Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantile Regression Approach for Analyzing Similarity of Gene Expressions under Multiple Biological Conditions

Temporal gene expression data contain ample information to characterize gene function and are now widely used in bio-medical research. A dense temporal gene expression usually shows various patterns in expression levels under different biological conditions. The existing literature investigates the gene trajectory using the mean function. However, temporal gene expression curves usually show a strong degree of heterogeneity under multiple conditions. As a result, rates of change for gene expressions may be different in non-central locations and a mean function model may not capture the non-central location of the gene expression distribution. Further, the mean regression model depends on the normality assumptions of the error terms of the model, which may be impractical when analyzing gene expression data. In this research, a linear quantile mixed model is used to find the trajectory of gene expression data. This method enables the changes in gene expression over time to be studied by estimating a family of quantile functions. A statistical test is proposed to test the similarity between two different gene expressions based on estimated parameters using a quantile model. Then, the performance of the proposed test statistic is examined using extensive simulation studies. Simulation studies demonstrate the good statistical performance of this proposed test statistic and show that this method is robust against normal error assumptions. As an illustration, the proposed method is applied to analyze a dataset of 18 genes in P. aeruginosa, expressed in 24 biological conditions. Furthermore, a minimum Mahalanobis distance is used to find the clustering tree for gene expressions.
Electromagnetic Interference Resisting Circuit

An electromagnetic interference (EMI) resisting circuit is described. It is improved from the classic Kuijk Bandgap with a PMOS pass device and an active load (PPDAL). Developed in 65 nm CMOS, the desired low reference voltage (441.3 mV) is achieved by substituting the BJT with MOSFET having a temperature coefficient (TC) of 10.65 ⁄ . The EMI resisting ability in terms of DC shift is up to 2V amplitude by applying a double differential-input pair and a power supply independent bias scheme. The total power consumption is 104 W.
Biochemical and Molecular Characteristics of a Novel Hyaluronic Acid Lyase from Citrobacter freundii

The Gram-negative strain of Citrobacter freundii, YNLX, has the ability to degrade hyaluronic acid. In this study, we expressed a C. freundii hyaluronic acid lyase, from polysaccharide lyase family 8, in Escherichia coli. The purified recombinant enzyme (rHynACF8) showed a substantially higher cleavage activity of hyaluronic acid than chondroitin sulfate. We found that its optimal pH and temperature are 5.5 and 35 °C, respectively. In addition, the enzyme activity was not notably affected by most metal ions. Km and kcat of rHynACF8 towards HA were 1.5 ± 0.01 mg/mL and 30.9 ± 0.5 /s, respectively. rHynACF8 is an endo-acting enzyme. Its cleavage products had dramatically increased antioxidant activity than hyaluronic acid in vitro (p < 0.001). As the molecular weight of hyaluronic acid decreased, the intramolecular interactions among antioxidant functional groups were removed; in the process of the cracking reaction, new double bonds formed and conjugated with the carbonyl group. We presumed that the structural change is the critical factor influencing antioxidant capacity. Overall, we found that rHynACF8 from Gram-negative bacteria with metal ion resistance, indicated the relationship between the function and structure of its antioxidant cleavage product.
Realtime Vehicle Counting Method Using Haar Cascade Classifier Model

The proliferation of digital camera technology has provided many digital images for object detection and counting in public places. This paper presents an experiment on the realtime vehicle counting method to be implemented in a single board computer. The proposed design's objective is to detect and count vehicles entering and exiting at entrances using haar cascade classifier algorithms and other automatic open and close door systems controlled by a single board computer (SBC). The proposed system was tested using raspberry pi 4 model B with a 4GB RAM platform. The empiric results using 3-minute video as input with a total of 113 passing vehicles the proposed method achieve of 91.2 % of average accuracy.
Some Automatically Generated Patches are More Likely to be Correct than Others: An Analysis of Defects4J Patch Features

Defects4J is a popular dataset against which many Java Automatic Program Repair (APR) tools benchmark their performance. However, recent evidence suggests that some APR tools overfit to Defects4J, producing plausible patches which are incorrect. What we do not currently know is whether there is any commonality in the features of these plausible patches that turn out not to be correct. We compare the features of Defects4J's human written patches in terms of those correctly patched by existing APR tools and those incorrectly patched. We found that 48.4% of Defects4J v1.5 have been automatically patched by existing APR tools; of which only 28.9% have been correctly patched leaving 19.5% incorrectly patched. We found patches of defects that added a method call, added a variable, or wrapped existing code with new code, such as a try/catch block were significantly associated with incorrect patches. Editing only a single line was significantly associated with correct patches. Our results suggest that current tools are weak at generating multi-line patches and synthesising new code especially when wrapping existing code. Our results highlight potential future areas of development for new APR approaches, such as developing a tool that effectively repairs defects that require a try/catch block. Our replication Package is available online11Replication Package available at: https://github.com/IncorrectDefects/ReplicationPackage.
Far-ultraviolet diffuse background and galaxy counts

We have used galaxy counts obtained at 2000 A down to a magnitude of 18.5 to calculate the ultraviolet integrated light of galaxies. The calculation is based on models developed to interpret the galaxy counts. Because of various sources of uncertainty, the extrapolated values lie in the range 40-130 photons cm −2 s −1 A −1 sr −1 . This extrapolated intensity is comparable to the extragalactic ultraviolet background estimated from direct background measurements, demonstrating that the integrated light of galaxies must be a significant contributor to the extragalactic ultraviolet background
SAVE-U: First Experiences with a Pre-Crash System for Enhancing Pedestrian Safety

This paper presents first results of the project SAVE-U (Sensors and system Architecture for VulnerablE road Users protection). It has been funded by the European Commission (EC) in the period between 2002 and 2005 (5 th IST framework program). The goal of this project is to enhance the safety of pedestrians in hazardous traffic situations (see Figure 1) (3). To be able to do this, special active countermeasures (actuators) can be integrated into the vehicles. This paper deals with a sensors system which is able to deploy such actuators in critical situations in a suitable way for the driver. Radar sensors (SiemensVDO/ Germany), color cameras and infrared cameras (CEA/ France) mounted into demonstrator vehicles observe the scene in the frontal area. The information of the individual sensors is fused and applied to a deployment algorithm for a braking system. In case of a dangerous situation the vehicle brakes automatically to decrease the vehicle speed and to increase the safety of the pedestrian. Two car manufacturers (Volkswagen (see Figure 4) (3) and DaimlerChrysler (9), both Germany) equipped their cars with this sensor platform for recognizing pedestrians and developed algorithms to provide their individual protection strategy. Both vehicles are tested by MIRA/ UK. This paper presents the first results of tests with the SAVE-U system in the Volkswagen vehicle.
Inadequate Response to Adenosine Infusion During Cardiac Stress Magnetic Resonance Imaging

Aim: To determine the factors associated with an inadequate response to adenosine infusion during cardiac stress magnetic resonance imaging (MRI). Study Design: It is a retrospective cohort study. Introduction: Stress cardiac MRI is a highly accurate and non-invasive method to diagnose coronary artery disease (CAD). Stress MRI is performed by inducing stress with adenosine infusion. There is an increase in systemic and myocardial blood flow (MBF) with vasodilator agents. Capillaries are maximally dilated in a diseased artery and cannot sustain increased myocardial oxygen demand. It results in delayed delivery of contrast, which leads to an area of perfusion defect in the myocardium. These perfusion defects can be accurately seen by cardiovascular magnetic resonance (CMR) and help in the prognosis of patients. Methods: A retrospective study on patients subjected to cardiac stress MRI was conducted in a Tertiary Care Cardiac Center from January 2019 to January 2022. In total, 99 patients underwent adenosine stress perfusion cardiac MRI. All patients received an adenosine infusion of 140 mcg/kg/min for 2 min. Subsequently, the dosage was increased by 20 mcg/kg/min every 2 min to a maximum of 210 mcg/kg/min until an adequate stress response was achieved. Adequate stress was defined as two or more of the following criteria: 1) Increase in heart rate >/= 10 beats per minute. 2) Decrease in systolic blood pressure SBP by >/= 10 mm Hg Symptoms like chest discomfort, breathlessness, and headache. Patients who satisfied two or more of the above criteria were labeled as responders and the patients who did not satisfy the above criteria with the maximum dose of 210 mcg/kg/min of adenosine infusion were labeled as non-responders. Multivariable logistic regression analysis with forward and backward stepwise selection was used to identify predictors in non-responders. Basic demographic variables with P value </= 0.2 were examined for inclusion in the model. A P value </= 0.05 was considered significant. Results: Nine patients (9.1%) showed inadequate stress response to adenosine infusion even with a maximum dose of 210 mcg/kg/min. Multivariate logistic regression analysis showed that left ventricular end-diastolic volume (LVEDV) was a predictor of inadequate response to adenosine infusion. Conclusion: Inadequate stress response to adenosine occurred in 9.1% of subjects with an infusion of 140–210 ug/kg/min. LVEDV is an independent and strong predictor in non-responders.
Efficacy of Exercise on Muscle Function and Physical Performance in Older Adults with Sarcopenia: An Updated Systematic Review and Meta-Analysis

This study aimed to analyze the efficacy of exercise interventions on muscle strength, muscle mass, and physical performance in older adults with sarcopenia. Randomized controlled studies assessing exercise effects on sarcopenia were searched in Web of Science, PubMed, Cochrane Library, ProQuest, EBSCOhost, Scopus, EMBASE, and VIP and CNKI up to 31 March 2022. Data were expressed as weighted/standardized mean difference (MD/SMD) with 95% confidence intervals (CI). I2 index was employed for heterogeneity. The initial search identified 5379 studies, and 23 studies involving 1252 participants met the inclusion criteria for further analysis. Results revealed that exercise interventions can significantly improve grip strength (MD = 2.38, 95%CI = 1.33–3.43), knee extension strength (SMD = 0.50, 95%CI = 0.36–0.64), muscle mass of lower extremities (MD = 0.28, 95%CI = 0.01–0.56), walking speed (SMD = 0.88, 95%CI = 0.49–1.27), and functional mobility (MD = −1.77, 95%CI = −2.11–−1.42) among older adults with sarcopenia. No significant exercise effects were found on fat-free muscle mass, appendicular muscle mass, skeletal muscle mass, and muscle mass of the upper extremities. The results of subgroup analysis indicated that both resistance training and multicomponent exercise could significantly increase the muscle strength, while aerobic exercise did not. The findings suggest that exercise intervention can effectively improve muscle function and physical performance in older adults with sarcopenia, but has limited effects on the muscle mass of the upper extremities. In addition, it is highly recommended to apply group-based and supervised resistance training and multicomponent exercise in the prevention and treatment of sarcopenia among the older population.
Analytical Approach to Matching Layer Design for Electric Field Maximization in Biological Tissues

The electromagnetic waves transmission inside biological tissues can be useful in several biomedical applications, such as rehabilitation and microwave imaging. In this context, an important point is to design a matching layer to enhance the penetration of the electric field into a target tissue. Here we present an analytical method to design a matching layer under the near-field regime, i.e. when the electromagnetic source, as for instance a short dipole antenna, lies in the proximity of the body. In particular, two cases are examined: when the matching layer only consists of a dielectric slab, and when it is composed by a metasurface printed on a dielectric substrate. The proposed approach is based on the wave-transmission chain matrix and on the Schelkunoff’s definition of wave impedance to consider the source. The body is modeled as a multilayered planar medium. An optimization procedure based on a stochastic algorithm is applied to determine the parameters of the matching layer which could realize the maximum electric field transmission inside the muscle. These parameters are then used to simulate the overall system with a numerical software. The results show that the matching layer comprising the metasurface is the most effective solution in terms of electric field maximization and dimensions of the substrate.
Towards JavaScript program repair with Generative Pre-trained Transformer (GPT-2)

The goal of Automated Program Repair (APR) is to find a fix to software bugs, without human intervention. The so-called Gener-ate and Validate (G&V) approach deemed to be the most popular method in the last few years, where the APR tool creates a patch and it is validated against an oracle. Recent years for Natural Language Processing (NLP) were of great interest, with new pre-trained models shattering records on tasks ranging from sentiment analysis to question answering. Usually these deep learning models inspire the APR community as well. These approaches usually require a large dataset on which the model can be trained (or fine-tuned) and evaluated. The criterion to accept a patch depends on the underlying dataset, but usually the generated patch should be exactly the same as the one created by a human developer. As NLP models are more and more capable to form sentences, and the sentences will form coherent paragraphs, the APR tools are also better and better at generating syntactically and semantically correct source code. As the Generative Pre-trained Transformer (GPT) model is now avail-able to everyone thanks to the NLP and AI research community, it can be fine-tuned to specific tasks (not necessarily on natural language). In this work we use the GPT-2 model to generate source code, to the best of our knowledge, the GPT-2 model was not used for Automated Program Repair so far. The model is fine-tuned for a specific task: it has been taught to fix JavaScript bugs automatically. To do so, we trained the model on 16863JS code snippets, where it could learn the nature of the observed programming language. In our experiments we observed that the GPT-2 model was able to learn how to write syntactically correct source code almost on every attempt, although it failed to learn good bug-fixes in some cases. Nonetheless it was able to generate the correct fixes in most of the cases, resulting in an overall accuracy up to 17.25%.
Efficient Robot Motion Planning Using Bidirectional-Unidirectional RRT Extend Function

In this article, based on the rapidly-exploring random tree (RRT), we propose a novel and efficient motion planning algorithm using bidirectional RRT search. First, a RRT extend function is used to organize the sampled states under kinodynamic constraints. Meanwhile, the bidirectional search strategy is implemented to grow a forward tree and backward tree simultaneously in the tree extension process. When these two trees meet each other, the backward tree will act as a heuristic to guide the forward tree to continuously grow toward the goal state, where the algorithm switches to unidirectional search mode. Therefore, the two-point boundary value problem (BVP) in the connection process is avoided, and the extension process gets much accelerated. We also prove that probabilistic completeness is guaranteed. Numerical simulations are conducted to demonstrate that the proposed algorithm performs much better than the state-of-the-art algorithms in different environments. Note to Practitioners—The motivation of this work is to develop an efficient sampling-based motion planning algorithm for mobile robots. Conventional sampling-based algorithms are time-consuming to find a feasible solution under differential constraints. When applying bidirectional search strategy to improve them, the complex 2-point BVP is required to solve. In this article, the backward free is regarded as a heuristic to guide the tree growth. On the one hand, the advantage of bidirectional search is retained. On the other hand, the 2-point BVP is avoided. Therefore, the bidirectional-unidirectional technique can achieve efficient robot motion planning. The proposed algorithm can be extended to other specified sampling-based algorithms to further improve their performance. Besides, it can be also applied to autonomous driving, service robot and medical robots to achieve efficient motion planning.
Synergistic Antitumoral Effect of Epigenetic Inhibitors and Gemcitabine in Pancreatic Cancer Cells

Epigenetic modifications could drive some of the molecular events implicated in proliferation, drug resistance and metastasis of pancreatic ductal adenocarcinoma (PDAC). Thus, epigenetic enzyme inhibitors could be the key to revert those events and transform PDAC into a drug-sensitive tumor. We performed a systematic study with five different epigenetic enzyme inhibitors (1, UVI5008, MS275, psammaplin A, and BIX01294) targeting either Histone Deacetylase (HDAC) 1 or 1/4, DNA methyltransferase 3a (DNMT3a), Euchromatic histone lysine methyltransferase 2 (EHMT2), or Sirtuin 1 (SIRT1), as well as one drug that restores the p53 function (P53R3), in three different human PDAC cell lines (SKPC-1, MIA PaCa-2, and BxPC-3) using 2D and 3D cell cultures. The synergistic effect of these antitumoral drugs with gemcitabine was tested and the most efficient combinations were characterized by RNA-seq. The inhibition of HDAC1/4 (MS275), HDAC1/4/SIRT1/DNMT3a (UVI5008) or EHMT2 (BIX01294) induced a significant reduction on the cell viability, even in gemcitabine-resistance cells. The combination of UVI5008 or MS275 with gemcitabine induced a synergistic effect at low concentration and the RNA-Seq analysis revealed some synergy candidate genes as potential biomarkers. Reverting aberrant epigenetic modifications in combination with gemcitabine offers an alternative treatment for PDAC patients, with an important reduction of the therapeutic dose.
Rheological Behavior and Dynamic Mechanical Properties for Interpretation of Layer Adhesion in FDM 3D Printing

Commercial filaments of poly(lactic acid) (PLA) composites with particulate filler, carbon fiber, and copper powder with different contents were fabricated by FDM 3D printing in XZ-direction at bed temperatures of 45 °C and 60 °C. The effects of additives and bed temperatures on layer adhesion, fracture behavior, and mechanical performance of the PLA composites 3D printing were evaluated. Rheological properties informed viscous nature of all filaments and interface bonding in the PLA composites, which improved printability and dimensional stability of the 3D printing. Crystallinity of the PLA composites 3D printing increased with increasing bed temperature resulting in an improvement of storage modulus, tensile, and flexural properties. On the contrary, the ductility of the 3D printing was raised when printed at low bed temperature. Dynamic mechanical properties, the degree of entanglement, the adhesion factor, the effectiveness coefficient, the reinforcing efficiency factor, and the Cole–Cole analysis were used to understand the layer adhesion, and the interfacial interaction of the composites as compared to the compression molded sheets. SEM images revealed good adhesion between the additives and the PLA matrix. However, the additives induced faster solidification and showed larger voids in the 3D printing, which indicated lower layer adhesion as compared to neat PLA. It can be noted that the combination of the additives and the optimized 3D printing conditions would be obtain superior mechanical performance even layer adhesion has been restricted.
Complex IgE sensitization patterns in ragweed allergic patients: Implications for diagnosis and specific immunotherapy

Abstract Background Ragweed (Ambrosia artemisiifolia) is one of the most important allergen sources, worldwide, causing severe respiratory allergic reactions in late summer and fall, in sensitized patients. Amb a 1 has been considered as the most important allergen in ragweed but 12 ragweed pollen allergens are known. The aim of our study was to investigate IgE reactivity profiles of ragweed allergic patients and to associate them with clinical symptoms. Methods IgE sensitization profiles from clinically well‐characterized ragweed allergic patients (n = 150) were analyzed using immunoblotted ragweed pollen extract. Immunoblot inhibition experiments were performed with two Amb a 1 isoforms and CCD markers and basophil activation experiments were performed with IgE serum before and after depletion of Amb a 1‐specific IgE. Results By IgE‐immunoblotting 19 different IgE reactivity patterns with and without Amb a 1‐sensitization were found. The majority of patients (>95%) suffered from rhino‐conjunctivitis, around 60% reported asthma‐like symptoms and about 25% had skin reactions. Patients with complex IgE sensitization profiles tended to have more clinical symptoms. Serum with and without Amb a 1‐specific IgE induced basophil activation. Conclusions Ragweed pollen allergic patients exhibit complex IgE reactivity profiles to ragweed allergens including Amb a 1 isoforms and cross‐reactive carbohydrates indicating the importance of Amb a 1 isoforms and additional allergens for diagnosis and allergen‐specific immunotherapy of ragweed allergy.