Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology) and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS) accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis.
Scalable data exchange with functional dependencies

The recent literature has provided a solid theoretical foundation for the use of schema mappings in data-exchange applications. Following this formalization, new algorithms have been developed to generate optimal solutions for mapping scenarios in a highly scalable way, by relying on SQL. However, these algorithms suffer from a serious drawback: they are not able to handle key constraints and functional dependencies on the target, i.e., equality generating dependencies (egds). While egds play a crucial role in the generation of optimal solutions, handling them with first-order languages is a difficult problem. In fact, we start from a negative result: it is not always possible to compute solutions for scenarios with egds using an SQL script. Then, we identify many practical cases in which this is possible, and develop a best-effort algorithm to do this. Experimental results show that our algorithm produces solutions of better quality with respect to those produced by previous algorithms, and scales nicely to large databases.
X-ray Microscopy and Root Cause Analysis in Electronic Packaging

Qualification of electronic package technologies requires electrical testing at standard JEDEC environmental test conditions. Finding an electrical failure through electrical test is straight forward; however, determining the root cause of the failure is generally much more difficult. Routine electronic packaging failure analysis utilizes a work flow with a minimum of 8 steps including electrical test, 2D Xray alignment of part to a dicing saw, dicing the package, mechanical polishing, ion milling, metal sputter coating, scanning electron microscopy imaging and root cause analysis. This traditional process provides two dimensional images of defects from the sample of interest. In this paper we describe an alternative failure analysis workflow involving X-ray microscopy, which effectively reduces the total number of analysis steps. Due to the non-destructive nature of X-ray, both 3 dimensional images of defects as well as 2 dimensional cross sections are effectively used to analyze true root cause of failures.
Growth and Brilliant Photo-Emission of Crystalline Hexagonal Column of Alq3 Microwires

We report the growth and nanoscale luminescence characteristics of 8-hydroxyquinolinato aluminum (Alq3) with a crystalline hexagonal column morphology. Pristine Alq3 nanoparticles (NPs) were prepared using a conventional reprecipitation method. Crystal hexagonal columns of Alq3 were grown by using a surfactant-assisted self-assembly technique as an adjunct to the aforementioned reprecipitation method. The formation and structural properties of the crystalline and non-crystalline Alq3 NPs were analyzed with scanning electron microscopy and X-ray diffraction. The nanoscale photoluminescence (PL) characteristics and the luminescence color of the Alq3 single NPs and their crystal microwires (MWs) were evaluated from color charge-coupled device images acquired using a high-resolution laser confocal microscope. In comparison with the Alq3 NPs, the crystalline MWs exhibited a very bright and sharp emission. This enhanced and sharp emission from the crystalline Alq3 single MWs originated from effective π-π stacking of the Alq3 molecules due to strong interactions in the crystalline structure.
A review of intrusion detection using anomaly based detection

Security from intruders in data mining and machine learning have been important area of research during the last few years. Today malicious attack is serious security threat. These malicious executables are created at the rate of thousands every year and create serious security problems. Intrusion Detection System (IDS) is used to Access unauthorized and malicious attacks over the network. Data mining techniques that can be applied to IDS to detect normal and abnormal behavior patterns. Intrusion detection systems analyzes network activities and identify suspicious activity in the network to improve accuracy and security and detect anomalies attacks. Data mining provide a way to analyze, classify, clean and eliminate the large amount of network data through intrusion detection system. Several privacy and security techniques and algorithms have been proposed recently. In this paper we provide techniques of research problem and achievements in the field of security of big data using anomaly based IDS. Intrusion detection is a software application for detecting and monitoring the network activities and protect from unknown and suspicious access of device.
Unintentional heating at implants when using electrosurgery

Electrosurgery is a commonly used device in the operating room, but it has some adverse effects, which are only partly described in literature. Interference issues are well described, but unintended heating in and around implants is not well studied. We simulated different scenarios using a Finite Element Model to investigate unintended heating caused by electrosurgery. We looked at different shapes, sizes, and active electrode placements. We found that all these factors play a role in the amount of heating.
Specificity of induced defenses, growth, and reproduction in lima bean (Phaseolus lunatus) in response to multispecies herbivory.

UNLABELLED • PREMISE OF THE STUDY Following herbivore attack, plants can either reduce damage by inducing defenses or mitigate herbivory effects through compensatory growth and reproduction. It is increasingly recognized that such induced defenses in plants are herbivore-specific, but less is known about the specificity of compensatory responses. Damage by multiple herbivores may also lead to synergistic effects on induction and plant fitness that differ from those caused by a single herbivore species. Although largely unstudied, the order of arrival and damage by different herbivore species might also play an important role in the impacts of herbivory on plants. • METHODS We investigated the specificity of defense induction (phenolics) and effects on growth (number of stems and leaves) and reproduction (number of seeds, seed mass, and germination rate) from feeding by two generalist leaf-chewing herbivores (Spodoptera eridania and Diabrotica balteata) on Phaseolus lunatus plants and evaluated whether simultaneous attack by both herbivores and their order of arrival influenced such dynamics. • KEY RESULTS Herbivory increased levels of leaf phenolics, but such effects were not herbivore-specific. In contrast, herbivory enhanced seed germination in an herbivore-specific manner. For all variables measured, the combined effects of both herbivore species did not differ from their individual effects. Finally, the order of herbivore arrival did not influence defense induction, plant growth, or seed number but did influence seed mass and germination. • CONCLUSIONS Overall, this study highlights novel aspects of the specificity of plant responses induced by damage from multiple species of herbivores and uniquely associates such effects with plant lifetime fitness.
Electronically conducting polymers as active electrode material for electrochemical supercapacitors

The electrochemical behavior of various conducting polymers has been evaluated so to find active electrode materials for electrochemical supercapacitors. Polyaniline, PANI, was prepared from non aqueous media on a carbon paper electrode and subsequently cycled in a non aqeuous electrolyte. A PANI-PANI electrochemical supercapacitor was tested and cycled over a cell voltage of 0.8 V. The electrochemical behavior of polypyrrole and PANI in the same electrolyte solution revealed that a cell voltage of about 1.5 V can be generated with a PPy-PANI based electrochemical supercapacitor. The approximate band gap of poly cyclopenta[2,1-b;3,4-b'] dithiophen-4-one, PCDT, was evaluated by cyclic voltammetry and a value of about 1 eV was obtained. The discharge capacity of a PCDT based electrochemical capacitor stabilized at 10 mC/cm 2 after 100 charge/discharge cycles. In this paper, a review of the work performed elsewhere is also presented together with the results from our laboratory.
Design of a hybrid magnetic and piezoelectric polymer microactuator

Microsensors and microactuators are considered to be the most crucial elements of micro-electromechanical systems (MEMS) and devices. There has been growing interest in the development of new microactuator technologies with an increasing requirement for low cost microswitch arrays providing large air gap and large force at the same time. In particular, large air gap/large force microactuators are essential for high voltage switching in automobile electronics, test equipment switchboards and in network remote reconfiguration. The necessity to reduce the size of actuators and at the same time increase the force and the air gap has placed severe constraints on the suitability of current microactuator technology for various applications. This has led to the development of new actuator technologies based on novel materials or modifying existing systems. As an effort in this direction, this thesis presents the details of the work on the design, fabrication and testing of a new hybrid microactuator, combining electromagnetic and piezoelectric actuation mechanisms. The design and fabrication of electromagnetic actuators using planar coils and a soft magnetic core has long been established. However, in many instances these designs are constrained by difficulties in the fabrication of the multi layer planar coils, which is tedious, often resulting in a low yield. Hence device performance is limited by the maximum coil currents and thereby the maximum force able to be generated. In order to overcome these problems, a hybrid actuator combining the electromagnetic system along side of a piezoelectric actuation is proposed. This has been demonstrated to assist in enhancing the total force and consequently achieving larger actuator displacements. In this research a hybrid microactuator with a footprint of 10 mm was designed, fabricated and tested. It can generate 330 μN force and cover 100 μm air gap as a microswitch.
The effects of volume relaxation and thermal mobilization of trapped radicals on the final conversion of photopolymerized diacrylates

Comparaison entre les mesures calorimetriques et de retrait au cours de la polymerisation photochimique. Influence de la structure moleculaire des composes de depart (hexanediol-1,6 diacrylate et bis(hydroxy-2 ethyl) bisphenol A dimethacrylate)
TreeFTL: Efficient RAM management for high performance of NAND flash-based storage systems

NAND flash memory is widely used for secondary storage today. The flash translation layer (FTL) is the embedded software that is responsible for managing and operating in flash storage system. One important module of the FTL performs RAM management. It is well-known to have a significant impact on flash storage system's performance. This paper proposes an efficient RAM management scheme called TreeFTL. As the name suggests, TreeFTL organizes address translation pages and data pages in RAM in a tree structure, through which it dynamically adapts to workloads by adjusting the partitions for address mapping and data buffering. TreeFTL also employs a lightweight mechanism to implement the least recently used (LRU) algorithm for RAM cache evictions. Experiments show that compared to the two latest schemes for RAM management in flash storage system, TreeFTL can reduce service time by 46.6% and 49.0% on average, respectively, with a 64MB RAM cache.
Efficacy of methanogenic biomass acclimation in mesophilic anaerobic digestion of ultrasound pretreated sludge

ABSTRACT Methanogenic biomass plays a key role with regard to methane production during anaerobic bioconversion of organic substrates. In this study, the effect of two different acclimated inocula on digestion performances was investigated by means of anaerobic batch tests on untreated and sonicated waste-activated sludge. Organics solubilization and removal kinetics, the abundance and physiological conditions of archaeal cells on ultimate methane yield were evaluated. The simultaneous presence of Methanosarcina and Methanosaeta in the archaeal biomass, the higher initial archaeal cells relative abundance and their occurrence in the aggregated forms were the main factors positively affecting the conversion into methane. The presence of the acclimated inoculum at the start-up influenced positively the methane improvement due to sonication, and the methane-specific production increased from 0.335 ± 0.03 to 0.420 ± 0.05 Nm3/kg VSfed. Moreover, the better physiological state of methanogens permitted to appreciate the effect of hydrolysis improvement by ultrasound pretreatment.
Calprotectin (S100A8/A9) should preferably be measured in EDTA-plasma; results from a longitudinal study of patients with rheumatoid arthritis

Abstract Calprotectin (S100A8/A9), a protein expressed in neutrophils and monocytes/macrophages in circulation and inflamed tissue, is associated with measures of disease activity in rheumatoid arthritis (RA) patients both when measured in ethylenediaminetetraacetic acid (EDTA)-plasma and in serum. We wanted to explore if EDTA-plasma or serum should be preferred for calprotectin as a marker of disease activity. Calprotectin was analysed in EDTA-plasma and serum by enzyme-linked immunosorbent assay (ELISA) at baseline in 141 RA patients, starting biologic disease-modifying anti-rheumatic drugs (bDMARDs), and after three months. Differences between plasma and serum levels of calprotectin were assessed by Wilcoxon signed rank test. Variability was assessed by quartile coefficient of dispersion. Spearman’s test explored correlations between calprotectin in plasma and serum and between calprotectin (plasma or serum) and clinical/ultrasound (US) measures of disease activity. Bland Altman plots were used for method comparisons. Conventional inflammatory markers were evaluated for comparison. Calprotectin had similar variability when measured in plasma and serum, but there was a significant difference in concentrations between plasma and serum (p < .001). The correlation coefficients at baseline between calprotectin measured in plasma/serum and measures of disease activity were rs = 0.62/0.46 for sum power Doppler score (PD), rs = 0.60/0.48 for assessor’s global visual analogue scale (VAS), rs = 0.59/0.43 for sum grey scale (GS) score and rs = 0.47/0.37 for swollen joint count of 32, all p < . 001. Similar differences were found after three months. Calprotectin measured in plasma showed the strongest associations with assessments of disease activity, and EDTA-plasma should preferably be used when evaluating disease activity in RA patients.
Multimodal 2D Brain Computer Interface

In this work we used multimodal, non-invasive brain signal recording systems, namely Near Infrared Spectroscopy (NIRS), disc electrode electroencephalography (EEG) and tripolar concentric ring electrodes (TCRE) electroencephalography (tEEG). 7 healthy subjects participated in our experiments to control a 2-D Brain Computer Interface (BCI). Four motor imagery task were performed, imagery motion of the left hand, the right hand, both hands and both feet. The signal slope (SS) of the change in oxygenated hemoglobin concentration measured by NIRS was used for feature extraction while the power spectrum density (PSD) of both EEG and tEEG in the frequency band 8-30Hz was used for feature extraction. Linear Discriminant Analysis (LDA) was used to classify different combinations of the aforementioned features. The highest classification accuracy (85.2%) was achieved by using features from all the three brain signals recording modules. The improvement in classification accuracy was highly significant (p = 0.0033) when using the multimodal signals features as compared to pure EEG features.
Postactivation Potentiation of the Plantar Flexors Does Not Directly Translate to Jump Performance in Female Elite Young Soccer Players

High-intensity muscle actions have the potential to temporarily improve muscle contractile properties (i.e., postactivation potentiation, PAP) thereby inducing acute performance enhancements. There is evidence that balance training can improve performance during strength exercises. Taking these findings together, the purpose of this study was to examine the acute effects of a combined balance and strength (B+S) exercise vs. a strength only (S) exercise on twitch contractile properties, maximum voluntary strength, and jump performance in young athletes. Female elite young soccer players (N = 12) aged 14–15 years conducted three experimental conditions in randomized order: S included 3 sets of 8–10 dynamic leg extensions at 80% of the 1-repetition maximum, B+S consisted of 3 sets of 40 s double-leg stances on a balance board prior to leg extensions (same as S), and a resting control period. Before and 7 min after exercise, participants were tested for their electrically-evoked isometric twitches (i.e., twitch peak torque, twitch rate of torque development) and maximal voluntary contraction (MVC) torque of the plantar flexor muscles. Additionally, countermovement (CMJ) and drop jump (DJ) performances (i.e., CMJ/DJ height, DJ ground contact time) were assessed. Significant effects of condition on twitch contractile properties (p < 0.05, d = 1.1) and jump performance outputs (p < 0.05, 1.1 ≤ d ≤ 1.2) were found. Post-hoc tests revealed that S compared to control produced larger PAP for twitch peak torques by trend (p = 0.07, d = 1.8, 33 vs. 21%) and significantly larger PAP for twitch rate of torque development (p < 0.05, d = 2.4, 55 vs. 43%). Following B+S compared to control, significant improvements in CMJ height (p < 0.01, d = 1.9, 3%) and DJ contact time were found (p < 0.01, d = 2.0, 10%). This study revealed protocol-specific acute performance improvements. While S resulted in significant increases in twitch contractile properties, B+S produced significant enhancements in jump performance. It is concluded that PAP effects in the plantar flexors may not directly translate to improved jump performance in female elite young soccer players. Therefore, the observed gains in jump performance following B+S are most likely related to neuromuscular changes (e.g., intramuscular coordination) rather than improved contractile properties.
Adaptive Plasticity in Wild Field Cricket’s Acoustic Signaling

Phenotypic plasticity can be adaptive when phenotypes are closely matched to changes in the environment. In crickets, rhythmic fluctuations in the biotic and abiotic environment regularly result in diel rhythms in density of sexually active individuals. Given that density strongly influences the intensity of sexual selection, we asked whether crickets exhibit plasticity in signaling behavior that aligns with these rhythmic fluctuations in the socio-sexual environment. We quantified the acoustic mate signaling behavior of wild-caught males of two cricket species, Gryllus veletis and G. pennsylvanicus. Crickets exhibited phenotypically plastic mate signaling behavior, with most males signaling more often and more attractively during the times of day when mating activity is highest in the wild. Most male G. pennsylvanicus chirped more often and louder, with shorter interpulse durations, pulse periods, chirp durations, and interchirp durations, and at slightly higher carrier frequencies during the time of the day that mating activity is highest in the wild. Similarly, most male G. veletis chirped more often, with more pulses per chirp, longer interpulse durations, pulse periods, and chirp durations, shorter interchirp durations, and at lower carrier frequencies during the time of peak mating activity in the wild. Among-male variation in signaling plasticity was high, with some males signaling in an apparently maladaptive manner. Body size explained some of the among-male variation in G. pennsylvanicus plasticity but not G. veletis plasticity. Overall, our findings suggest that crickets exhibit phenotypically plastic mate attraction signals that closely match the fluctuating socio-sexual context they experience.
2 – Fiber-fiber and fiber-wall interactions during the flow of non-dilute suspensions

Publisher Summary Short-fiber composites are reinforced by particles that are slender, but whose length is small compared to the overall dimensions of the part. They include fiber-reinforced thermoplastics for injection molding and extrusion, sheet molding compounds and short-fiber GMTs (glass-mat reinforced thermoplastics). Short-fiber composites can be processed by fast, highly-automated methods such as injection or compression molding. In these processes, the fibers and the resin are transported as a suspension into the mold cavity. The properties of a short-fiber composite part are highly dependent on the way the part is manufactured. As the resin or molding compound deforms to achieve the desired shape, the orientation of the fibers is changing. Fiber orientation changes stop when the matrix solidifies and the orientation pattern becomes part of the microstructure of the finished article. To design short-fiber composite parts effectively, the way that processing-induced fiber orientation influences the properties of the finished part must be anticipated. Hence, the flow of fiber suspensions needs to be understood in order to predict the orientation distribution of the fibers.
Implementation of random parameter filtering using OpenMP

This paper proposes the use of OpenMP for random parameter filtering. The use of large numbers of samples during ray tracing rendering results in high quality images yet requires long processing times. On the other hand, the use of a small number of samples results in noise. For the purposes of reducing processing time and removing noise, this study undertook rendering using a small number of samples and subsequently undertook random parameter filtering. In order to speed up the process of random parameter filtering, this study applied OpenMP. The use of OpenMP resulted in a 5.8 times greater improvement in performance.