Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification of explosives transformation products in plant tissue

Explosives contamination in surface or groundwater used for the irrigation of food crops and phytoremediation of explosives‐contaminated soil or water using plant‐assisted biodegradation have brought about concerns as to the fate of explosives in plants. Liquid scintillation counting, high‐performance liquid chromatography, and gel permeation chromatography were utilized to characterize explosives (hexahydro‐1,3,5‐trinitro‐1,3,5‐triazine and trinitrotoluene) and their metabolites in plant tissues obtained from three separate studies. Analyzing tissues of yellow nutsedge (Cyperus esculentus), corn (Zea mays), lettuce (Lacuta sativa), tomato (Lyopersicum esculentum), radish (Raphanus sativus), and parrot feather (Myriophyllum aquaticum) from three studies where exposure to explosives at nontoxic levels (1–2 mg/L in water) occurred showed that extensive transformation of the explosive contaminant occurred, variations were noted in uptake and transformation between terrestrial and aquatic plants, the products had significantly higher polarity and water solubility than the parent compounds, and the molecular sizes of the transformation products were significantly greater than those of the parent compounds (approximately 300 times greater).
Self-Formed InGaAs Quantum Dot Lasers with Multi-Stacked Dot Layer

Systematic investigation of lasing characteristics of self-formed InGaAs quantum dot lasers with multi-stacked dot layer is reported. We show that the lasing wavelength is strongly dependent on the number of quantum dot layers and the cavity length. Discontinuous shifts of the lasing wavelength from a high-order subband to a lower-order subband are clearly observed with increasing number of quantum dot layers and with decreasing cavity loss. The possibility of lasing at the ground state of quantum dots is also quantitatively discussed.
Damping Controller Design for Nanopositioners: A Mixed Passivity, Negative-Imaginary, and Small-Gain Approach

A design of a damping controller to damp the first resonant mode of a piezoelectric tube scanner (PTS) used in most commercial atomic force microscopes (AFMs) is proposed in this study. The design of the controller is carried out by proposing a novel analytical framework. The analytical framework examines the finite-gain stability for a positive feedback interconnection between two stable linear time-invariant systems, where one system has mixed passivity, negative-imaginary, and small-gain properties and the other system has mixed negative-imaginary, negative-passivity, and small-gain properties. Experimental results are presented to show the effectiveness of the proposed analytical framework to design the proposed controller.
Incidence of ultrasound‐detected asymptomatic long‐term central vein catheter‐related thrombosis and fibrin sheath in cancer patients

Most central venous catheter (CVC)‐related deep vein thromboses (DVT) are asymptomatic and their incidence and clinical relevance are still under debate. Data on CVC‐related fibrin sheaths are scarce. We investigated the incidence of asymptomatic DVT and fibrin sheaths in cancer patients with long‐term CVC implantation who underwent Doppler ultrasound surveillance at 1, 6, and 12 months after implantation. Effects of low‐weight molecular heparin (LWMH) therapy on DVT and fibrin sheaths were also analyzed.
Genetic diversity among Mycobacterium avium complex strains recovered from children with and without human immunodeficiency virus infection.

The genetic diversity and molecular epidemiology of Mycobacterium avium complex (MAC) infections in children with and without human immunodeficiency virus (HIV) infection were evaluated. Isolates recovered from 136 children were subtyped by sequence analysis of a 360-bp region of the gene (hsp65) encoding a 65-kDa heat-shock protein. Twenty-one distinct hsp65 alleles were identified. On the basis of hsp65 genotype, 6 isolates were not MAC organisms. Of the remaining 130 samples, 61% were M. avium, 37% were Mycobacterium intracellulare, and 2% were species nonspecific MAC. Eighty-eight percent of the isolates obtained from HIV-infected children were M. avium. In contrast, only 38% of the isolates obtained from children without HIV infection were M. avium (chi2 test, P < .001). M. avium isolates were further subtyped by Southern blot analysis with insertion element IS1245. Taken together, no evidence for a single clonal M. avium strain causing infection was detected.
Evaluation of Optimization Solvers in Mathematica with focus on Optimal Control Problems

This thesis involves optimization of optimal control problems using collocation methods in Wolfram SystemModeler and Mathematica. Three optimization solvers are evaluated and compared: FindMinimum in Mathematica, IPOPT and KNITRO. They are evaluated by letting them solve optimal control problems with use of the numerical method direct collocation. Two test problems are used; they represent a batch reactor and a free floating robot. An interface between IPOPT and Mathematica is created. Direct collocation is based on discretizing the state and control variables of the optimal control problem with use of collocation points. In this thesis three numerical methods are used to approximate the derivatives of the state variables in the optimal control problem. The three methods are Euler method, backward differentiation method and the use of Lagrange basis polynomials. The results are obtained by investigating the optimal trajectories of the variables, the optimal cost function, the number of iterations and the total time spent during optimization. The conclusion is that FindMinimum is not as good as the other two solvers. It performs worst in all studied aspects. The main reason is that it does not have a good algorithm to solve constrained optimization problems. IPOPT and KNITRO are equally good with respect to number of iterations and optimal results, but in the timing aspect is IPOPT slower because of slow function evaluations. Acknowledgements This thesis has been performed at Wolfram MathCore in Linköping. I would like to thank my supervisor Peter Aronsson and all colleagues at Wolfram MathCore. I would also like to thank my supervisor and examiner Stig Larsson at the Department of Mathematical Sciences, Chalmers University. Rebecka Nylin, Gothenburg June 7, 2013
Kinetic studies by fluorescence resonance energy transfer employing a double-labeled oligonucleotide: hybridization to the oligonucleotide complement and to single-stranded DNA.

A single 16-base oligodeoxyribonucleotide was labeled at the 3'-end with fluorescein and at the 5'-end with x-rhodamine (R*oligo*F); the chromophores served as a donor/acceptor pair, respectively, for Förster resonance energy transfer. We exploited the striking differences in the steady-state emission spectra of the R*oligo*F as a single strand and in a duplex structure to signal hybridization in solution and to determine the kinetics of duplex formation as the probe bound to its oligomer complement and to its target sequence in M13mp18(+) phage DNA. The binding followed second-order kinetics; in 0.18 M NaCl (pH 8) with 25% formamide, the rate constant for binding to the oligomer complement was 5.7 x 10(5) M-1 s-1, and that to M13mp18(+) was 5.7 x 10(4) M-1 s-1. The source of the 10-fold decrease in the rate of binding to M13mp18(+) was examined to differentiate between multiple nonproductive nucleation and rapid fluctuations in the structure around the target site. From simulations based on each model combined with associated experimental results, we concluded that the slower binding was due to rapid structural fluctuations around the target site, with an effective target concentration 0.1 of that of the total. Comparisons of total fluorescein emission derived from both steady-state and lifetime measurements suggest that the 5'-x-rhodamine induces a conformational change that affects the interaction at the 3'-end between the fluorescein and the polymer. The effects of salt on the fluorescence were complex. (ABSTRACT TRUNCATED AT 250 WORDS)
Weapon Carrying Among Victims of Bullying

In this study of a nationally representative sample of high school students, we investigate the risks of weapon carrying by victims of bullying who have additional indicators of peer aggression. OBJECTIVES: To examine, in a large, nationally representative sample of high school students, the association between bullying victimization and carrying weapons to school and to determine to what extent past experience of 1, 2, or 3 additional indicators of peer aggression increases the likelihood of weapon carrying by victims of bullying (VoBs). METHODS: National data from the 2015 Youth Risk Behavior Survey were analyzed for grades 9 to 12 (N = 15 624). VoB groups were determined by self-report of being bullied at school and additional adverse experiences: fighting at school, being threatened or injured at school, and skipping school out of fear for one’s safety. Weapon carrying was measured by a dichotomized (ie, ≥1 vs 0) report of carrying a gun, knife, or club on school property. VoB groups were compared with nonvictims with respect to weapon carrying by logistic regression adjusting for sex, grade, and race/ethnicity. RESULTS: When surveyed, 20.2% of students reported being a VoB in the past year, and 4.1% reported carrying a weapon to school in the past month. VoBs experiencing 1, 2, or 3 additional risk factors were successively more likely to carry weapons to school. The subset of VoBs who experienced all 3 additional adverse experiences were more likely to carry weapons to school compared with nonvictims (46.4% vs 2.5%, P < .001). CONCLUSIONS: Pediatricians should recognize that VoBs, especially those who have experienced 1 or more indicators of peer aggression in conjunction, are at substantially increased risk of weapon carrying.
Fair downlink data distribution

Downlink data distribution refers to the problem of distributing data from a base station to the mobile terminals within its radiation coverage. Because the condition or quality of the channel connecting a mobile terminal and its base station is not only time varying but also location dependent, fair data distribution on the downlink is a challenging problem and has received considerable attention from the research community. Data distribution is performed through a scheduler implemented at the base station. Elsewhere, we treated the problem for realtime traffic (Kuo, C. and Chang, J. F., IEEE ICCCN'03). We extend the treatment to a hybrid of both realtime plus non-realtime traffic. Numerical results show that our proposed scheduling algorithm has corrected the fairness problem.
Effects of Neutral Detergent Fiber from Rice Straw on Blood Metabolites and Productivity of Dairy Cows in the Tropics

This study aimed to assess the effects of neutral detergent fiber (NDF) from rice straw on blood metabolites and productivity of dairy cows in the tropics. Eight Holstein×indigenous (75-87.5% Holstein) were randomly allocated to dietary treatments according to a double 4×4 Latin square design. Contents of roughage NDF from rice straw were 12.8, 14.8, 16.8 and 18.8% dry matter (DM) and concentrate NDF content was 10.2% DM, so that levels of dietary NDF were 23, 25, 27 and 29% DM. Dietary treatments were isonitrogenous and isocaloric diets. The average maximum and minimum temperature humidity index during the experimental period were 85.6 and 76.9, respectively. Plasma glucose (p 0.05). Decreased rectal temperature and concentrations of serum cortisol were associated with decreasing levels of β-hydroxybutyrate and serum urea, but with increased concentrations of plasma glucose, DMI and 4% fat corrected milk indicating that lactating cows fed lower fiber diets were in lower oxidative stress. Therefore higher intake and metabolic efficiency in dairy cows fed diets lower in roughage NDF from rice straw would be of an advantage in productive systems under tropical conditions. (Asian-Aust. J. Anim. Sci. 2006. Vol 19, No. 3 : 356-362)
Arabidopsis HMA2, a Divalent Heavy Metal-Transporting PIB-Type ATPase, Is Involved in Cytoplasmic Zn2+ Homeostasis1

PIB-type ATPases transport heavy metal ions (Cu+, Cu2+, Zn2+, Cd2+, Co2+, etc.) across biological membranes. Several members of this subfamily are present in plants. Higher plants are the only eukaryotes where putative Zn2+-ATPases have been identified. We have cloned HMA2, a PIB-ATPase present in Arabidopsis (Arabidopsis thaliana), and functionally characterized this enzyme after heterologous expression in yeast (Saccharomyces cerevisiae). HMA2 is a Zn2+-dependent ATPase that is also activated by Cd2+ and, to a lesser extent, by other divalent heavy metals (Pb2+, Ni2+, Cu2+, and Co2+). The enzyme forms an acid-stable phosphorylated intermediate and is inhibited by vanadate. HMA2 interacts with Zn2+ and Cd2+ with high affinity (Zn2+ K1/2 = 0.11 ± 0.03 μm and Cd2+ K1/2 = 0.031 ± 0.007 μm). However, its activity is dependent on millimolar concentrations of Cys in the assay media. Zn2+ transport determinations indicate that the enzyme drives the outward transport of metals from the cell cytoplasm. Analysis of HMA2 mRNA suggests that the enzyme is present in all plant organs and transcript levels do not change in plants exposed to various metals. Removal of HMA2 full-length transcript results in Zn2+ accumulation in plant tissues. hma2 mutant plants also accumulate Cd2+ when exposed to this metal. These results suggest that HMA2 is responsible for Zn2+ efflux from the cells and therefore is required for maintaining low cytoplasmic Zn2+ levels and normal Zn2+ homeostasis.
Title : Twice weekly , in-school jumping improves lean mass , particularly in adolescent boys Running Title : Brief jumping bouts improve lean mass in boys Authors and Institutions :

Objective: To determine the effect of a twice-weekly, school-based, 10 minute jumping regime on muscle and fat tissue in healthy adolescent boys and girls. Methods: We replaced regular warm up activities with jumping in physical education (PE) classes of early high school students for 8 months to observe the effect on muscle and fat tissue. A total of 99 adolescents (46M, 53F; 13.8  0.4 years) volunteered to participate. Intervention group subjects performed ten minutes of varied jumping activity, while control subjects performed a regular PE warm-up. Biometrics, Tanner staging, age of peak height velocity (PHV), vertical jump, whole body lean tissue, and fat mass (DXA-derived) were measured at baseline and follow-up. Physical activity was determined by questionnaire. Results: There were no differences in any measured variable between control and intervention groups at baseline. Boys had a significantly older age of PHV than girls (p = 0.02). No group differences were detected for 8-month change in height, weight or maturity measures for the combined sample; however at 8-months jumpers had accrued greater lean tissue mass than controls (p = 0.002). Sex-specific analysis revealed that intervention group boys had gained more lean tissue mass than controls (p = 0.016) and experienced significant fat loss (p = 0.010) than controls, an effect that was not observed in the girls. Conclusion: Regular, short duration, jumping activity during adolescence increased lean tissue mass and boys additionally lost fat mass. Sex-specific and/or maturation-specific factors may explain the disparity in effect.
Decreased endothelial progenitor cells and increased serum glycated albumin are independently correlated with plaque-forming carotid artery atherosclerosis in type 2 diabetes patients without documented ischemic disease.

BACKGROUND The aim of the present study was to investigate the serum levels of endothelial progenitor cells (EPCs) in type 2 diabetic patients without documented ischemic disease and the association between EPCs and atherosclerotic plaque formation in the carotid artery. METHODS AND RESULTS A clinic-based, prospective study of type 2 diabetic patients was conducted. A total of 73 subjects were enrolled in this study after cardiac magnetic resonance imaging and ankle-brachial index measurements to exclude patients with ischemic disease. Plaque formation in the carotid artery was measured on ultrasonography. Circulating EPCs (CD34(+)/CD133(+)/CD309(+) cells) were counted on flow cytometry. Compared to subjects without carotid artery plaques, patients with plaques were significantly older (P=0.006) and had decreased EPC count (P=0.027). Serum glycated albumin (GA) level and the GA/glycated hemoglobin ratio tended to decrease in patients with plaques (P=0.091 and 0.067, respectively). Other cardiovascular disease risk factors were not significantly different between the 2 groups. On binary logistic regression analysis old age, low EPC count, and high serum GA level were independently correlated with carotid artery plaque formation. CONCLUSIONS EPC count and serum GA level appear to be a protective and an aggravating factor for endothelial damage, respectively, and therefore, a reduced EPC count or an increased GA level results in atherosclerotic plaque formation in type 2 diabetic patients.
FoxC 1 promotes epithelial-mesenchymal transition through PBX 1 dependent transactivation of ZEB 2 in esophageal cancer

Esophageal cancer (EC) was one of the most lethal malignancies worldwide with intricate mechanisms. Here we reported that Forkhead box C1 (FoxC1), a member of the forkhead family transcription factors, was upregulated in EC tissues and cell lines in comparison with controls. FoxC1 levels were negatively correlated with tumor stage, lymph node metastasis and survival status of EC patients. Knockdown of FoxC1 inhibited the proliferation, colony formation and epithelial-mesenchymal transition (EMT) of EC cells, while overexpression of FoxC1 promoted these biological behaviors. Mechanically, serial deletion and chromatin immunoprecipitation assays showed that ZEB2, a well-reported transcriptional suppressor of E-cadherin, was a direct transcriptional target of FoxC1. Moreover, FoxC1 was recruited to the ZEB2 promoter by its interaction with the pioneer transcription factor preB-cell leukemia homeobox 1 (PBX1). Importantly, significant correlation between levels of FoxC1 and ZEB2 was observed in EC tissues and the two proteins could be used as prognostic biomarkers together. Hence, our results revealed a critical role of FoxC1 in the EMT process of EC and uncovered a novel mechanism for the regulation of ZEB2-E-cadherin axis in EC.
Effect of Adrenergic Agents on the Secretion of Gastrointestinal Immunoreactive Glucagon in Depancreatized Dogs

To elucidate the mode of action of adrenergic agents on gastric A cells, the effects of infusion of adrenergic agonists and antagonists on the secretion of gastrointestinal immunoreactive glucagon (gastrointestinal IRG) from gastric A cells were investigated in 45 conscious, depancreatized dogs untreated with insulin. Large amounts (0.6 μg/kg/min) of epinephrine, norepinephrine, and isoproterenol stimulated the release of gastrointestinal (RG, and catecholamine-induced gastrointestinal IRG release was completely abolished by simultaneous infusion of the specific beta receptor-blocking compound, propranolol, but not by alpha receptor blockade with phentolamine. These findings suggest that, when adrenergic agonists are infused in large amounts, they may act through a beta receptor to increase the release of gastrointestinal IRG.
Detection of central venous catheter‐related bloodstream infections in haematooncological patients

Catheter‐related bloodstream infections (CRBSIs) are currently detected in patients with clinically suspicion. The aim of our study was to evaluate whether CRBSIs could be anticipated and detected in a subclinical stage by peptide nucleic acid fluorescence in situ hybridization (PNA FISH) using universal hybridization probes or acridine orange leucocyte cytospin (AOLC) tests in haematooncological patients with central venous catheters (CVCs) in situ.
An Extension of Locally Linear Embedding for Pose Estimation of 3D Object

Diverse pose estimation of 3D object in the whole view-space is a problem perplexed many researchers. In this paper we propose an algorithm extended from LLE which can estimate the arbitrary pose of 3D object in the whole view space. First, we compute the eigen-images of training set by introducing the idea of PCA using the low-dimensional embedding coordinate deduced from LLE. For a new sample we can compute its projection to the eigen-images, and the nearest training images from the new sample are the estimation poses. Next, we set different weight for different projection direction depends on its eigen-value when computing the distance between the new sample and the training images. Experimental results obtained demonstrated that the performance of the proposed method could estimate the diverse pose of 3D object efficiently and precisely, also our algorithm can be extended to real-time pose estimate, is of a potential future.
Word-Based Grammars for PPM

The Prediction by Partial Matching (PPM) compression algorithm is considered one of the most efficient methods for compressing natural language text. Despite the advances of the PPM method for the English language to predict upcoming symbols or words, more research is required to devise better compression methods for other languages, such as Arabic due, for example, to the rich morphological nature of the Arabic text, where a word can take many different forms. In this paper, we propose a new method that achieves the best compression rates not only for Arabic text but also for other languages that use Arabic script in their writing system such as Persian. Our word-based method constructs a context-free grammar (CFG) for the text and this grammar is then encoded using PPM to achieve excellent compression rates.
Evolutionarily accelerated invasions: the rate of dispersal evolves upwards during the range advance of cane toads

Human activities are changing habitats and climates and causing species’ ranges to shift. Range expansion brings into play a set of powerful evolutionary forces at the expanding range edge that act to increase dispersal rates. One likely consequence of these forces is accelerating rates of range advance because of evolved increases in dispersal on the range edge. In northern Australia, cane toads have increased their rate of spread fivefold in the last 70 years. Our breeding trials with toads from populations spanning the species’ invasion history in Australia suggest a genetic basis to dispersal rates and interpopulation genetic variation in such rates. Toads whose parents were from the expanding range front dispersed faster than toads whose parents were from the core of the range. This difference reflects patterns found in their field‐collected mothers and fathers and points to heritable variance in the traits that have accelerated the toads’ rate of invasion across tropical Australia over recent decades. Taken together with demonstrated spatial assortment by dispersal ability occurring on the expanding front, these results point firmly to ongoing evolution as a driving force in the accelerated expansion of toads across northern Australia.