Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamically updated region based memetic algorithm for the 2013 CEC Special Session and Competition on Real Parameter Single Objective Optimization

In this paper, we present a memetic algorithm which combines in a local search chaining framework, a steady-state genetic algorithm as evolutionary algorithm and a CMA-ES as local search method. It is an extension of an already presented algorithm which uses a region-based niching strategy and which has proven to be very efficient on real parameter optimisation problems. In this new version, we propose to dynamically update the niche size in order to make it less dependent to such critical parameter. In addition, we used an automatic configuration tool to optimise its parameters, and show that the optimised version of this algorithm is significantly better than with its default parameters. We tested this algorithm on the Special Session and Competition on Real-Parameter Optimization of the IEEE Congress on Evolutionary 2013 benchmark.
Advanced Data-Mining Strategies for the Analysis of Direct-Infusion Ion Trap Mass Spectrometry Data from the Association of Perennial Ryegrass with Its Endophytic Fungus, Neotyphodium lolii1[W][OA]

Direct-infusion mass spectrometry (MS) was applied to study the metabolic effects of the symbiosis between the endophytic fungus Neotyphodium lolii and its host perennial ryegrass (Lolium perenne) in three different tissues (immature leaf, blade, and sheath). Unbiased direct-infusion MS using a linear ion trap mass spectrometer allowed metabolic effects to be determined free of any preconceptions and in a high-throughput fashion. Not only the full MS1 mass spectra (range 150–1,000 mass-to-charge ratio) were obtained but also MS2 and MS3 product ion spectra were collected on the most intense MS1 ions as described previously (Koulman et al., 2007b). We developed a novel computational methodology to take advantage of the MS2 product ion spectra collected. Several heterogeneous MS1 bins (different MS2 spectra from the same nominal MS1) were identified with this method. Exploratory data analysis approaches were also developed to investigate how the metabolome differs in perennial ryegrass infected with N. lolii in comparison to uninfected perennial ryegrass. As well as some known fungal metabolites like peramine and mannitol, several novel metabolites involved in the symbiosis, including putative cyclic oligopeptides, were identified. Correlation network analysis revealed a group of structurally related oligosaccharides, which differed significantly in concentration in perennial ryegrass sheaths due to endophyte infection. This study demonstrates the potential of the combination of unbiased metabolite profiling using ion trap MS and advanced data-mining strategies for discovering unexpected perturbations of the metabolome, and generating new scientific questions for more detailed investigations in the future.
Erythrocytes as Volume Markers in Experimental PD Show that Albumin Transport in the Extracellular Space Depends on PD Fluid Osmolarity

♦ Background: Macromolecules, when used as intraperitoneal volume markers, have the disadvantage of leaking into the surrounding tissue. Therefore, 51Cr-labeled erythrocytes were evaluated as markers of intraperitoneal volume and used in combination with 125I-labeled bovine serum albumin to study albumin transport into peritoneal tissues in a rat model of peritoneal dialysis (PD). ♦ Methods: Single dwells of 20 mL of lactate-buffered filter-sterilized PD fluid at glucose concentrations of 0.5%, 2.5%, and 3.9% were performed for 1 or 4 hours. Tissue biopsies from abdominal muscle, diaphragm, liver, and intestine, and blood and dialysate samples, were analyzed for radioactivity. ♦ Results: The dialysate distribution volume of labeled erythrocytes, measured after correction for lymphatic clearance to blood, was strongly correlated with, but constantly 3.3 mL larger than, drained volumes. Erythrocyte activity of rinsed peritoneal tissue biopsies corresponded to only 1 mL of dialysate, supporting our utilization of erythrocytes as markers of intraperitoneal volume. The difference between the distribution volumes of albumin and erythrocytes was analyzed to represent the albumin loss into the peritoneal tissues, which increased rapidly during the first few minutes of the dwell and then leveled out at 2.5 mL. It resumed when osmotic ultrafiltration turned into reabsorption and, at the end of the dwell, it was significantly lower for the highest osmolarity PD fluid (3.9% glucose). Biopsy data showed the lowest albumin accumulation and edema formation in abdominal muscle for the 3.9% fluid. ♦ Conclusion: Labeled erythrocytes are acceptable markers of intraperitoneal volume and, combined with labeled albumin, provided novel kinetic data on albumin transport in peritoneal tissues.
Predicting Chemical Reaction Type and Reaction Products with Recurrent Neural Networks

Synthesizing chemical molecules is a necessary and often time-consuming process in fields like drug discovery and materials science. Here, we use recurrent neural networks to automate two tasks in chemical synthesis: 1) classifying the type of reaction two molecules will participate in, and 2) generating the correct products given the reactants and reaction type. We achieve 96% accuracy and 99% AUPRC in the task of reaction type classification, significantly improving on the baseline and previous approaches. In addition, our model for reaction-type generation stabilizes at 87.6% molecular similarity between the predicted and actual products, and reaches 96.6%. We demonstrate considerable improvement over rule-based prediction systems. These two completely data-driven systems can be useful to synthetic chemists seeking to predict the outcome of chemical reactions.
Improving threshold assignment for cluster head selection in hierarchical wireless sensor networks

WSNs (wireless sensor networks) are networks that hundreds or thousands of nodes poured in a field and nodes try to send sensed event to base station (BS). In many cases, the BS isn't in the field and is so far away from nodes. Energy efficiency is one of the major concerns in wireless sensor networks since it impacts the network lifetime. So instead of transmitting directly to BS, in hierarchical network, we choose a cluster head (CH) to send aggregated data from neighbors to BS. In this paper we investigate a new threshold assignment for LEACH and xLEACH that improves energy consumption. We insert the distances of nodes from BS in threshold assignment in order to unbalance the CH selection to reduce energy consumption in the network.
Synthetic learning agents in game-playing social environments

This paper investigates the performance of synthetic agents in playing and learning scenarios in a turn-based zero-sum game and highlights the ability of opponent-based learning models to demonstrate competitive playing performances in social environments. Synthetic agents are generated based on a variety of combinations of some key parameters, such as exploitation-vs-exploration trade-off, learning back-up and discount rates, and speed of learning, and interact over a very large number of games on a grid infrastructure; experimental data is then analysed to generate clusters of agents that demonstrate interesting associations between eventual performance ranking and learning parameters’ set-up. The evolution of these clusters indicates that agents with a predisposition to knowledge exploration and slower learning tend to perform better than exploiters, which tend to prefer fast learning. Observing these clusters vis-à-vis the playing behaviours of the agents makes it also possible to investigate how to select opponents best from a group; initial results suggest that good progress and stable evolution arise when an agent faces opponents of increasing capacity, and that an agent with a good learning mechanism set-up progresses better when it faces less favourably set-up agents.
Pick Your Flavor of Random Forest

The ModelMap package (Freeman, 2009) for R ( R Development Core Team, 2008) has added two additional variants of random forests: quantile regression forests and conditional inference forests. The quantregForest package (Meinshausen and Schiesser, 2015) is used for quantile regression forest (QRF) models. QRF models provide the ability to map the predicted median and individual quantiles. This makes it possible to map lower and upper bounds for the predictions without relying on the assumption that the predictions of individual trees in the model follow a normal distribution. The party package (Hothorn et al., 2006; Strobl et al., 2007, 2008) is used for conditional inference forest (CF) models. CF models offer two advantages over traditional RF models: they avoid RF’s bias towards predictor variables with higher numbers of categories; and, they provide a conditional importance measure, allowing a better understanding of the relative importance of correlated predictor variables.
A novel multiple-heuristic approach for singularity-free motion planning of spatial parallel manipulators

SUMMARY The issue of motion planning for closed-loop mechanisms, such as parallel manipulators or robots, is still an open question. This paper proposes a novel approach for motion planning of spatial parallel robots. The framework for the geometric modeling is based on the visibility graph methodology. It is opted for a multiple-heuristics approach, where different influences are integrated in a multiplicative way within the heuristic cost function. Since the issue of singularities is a fundamental one for parallel robots, it is emphasized on the avoidance of such configurations. To include singularity-free planning within the heuristic approach, two heuristic functions are proposed, the inverse local dexterity as well as a novel defined “next-singularity” function, in such a way, well conditioned motions can be provided by a single planning procedure. The success of the method is illustrated by some examples.
Selective vulnerability of embryonic cell populations to ethanol-induced apoptosis: implications for alcohol-related birth defects and neurodevelopmental disorder.

BACKGROUND Ethanol-induced cell death has been characterized in very few stages of embryogenesis. This investigation comprehensively maps patterns of both programmed and ethanol-induced cell death in the central nervous system and craniofacial region at 0.5-day intervals from gestational day (GD) 6.5 to 11 in mice. METHODS A teratogenic dosage of ethanol (2.9 g/kg) or vehicle was administered via two intraperitoneal injections to pregnant C57BL/6J mice at various stages of gestation. Cell death patterns were characterized using Nile blue sulfate vital staining and histological analysis of plastic sections. Confocal laser scanning microscopy of LysoTracker Red-stained specimens allowed for three-dimensional visualization of areas of apoptosis and precise sectional imaging of mouse embryos. Apoptosis was also documented using a TUNEL technique on histological sections. RESULTS Normal programmed cell death in control embryos was noted in the prechordal plate region at GD 8, the neuroepithelium of the fourth ventricle and anterior neuropore at GD 9, and within the ganglia of cranial nerves V, VII-VIII, IX, and X at GD 10. Acute maternal ethanol administration 12 hr before examination resulted in a dramatic increase in apoptosis within sites of programmed cell death in the embryo. Moreover, ethanol-exposed specimens exhibited stage-dependent excessive cell death in other distinct cell populations, particularly within the developing central nervous system. Ethanol-induced apoptosis was notable as follows: GD 7.5-neuroectoderm; GD 8-neural plate and primitive streak; GD 9-alar plate and presumptive neural crest of the rostral hindbrain, especially at the mesencephalon/rhombencephalon junction; GD 9.5-10-branchial arches and rhombomeres; and GD 11-diencephalon, basal ganglia, pons, and developing cerebellum. CONCLUSIONS The results of this study revealed developmental stage-specific cell populations of the developing brain and craniofacial region that are vulnerable to ethanol-induced apoptosis and provide new insight relative to the genesis of alcohol-related birth defects.
The business process management software for successful quality management and organization: A case study from the University of Split School of Medicine.

OBJECTIVE Our aim was to describe a comprehensive model of internal quality management (QM) at a medical school founded on the business process analysis (BPA) software tool. METHODS BPA software tool was used as the core element for description of all working processes in our medical school, and subsequently the system served as the comprehensive model of internal QM. RESULTS The quality management system at the University of Split School of Medicine included the documentation and analysis of all business processes within the School. The analysis revealed 80 weak points related to one or several business processes. CONCLUSION A precise analysis of medical school business processes allows identification of unfinished, unclear and inadequate points in these processes, and subsequently the respective improvements and increase of the QM level and ultimately a rationalization of the institution's work. Our approach offers a potential reference model for development of common QM framework allowing a continuous quality control, i.e. the adjustments and adaptation to contemporary educational needs of medical students.
An Introductory Guide to References on Conservation Laws

These pages originate as a follow up to the course Conservation Laws delivered by the author at the University of Warsaw in the week 12-16.05. 2014. Clearly, not all the theory of Conservation Laws is considered, several subjects are only superficially covered, while others are entirely omitted and the space devoted to the various research directions is not related to their relevance. Unfortunately, these choices reflect the author’s limited knowledge, rather than his interests.
Prenatal Androgenization Induces Anxiety-Like Behavior in Female Rats, Associated with Reduction of Inhibitory Interneurons and Increased BDNF in Hippocampus and Cortex

Anxiety is one of the most frequent psychiatric disorders. Despite the fact that most studies describe an anxiolytic effect of testosterone, hyperandrogenemia in mothers is assumed to be related to an increased risk of mood disorders in their offspring. An increasing body of scientific evidence suggests that an altered expression of interneuronal markers of the hippocampus may be the cause of anxiety. The aim of this study was to examine the influence of maternal hyperandrogenemia on behavioral parameters of anxiety-like behavior, neuropeptide Y (NPY) and parvalbumin (PV) expression in the hippocampus, and the level of the brain-derived neurotrophic factor (BDNF) in the hippocampus and cerebral cortex. Pregnant female Wistar albino rats were treated with testosterone undecanoate on the 20th day of gestation. Anxiety-like behavior in adult female offspring was evaluated by the elevated plus maze test and the open field. The number of PV and NPY immunoreactive cells in the hippocampus was determined immunohistochemically. The level of BDNF expression in the hippocampus and cerebral cortex was analyzed with the Western blot test. Prenatal hyperandrogenization increased anxiety-like behavior in female offspring and decreased expression of NPY+ and PV+ in the CA1 region of the hippocampus as compared to the control group. BDNF expression in the hippocampus and cerebral cortex of prenatally androgenized female offspring was significantly increased in comparison with the controls. Prenatal hyperandrogenization may be the cause of anxiety-like behavior in female offspring. Decrease in NPY and PV expression in the hippocampus may explain the possible mechanism of hyperandrogenization induced anxiety.
Performance Improvement of Optically Controlled Microwave Switch by Introducing Complementary Split-Ring Resonator

An optically controlled microwave switch (OCMS) with improved performance is demonstrated by introducing a complementary split-ring resonator (CSRR). The CSRR is etched in the metal ground and placed just below the microstrip gap that is bridged by a piece of high-resistivity silicon dice. Thanks to the deep transmission zero offered by the CSRR, high isolation in the off state can be achieved by controlling the position of transmission zero of the CSRR. Meanwhile, the microstrip gap is allowed to be designed with smaller size for reducing the insertion loss of the OCMS in its on state. Measurements are performed for comparison between the traditional OCMS and the proposed one. The comparison illustrates that the CSRR is an attractive method to improve the performance of the OCMS, with which a reduction of the insertion loss in the on state and an increase of the isolation in the off state are achieved.
Evidence that TMEM67 causes polycystic kidney disease through activation of JNK/ERK‐dependent pathways

TMEM67 mutations are associated with severe autosomal recessive polycystic kidney disease (ARPKD) in both humans and animals. However, the molecular mechanisms underlying the pathogenesis of PKD caused by TMEM67 mutations remain to be determined. We have investigated the possible signalling pathways involved in the pathogenesis of PKD. Overexpression of TMEM67 in human embryonic kidney (HEK293) cells triggered the activation of overall tyrosine phosphorylated proteins, extracellular signal‐regulated kinase (ERK) and c‐jun N‐terminal KINASE (JNK). Activation was suppressed by pharmacological inhibitors of ERK or JNK. Activation of the mammalian target of rapamycin (mTOR) or p70s kinase (S6K) did not occur, although elevated phosphorylation of eIF4E‐binding protein 1 (4E‐BP1), a target of S6K, was seen. In animal studies, activation of a variety of signalling molecules was linked to ERK, JNK and 4E‐BP1. Significant induction of phosphorylation of tyrosine phosphorylated proteins, ERK and 4E‐BP1, at different postnatal ages was detected in mutant kidneys of B6C3Fe a/a‐bpck mice, a cystic renal disease mouse model caused by TMEM67 loss of function mutation. Based on these in vitro and in vivo observations, we propose that TMEM67 mutations cause PKD through ERK‐ and JNK‐dependent signalling pathways, which may provide novel insight into the therapy of polycystic kidney diseases.
The Structural Mechanism for Iron Uptake and Release by Transferrins

Transferrins are a group of iron-binding proteins that control the levels of iron in the body fluids of vertebrates by their ability to bind two Fe3+ and two CO3 2-. The transferrin molecule, with a molecular mass of about 80 kDa, is folded into two similarly sized homologous N- and C-lobes that are stabilized by many intrachain disulfides. As observed by X-ray crystallography, each lobe is further divided into two similarly sized domains, domain 1 and domain 2, and an Fe3+-binding site is within the interdomain cleft. Four of the six Fe3+ coordination sites are occupied by protein ligands (2 Tyr residues, 1 Asp, and 1 His) and the other two by a bidentate CO3 2-. Upon uptake and release of Fe3+, transferrins undergo a large-scale conformational change dependng on a common structural mechanism: domains 1 and 2 rotate as rigid bodies around a rotation axis that passes through the two antiparallel β-strands linking the domains. The extent of the rotaion is, however, variable for different transferrin species and lobes. As a Fe3+ release mechanisms at low pH from the N-lobes of serum transferrin and ovotransferrin, the structral evidence for ‘dilysine trigger mechanism’ is shown. A structural mechanism for the Fe3+ release in presence of a non-synergistic anion is proposed on the basis of the sulfate-bound apo crystal structure of the ovotransferrin N-lobe. Domain-opened structures with the coordinated Fe3+ by the two tyrosine residues are demonstrated in fragment and intact forms, and their functional implications as a possible intermediate for iron uptake and release are discussed.
Teacher Stress and Teacher Self-Efficacy as Predictors of Engagement, Emotional Exhaustion, and Motivation to Leave the Teaching Profession

The purpose of this study was to explore how seven potentially stressful school context variables (potential stressors) predicted senior high school teachers’ experiences of teacher self-efficacy, emotional stress, emotional exhaustion, engagement in teaching, and motivation to leave the teaching profession. A total of 523 Norwegian teachers in senior high school participated in the study. Four of the potential stressors were significantly but differently related to self-efficacy and emotional stress and indirectly to emotional exhaustion, engagement, and motivation to leave the profession. The study shows that different potential stressors predict emotional exhaustion, engagement, and motivation through different psychological processes. SEM-analysis indicated two main routes to teachers’ motivation to leave the profession: 1) one route from time pressure via emotional stress and exhaustion to motivation to quit and 2) another route from lack of supervisory support and trust, low student motivation and value conflicts via lower self-efficacy and lower engagement to motivation to quit.
Maximal physiological parameters during partial body-weight support treadmill testing.

PURPOSE This study investigated maximal cardiometabolic response while running in a lower body positive pressure treadmill (antigravity treadmill (AG)), which reduces body weight (BW) and impact. The AG is used in rehabilitation of injuries but could have potential for high-speed running, if workload is maximally elevated. METHODS Fourteen trained (nine male) runners (age 27 ± 5 yr; 10-km personal best, 38.1 ± 1.1 min) completed a treadmill incremental test (CON) to measure aerobic capacity and heart rate (VO(2max) and HR(max)). They completed four identical tests (48 h apart, randomized order) on the AG at BW of 100%, 95%, 90%, and 85% (AG100 to AG85). Stride length and rate were measured at peak velocities (V(peak)). RESULTS VO(2max) (mL.kg(-1). min(-1)) was similar across all conditions (men: CON = 66.6 (3.0), AG100 = 65.6 (3.8), AG95 = 65.0 (5.4), AG90 = 65.6 (4.5), and AG85 = 65.0 (4.8); women: CON = 63.0 (4.6), AG100 = 61.4 (4.3), AG95 = 60.7 (4.8), AG90 = 61.4 (3.3), and AG85 = 62.8 (3.9)). Similar results were found for HR(max), except for AG85 in men and AG100 and AG90 in women, which were lower than CON. V(peak) (km.h(-1)) in men was 19.7 (0.9) in CON, which was lower than every other condition: AG100 = 21.0 (1.9) (P < 0.05), AG95 = 21.4 (1.8) (P < 0.01), AG90 = 22.3 (2.1) (P < 0.01), and AG85 = 22.6 (1.6) (P < 0.001). In women, V(peak) (km.h(-1)) was similar between CON (17.8 (1.1) ) and AG100 (19.3 (1.0)) but higher at AG95 = 19.5 (0.4) (P < 0.05), AG90 = 19.5 (0.8) (P < 0.05), and AG85 = 21.2 (0.9) (P < 0.01). CONCLUSIONS The AG can be used at maximal exercise intensities at BW of 85% to 95%, reaching faster running speeds than normally feasible. The AG could be used for overspeed running programs at the highest metabolic response levels.