Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid Detection of mecA and femA Genes by Loop-Mediated Isothermal Amplification in a Microfluidic System for Discrimination of Different Staphylococcal Species and Prediction of Methicillin Resistance

Staphylococcal infection is one of the most pressing problems in modern medicine due to the increasing antibiotic resistance with the overuse of antibiotics. Conventional methods for identification and antimicrobial susceptibility testing (AST) generally take 3–7 days and require skilled technicians. In this study, a microfluidic device based on loop-mediated isothermal amplification (LAMP) was developed, which could discriminate Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, and Staphylococcus hominis and predict their methicillin resistance by targeting the mecA and femA genes within 70 min including the hands-on time. Multiplex and real-time detection was achieved in a closed system without aerosol contamination. The limits of detection (LODs) for S. aureus, S. epidermidis, S. hominis, and methicillin-resistant S. aureus (MRSA) were 20 CFU/reaction, while that for S. haemolyticus was 200 CFU/reaction. A total of 102 positive cultures of cerebrospinal fluid (CSF) were also tested, and the results were in good agreement with those from conventional methods. Furthermore, mixed cultures were readily identified by our method. The portable and integrated device is rapid, accurate, and easy to use, which can provide information for prompt institution of proper antimicrobial therapy and has great potential for clinical applications, especially in resource-limited settings.
Shensong Yangxin Protects Against Metabolic Syndrome-Induced Ventricular Arrhythmias by Inhibiting Electrical Remodeling

Shensong Yangxin (SSYX) is a traditional Chinese medicine, which has been proven to improve the clinical symptoms of arrhythmia. However, the role of SSYX in metabolic syndrome (MetS)-induced electrical remodeling remains to be fully elucidated. Here, we sought to clarify whether SSYX can alter the electrophysiological remodeling of cardiac myocytes from MetS rats by regulating transient outward potassium current (I to) and calcium current (I Ca-L). Male Wistar rats were subjected to 16 weeks of high-carbohydrate, high-fat to produce a MetS model group. SSYX (0.4 g/kg) was administrated by daily gavage 8 weeks following high-carbohydrate, high-fat for 8 weeks. In vivo electrophysiological study was performed to evaluated ventricular arrhythmias (VA) vulnerability and electrophysiological properties. The potential electrical mechanisms were estimated by whole-cell patch-clamp and molecular analysis. The H9C2 cells were used to verify the protective role of SSYX in vitro. After 16-week high-carbohydrate, high-fat feeding, MetS model rats showed increased body weight (BW), blood pressure (BP), blood sugar (BS), heart rate (HR) and heart weights to tibia length (HW/TL) ratio. Furthermore, MetS rats depicted increased VA inducibility, shortened effective refractory period (ERP) and prolonged action potential duration (APD). Lower I Ca-L and I to current densities were observed in MetS rats than CTL rats. Additionally, MetS rats exhibited significantly increased cardiac fibrosis, decreased Cx43 expression and protein levels of Cav1.2, Kv4.2, Kv4.3 than CTL group. As expected, these MetS-induced effects above were reversed when SSYX was administrated. Mechanistically, SSYX administrated significantly down-regulated the TLR4/MyD88/CaMKII signaling pathway both in vivo and in vitro. Collectively, our data indicated that the electrical remodeling induced by MetS contributed to the increased VA susceptibility. SSYX protects against MetS-induced VA by inhibiting electrical remodeling through TLR4/MyD88/CaMKII signaling pathway.
Mutations in Two Aphid-Regulated β-1,3-Glucanase Genes by CRISPR/Cas9 Do Not Increase Barley Resistance to Rhopalosiphum padi L

Callose deposition is induced in plants by various stress factors such as when plants are attacked by herbivores and pathogens. In the case of aphids, callose plugging of aphid-damaged phloem sieve tubes is expected to reduce aphid access to the phloem sap, while aphid-induced upregulation of callose-degrading β-1,3-glucanase genes in the host plant might counteract this negative effect on aphid performance. We have tested this hypothesis with barley mutants in which one or both of two β-1,3-glucanase genes (1636 and 1639) have been mutated by CRISPR/Cas9 technique in cv. Golden Promise. These two genes were previously found to be upregulated by the cereal pest Rhopalosiphum padi L. in susceptible barley genotypes. Four 1636/1639 double mutant, three 1636 single mutant and two 1639 single mutant lines were tested for aphid resistance along with control lines. All mutant lines had single base insertions, causing frame shifts and premature stop codons. Three of the four double mutant lines showed significantly reduced β-1,3-glucanase activity, and bacterial flagellin-induction resulted in significantly more callose formation in the leaves of double mutant compared to control and single mutant lines. However, we found no effect of these modified plant traits on barley resistance to R. padi. Both genes were confirmed to be upregulated by R. padi in Golden Promise. The gene 1637 is another β-1,3-glucanase gene known to be upregulated by R. padi in barley and was here found to be higher expressed in a double mutant line when compared with a control line. If this can compensate for the general reduction of β-1,3-glucanase activity in the double mutants is difficult to discern since phloem concentrations of these proteins are unknown.
Time complexity analysis of the dominance degree approach for non-dominated sorting

Non-dominated sorting is a procedure which is heavily used by many evolutionary multiobjective algorithms. Despite it can be done in polynomial time, it remains an asymptotical bottleneck in many of these algorithms. What is more, some algorithms for non-dominated sorting, which are fast on average, are ridiculously slow in the worst case. Here we prove that a recent algorithm, the dominance degree approach from the paper "Ranking Vectors by Means of the Dominance Degree Matrix" by Zhou et al., has the worst-case time complexity of Θ(M N2 + N3). The Θ(N3) term, which is unusually high for this problem, indicates that this particular algorithm can not be recommended for performance-critical applications.
Preliminary study of adaptive grid-based decomposition on many-objective evolutionary optimization

This work proposes a method to adaptively determine the grid granularity for the grid decomposition-based evolutionary algorithm for many-objective optimization. The decomposition of the objective space is one of the promising approaches for evolutionary many-objective optimization. Although the weight-based decomposition is frequently employed recently, it has been known that the grid-based decomposition is also effective for many-objective optimization. The grid-based evolutionary algorithm (GrEA) decomposes the objective space into a grid environment with the grid division parameter. The grid division parameter determines the grid granularity and affects search performance. To find out an appropriate grid division parameter, we need to perform a parameter tuning, which executes multiple runs with different parameters and is generally time-consuming. In this work, we propose an adaptive GrEA (A-GrEA) automatically determines the grid division parameter during a single run of the search. Experimental results using WFG variant problems with 6 to 10 objectives show that the proposed A-GrEA does not only to determine the grid division parameter adaptively but also achieves comparative or higher search performance than the conventional GrEA with the best grid division parameter, MOEA/D, and NSGA-III.
Improving an evolutionary wrapper for attack detection by including feature importance information

Detect attacks is a major problem in cybersecurity, due to its wide variety of types, behaviors and dynamic structure. In this paper, we include a special crossover operator, which considers the features importance, providing additional information to a wrapped evolutionary algorithm, which uses random forest as classification technique. Results show that random forest improves its classification quality, when the wrapper evolutionary algorithm includes feature importance information for feature selection
Influences of Sensor Placement Site and Subject Posture on Measurement of Respiratory Frequency Using Triaxial Accelerometers

Introduction Respiration frequency (RF) could be derived from the respiratory signals recorded by accelerometers which detect chest wall movements. The optimum direction of acceleration for accurate RF measurement is still uncertain. We aim to investigate the effect of measure site, posture, and direction of acceleration on the accuracy of accelerometer-based RF estimation. Methods In supine and seated postures respectively, respiratory signals were measured from 34 healthy subjects in 70 s by triaxial accelerometers located at four sites on the body wall (over the clavicle, laterally on the chest wall, over the pectoral part of the anterior chest wall, on the abdomen in the midline at the umbilicus), with the reference respiratory signal simultaneously recorded by a strain gauge chest belt. RFs were extracted from the accelerometer and reference respiratory signals using wavelet transformation. To investigate the effect of measure site, posture, and direction of acceleration on the accuracy of accelerometer-based RF estimation, repeated measures multivariate analysis of variance, linear regression, Bland-Altman analysis, and Scheirer-Ray-Hare test were performed between reference and accelerometer-based RFs. Results There was no significant difference in accelerometer-based RF estimation between seated and supine postures, among four accelerometer sites, or between seated or supine postures (p > 0.05 for all). The error of accelerometer-based RF estimation was less than 0.03 Hz (two breaths per minute) at any site or posture, but was significantly smaller in supine posture than in seated posture (p < 0.05), with narrower limits of agreement in Bland-Altman analysis and higher accuracy in linear regression (R2 > 0.61 vs. R2 < 0.51). Conclusion Respiration frequency can be accurately measured from the acceleration of any direction using triaxial accelerometers placed at the clavicular, pectoral and lateral sites on the chest as well the mid abdominal site. More accurate RF estimation could be achieved in supine posture compared with seated posture.
Two-year response of American chestnut (Castanea dentata) seedlings to shelterwood harvesting and fire in a mixed-oak forest ecosystem

The American chestnut (Castanea dentata (Marsh.) Borkh. ) was once an important tree species in the east- ern United States prior to its devastation by the chestnut blight. The American Chestnut Foundation will soon release seeds that are blight resistant. However, the necessary site requirements for restoration efforts have not yet been ex- plored. The goal of this study was to evaluate the survival and growth of chestnut seedlings within a diverse forest management regime. Seedlings were experimentally grown for 2 years in three mixed-oak forests subjected to thinning, burning, thinning followed by burning, and an untreated control. Seedling biomass parameters were most influenced by treatments that increased light availability. Soil chemistry and texture parameters were also correlated (p < 0.05) with chestnut biomass. Thus, site fertility should also be considered in reintroduction efforts. While site quality may influ- ence growth, light conditions appear to be overwhelmingly important. Therefore, we recommend that American chest- nut seeds be planted in areas with moderate to high light conditions (recently disturbed), with low surrounding competing vegetation (possibly after a burn) for optimal growth benefits. Resume : Avant d'etre decime par la brulure, le châtaignier d'Amerique (Castanea dentata (Marsh.) Borkh. ) etait une espece importante dans l'est des Etats-Unis. La « American Chesnut Foundation » va bientot distribuer des graines de châtaignier resistant a la brulure. Cependant, les conditions de station requises pour orienter les efforts de restauration n'ont pas encore ete examinees. Le but de cette etude consistait a evaluer le taux de survie et la croissance de semis de châtaignier en fonction de divers regimes d'amenagement forestier. Les semis ont ete cultives experimentalement pendant deux ans dans trois forets melangees de chenes soumises a une eclaircie, a un brulage et a une eclaircie suivie d'un brulage avec un temoin non traite. Les parametres de biomasse des semis etaient surtout influences par les traite- ments qui augmentaient la disponibilite de la lumiere. Les parametres de chimie et de texture du sol etaient egalement correles (p < 0,05) a la biomasse du châtaignier. Par consequent, la fertilite de la station devrait aussi etre consideree dans les efforts de reintroduction. La qualite de station peut influencer la croissance mais les conditions de lumiere ont une importance predominante. Par consequent, les auteurs recommandent que les graines de châtaignier d'Amerique soient plantees dans des endroits ou les conditions de lumiere vont de moderees a elevees (endroits recemment pertur- bes) avec peu de vegetation competitrice environnante (possiblement apres un brulage) pour beneficier d'une croissance optimale. (Traduit par la Redaction) McCament and McCarthy 749
Improving NSGA-III for flexible job shop scheduling using automatic configuration, smart initialization and local search

This paper provides a short summary of a novel algorithm tailored towards multi-objective flexible job shop scheduling problems (FJSP). The result shows that for challenging real-world problems in combinatorial optimization, off-the-shelf implementations of multi-objective optimization evolutionary algorithms (MOEAs) might not work, but by using various adaptations, these methods can be tailored to provide excellent results. This is demonstrated for a state of the art MOEA, that is NSGA-III, and the following adaptations: (1) initialization approaches to enrich the first-generation population, (2) various crossover operators to create a better diversity of offspring, (3) parameter tuning, to determine the optimal mutation probabilities, using the MIP-EGO configurator, (4) local search strategies to explore the neighborhood for better solutions. Using these measures, NSGA-III has been enabled to solve benchmark multi-objective FJSPs and experimental results show excellent performance.
An efficient evolutionary solution to the joint order batching - order picking planning problem

This paper introduces an innovative solution to the joint Order Batching - Order Picking Planning Problem. Previous research on this field has mainly focused on solving the two problems separately. Failing to consolidate the two components, however, this approach leads to sub-optimal solutions. In this work we propose a Genetic Algorithm for Joint Optimization (GAJO), which optimizes the integrated problem. Thorough experimentation shows GAJO to be both more effective and faster than the baseline models.
A many-objective route planning benchmark problem for navigation

Route planning is one of the key elements in logistics, mobile robotics, and other applications, where engineers face many conflicting objectives. However, most of the current route planning algorithms consider merely up to three objectives. In this paper, we propose a scalable many-objective benchmark problem covering most of the key features for routing applications based on real-world data. We define five objective functions representing distance, travelling time, delays, and two route-specific features such as curvature and elevation. We define one instance for this test problem and provide its true Pareto-front to analyse the problem difficulties. We apply three well-known evolutionary algorithms. Since this test benchmark can be easily transferred to real-world routing problems, we construct a routing problem from OpenStreetMap data. We evaluate the three optimisation algorithms and observe that we can provide promising results for such a real-world application. The proposed benchmark represents a scalable many-objective route planning optimisation problem enabling researchers and engineers to evaluate their navigation and routing approaches.
Evolving an artificial creole

There has been a significant amount of research on computational modeling of language evolution to understand the origins and evolution of communication [5--8]. However, there has relatively been relatively little computational modeling of environmental factors that enable the evolution of creole languages [2, 9], specifically, modeling lexical term transmission between intersecting language groups, within the context of artificial creole language evolution [4]. This study used an iterative agent-based naming game [8] simulation to investigate the impact of population size and lexical similarity [7] of interacting language groups on the evolution of an artificial creole lexicon. We applied the synthetic methodology [6], using agent-based artificial language evolution as an experimental platform to investigate two objectives. First, to investigate the impact of population size of interacting groups (with differing lexicons) on the evolution of a common (creole) lexicon. Second, to evaluate the concurrent impact of lexical similarity between interacting agent groups on the evolution of a creole lexicon.
Individual and Environmental Predictors of Age of First Intercourse and Number of Children by Age 27

Reproductive behavior characteristics may be influenced by both social and individual factors. Recent studies have revealed that personality traits might be related to reproductive characteristics in adulthood. Little is known about potential mediators or moderators of relations between personality and reproductive behavior. The present study examines the relation between personality traits measured in early adolescence and the number of children people have by age 27, with an attempt to identify moderation and mediation effects. We used data from the longitudinal cohort (N = 585) collected as a part of the Child Development Project. Personality was measured with the use of Lanthier’s Big Five Personality Questionnaire. Results from regression analyses and structural equation models showed that four of the five personality traits (except extraversion) were related to the number of children individuals had by age 27, and these associations were mediated by the age of first intercourse and participants’ familial and educational plans. We also identified moderation effects of IQ and SES both on the associations of personality traits with mediators and the number of children by age 27.
Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and Its Inhibitors

Reliable prediction of binding affinities for ligand-receptor complex has been the primary goal of a structure-based drug design process. In this respect, alchemical methods are evolving as a popular choice to predict the binding affinities for biomolecular complexes. However, the highly flexible protein-ligand systems pose a challenge to the accuracy of binding free energy calculations mostly due to insufficient sampling. Herein, integrated computational protocol combining free energy perturbation based absolute binding free energy calculation with free energy landscape method was proposed for improved prediction of binding free energy for flexible protein-ligand complexes. The proposed method is applied to the dataset of various classes of p53-MDM2 (murine double minute 2) inhibitors. The absolute binding free energy calculations for MDMX (murine double minute X) resulted in a mean absolute error value of 0.816 kcal/mol while it is 3.08 kcal/mol for MDM2, a highly flexible protein compared to MDMX. With the integration of the free energy landscape method, the mean absolute error for MDM2 is improved to 1.95 kcal/mol.
Structural Brain Lesions and Gait Pathology in Children With Spastic Cerebral Palsy

The interaction between brain damage and motor function is not yet fully understood in children with spastic cerebral palsy (CP). Therefore, a semi-quantitative MRI (sqMRI) scale was used to explore whether identified brain lesions related to functional abilities and gait pathology in this population. A retrospective cohort of ambulatory children with spastic CP was selected [N = 104; 52 bilateral (bCP) and 52 unilateral (uCP)]. Extent and location-specific scores were defined according to the sqMRI scale guidelines. The gross motor function classification system (GMFCS), the gait profile score (GPS), GPSs per motion plane, gait variable scores (GVS) and multiple-joint (MJ) gait patterns were related to brain lesion scores. In all groups, the global total brain scores correlated to the GPS (total: rs = 0.404, p ≤ 0.001; bCP: rs = 0.335, p ≤ 0.05; uCP: rs = 0.493, p ≤ 0.001). The global total hemispheric scores correlated to the GMFCS (total: rs = 0.392, p ≤ 0.001; bCP: rs = 0.316, p ≤ 0.05; uCP: rs = 0.331, p ≤ 0.05). The laterality scores of the hemispheres in the total group correlated negatively to the GMFCS level (rs = −0.523, p ≤ 0.001) and the GVS-knee sagittal (rs = −0.311, p ≤ 0.01). Lesion location, for the total group demonstrated positive correlations between parietal lobe involvement and the GPS (rs = 0.321, p ≤ 0.001) and between periventricular layer damage and the GMFCS (rs = 0.348, p ≤ 0.001). Involvement of the anterior part of the corpus callosum (CC) was associated with the GVS-hip sagittal in all groups (total: rpb = 0.495, p ≤ 0.001; bCP: rpb = 0.357, p ≤ 0.05; uCP: rpb = 0.641, p ≤ 0.001). The global total hemispheric and laterality of the hemispheres scores differentiated between the minor and both the extension (p ≤ 0.001 and p ≤ 0.001) and flexion (p = 0.016 and p = 0.013, respectively) MJ patterns in the total group. Maximal periventricular involvement and CC intactness were associated with extension patterns (p ≤ 0.05 and p ≤ 0.001, respectively). Current findings demonstrated relationships between brain structure and motor function as well as pathological gait, in this cohort of children with CP. These results might facilitate the timely identification of gait pathology and, ultimately, guide individualized treatment planning of gait impairments in children with CP.
Use of a video imaging system for estimating leaf surface area of pinus sylvestris seedlings

A method is described for a rapid, nondestructive estimation of the surface area of the shoot system of intact pine seedlings. A video camera and image analyzer were used to quantify the area of a video image of pine seedling shoots. Surface area values were displayed in dimensionless units, referred to as silhouette area. Silhouette area was significantly correlated with several other methods of estimating needle surface area, including dry weight, calculation based on measurement of linear dimensions, volume displacement, and optical planimetry. Correspondence between dry weight, or surface area estimates based on dry weight, and silhouette area was relatively low (r2 0.9) when shoot area was estimated from volume displacement or optical planimetry.