Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural network-based taxonomic clustering for metagenomics

Metagenomic studies inherently involve sampling genetic information from an environment potentially containing thousands of distinctly different microbial organisms. This genetic information is sequenced producing many short fragments (<500 base pair (bp)); each is tentatively a small representative of the DNA coding structure. Any of the fragments may belong to any of the organisms in the sample, but the relationship is unknown a priori. Furthermore, most of these organisms have not been identified and correspondingly are not represented in any of the publicly available search databases. Our goal is to be able to predict the taxonomic classification of an organism based on the fragments obtained from an environmental sample that may include many (some previously unidentified) organisms. To elucidate the diversity and composition of the sample, we first use a supervised naïve Bayes classifier to score the fragments of known genomes, followed by an unsupervised clustering to group fragments from similar organisms together. We are then free to analyze each cluster separately. This is challenging since we are not interested in similar sequences, but sequences that come from similar genomes, which are known to vary widely intra-genomically. Our dataset comprises of an extremely challenging scenario involving clustering fragments at the phyla level, where none of the phyla have been previously seen or identified. We present two variations of our proposed approach, one based on ART and K-means. We show that ART can cluster 500bp fragments from 17 novel phyla at an overall isolation/grouping that is 10% better than K-means and nearly 7 times over chance.
Behavior of sandwich wall panels with GFRP face sheets and a foam-GFRP web core loaded under four-point bending

In this paper, a simple and innovative sandwich panel with GFRP face sheets and a foam-GFRP web core (GFFW panels) is developed. An experimental study was carried out to validate the effectiveness of this panel for increasing the bending strength. The effects of web thickness, web spacing, web height and face sheet thickness on bending stiffness and energy dissipation were also investigated. Test results demonstrate that compared to the normal foam-core sandwich panels, a maximum of approximately 640% increase in the ultimate bending strength can be achieved. Meanwhile, the bending stiffness and energy dissipation can be enhanced by increasing web thickness, web height and face sheet thickness. An analytical model was developed to predict the ultimate bending strength of GFFW panels. The formulae to calculate the equivalent bending stiffness, shear modulus and mid-span deflection were also derived. A comparison of the analytical and experimental results showed that the analytical model accurately predicted the ultimate bending strengths and min-span deflections of the GFFW panels under four-point bending. Furthermore, the finite element analysis was extended to nvestigate the effects of foam density and shear span-to-depth ratio which were not considered in the tests. The numerical results revealed that increasing foam density and decreasing the shear span-to-depth ratio can improve the bending strength and stiffness of the panels.
Pose estimation and trajectory derivation from underwater imagery

Obtaining underwater imagery is normally a costly affair since expensive equipment such as multi-beam sonar scanners need to be utilized. Even though such scanners provide imagery in form of 3D point clouds, the tasks of locating accurate and dependable correspondences between point clouds and registration can be quite slow. Registered 3D point clouds can provide pose estimation and trajectory information vital to the navigation of a robot, however, the slow speed of point cloud registration normally means that maps are generated offline for later use. Furthermore, any algorithm must be robust against artifacts in 3D range data as sensor motion, reflection and refraction are commonplace. In our work we describe the use of the SIFT feature detector on scaled images based on point clouds captured by sonar in order to register them in real-time. This online registration approach is used to derive navigational information vital to underwater vehicles. The algorithm utilizes the known point correspondence registration algorithm in order to achieve real-time registration of point clouds, thereby generating 3D maps in real-time and providing 3D pose estimation and trajectory information.
RELAX-IV : a faster version of the RELAX code for solving minimum cost flow problems

The structure of dual ascent methods is particularly well-suited for taking advantage of good initial dual solutions of minimum cost flow problems. For this reason, these methods are extremely efficient for reoptimization and sensitivity analysis. In the absence of prior knowledge of a good initial dual solution, one may attempt to find such a solution by means of a heuristic initialization. RELAX-IV is a minimum cost flow code that combines the RELAX code of [BeT88a], [BeT88b] with an initialization based on a recently proposed auction/sequential shortest path algorithm. This initialization is shown to be extremely helpful in speeding up the solution of difficult problems, involving for example long augmenting paths, for which the relaxation method has been known to be slow. On the other hand, this initialization procedure does not significantly deteriorate the performance of the relaxation method for the types of problems where it has been known to be very fast.
Conjectural Variation-Based Bidding Strategies with Q-Learning in Electricity Markets

A novel conjectural variation-based bidding strategy combined with a Q-learning algorithm is presented in this paper. Generation companies are modeled as adaptive agents in the electricity markets. Conjectural variation is introduced to model rivals' reaction to one generation company's bidding strategy. Q-learning is used to model the bidding behavior of generation companies that can learn and adjust their strategies over time. SA-Q-learning algorithm with Metropolis criterion is applied to balance exploitation and exploration in the reinforcement learning process. A series of stage games represented by short-term market clearings form a repeated game for generation companies. Interactions among market participants can be studied accordingly by the proposed agent-based simulation approach. Case studies demonstrate the learning process and corresponding equilibriums.
Polyacrylic acid/poly(vinyl sulfonic acid, sodium salt) copolymer hydrogel actuator under an electric field

Random copolymer hydrogel actuators, composed of poly(acrylic acid) and poly(vinyl sulfonic acid, sodium salt), were prepared. The swelling ratios at various temperatures and pHs, the deswelling water ratio and contraction/expansion behavior under an electric field for the hydrogel actuators were measured. The hydrogels exhibited very high swelling ratios, in the range of 8200 ~ 18000%, at 37 °C, and showed temperature/pH dependent swelling behavior. The deswelling water ratio of the CO1 hydrogel sample showed about an 80% weight reduction under a 5 V applied voltage. When the hydrogel actuator in various pH buffer solutions is subjected to an electric field, the hydrogel actuator was contracted. When the electric stimulus was removed, the hydrogel actuator was expanded on its original size. The hydrogel actuator also showed stepwise contraction/expansion behavior depending on the electric stimulus.
When countries do not do what they say: Systematic discrepancies between exchange rate regime announcements and de facto policies

We study the apparent disconnect between what countries announce to be their exchange rate regime and what they de facto implement. Even though discrepancies between announcements and de facto polices are frequent, there is a lack of understanding of actual patterns and underlying reasons. We contribute to the literature by identifying a number of robust stylized facts by means of an in-depth analysis of a large cross-country dataset. A key insight is that countries that operate under intermediate de facto regimes tend to announce fixed or flexible exchange rate regimes. The exact nature of deviations is related to country characteristics such as trade structure, financial development, and financial openness. Furthermore, regime discrepancies have followed secular trends, which are most likely related to financial globalization and changes in monetary policy design.
Thermomagnetic instability and correlated deformation in the type-II superconducting films

Flux avalanches and it induced thermal stress (strain) in the superconducting film is investigated. Numerical simulation of the nonlinear and nonlocal electromagnetics of superconductors are performed by using the iteration scheme based on the fast Fourier transform technique. Local thermal stress and strain causing by the sharp increase of temperature during the dendritic avalanche process are obtained for the superconducting film subjected to an increasing magnetic field.
PEpiD: A Prostate Epigenetic Database in Mammals

Epigenetic mechanisms play key roles in initiation and progression of prostate cancer by changing gene expression. The Prostate Epigenetic Database (PEpiD: http://wukong.tongji.edu.cn/pepid) archives the three extensively characterized epigenetic mechanisms DNA methylation, histone modification, and microRNA implicated in prostate cancer of human, mouse, and rat. PEpiD uses a distinct color scheme to present the three types of epigenetic data and provides a user-friendly interface for flexible query. The retrieved information includes Refseq ID, gene symbol, gene alias, genomic loci of epigenetic changes, tissue source, experimental method, and supportive references. The change of histone modification (hyper or hypo) and the corresponding gene expression change (up or down) are also indicated. A graphic view of DNA methylation with exon-intron structure and predicted CpG islands is provided as well. Moreover, the prostate-related ENCODE tracks (DNA methylation, histone modifications, chromatin remodelers), and other key transcription factors with reported roles in prostate are displayed in the browser as well. The reversibility of epigenetic aberrations has made them potential markers for diagnosis and prognosis, and targets for treatment of cancers. This curated information will improve our understanding of epigenetic mechanisms of gene regulation in prostate cancer, and serve as an important resource for epigenetic research in prostate cancer.
Motion blur kernel estimation via salient edges and low rank prior

Blind image deblurring, i.e., estimating a blur kernel from a single input blurred image is a severely ill-posed problem. In this paper, we show how to effectively apply low rank prior to blind image deblurring and then propose a new algorithm which combines salient edges and low rank prior. Salient edges provide reliable edge information for kernel estimation, while low rank prior provides data-authentic priors for the latent image. When estimating the kernel, the salient edges are extracted from an intermediate latent image solved by combining the predicted edges and low rank prior, which help preserve more useful edges than previous deconvolution methods do. By solving the blind image deblurring problem in this fashion, high-quality blur kernels can be obtained. Extensive experiments testify to the superiority of the proposed method over state-of-the-art algorithms, both qualitatively and quantitatively.
Volatile constituents and antioxidant activity of flowers, stems and leaves of Nasturtium officinale R. Br.

GC–MS analyses of the essential oils of leaves, stems and flower of Nasturtium officinale resulted in the identification of 9, 8 and 15 compounds, representing 97%, 100% and 94.7% of the oils, respectively. The main compounds of the oil of leaves were myristicin (57.6%), α-terpinolene (8.9%) and limonene (6.7%). Caryophyllene oxide (37.2%), p-cymene-8-ol (17.6%), α-terpinolene (15.2%) and limonene (11.8%) were the main components in stems, whereas limonene (43.6%), α-terpinolene (19.7%), p-cymene-8-ol (7.6%) and caryophyllene oxide (6.7%) were the major constituents in the oil of flowers. All the samples were subjected to a screening for their possible antioxidant activities using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and β-carotene-linoleic acid assays. In the above tests, methanol extracts of leaves showed higher antioxidant activity than the oils and methanol extracts of stems and flowers.
Membrane Modification : Technology and Applications

Membranes in Nuclear Science and Technology: Membrane Modification as a Tool for Performance Improvement Grazyna Zakrzewska-Trznadel and Mohamed Khayet Use of Impedance Spectroscopy for Characterization of Modified Membranes Juana Benavente Reduction of Membrane Fouling by Polymer Surface Modification Victor Kochkodan Modifications of Polymeric Membranes by Incorporating Metal/Metal Oxide Nanoparticles Law Yong Ng, Abdul Wahab Mohammad, and Nidal Hilal Development of Antifouling Properties and Performance of Nanofiltration Membranes by Interfacial Polymerization and Photografting Techniques Mazrul N. Abu Seman, Mohamed Khayet, and Nidal Hilal Integrating Hydrophobic Surface-Modifying Macromolecules into Hydrophilic Polymers to Produce Membranes for Membrane Distillation Mohammed Qtaishat, Mohamed Khayet, and Takeshi Matsuura Plasma Modification of Polymer Membranes Marek Bryjak and Irena Gancarz Surface Modification of Electrospun Nanofiber and Nanofibrous Membranes Carmen Garcia-Payo and Mohamed Khayet Development of Membranes for Pervaporation by Membrane Surface Modification and Incorporation of Inorganic Particles Kailash Chandra Khulbe, Chaoyang Y. Feng, and Takeshi Matsuura Tailor-Made Polymeric Membranes for Advanced Crystallization of Biomolecules Efrem Curcio, Enrica Fontananova, and Gianluca Di Profio Chemical Cross-Linking Modifications of Polymeric Membranes for Gas Separation Applications Ahmad Fauzi Ismail and Farhana Aziz Development of Fuel Cell Polymer Electrolyte Membranes by Radiation-Induced Grafting with Electron-Beam Irradiation Mohamed Mahmoud Nasef Modification of Sulfonated Poly(Ether Ether Ketone) for DMFC Application Ahmed Fauzi Ismail, Mohammad Noorul Anam Norddin, Juhana Jaafar, and Takeshi Matsuura Nanofiltration Membrane in Textile Effluent Treatment Ahmad Fauzi Ismail and Woei Jye Laua Future Prospects Nidal Hilal, Mohamed Khayet, and Chris J. Wright
PBN: towards practical activity recognition using smartphone-based body sensor networks

The vast array of small wireless sensors is a boon to body sensor network applications, especially in the context awareness and activity recognition arena. However, most activity recognition deployments and applications are challenged to provide personal control and practical functionality for everyday use. We argue that activity recognition for mobile devices must meet several goals in order to provide a practical solution: user friendly hardware and software, accurate and efficient classification, and reduced reliance on ground truth. To meet these challenges, we present PBN: Practical Body Networking. Through the unification of TinyOS motes and Android smartphones, we combine the sensing power of on-body wireless sensors with the additional sensing power, computational resources, and user-friendly interface of an Android smartphone. We provide an accurate and efficient classification approach through the use of ensemble learning. We explore the properties of different sensors and sensor data to further improve classification efficiency and reduce reliance on user annotated ground truth. We evaluate our PBN system with multiple subjects over a two week period and demonstrate that the system is easy to use, accurate, and appropriate for mobile devices.
Comparison of a 4-Day versus 2-Day Low Fiber Diet Regimen in Barium Tagging CT Colonography in Incomplete Colonoscopy Patients

Our aim was to compare the amount of residual feces, residual fluid, the tagging quality, and patient compliance using 4-day versus 2-day low fiber diet regimen in barium tagging CT colonography in incomplete colonoscopy patients. Methods. A total of 101 patients who underwent CT colonography were assigned to 2-day diet group (n = 56) and 4-day diet group (n = 45). Fecal tagging was achieved with barium sulphate while bisacodyl and sennoside B were used for bowel preparation. Residual solid stool was divided into two groups measuring <6 mm and ≥6 mm. We graded the residual fluid, tagging quality for solid stool, and fluid per bowel segment. We performed a questionnaire to assess patient compliance. Results. 604 bowel segments were evaluated. There was no significant difference between 2-day and 4-day diet groups with respect to residual solid stool, residual fluid, tagging quality for stool, and fluid observed in fecal tag CT colonography (P > 0.05). The prevalence of moderate discomfort was significantly higher in 4-day group (P < 0.001). Conclusion. Our study shows that 2-day limited bowel preparation regimen for fecal tag CT colonography is a safe and reasonable technique to evaluate the entire colon, particularly in incomplete conventional colonoscopy patients.
Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin

Significance The Microrchidia (MORC) family of ATPases are important regulators of gene silencing in multiple organisms but little is known about their molecular behavior. In this study, we used crystallography and native mass spectrometry to show that MORC3 forms dimers when it binds to nonhydrolyzable ATP analogues. We also determined that the CW zinc finger-like domain of MORC3 can bind euchromatic histone H3 lysine 4 (H3K4) methylation and that MORC3 localizes to H3K4me3-marked chromatin. The MORC3 crystal structure provides details as to the intermolecular interactions that allow dimerization and the binding to ATP and histones. This work reveals key molecular activities of MORC3 that might apply to other MORC family members in eukaryotic organisms. Microrchidia (MORC) proteins are GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPases that function in gene regulation in multiple organisms. Animal MORCs also contain CW-type zinc finger domains, which are known to bind to modified histones. We solved the crystal structure of the murine MORC3 ATPase-CW domain bound to the nucleotide analog AMPPNP (phosphoaminophosphonic acid-adenylate ester) and in complex with a trimethylated histone H3 lysine 4 (H3K4) peptide (H3K4me3). We observed that the MORC3 N-terminal ATPase domain forms a dimer when bound to AMPPNP. We used native mass spectrometry to show that dimerization is ATP-dependent, and that dimer formation is enhanced in the presence of nonhydrolyzable ATP analogs. The CW domain uses an aromatic cage to bind trimethylated Lys4 and forms extensive hydrogen bonds with the H3 tail. We found that MORC3 localizes to promoters marked by H3K4me3 throughout the genome, consistent with its binding to H3K4me3 in vitro. Our work sheds light on aspects of the molecular dynamics and function of MORC3.
Binary recombinase systems for high-resolution conditional mutagenesis

Conditional mutagenesis using Cre recombinase expressed from tissue specific promoters facilitates analyses of gene function and cell lineage tracing. Here, we describe two novel dual-promoter-driven conditional mutagenesis systems designed for greater accuracy and optimal efficiency of recombination. Co-Driver employs a recombinase cascade of Dre and Dre-respondent Cre, which processes loxP-flanked alleles only when both recombinases are expressed in a predetermined temporal sequence. This unique property makes Co-Driver ideal for sequential lineage tracing studies aimed at unraveling the relationships between cellular precursors and mature cell types. Co-InCre was designed for highly efficient intersectional conditional transgenesis. It relies on highly active trans-splicing inteins and promoters with simultaneous transcriptional activity to reconstitute Cre recombinase from two inactive precursor fragments. By generating native Cre, Co-InCre attains recombination rates that exceed all other binary SSR systems evaluated in this study. Both Co-Driver and Co-InCre significantly extend the utility of existing Cre-responsive alleles.
XPath whole query optimization

Previous work reports about SXSI, a fast XPath engine which executes tree automata over compressed XML indexes. Here, reasons are investigated why SXSI is so fast. It is shown that tree automata can be used as a general framework for fine grained XML query optimization. We define the "relevant nodes" of a query as those nodes that a minimal automaton must touch in order to answer the query. This notion allows to skip many subtrees during execution, and, with the help of particular tree indexes, even allows to skip internal nodes of the tree. We efficiently approximate runs over relevant nodes by means of on-the-fly removal of alternation and non-determinism of (alternating) tree automata. We also introduce many implementation techniques which allows us to efficiently evaluate tree automata, even in the absence of special indexes. Through extensive experiments, we demonstrate the impact of the different optimization techniques.
A Chosen-IV Key Recovery Attack on Py and Pypy

In this paper, we propose an effective key recovery attack on stream ciphers Py and Pypy with chosen IVs. Our method uses an internal-state correlation based on the vulnerability that the randomization of the internal state in the KSA is inadequate, and it improves two previous attacks proposed by Wu and Preneel (a WP-1 attack and a WP-2 attack). For a 128-bit key and a 128-bit IV, the WP-1 attack can recover a key with 223 chosen IVs and time complexity 272. First, we improve the WP-1 attack by using the internal-state correlation (called a P-1 attack). For a 128-bit key and a 128-bit IV, the P-1 attack can recover a key with 223 chosen IVs and time complexity 248, which is 1/224 of that of the WP-1 attack. The WP-2 attack is another improvement on the WP-1 attack, and it has been known as the best previous attack against Py and Pypy. For a 128-bit key and a 128-bit IV, the WP-2 attack can recover a key with 223 chosen IVs and time complexity 224. Second, we improve the WP-2 attack by using the internal-state correlation as well as the P-1 attack (called a P-2 attack). For a 128-bit key and a 128-bit IV, the P-2 attack can recover a key with 223 chosen IVs and time complexity 224, which is the same capability as that of the WP-2 attack. However, when the IV size is from 64bits to 120bits, the P-2 attack is more effective than the WP-2 attack. Thus, the P-2 attack is the known best attack against Py and Pypy.
Changes in the Reflux Symptom Index After Multilevel Surgery for Obstructive Sleep Apnea

Objectives This study evaluated whether the symptoms of laryngopharyngeal reflux (LPR) change after multilevel surgery for obstructive sleep apnea (OSA). Methods Patients who underwent multilevel surgery for OSA between April 2009 and September 2014 were enrolled in this study. All patients underwent preoperative polysomnography prior to surgery and were asked to complete the reflux symptom index (RSI) questionnaire before and after surgery. Results Of 73 enrolled patients, 24 (33%) reported an RSI score >13 and were thus classified as having reflux. The mean RSI score before surgery was 11.48±7.95; this number decreased to 4.95±6.19 after surgery (P<0.001). The rate of positive RSI responses was 33% before surgery and 9% after surgery. Each variable that comprised the RSI improved significantly after surgery, except for difficulty with swallowing. Regarding the degree of RSI improvement after surgery, there were no significant differences between subgroups according to sex, age, body mass index, OSA severity, or surgical outcome. Conclusion LPR symptoms are prevalent in OSA patients. Treatment for OSA using multilevel surgery potentially reduces the symptoms of LPR.