Italy and elsewhere.