Miracle-dz/UniFAR-FTUs huggingface dataset:
Feature selection and classification by using grid computing based evolutionary approach for the microarray data

The cancer classification through gene expression patterns becomes one of the most promising applications of the microarray technology. It is also a significant procedure in bioinformatics. In this study a grid computing based evolutionary mining approach is proposed as discriminant function for gene selection and tumor classification. The proposed approach is based on the grid computing infrastructure for establishing the best attributes set. The discriminant analysis based on vector distant of median method as the evaluation function of genetic algorithm which lays stress on find the key attributes set of the data set to establish the best attributes set for constructing a classification response model with highest accuracy. We show experimentally that the proposed approach for several benchmarking cancer microarray data sets can work effectively and efficiently, and the results of the proposed methods are superior to or as well as other existing methods in literatures.
The Social World of Twitter: Topics, Geography, and Emotions

Debate is open as to whether social media communities resemble real-life communities, and to what extent. We contribute to this discussion by testing whether established sociological theories of real-life networks hold in Twitter. In particular, for 228,359 Twitter profiles, we compute network metrics (e.g., reciprocity, structural holes, simmelian ties) that the sociological literature has found to be related to parts of one's social world (i.e., to topics, geography and emotions), and test whether these real-life associations still hold in Twitter. We find that, much like individuals in real-life communities, social brokers (those who span structural holes) are opinion leaders who tweet about diverse topics, have geographically wide networks, and express not only positive but also negative emotions. Furthermore, Twitter users who express positive (negative) emotions cluster together, to the extent of having a correlation coefficient between one's emotions and those of friends as high as 0.45. Understanding Twitter's social dynamics does not only have theoretical implications for studies of social networks but also has practical implications, including the design of self-reflecting user interfaces that make people aware of their emotions, spam detection tools, and effective marketing campaigns.
Serotonergic mechanisms of the lateral parabrachial nucleus and cholinergic-induced sodium appetite.

Central cholinergic mechanisms are suggested to participate in osmoreceptor-induced water intake. Therefore, central injections of the cholinergic agonist carbachol usually produce water intake (i.e., thirst) and are ineffective in inducing the intake of hypertonic saline solutions (i.e., the operational definition of sodium appetite). Recent studies have indicated that bilateral injections of the serotonin receptor antagonist methysergide into the lateral parabrachial nucleus (LPBN) markedly increases salt intake in models involving the activation of the renin-angiotensin system or mineralocorticoid hormones. The present studies investigated whether sodium appetite could be induced by central cholinergic activation with carbachol (an experimental condition where only water is typically ingested) after the blockade of LPBN serotonergic mechanisms with methysergide treatment in rats. When administered intracerebroventricularly in combination with injections of vehicle into both LPBN, carbachol (4 nmol) caused water drinking but insignificant intake of hypertonic saline. In contrast, after bilateral LPBN injections of methysergide (4 microg), intracerebroventricular carbachol induced the intake of 0.3 M NaCl. Water intake stimulated by intracerebroventricular carbachol was not changed by LPBN methysergide injections. The results indicate that central cholinergic activation can induce marked intake of hypertonic NaCl if the inhibitory serotonergic mechanisms of the LPBN are attenuated.
Continuous subcutaneous insulin infusion (CSII) of insulin aspart versus multiple daily injection of insulin aspart/insulin glargine in type 1 diabetic patients previously treated with CSII.

OBJECTIVE Multiple daily injection (MDI) therapy of bolus insulin aspart and basal insulin glargine was compared with continuous subcutaneous insulin infusion (CSII) with aspart in type 1 diabetic patients previously treated with CSII. RESEARCH DESIGN AND METHODS One hundred patients were enrolled in a randomized, multicenter, open-label, crossover study. After a 1-week run-in period with aspart by CSII, 50 subjects were randomly assigned to MDI therapy (aspart immediately before each meal and glargine at bedtime) and 50 subjects continued CSII. After 5 weeks of the first treatment, subjects crossed over to the alternate treatment for 5 weeks. During the last week of each treatment period, subjects wore a continuous glucose monitoring system for 48-72 h. RESULTS Mean serum fructosamine levels were significantly lower after CSII therapy than after MDI therapy (343 +/- 47 vs. 355 +/- 50 micromol/l, respectively; P = 0.0001). Continuous glucose monitoring profiles over a 24-h time period showed that glucose exposure was 24 and 40% lower for CSII than MDI as measured by area under the curve (AUC) glucose >/=80 mg/dl (1,270 +/- 742 vs. 1,664 +/- 1,039 mg . h . dl(-1); P < 0.001) and AUC glucose >/=140 mg/dl (464 +/- 452 vs. 777 +/- 746 mg . h . dl(-1), CSII vs. MDI, respectively; P < 0.001). Similar percentages of subjects reported hypoglycemic episodes (CSII: 92%, MDI: 94%) and nocturnal (12:00 a.m. to 8:00 a.m.) hypoglycemic episodes (CSII: 73%, MDI: 72%). Major hypoglycemia was infrequent (CSII: two episodes, MDI: five episodes). CONCLUSIONS In a trial of short duration, CSII therapy with insulin aspart resulted in lower glycemic exposure without increased risk of hypoglycemia, as compared with MDI with insulin aspart and glargine.
Neurological complications in late-stage hospitalized patients with HIV disease

Background and Objective: The nervous system is the most frequent and serious targets of human immunodeficiency virus (HIV) infection. In spite of a wide prevalence of neurological manifestations in HIV there are not many studies to look into it, especially from this part of the world. We investigated various neurological manifestations of HIV and their association with CD4 and CD8 counts at the time of presentation. Materials and Methods: All HIV-infected patients who presented to 750 bedded teaching hospital in North India were subjected to thorough neurological and neuropsychological evaluation. Wherever indicated, neuroimaging, cerebrospinal fluid study, electromyography, and nerve-conduction studies were performed to confirm the diagnosis. CD4 and CD8 counts were calculated. Results: A total of 416 HIV-positive patients were seen. Of them 269 were males. A total of 312 neurological events were identified in 268 patients having evidence of neurological involvement. HIV-associated dementia (HAD) was the most common cause of morbidity (33.65%), followed by CNS infections (21.63%). Most common CNS infection was tuberculosis (65.56%). CD4 counts in CNS infections and HAD were 64.8/μl and 83.52/μl, respectively. Most of the patients in our study had low scores on MMSE (22.32). Conclusions: Even in the absence of overt neurological disease, subclinical involvement in the form of subtle cognitive and motor decline is found to occur with greater frequency. Most of these patients have lower CD4 and CD8 counts, thus substantiating the proposition that neuroAIDS is a late manifestation. Significant correlation exists between CD4 counts and type of neurological manifestation. We concluded that neuropsychological assessment should be mandatory for all HIV-positive patients.
A method of analysis for T-2 toxin and neosolaniol by UPLC-MS/MS in apple fruit inoculated with Trichothecium roseum

Trichothecenes are one of the most important groups of mycotoxins produced by Trichothecium roseum, which causes core rot of apple. A reliable and sensitive method was developed and successfully applied for the rapid detection of trichothecenes including T-2 toxin and neosolaniol in harvested apple using UPLC-MS/MS. After the extraction of the two mycotoxins from the apple matrix with methanol/water (80/20, v/v), the concentrated extracts were cleaned-up by PriboFast M270 columns and then analysed by UPLC-MS/MS. T-2 toxin and neosolaniol were effectively separated as unique peaks. The validity of this method was established by its linearity (R2 ≥ 0.9995), precision (relative standard deviation ≤ 3.6%), accuracy, selectivity, limit of detection of 2–5 μg kg–1, limit of quantification of 5–10 μg kg–1 and average recovery of 73–96%. Levels of T-2 toxin were found in the range 7.1–128.4 µg kg–1 in the core rot lesion of three cultivars apple (cvs. Red Delicious, Fuji and Ralls). T-2 was detected not only in the lesion, but also in the tissue without any disease symptoms. However, neosolaniol was only detected in the lesion on ‘Red Delicious’ apples. In addition, the concentration of T-2 toxin in the susceptible cultivar (cv. Fuji) was significantly higher than that in the resistant one (cv. Ralls). This method proved to be suitable at detecting T-2 and neosolaniol simultaneously in apples infected with T. roseum.
A probabilistic method for identifying start codons in bacterial genomes

As the pace of genome sequencing has accelerated, the need for highly accurate gene prediction systems has grown. Computational systems for identifying genes in prokaryotic genomes have sensitivities of 98-99% or higher (Delcher et al., Nucleic Acids Res., 27, 4636-4641, 1999). These accuracy figures are calculated by comparing the locations of verified stop codons to the predictions. Determining the accuracy of start codon prediction is more problematic, however, due to the relatively small number of start sites that have been confirmed by independent, non-computational methods. Nonetheless, the accuracy of gene finders at predicting the exact gene boundaries at both the 5' and 3' ends of genes is of critical importance for microbial genome annotation, especially in light of the important signaling information that is sometimes found on the 5' end of a protein coding region. In this paper we propose a probabilistic method to improve the accuracy of gene identification systems at finding precise translation start sites. The new system, RBSfinder, is tested on a validated set of genes from Escherichia coli, for which it improves the accuracy of start site locations predicted by computational gene finding systems from the range 67-77% to 90% correct.
The Flathead Mutation Causes CNS-Specific Developmental Abnormalities and Apoptosis

We describe a new mutation, flathead(fh), that arose spontaneously in an inbred colony of Wistar rats. The mutation is autosomal recessive, and the behavioral phenotype of fh/fh rats includes spontaneous seizures, tremor, impaired coordination, and premature death. A striking feature of the fh mutation is a dramatic reduction in brain size (40% of normal at birth). In contrast, no abnormalities are evident in the peripheral nervous system or in other tissues outside of the CNS. Although bromodeoxyuridine incorporation assays indicate that the rate of cell proliferation in thefh/fh cortex is similar to that of unaffected animals,in situ terminal deoxynucleotidyl transferase-mediated dUTP-biotin end-labeling assays reveal a dramatic increase in apoptotic cell death beginning after embryonic day 16 (E16). At E18 there is a 20-fold increase in cell death in the ventricular zone offh/fh neocortex, and at postnatal day 1 (P1), the number of apoptotic cells is still two times that of normal. However, by P8 the extent of cell death in fh/fh is comparable to that of unaffected littermates, indicating that the reduction in brain growth is caused by abnormally high apoptosis during a discrete developmental period. Late-developing structures such as the cerebellum, neocortex, hippocampus, and retina are most severely affected by the fh mutation. Within these structures, later-generated neuronal populations are selectively depleted. Together, these results suggest that the flathead gene is essential for a developmental event required for the generation and maturation of late-born cell populations in the brain.
Merging Stratified Knowledge Bases under Constraints

In this paper, we propose a family of operators for merging stratified knowledge bases under integrity constraints. The operators are defined in a model-theoretic way. Our merging operators can be used to merge stratified knowledge bases where no numerical information is available. Furthermore, the original knowledge bases to be merged can be individually inconsistent. Both logical properties and computational complexity issues of the operators are studied.
Consuming Iron Biofortified Beans Increases Iron Status in Rwandan Women after 128 Days in a Randomized Controlled Feeding Trial.

BACKGROUND Food-based strategies to reduce nutritional iron deficiency have not been universally successful. Biofortification has the potential to become a sustainable, inexpensive, and effective solution. OBJECTIVE This randomized controlled trial was conducted to determine the efficacy of iron-biofortified beans (Fe-Beans) to improve iron status in Rwandan women. METHODS A total of 195 women (aged 18-27 y) with serum ferritin <20 μg/L were randomly assigned to receive either Fe-Beans, with 86 mg Fe/kg, or standard unfortified beans (Control-Beans), with 50 mg Fe/kg, 2 times/d for 128 d in Huye, Rwanda. Iron status was assessed by hemoglobin, serum ferritin, soluble transferrin receptor (sTfR), and body iron (BI); inflammation was assessed by serum C-reactive protein (CRP) and serum α1-acid glycoprotein (AGP). Anthropometric measurements were performed at baseline and at end line. Random weekly serial sampling was used to collect blood during the middle 8 wk of the feeding trial. Mixed-effects regression analysis with repeated measurements was used to evaluate the effect of Fe-Beans compared with Control-Beans on iron biomarkers throughout the course of the study. RESULTS At baseline, 86% of subjects were iron-deficient (serum ferritin <15 μg/L) and 37% were anemic (hemoglobin <120 g/L). Both groups consumed an average of 336 g wet beans/d. The Fe-Beans group consumed 14.5 ± 1.6 mg Fe/d from biofortified beans, whereas the Control-Beans group consumed 8.6 ± 0.8 mg Fe/d from standard beans (P < 0.05). Repeated-measures analyses showed significant time-by-treatment interactions for hemoglobin, log serum ferritin, and BI (P < 0.05). The Fe-Beans group had significantly greater increases in hemoglobin (3.8 g/L), log serum ferritin (0.1 log μg/L), and BI (0.5 mg/kg) than did controls after 128 d. For every 1 g Fe consumed from beans over the 128 study days, there was a significant 4.2-g/L increase in hemoglobin (P < 0.05). CONCLUSION The consumption of iron-biofortified beans significantly improved iron status in Rwandan women. This trial was registered at clinicaltrials.gov as NCT01594359.
miR-409-3p/-5p Promotes Tumorigenesis, Epithelial-to-Mesenchymal Transition, and Bone Metastasis of Human Prostate Cancer

Purpose: miR-409-3p/-5p is a miRNA expressed by embryonic stem cells, and its role in cancer biology and metastasis is unknown. Our pilot studies demonstrated elevated miR-409-3p/-5p expression in human prostate cancer bone metastatic cell lines; therefore, we defined the biologic impact of manipulation of miR-409-3p/-5p on prostate cancer progression and correlated the levels of its expression with clinical human prostate cancer bone metastatic specimens. Experimental Design: miRNA profiling of a prostate cancer bone metastatic epithelial-to-mesenchymal transition (EMT) cell line model was performed. A Gleason score human tissue array was probed for validation of specific miRNAs. In addition, genetic manipulation of miR-409-3p/-5p was performed to determine its role in tumor growth, EMT, and bone metastasis in mouse models. Results: Elevated expression of miR-409-3p/-5p was observed in bone metastatic prostate cancer cell lines and human prostate cancer tissues with higher Gleason scores. Elevated miR-409-3p expression levels correlated with progression-free survival of patients with prostate cancer. Orthotopic delivery of miR-409-3p/-5p in the murine prostate gland induced tumors where the tumors expressed EMT and stemness markers. Intracardiac inoculation (to mimic systemic dissemination) of miR-409-5p inhibitor–treated bone metastatic ARCaPM prostate cancer cells in mice led to decreased bone metastasis and increased survival compared with control vehicle–treated cells. Conclusion: miR-409-3p/-5p plays an important role in prostate cancer biology by facilitating tumor growth, EMT, and bone metastasis. This finding bears particular translational importance as miR-409-3p/-5p appears to be an attractive biomarker and/or possibly a therapeutic target to treat bone metastatic prostate cancer. Clin Cancer Res; 20(17); 4636–46. ©2014 AACR.
Dynamical cubes and a criteria for systems having products extensions

For minimal $\mathbb{Z}^{2}$-topological dynamical systems, we introduce a cube structure and a variation of the regionally proximal relation for $\mathbb{Z}^2$ actions, which allow us to characterize product systems and their factors. We also introduce the concept of topological magic systems, which is the topological counterpart of measure theoretic magic systems introduced by Host in his study of multiple averages for commuting transformations. Roughly speaking, magic systems have a less intricate dynamic and we show that every minimal $\mathbb{Z}^2$ dynamical system has a magic extension. We give various applications of these structures, including the construction of some special factors in topological dynamics of $\mathbb{Z}^2$ actions, and a computation of the automorphism group of the minimal Robinson tiling.
Engineering of Saccharomyces cerevisiae for Efficient Anaerobic Alcoholic Fermentation of l-Arabinose

ABSTRACT For cost-effective and efficient ethanol production from lignocellulosic fractions of plant biomass, the conversion of not only major constituents, such as glucose and xylose, but also less predominant sugars, such as l-arabinose, is required. Wild-type strains of Saccharomyces cerevisiae, the organism used in industrial ethanol production, cannot ferment xylose and arabinose. Although metabolic and evolutionary engineering has enabled the efficient alcoholic fermentation of xylose under anaerobic conditions, the conversion of l-arabinose into ethanol by engineered S. cerevisiae strains has previously been demonstrated only under oxygen-limited conditions. This study reports the first case of fast and efficient anaerobic alcoholic fermentation of l-arabinose by an engineered S. cerevisiae strain. This fermentation was achieved by combining the expression of the structural genes for the l-arabinose utilization pathway of Lactobacillus plantarum, the overexpression of the S. cerevisiae genes encoding the enzymes of the nonoxidative pentose phosphate pathway, and extensive evolutionary engineering. The resulting S. cerevisiae strain exhibited high rates of arabinose consumption (0.70 g h−1 g [dry weight]−1) and ethanol production (0.29 g h−1 g [dry weight]−1) and a high ethanol yield (0.43 g g−1) during anaerobic growth on l-arabinose as the sole carbon source. In addition, efficient ethanol production from sugar mixtures containing glucose and arabinose, which is crucial for application in industrial ethanol production, was achieved.
The Global Trace Graph, a Novel Paradigm for Searching Protein Sequence Databases

Motivation: Propagating functional annotations to sequence-similar, presumably homologous proteins lies at the heart of the bioinfor-matics industry. Correct propagation is crucially dependent on the accurate identification of subtle sequence motifs that are conserved in evolution. The evolutionary signal can be difficult to detect because functional sites may consist of non-contiguous residues while segments in-between may be mutated without affecting fold or function. Results: Here, we report a novel graph clustering algorithm in which all known protein sequences simultaneously self-organize into hypothetical multiple sequence alignments. This eliminates noise so that non-contiguous sequence motifs can be tracked down between extremely distant homologues. The novel data structure enables fast sequence database searching methods which are superior to profile-profile comparison at recognizing distant homo-logues. This study will boost the leverage of structural and functional genomics and opens up new avenues for data mining a complete set of functional signature motifs.
International Journal of Hospitality Management Linkages among Business Strategy, Uncertainty and Performance in the Hospitality Industry: Evidence from an Emerging Economy

This study investigates linkages among business strategy, environmental uncertainty, and performance in an emerging economy. The hotel sector in Turkey's hospitality industry is investigated. Generic strategies were self-reported with regard to typologies develop by Porter, and Miles and Snow. Partial support was found for direct linkages between environmental uncertainty and both financial and non-financial performance. Defenders exhibited the highest value in competitive uncertainty, but the difference was not significant. Prospectors, analyzers, and defenders outperformed reactors in terms of both financial and non-financial performance. Overall, defender/cost leadership and prospector/focus strategies appear to be the best options for Turkish hotels. Following Porter's admonition, hotels in Turkey seeking to combine low cost and differentiation approaches are likely to end up " stuck in the middle. " Implications for managers and future research are discussed.
Hydrosurgery is Effective for Debridement of Diabetic Foot Wounds.

INTRODUCTION Diabetic foot wounds are serious complications of diabetes mellitus. Surgical debridement is a very important part of the management of diabetic wounds. Sharp debridement using the scalpel is normally performed. Versajet II hydrosurgery system is an alternative technique for debridement. To our knowledge, this is the fi rst study conducted to evaluate the use of hydrosurgery debridement for diabetic foot wounds. MATERIALS AND METHODS This pilot study included 15 consecutive patients with diabetic foot wounds who were admitted to the National University Hospital (NUH) and were managed by the Diabetic Foot Team from June 2012 to December 2012. All wounds underwent hydrosurgery debridement. Patients' demographic details, clinical details on wound assessments, and outcome were recorded and analysed. RESULTS The Versajet II hydrosurgery system was found to show some advantages over standard surgical scalpel debridement. It allowed adequate debridement whilst preserving more viable tissue to promote rapid healing. It could be manoeuvred over complex wound terrain. The time required for debridement was short--an average of 9.5 minutes. Good wound healing was achieved in all 15 cases. Only 1 Versajet debridement was required in 13 cases and 2 required an extra debridement. Twelve wounds were healed by split thickness skin grafting (STSG) and 3 wounds by secondary healing. Two of the STSG were infected but they were subsequently healed by dressings via secondary healing. CONCLUSION Although good wound healing was achieved in all 15 cases, further study that uses a larger cohort and a randomised controlled trial is required to fully evaluate the effectiveness, or otherwise, of the Versajet II hydrosurgery system for the debridement of diabetic foot wounds.
Nash equilibria in random games

We consider Nash equilibria in 2-player random games and analyze a simple Las Vegas algorithm for finding an equilibrium. The algorithm is combinatorial and always finds a Nash equilibrium; on m /spl times/ n payoff matrices, it runs in time O(m/sup 2/n log log n + n/sup 2/m log log m) with high probability. Our main tool is a polytope formulation of equilibria.