Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA-Seq Analysis of Diverse Rice Genotypes to Identify the Genes Controlling Coleoptile Growth during Submerged Germination

The rate of coleoptile elongation varies between different rice varieties that are grown under water during the germination stage. Compared to sensitive varieties, submergence-tolerant rice exhibits substantial coleoptile elongation in order to uptake oxygen (O2) from the surface and thus have a better chance to survive water stress. We conducted RNA-seq analysis in order to investigate 7-day-old shoot transcriptome dynamics in six rice genotypes that exhibit different coleoptile elongation rates under water. This enabled us to identify the genes involved in photosynthesis, lipid metabolism, glycolysis, anaerobic fermentation, hormone synthesis, cell wall growth and elongation, and to demonstrate that these genes are differentially regulated within, and between, genotypes. Further, in addition to determining how allelic variation affects anaerobic germination, we compared the expression patterns and genomic sequences of six genotypes; this enabled us to discover that some genes carry small-to-large deletions in the coding region of sensitive varieties. These structural variations may explain the absence of transcripts in the dataset, as well as the failure of sensitive variety to respond to submergence. On the basis of these results, we hypothesize that transcriptional regulation enhances coleoptile elongation. Although this is an area for future research, the outcome of this study is expected to facilitate rice breeding for direct-seeding.
Noisy Text Clustering

This work presents document clustering experiments performed over noisy texts (i.e. text that have been extracted through an automatic process like speech or character recognition). The effect of recognition errors on different clustering techniques is measured through the comparison of the results obtained with clean (manually typed texts) and noisy (automatic speech transcripts affected by $30%$ Word Error Rate) versions of the TDT2 corpus ($\sim600$ hours of spoken data from broadcast news). The results suggest that clustering can be performed over noisy data with an acceptable performance degradation.
Determination of optical properties and blood oxygenation in tissue using continuous NIR light

The authors introduce a simple method to characterize optical properties and blood oxygenation in tissue using spatially resolved, steady-state reflectance. The method considers multiple source-detector separations larger than 2 cm, i.e. 20 times the optical mean free path in tissue, and makes an approximation to linearize the relationship between the separation and reflectance. Simulation results show that errors of the algorithm due to the approximation are less than 10%. Using a calibration sample, the authors calculate from the slope and intercept the absorption and reduced scattering coefficients, mu a, and mu 's, of a tissue-like solution, and experimental results confirm the usefulness of the method for quantitation of haemoglobin saturation in tissue.
Model Identification And Controller Design For An Electropneumatic Actuator System With Dead Zone Compensation

abstract Pneumatic actuator system is inexpensive, high power to weight ratio, cleanliness and ease of maintenance make it’s a choice compared to hydraulic actuator and electromagnetic actuator. Nonetheless, the steady state error of the system is high due to the dead zone of the valve. In this paper, an Auto-Regressive with External Input (ARX) model structure is chosen to represent the pneumatic actuator system. The recursive least square method is used to estimate the model parameters. The poleassignment controller is then developed for position tracking. To cater the problem of high in steady state error, the dead zone compensation is added to the system. The dead zone controller was designed based on the inverse dead zone model and the dead zone compensation designed based on the desired error. The proposed method is then experimentally with varies load and compares with Nonlinear PID controller. The result shows that the proposed controller reduced the overshoot and steady state error of the pneumatic actuator system to no overshoot and 0.025mm respectively.
Epidural analgesia in British obstetrics.

SUMMARY Experiences with 300 continuous and 62 single-shot epidural blocks administered during labour are presented. The main indications for continuous epidural analgesia were inco-ordinate uterine action, severe pre-eclampsia and failure of orthodox analgesic drugs to produce satisfactory pain relief. The method can also be used with benefit in selected cases of cardiac and respiratory disease. In hypertonic inco-ordinate uterine action graphical analysis of labour demonstrates an increased rate of cervical dilatation after epidural block in 70 per cent of cases. In pre-eclampsia a satisfactory reduction of systolic and diastolic blood pressure is produced. Analgesia is virtually complete and the complication rate is acceptably low in experienced hands. Single-shot epidural analgesia is excellent for forceps delivery and blood loss at delivery is reduced. Epidural analgesia has a valuable therapeutic role in obstetrics and is one of the benefits which result from the introduction of a 24-hour resident obstetric anaesthetic service.
Automatic analysis of the difference image for unsupervised change detection

One of the main problems related to unsupervised change detection methods based on the "difference image" lies in the lack of efficient automatic techniques for discriminating between changed and unchanged pixels in the difference image. Such discrimination is usually performed by using empirical strategies or manual trial-and-error procedures, which affect both the accuracy and the reliability of the change-detection process. To overcome such drawbacks, in this paper, the authors propose two automatic techniques (based on the Bayes theory) for the analysis of the difference image. One allows an automatic selection of the decision threshold that minimizes the overall change detection error probability under the assumption that pixels in the difference image are independent of one another. The other analyzes the difference image by considering the spatial-contextual information included in the neighborhood of each pixel. In particular, an approach based on Markov Random Fields (MRFs) that exploits interpixel class dependency contexts is presented. Both proposed techniques require the knowledge of the statistical distributions of the changed and unchanged pixels in the difference image. To perform an unsupervised estimation of the statistical terms that characterize these distributions, they propose an iterative method based on the Expectation-Maximization (EM) algorithm. Experimental results confirm the effectiveness of both proposed techniques.
Proteomic and Transcriptomic Analyses of Swine Pathogen Erysipelothrix rhusiopathiae Reveal Virulence Repertoire

E. rhusiopathiae is the causative agent of erysipelas in animals and erysipeloid in humans, but its pathogenicity is poorly understood. To identify virulence factors associated with E. rhusiopathiae and screen engineered vaccine candidates, we used proteomics and transcriptomics to compare the highly virulent strain HX130709 with an isogenic avirulent derivative, HX130709a. 1,299 proteins and 1,673 transcribed genes were identified and 1,292 of the proteins could be associated with genes. In a comparison between HX130907 and HX130709a, 168 proteins and 475 genes exhibited differences in regulation level. Among these, levels for 61 proteins and transcripts were positively or negatively correlated. Gene Ontology (GO) analysis suggests that many of the down-regulated proteins in the attenuated strain have catalytic or binding functions. Potential protein-protein interactions suggest that some of the down-regulated proteins may regulate PTS, GMP synthase and ribosomal proteins. Morphological results showed that HX130709 and HX130709a have similar colony and capsule morphology. Growth curves and pyruvate measurements suggest that TCA cycle and saccharide phosphorylation levels were decreased and gluconeogenesis was increased in HX130709a. Our study confirms that SpaA and neuraminidase, but not hyaluronidase and capsule, are associated with virulence in E. rhusiopathiae. We conclude that the virulence of E. rhusiopathiae may be associated with slow reactions of the TCA cycle and down-regulation of selected proteins.
QoS issues in EPON

One of the key issues for the Ethernet passive optical network (EPON) is the ability of the Multi-point control protocol (MPCP) to support quality of service (QoS). In a variety of dynamic bandwidth allocation algorithms, which make use of the threshold reporting, were compared with respect to their QoS support and efficiency. Two of these algorithms, referred to as R-FPSA and R-IPSA, are studied in more detail in this paper by considering both symmetric and asymmetric traffic conditions. Moreover, a slight improvement has been made to the scheduling algorithm to further improve its performance. We demonstrate that the QoS support of high priority traffic is not influenced by the presence of best effort traffic when using R-IPSA, as opposed to R-FPSA that favors ONUs with lots of best effort traffic. While slightly higher delays for some priorities are observed with R-IPSA, it realizes better fairness and efficiency when compared to R-FPSA.
Disease-associated missense mutations in bestrophin-1 affect cellular trafficking and anion conductance

Bestrophin-1, an integral membrane protein encoded by the BEST1 gene, is localized predominantly to the basolateral membrane of the retinal pigment epithelium. Mutations in the BEST1 gene have been associated with Best vitelliforme macular dystrophy (BMD), a central retinopathy with autosomal dominant inheritance and variable penetrance. Over 120 disease-causing mutations are known, the majority of which result in amino acid substitutions within four mutational hot-spot regions in the highly conserved N-terminal half of the protein. Although initially thought to impair Cl− channel function, the molecular pathology of BEST1 mutations is still controversial. We have analyzed the subcellular localization of 13 disease-associated BEST1 mutant proteins in polarized MDCK II cells, an established model of apical to basolateral protein sorting. Immunostaining demonstrated that nine of the 13 mutant proteins failed to integrate into the cell membrane. The defective proteins were predominantly retained in the cytoplasm, whereas wild-type bestrophin-1 revealed cell membrane localization. Functional analysis of I− fluxes in HEK-293 cells showed that all mutants exhibited a significant reduction in anion conductance. Our data indicate that defective intracellular trafficking could be a common cause of BMD accompanied by impaired anion conductance, representing a loss of anion channel function that is probably due to mistargeting of mutant protein.
Towards deep reasoning with respect to natural language text in scientific domains

In this paper we take some initial steps towards deep reasoning with respect to natural language text in scientific domains. In particular we consider answering Why and How questions with respect to a high school Biology text. In comparison to other kinds of questions, Why and How questions (the later referred to as procedural questions by some) have been less explored in the Question Answering literature. However, they have been considered to a greater degree in the Reasoning about Actions literature and in the Knowledge Representation and Reasoning literature. In this paper we borrow some ideas from those literature and use answer set programming (ASP) as the knowledge representation language. A key concern in our representation of natural language statements and questions is that one should be able to obtain the ASP representation of natural language text in an automated way. We also briefly discuss how some of the background knowledge needed for deep reasoning can be obtained automatically and how various levels of approximate reasoning can be done.
Apoptotic sperm biomarkers and the correlation between conventional sperm parameters and clinical characteristics

The principal aim of this retrospective study was to examine the relationship between sperm apoptotic biomarkers and the patient's biclinical characteristics, the conventional sperm parameters and the results of assisted reproductive technology. Sperm analysis, activated caspases, annexin V staining for phosphatidylserine (PS) externalisation and labelling assay for DNA fragmentation were assessed in 122 males of infertile couples. Fifty‐seven couples were allocated to the natural conception group, and 65 couples underwent IVF or ICSI. Semen of IVF/ICSI patients showed a higher proportion of apoptotic spermatozoa in their spermatozoa when compared with a natural conception group (p < .05). Sperm apoptotic biomarkers correlated with age, FSH, and conventional sperm parameters. DNA fragmentation correlated positively with the percentage of semen having externalised PS (r = .78, p = 0) and activated caspases (r = .71, p = 0). Patients without clinical pregnancy had higher frequency of DNA fragmentation, externalised PS and activated caspases compared to patients with clinical pregnancy (p < .001). The best specificity and greater sensitivity were obtained with the test of the DNA fragmentation compared to the other biomarkers. Among the apoptotic biomarkers, only DNA fragmentation was found to predict natural or assisted pregnancy better than conventional sperm parameters.
Detection of Malicious Node in Wireless Ad Hoc Network by Using Acknowledgement Based Approach

Providing secure communication in different environments is very vital in an adhoc network. One of the important security threats in wireless adhoc networks are routing attacks. These attacks are used to disconnect a sensor network from its central base station. Ad hoc on-demand distance vector (AODV) is a dynamic routing protocol that is not designed to consider security as a goal. In this research, a novel solution AODV Malicious node Detection and Removal (AODV- MDR) has been proposed. During route discovery of AODV-MDR, every intermediate node who claims that it has a fresh path to destination, must send Gratuitous Route Reply to the destination and destination sends acknowledgement back to the source through the same intermediate node. Based on the received acknowledgement, source node confirms the authenticity of claimed path and also applies hop count verification. Results revealed that the proposed scheme detect malicious node with great accuracy. Moreover, AODV-MDR works without any overhead of encryption and hashing.
Impacts of Spark Discharge Current and Duration on Flame Development of Lean Mixtures Under Flow Conditions

Lean or diluted combustion has been considered as an effective strategy to improve the thermal efficiency of spark ignition engines. Under lean or diluted conditions, the combustion speed is reduced by the diluting gas. In order to speed up the combustion, in-cylinder flow is intentionally enhanced to promote the flame propagation. However, it is observed that the flow may make the spark ignition process more challenging due to the shortened discharge duration, the frequent re-strikes of spark plasma and the more complicated interactions between the flow and the flame. In this research, the effects of spark discharge current level and discharge duration on flame kernel development and flame propagation of lean methane air mixture are investigated under flow velocity of about 25 m/s and background pressure of 4 bar abs in an optical combustion chamber. A dual coil ignition system and an in-house developed current management module are used to create different discharge current levels. The average discharge current levels range from 55 mA, 190 mA, up to 250 mA. Detached flame kernel is observed under some test conditions. The flame propagation speed with the detached flame is generally slower than the flame developed from a flame kernel attached to the spark plug. The flame detachment is related to both the discharge current level and the discharge duration. When the discharge current level is high at 250 mA, the detached flame is observed at shorter discharge duration of 0.8 ms, while when the discharge current is low at 190 mA, detached flame can happen at longer discharge duration of 1.3 ms. Various discharge current and discharge durations are adopted to initiate the combustion in a single-cylinder engine operating with lean gasoline air mixture. It is shown from the results that a higher discharge current level and longer discharge duration are beneficial for controlling the combustion phasing and improving the operation stability of the engine.
Tube-based MPC for the energy management of hybrid electric vehicles with non-parametric driving profile prediction

Advanced control approaches designed to enhance the fuel economy of hybrid electric vehicles are being accommodated to overcome the drawbacks of the control strategies introduced earlier which mostly rely on backward vehicle simulations. In such simulations the driver actions although being essential exogenous disturbance are not modeled. To overcome this shortcoming, a tube-based model predictive controller for the fuel optimization of hybrid electric vehicles is presented in this contribution. The controller is robust with respect to the uncertainties in the driver torque demand which might result from the driving style or traffic conditions. Associated with the MPC controller driving profile prediction is conducted based on an adopted non-parametric driver model. The controller performance is evaluated in simulations on real world driving cycles. In addition the real-time capability of the introduced control concept and the possibility for its further assessment on a rapid control prototyping platform are adduced.
Long-term use of thiazolidinediones and the associated risk of pneumonia or lower respiratory tract infection: systematic review and meta-analysis

Introduction The peroxisome proliferator-activated receptor-γ agonists rosiglitazone and pioglitazone activate glucocorticoid receptors and have an immunomodulatory effect. The authors aimed to systematically determine the risk of pneumonia or lower respiratory tract infections associated with thiazolidinediones. Methods Systematic searches of MEDLINE, EMBASE, regulatory documents and trial registries were carried out for randomised controlled trials of thiazolidinediones with no date restrictions through March 2010. The authors selected long-term (≥1 year) randomised controlled trials of thiazolidinediones versus a placebo, metformin or sulfonylurea control for prevention or treatment of type 2 diabetes that reported on pneumonia or lower respiratory tract infection adverse events or serious adverse events (hospitalisation, disability or death). Relative risks (RRs) were estimated using a fixed-effects meta-analysis, and statistical heterogeneity was assessed using the I2 statistic. Results Thirteen trials (n=17 627, including 8163 patients receiving thiazolidinediones and 9464 patients receiving control therapy) with a duration of follow-up of 1–5.5 years were included after a detailed screening of 58 studies. Thiazolidinediones were associated with a statistically significantly increased risk for any pneumonia or lower respiratory tract infection (n=130/8163 vs 100/9464; RR 1.40; 95% CI 1.08 to 1.82; p=0.01; I2=0%) and serious pneumonia or lower respiratory tract infection (n=111/7391 vs 87/8692; RR 1.39; 95% CI 1.05 to 1.83; p=0.02; I2=0%). Interpretation Long-term thiazolidinedione use is associated with a modestly increased risk of any pneumonia or lower respiratory tract infection and serious pneumonia or lower respiratory tract infection in patients with type 2 diabetes.
Flexibility of a Eukaryotic Lipidome – Insights from Yeast Lipidomics

Mass spectrometry-based shotgun lipidomics has enabled the quantitative and comprehensive assessment of cellular lipid compositions. The yeast Saccharomyces cerevisiae has proven to be a particularly valuable experimental system for studying lipid-related cellular processes. Here, by applying our shotgun lipidomics platform, we investigated the influence of a variety of commonly used growth conditions on the yeast lipidome, including glycerophospholipids, triglycerides, ergosterol as well as complex sphingolipids. This extensive dataset allowed for a quantitative description of the intrinsic flexibility of a eukaryotic lipidome, thereby providing new insights into the adjustments of lipid biosynthetic pathways. In addition, we established a baseline for future lipidomic experiments in yeast. Finally, flexibility of lipidomic features is proposed as a new parameter for the description of the physiological state of an organism.
The Influence of Ultrasound Enhancement during Friction Stir Welding of Aluminum to Steel

The innovative joining process of friction stir welding (FSW) offers a wide range of advantages for welding similar as well as dissimilar materials. Even for the field of poorly weldable material combinations like aluminum to steel with their strongly differing physical properties the method of FSW proved its capability for realizing dissimilar joints with tensile strengths up to more than 80 % of the aluminum base material. Trying to improve this value and other properties of the joints several approaches for hybrid friction stir welding processes were tested in the scientific community, whereas the ultrasound enhancement of FSW (USE-FSW) looked as one of the most promising reaching good results. To gain a deeper knowledge of the influence of the ultrasound on the friction stir welds different investigations were carried out in this paper. Therefore the method of USE-FSW was applied on two dissimilar aluminum/steel-joints with varying carbon content of the steel in this work. The material combinations AA6061/SAE1006 and AA6061/SAE1045 were welded successfully with and without additional power ultrasound. Afterwards a comparison between FSW-and USE-FSW-joints was carried out regarding the microstructure of the nugget and interface (IF) by light-microscopy as well as scanning electron microscopy. Furthermore the mechanical properties were characterized in a first step.
Sparse recovery with pre-Gaussian random matrices

For an m×N underdetermined system of linear equations with independent pre-Gaussian random coefficients satisfying simple moment conditions, it is proved that the s-sparse solutions of the system can be found by l1-minimization under the optimal condition m≥csln(eN/s). The main ingredient of the proof is a variation of a classical Restricted Isometry Property, where the inner norm becomes the l1-norm and the outer norm depends on probability distributions.
Organisational learning capability, product innovation performance and export intensity

The hypothesis that managerial characteristics which facilitate the organisational learning process can provide firms with a basis for competitive advantage has received a great deal of attention. While there is evidence that organisational learning affects export intensity, we argue that intermediate variables, such as innovation, should be used in order to evaluate its impact in organisations. This study shows that firms with a higher organisational learning capability tend to be more innovative, and for this reason, they are more likely to export a higher share of their production. From a longitudinal perspective, we use structural equation modeling on a database from Italian and Spanish ceramic tile producers, worldwide leaders in terms of technology. The database combines primary and secondary data. The results support our theoretical conjectures. Findings improve our understanding of the antecedents of export intensity and are related to previous research.