Miracle-dz/UniFAR-FTUs huggingface dataset:
CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices

K-mer based methods are used ubiquitously in the field of computational biology. However, determining the optimal value of k for a specific application often remains heuristic. Simply reconstructing a new k-mer set with another k-mer size is computationally expensive, especially in metagenomic analysis where data sets are large. Here, we introduce a hashing-based technique that leverages a kind of bottom-m sketch as well as a k-mer ternary search tree (KTST) to obtain k-mer based similarity estimates for a range of k values. By truncating k-mers stored in a pre-built KTST with a large k = kmax value, we can simultaneously obtain k-mer based estimates for all k values up to kmax. This truncation approach circumvents the reconstruction of new k-mer sets when changing k values, making analysis more time and space-efficient. For example, we show that when using a KTST to estimate the containment index between a RefSeq-based microbial reference database and simulated metagenome data for 10 values of k, the running time is close to 10x faster compared to a classic MinHash approach while using less than one-fifth the space to store the data structure. A python implementation of this method, CMash, is available at https://github.com/dkoslicki/CMash. The reproduction of all experiments presented herein can be accessed via https://github.com/KoslickiLab/CMASH-reproducibles.
Fiber composite materials via coaxial, dual or blend electrospinning

Abstract Electrospinning (ES) is a suitable and cost effective method to mimic the chemical composition, morphology, and functional surface of natural tissues, for example of the nervous, dermal, vascular, and musculoskeletal systems. This technique is a versatile tool to obtain tailored fibrous scaffolds from various polymer materials. By varying the diameter, porosity, orientation, layering, surface structuring, mechanical properties and biodegradability of the fibers the properties can be adapted for specific applications ranging from implantable medical devices to wound repair and protective clothing. Especially the combination of different polymer types offers a high potential. In this study electrospun two-component nonwoven structures of thermoplastic copolyester elastomer (TPC-ET) and bioresorbable polylactide (PLLA) were fabricated, using different ES setups. A comparative evaluation in terms of porosity, thermal and mechanical properties as well as required fabrication effort, was performed. Nonwovens made from polymer blends and coaxial spun core-sheath fibers showed similar tensile strength, which was higher than dual electrospun fabrics. Porosity was found to be in the range of 80 - 90%. By modifying the polymer solution and process parameters multicomponent nonwoven structures with tailored properties and drug release profiles can be manufactured.
Revised International Staging System (R-ISS) stage-dependent analysis uncovers oncogenes and potential immunotherapeutic targets in multiple myeloma (MM)

Multiple myeloma (MM) accounts for ~10% of all haematologic malignancies. Little is known about high intratumour heterogeneities in patients stratified by the Revised International Staging System (R-ISS). Herein, we constructed a single-cell transcriptome atlas to compare differential expression patterns among stages. We found that a novel cytotoxic plasma cell (PC) population exhibited with NKG7 positive was obviously enriched in stage II patients. Additionally, a malignant PC population with significantly elevated expression of MKI67 and PCNA was associated with unfavourable prognosis and Epstein-Barr virus (EBV) infection in our collected samples. Moreover, ribonucleotide reductase regulatory subunit M2 (RRM2) was found and verified to promote proliferation of MM cell lines, suggesting RRM2 may serve as a detrimental marker in MM. The percentages of CD8+ T cells and NKT cells decreased along with R-ISS stages, reflecting the plasticity of the tumour immune microenvironment. Importantly, their crosstalks with myeloid cells and PC identified several potential immunotargets such as SIRPA-CD47 and CD74-MIF, respectively. Collectively, this study provided an R-ISS-related single-cell MM atlas and revealed the clinical significance of novel PC clusters, as well as potential immunotargets in MM progression.
LEXAS: a web application for life science experiment search and suggestion

Motivation In cellular biology, researchers design wet experiments by reading the relevant articles and considering the described experiments and results. Today, researchers spend a long time exploring the literature in order to plan experiments. Results To accelerate experiment planning, we have developed a web application named LEXAS (Life-science EXperiment seArch and Suggestion). LEXAS curates the description of biomedical experiments and suggests the experiments on genes that could be performed next. To develop LEXAS, we first retrieved the descriptions of experiments from full-text biomedical articles archived in PubMed Central. Using these retrieved experiments and biomedical knowledgebases and databases, we trained a machine learning model that suggests the next experiments. This model can suggest not only reasonable genes but also novel genes as targets for the next experiment as long as they share some critical features with the gene of interest. Availability and implementation LEXAS is available at https://lexas.f. u-tokyo.ac. jp/ and provides users with two interfaces: search and suggestion. The search interface allows users to find a comprehensive list of experiment descriptions, and the suggestion interface allows users to find a list of genes that could be analyzed along with possible experiment methods. The source code is available at https://github.com/lexas-f-utokyo/lexas. Contact ito-delightfully-kei@g.ecc. u-tokyo.ac. jp Supplementary information Supplementary data are available at Bioinformatics online.
A STUDY MODEL ON THE IMPACT OF VARIOUS INDICATORS IN THE PERFORMANCE OF STUDENTS IN HIGHER EDUCATION

In this technology revolutionized century knowledge has become a vital resource. Also, Education has been viewed as a crucial factor in contributing to the welfare of the country. Higher education does categorize the students by their academic performance. In higher education institutions a substantial amount of knowledge is hidden and need to be extracted using Knowledge Discovery process. Data mining helps to extract the knowledge from available dataset and should be created as knowledge intelligence for the benefit of the institution. Many factors influence the academic performance of the student. The study model is mainly focused on exploring various indicators that have an effect on the academic performance of the students. The study result shows the impact of various factors affecting the students of higher education system. The extracted information that describes student performance can be stored as intelligent knowledge for decision making to improve the quality of education in institutions.
Center Impedance Method for Damping Measurement

Damping materials are used extensively for reduction of vibration and noise. These damping materials have viscoelastic characteristics and are used by automotive and other industries. Testing of these materials is important in order to predict their performance and traditionally the damping properties are measured by the Oberst method. This paper discusses an alternate method called the Center Impedance method where force and response are measured directly and the damping properties are obtained. The Center Impedance method is easy to use requiring only standard vibration equipment for excitation, namely, shaker, and is easy to control the experiment for repeatability. Results of beams tested by both Oberst and Center Impedance methods are presented in order to validate this test method.
Traditional versus Neural Network Classification Methods for Facial Emotion Recognition

Abstract Facial emotion recognition (FER) is a topic that has gained interest over the years for its role in bridging the gap between Human and Machine interactions. This study explores the potential of real time FER modelling, to be integrated in a closed loop system, to help in treatment of children suffering from Autism Spectrum Disorder (ASD). The aim of this study is to show the differences between implementing Traditional machine learning and Deep learning approaches for FER modelling. Two classification approaches were taken, the first approach was based on classic machine learning techniques using Histogram of Oriented Gradients (HOG) for feature extraction, with a k-Nearest Neighbor and a Support Vector Machine model as classifiers. The second approach uses Transfer Learning based on the popular “Alex Net” Neural Network architecture. The performance of the approaches was based on the accuracy of randomly selected validation sets after training on random training sets of the Oulu-CASIA database. The data analyzed shows that traditional machine learning methods are as effective as deep neural net models and are a good compromise between accuracy, extracted features, computational speed and costs.
Microchip Transfer Process for Implantable Flexible Bioelectronic Devices

Abstract The demands on flexible implants for recording of neural signals and electrical stimulating have increased in recent years with regard to their functionality, miniaturization, and spatial resolution. These requirements can be met best by embedding powerful complementary metal oxide semiconductor (CMOS) microchips into thin biocompatible polymer substrates. So-called chip-in-foil systems thus combine mechanical properties of a polymer substrate and performance of CMOS technology. The development of a process for direct transfer of multiple CMOS microchips (edge length <400 μm) simultaneously into thin polyimide (PI) substrates is subject of this study. It allows the use of standard microelectromechanical systems (MEMS) processes for further levelled superficial layer build-up. This is achieved with the help of a silicon carrier wafer equipped with cavities for precise chip placement and a sacrificial layer to facilitate release of the chip-in-foil systems. In a post-processing step all silicon chips are thinned down to 100 μm. With this process a transfer yield of 100 % (n = 34) was achieved for the silicon chips on a die level. Chip rotational error on substrates was determined to be as low as 0.21° ± 0.10°. Die adhesion was examined by shear tests, resulting in shear strength of 58.1 MPa ± 13.7 MPa, which dropped to 15.2 MPa ± 10.5 MPa after accelerated ageing in 60 °C phosphate buffered saline solution (PBS) for 16 days (equivalent to 78 days at 37 °C). This study demonstrated a reliable microchip transfer process with low positioning error into flexible PI substrates with post-processing thinning of the dies. The use of a carrier silicon wafer allowed precise electrical interconnect fabrication with standard MEMS processing techniques and without handling of thin and fragile chips. These results are a prerequisite to meet needs of reliability and structural biocompatibility in implantable flexible bioelectronic devices.
Finite Element Modelling of a Hearing Contact Lens Coupled to the Middle Ear

Abstract Hearing contact lens (HCL) is a new type of hearing aid devices. One of its main components is a piezoelectric actuator (PEA). In order to evaluate and maximize the HCL’s performance, a model of the HCL coupled to the middle ear was developed using finite element (FE) approach. To validate the model, vibrational measurements on the HCL and temporal bones were performed using a Laser-Doppler-Vibrometer (LDV). The model was validated step by step starting with HCL only. Then a silicone cap was fitted onto the HCL to provide an interface between the HCL and the tympanic membrane. The HCL was placed on the tympanic membrane and additional measurements were performed to validate the coupled model. The model was used to evaluate the sensitivity of geometrical and material parameters with respect to performance measures of the HCL. Moreover, deeper insight was gained into the feedback behavior, which causes whistling sounds, and the contact between the HCL and tympanic membrane.
Evaluation of Streptococcus oralis adhesion and biofilm formation on laser-processed titanium

Abstract To prevent implant-associated infections, surface modifications need to be developed that prevent bacterial colonisation and biofilm formation. In the present study, titanium surfaces were processed by nanosecond-pulsed laser ablation to generate a variety of different structures (anatase, rutile, Osteon, as well as Osteon additionally coated with silver and clove nanoparticles). Analysis of adhesion and biofilm formation of the oral pioneer bacterium Streptococcus oralis could demonstrate antibacterial properties of anatase surfaces. For clinical translation, the effect should be enhanced by further adaption and combined with the osseointegrative Osteon structure
Computation analysis and optimal design of a high speed response and low power micro valve

This study was conducted to analyze the special quality of a very low power consumption type of pneumatic on-off micro valve, and to numerically investigate its flow characteristic depending upon a change in stroke. As a result, it was identified that an enough electromagnetic force (2.4N) acted on the solenoid so that the poppet of the micro valve might run a stroke (0.3 mm) at the high response speed (5ms), and that the yoke caused no magnetic force to be emitted. It was identified that the dynamic presstre acting on the poppet wall was little reduced when the poppet stroke was 0.4 mm or less, but that as it got to be beyond 0.4 mm, it was remarkably reduced and when it was 0.8mm, it went down to 40%.
Incentives to Licence Virtual Mobile Network Operators (MVNOs)

A vivid debate about the intensity of competition in mobile telecommunications markets has recently emerged in many jurisdictions. Given that radio spectrum is a scarce resource which limits the number of mobile network operators (MNOs) that can use their own radio spectrum to provide services, one idea has been to require MNOs to sell or lease spare spectrum capacities to so-called mobile virtual network operators (MVNOs), i.e. operators that provide mobile communications services without their own radio spectrum. One aspect of this policy debate is on the appropriate regulatory framework: Should MNOs be required by regulation to open up their networks for MVNOs and if so, under which terms and conditions? Or, are the MNOs’ incentives to rent out their spare capacities sufficient to facilitate entry by MVNOs? In January 2006, for example, the European Commission has answered the latter question with a "no" and endorsed a measure proposed by the Spanish national regulator, CMT, to regulate access to the networks of the three Spanish MNOs (Telefonica, Vodafone, and Armena) by MVNOs (see European Commission, 2006). Both the European Commission and the Spanish regulator CMT consider the current state of competition in the Spanish mobile telecommunications market to be unsatisfactory, and both authorities expect MVNOs to intensify competition in that market.
Dynamic Deflection of a Bridge versus Speed of Vehicle Motion

The vehicle-bridge interaction (VBI) is the actual problem of many work places. The mid-span deflection of a bridge versus speed vehicle motion is interested from a practical point of view. Within the solution of the task the numerical methods based on Finite Element Method (FEM) are applied mainly. The task of VBI described in the submitted article is solved by using commercial software ANSYS. The 2-D sprung model of vehicle is modeled as combination of mass, spring and beam elements. The bridge with the mid-range is modeled by simple beam created with beam elements.
The differential analysis for temperature distribution diagnostics of arc current-carrying region in sheet slanting tungsten electrode inert gas welding with the electrostatic probe

Abstract An electrostatic probe differential analysis method is used to diagnose the arc current-carrying region of the sheet slanting tungsten electrode. Based on the local thermal equilibrium condition and energy transition model with charged particles collision, the temperature distribution in the current-carrying region of different welding process parameters is solved by saturated ion current. The results show that the temperature distribution range in the width direction of sheet slanting tungsten electrode expands, the arc high-temperature region shifts integrally, and the temperature in the thickness direction of sheet slanting tungsten electrode would be symmetrical. The guide effect of the hypotenuse of sheet slanting tungsten electrode for arc current and the inertia drag effect of arc would mainly change the temperature distribution. The variation of the inclination angle of the hypotenuse of sheet slanting tungsten electrode will aggravate the shift of the arc high-temperature region. The larger inclination angle will enhance the guiding effect, and then the inertia drag effect would be in a dominant position with a smaller inclination angle. With the increase of welding current, both the arc stiffness and the guiding effect would be intensified, the latter should make the arc high-temperature zone shift to the position with a small discharge gap.
Design Optimization and Performance of a Novel 6-Slot 5-Pole PMFSM with Hybrid Excitation for Hybrid Electric Vehicle

With growing concerns over our environment, more and more people in automakers, governments and customers think that the electric drive becomes more attractive research. Since electric motors play an important role in both EVs and HEVs, it is a pressing need for researchers to develop advanced electric machines. As one of the candidates, permanent magnet flux switching machine (PMFSM) with additional coil excitation has several attractive features compared to interior permanent magnet synchronous machines (IPMSM) conventionally employed in HEV. The variable flux control capability and robust rotor structure make this machine becoming more attractive to apply for high speed motor drive system coupled with reduction gear. This paper presents an investigation into design possibility of 6-slot 5-pole PMFSM with hybrid excitation for traction drives in HEVs. An improved design is examined to gain a better performance in its maximum torque and power production. The final designed machine enables to keep much power density compared to existing IPMSM installed on the commercial SUV-HEV.
Long Non-coding RNAs Gabarapl2 and Chrnb2 Positively Regulate Inflammatory Signaling in a Mouse Model of Dry Eye

Purpose: To elucidate the expression profile and the potential role of long non-coding ribonucleic acids (RNAs) (lncRNAs) in a dry eye disease (DED) model. Methods: A DED model was established in C57BL/6J mice with 0.2% benzalkonium chloride (BAC) twice a day for 14 days. The differentially expressed lncRNAs were detected by RNA-seq technology (Gene Expression Omnibus, GEO GSE186450) and the aberrantly expressed lncRNAs were further verified by RT-qPCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to predicate the related candidate genes and potential pathological pathways. Cells from a human corneal epithelial cell line (HCECs) were cultured under hyperosmolarity. The regulation of inflammatory factors by silencing potential targeted lncRNAs was verified in vitro in HCECs. Results: In our study, a significant increase in corneal fluorescence staining and a reduction in tear production were observed in DED mice at all follow-ups compared with the controls, and the differences were increasing over time. In total, 2,649 upregulated and 704 downregulated lncRNAs were identified in DED mice. We selected six aberrantly expressed and most abundant lncRNAs and performed RT-qPCR using the samples for RNA-seq. Chrnb2, Gabarapl2, and Usp31 were thereby confirmed as the most significantly altered lncRNAs. Pathway analysis revealed that the neuroactive ligand–receptor interaction signaling pathway was the most enriched, followed by the calcium signaling pathway and cytokine–cytokine receptor interaction. Following treatment of Gabarapl2 siRNA and Chrnb2 siRNA, tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, and IL-6 were significantly downregulated in the HCECs. Conclusion: Our study suggests that Chrnb2 and Gabarapl2 may be involved in the inflammation response by regulating TNF-α, IL-1β, and IL-6 in DED. These candidate lncRNAs may be both potential biomarkers and therapeutic targets for DED.
Editorial: LncRNAs in Cancer Metastasis and Therapy Resistance

Long noncoding RNA transcripts (lncRNAs) are being revealed by complementary DNA cloning and genome tiling array studies in animals. Differently from structured RNAs (RNAs, snoRNAs, etc), lncRNAs have been named regulatory RNAs (1, 2). With the finding that microRNAs can be sponged by lncRNAs, named competitive endogenous RNAs (ceRNAs), an alternative function of these RNA molecules is in the assembling of protein complexes, thanks to a tridimensional RNA structure able to interact with proteins involved in transcription, mRNA splicing, epigenetic regulation, chromatin opening or compaction (3). It was shown in bacteria that any species of RNA with a sequence complementary to an mRNAmay regulate its stability (avoiding access to ribonucleases) or may block translation by masking the Shine-Dalgarno region or giving access to an alternative internal transcription start site. LncRNAs are relatively long RNA sequences (more than 200 nucleotides) long that impact the cellular gene expressions and functions in ways that are just beginning to be explored. The metastasis of human cancers as well as acquired resistance against the administered therapeutics are two major factors responsible for the cancer-associated mortality. In a small number of cases lncRNAs are translated into short peptides, and in this case both RNAs and peptides may have a functional role. The big question is whether these transcripts are relevant. To this aim, there are today technologies available such as transient RNA silencing, gene overexpression, and highthroughput CRISPR/Cas genome editing methods that in principle could generate cell lines with all the possible combinations of silenced genes. In search of novel biomarkers as well as potential therapeutic targets of cancer metastasis and cancer drug resistance, the focus in recent years has turned to lncRNAs. What started with studies on relative expression of lncRNAs with the aim to define their utility as diagnostic biomarkers, has evolved into explorations of the possible functional role that these ncRNAs possibly play. One of the relatively more explored functions of lncRNAs is their ability to sponge and regulate the expression of microRNAs (miRNAs), the other ncRNAs that are much shorter in length. This indirectly opens the flood gates to endless possibilities of regulation of gene expression, as miRNAs represent a much better explored subtype of ncRNA. However, regulation through miRNAs is perhaps not the only mode of lncRNAs functionality, as being revealed through continued interest and evaluations. The list of lncRNAs known to cancer researchers is ever expanding, as is the evidence linking their possible role as diagnostic as well as prognostic markers. Concerning lncRNAs, there are published reports on lncRNAs in almost all cancers that affect humans. There is evidence