Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic peripheral nerve stimulation can produce cortical activation similar to punctate mechanical stimuli

During contact, phasic and tonic responses provide feedback that is used for task performance and perceptual processes. These disparate temporal dynamics are carried in peripheral nerves, and produce overlapping signals in cortex. Using longitudinal intrafascicular electrodes inserted into the median nerve of a nonhuman primate, we delivered composite stimulation consisting of onset and release bursts to capture rapidly adapting responses and sustained stochastic stimulation to capture the ongoing response of slowly adapting receptors. To measure the stimulation’s effectiveness in producing natural responses, we monitored the local field potential in somatosensory cortex. We compared the cortical responses to peripheral nerve stimulation and vibrotactile/punctate stimulation of the fingertip, with particular focus on gamma band (30–65 Hz) responses. We found that vibrotactile stimulation produces consistently phase locked gamma throughout the duration of the stimulation. By contrast, punctate stimulation responses were phase locked at the onset and release of stimulation, but activity maintained through the stimulation was not phase locked. Using these responses as guideposts for assessing the response to the peripheral nerve stimulation, we found that constant frequency stimulation produced continual phase locking, whereas composite stimulation produced gamma enhancement throughout the stimulus, phase locked only at the onset and release of the stimulus. We describe this response as an “Appropriate Response in the gamma band” (ARγ), a trend seen in other sensory systems. Our demonstration is the first shown for intracortical somatosensory local field potentials. We argue that this stimulation paradigm produces a more biomimetic response in somatosensory cortex and is more likely to produce naturalistic sensations for readily usable neuroprosthetic feedback.
Bias field angle dependence of the self-oscillation of spin torque oscillators having a perpendicularly magnetized free layer and in-plane magnetized reference layer

We report on the oscillation behavior of spin torque oscillators having a perpendicularly magnetized free layer and in-plane magnetized reference layer as a function of bias field angle. The measurement results show that both emission power and oscillation frequency are strongly dependent on the bias field angle. When the bias field was tilted by only a few degrees away from the axis normal to the film toward either parallel or antiparallel configuration, the power increased by about 1.5 times or decreased by two orders of magnitude, and the peak frequency varied by about ±1 GHz.
Classical Electron-Ion Coulomb Bremsstrahlung in Weakly Coupled Plasmas

In weakly coupled plasmas the classical electron-ion Coulomb bremsstrahlung process are investigated. The cross section for the electron-ion Coulomb bremsstrahlung in weakly-coupled plasmas is obtained by the Debye-Hückel model with the modified hyperbolic-orbit trajectory method. The results show that the plasma-screening effects on the scaled doubly differential bremsstrahlung radiation (SDDBR) cross section increase as the radiation frequency increases. For a given projectile electron energy, the SDDBR cross section obtained by the modified hyperbolic-orbit trajectory method and by the straight-line trajectory method tend to the same value with increasing radiation photon energy. The SDDBR cross sections using the modified hyperbolic-orbit trajectory method are increased by the plasma screening in the small impact parameter domain and decreased for large and intermediate impact parameters with increasing radiation frequency.
Scintillation Characteristics of Doped PbWO 4 Crystals

Emission spectra, longitudinal transmission and light output for the Sb-doped and Y-doped PbWO4 crystals are presented. Scintillation decay kinetics has been measured by using gate integration and the single photon counting method with blue and green filters. Radiation hardness has also been measured by using 60Co γ-ray irradiation under different dose rates and different dose rate profiles. The light yield and radiation hardness of the Sb-doped and Y-doped PbWO4 crystals are improved as compared to the undoped crystals and are suitable for the requirements of compact muon solenoid.
EasyCellType: marker-based cell-type annotation by automatically querying multiple databases

Abstract Motivation Cell label annotation is a challenging step in the analysis of single-cell RNA sequencing (scRNA-seq) data, especially for tissue types that are less commonly studied. The accumulation of scRNA-seq studies and biological knowledge leads to several well-maintained cell marker databases. Manually examining the cell marker lists against these databases can be difficult due to the large amount of available information. Additionally, simply overlapping the two lists without considering gene ranking might lead to unreliable results. Thus, an automated method with careful statistical testing is needed to facilitate the usage of these databases. Results We develop a user-friendly computational tool, EasyCellType, which automatically checks an input marker list obtained by differential expression analysis against the databases and provides annotation recommendations in graphical outcomes. The package provides two statistical tests, gene set enrichment analysis and a modified version of Fisher’s exact test, as well as customized database and tissue type choices. We also provide an interactive shiny application to annotate cells in a user-friendly graphical user interface. The simulation study and real-data applications demonstrate favorable results by the proposed method. Availability and implementation https://biostatistics.mdanderson. org/shinyapps/EasyCellType/; https://bioconductor.org/packages/devel/bioc/html/EasyCellType.html. Supplementary information Supplementary data are available at Bioinformatics Advances online.
Fuzzy reliability optimization models for redundant systems

In this paper, a special class of redundancy optimization problem with fuzzy random variables is presented. In this model, fuzzy random lifetimes are considered as basic parameters and the Er-expected of system lifetime is used as a major type of system performance. Then a redundancy optimization problem is formulated as a binary integer programming model. Furthermore, illustrative numerical examples are also given to clarify the methods discussed in this paper.
Depth from Defocus Using Geometric Optics Regularization

This paper formulates the problem of recovering depth information of the scene from two defocused images as the minimization of the information divergence between the two measured defocused images based on geometric optics regularization. This geometric optics regularization term is attained according to different relative position of image plane and image focus. The experimental results show that the quality of the estimated depth is significantly better than that obtained without the geometric optics regularization.
History of advances in genetic engineering of viruses before COVID-19 pandemic

Background: On December 31, 2019, the World Health Organization’s China Country Office was alerted to cases of pneumonia of unknown cause detected in Wuhan City, Hubei Province of China. Methods: Due to the fact that to date, the question of the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has not been resolved yet, the author analyzed the main advances in the development of genetic engineering of viruses that took place before the onset of the COVID-19 pandemic. Results: The first artificial genetically modified viruses could appear in nature in the mid-1950s. The technique of nucleic acid hybridization was developed by the end-1960s. In the late 1970s, a method called the “reverse genetics” emerged to synthesize ribonucleic acid and deoxyribonucleic acid molecules. In the early 1980-s, it became possible to combine the genes of different viruses and insert the genes of one virus into the genome of another virus. Since that time, the production of vector vaccines began. At present, by modern technologies one can assemble any virus based on the nucleotide sequence available in the virus database or designed by a computer as a virtual model. Conclusion: Scientists around the world are invited to answer the call of Neil Harrison and Jeffrey Sachs of Columbia University, for a thorough and independent investigation into the origin of SARS-CoV-2. Only a full understanding of the origin of the new virus can minimize the likelihood of a similar pandemic in the future.
Challenges, Concerns, and Experiences of Community-Dwelling Older Women with Chronic Low Back Pain—A Qualitative Study in Hong Kong, China

Background and Objectives: Although chronic low back pain (CLBP) is known to negatively affect multiple aspects of the lives of older people, prior qualitative studies mainly focused on the lived experiences of older people with CLBP in Western countries. Given cultural and contextual differences and poor understanding of CLBP in older women with CLBP, it is important to better understand the concerns and lived experiences of Chinese older women with CLBP. The current study aimed to investigate the experiences, challenges, concerns, and coping strategies of older women with CLBP in Hong Kong. Research Design and Methods: A total of 15 community-dwelling older women with CLBP aged ≥60 years were recruited from a physiotherapy clinic or a community center for semi-structured interviews. The interviews were audio recorded and transcribed ‘verbatim’. The transcription was imported to NVivo 12 software. Thematic analysis was conducted using Braun and Clarke’s method. Results: Five themes were identified: (1) physical impacts of CLBP on daily life; (2) psychological influences of CLBP; (3) management of CLBP; (4) family support; and (5) social activities and support. Discussion and implications: Negative physical and psychosocial impacts of CLBP were common among older women, and they adopted diverse pain management strategies, although some of their treatment options were influenced by the Chinese culture. Misbeliefs and responses of family and friends also affected their management strategies. Elderly community centers are a significant source of social support for older women with CLBP, making it an ideal platform for establishing self-help groups to facilitate their self-management of CLBP.
Increased ENT2 expression and its association with altered purine metabolism in cell lines derived from different stages of colorectal cancer

Colorectal cancer (CRC) is one of the most prevalent malignant cancer types worldwide. Although the purine metabolism pathway is vital for cancer cell survival, little is known about the role of equilibrative nucleoside transporter 2 (ENT2) in CRC development and its association with purine metabolites. The aim of the present study was to evaluate the levels of hypoxanthine phosphoribosyl transferase (HPRT), hypoxanthine and uric acid (UA), as well as xanthine oxidase (XO) activity, and investigate their association with ENT2 expression levels in a normal human colon cell line and CRC cell lines derived from different stages of CRC. These analyses were performed using the normal colon CCD-841CoN cell line and a panel of human CRC cell lines comprising SW480, HCT15 and HCT116, which represent Dukes' B, C and D stages, respectively. Reverse transcription-quantitative PCR was performed to determine the level of ENT2 mRNA expression. In cells of all CRC stages, the levels of HPRT and hypoxanthine were significantly higher (P<0.05), while XO activity and UA levels were significantly decreased (P<0.05), compared with those in the CCD-841CoN cell line. ENT2 expression was found to be elevated in cells derived from all stages of CRC. The Dukes' D stage cell line had higher levels of HPRT and hypoxanthine, although its ENT2 level was not significantly lower than that of the Dukes' B and C stage cell lines. Increased levels of HPRT and hypoxanthine in various stages of CRC may indicate an increase in the activity of the salvage pathway. The increased expression of ENT2 implies the importance of the ENT2 protein in facilitating hypoxanthine transport, which is required for enhanced DNA synthesis via hypoxanthine recycling. In conclusion, ENT2 may have potential as a target in the development of CRC therapeutics.
Inhibition of Rab1B Impairs Trafficking and Maturation of SARS-CoV-2 Spike Protein

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) utilizes cellular trafficking pathways to process its structural proteins and move them to the site of assembly. Nevertheless, the exact process of assembly and subcellular trafficking of SARS-CoV-2 proteins remains largely unknown. Here, we have identified and characterized Rab1B as an important host factor for the trafficking and maturation of the spike protein (S) after synthesis at the endoplasmic reticulum (ER). Using confocal microscopy, we showed that S and Rab1B substantially colocalized in compartments of the early secretory pathway. Co-expression of dominant-negative (DN) Rab1B N121I leads to an aberrant distribution of S into perinuclear spots after ectopic expression and in SARS-CoV-2-infected cells caused by either structural rearrangement of the ERGIC or Golgi or missing interaction between Rab1B and S. Western blot analyses revealed a complete loss of the mature, cleaved S2 subunit in cell lysates and culture supernatants upon co-expression of DN Rab1B N121I. In sum, our studies indicate that Rab1B is an important regulator of trafficking and maturation of SARS-CoV-2 S, which not only improves our understanding of the coronavirus replication cycle but also may have implications for the development of antiviral strategies.
Application of Drug Efficiency Index Metric for Analysis of Post-Traumatic Stress Disorder and Treatment Resistant Depression Gene Expression Profiles

Post-traumatic stress disorder (PTSD) is a severe mental illness with grave social, political, economic, and humanitarian implications. To apply the principles of personalized omics-based medicine to this psychiatric problem, we implemented our previously introduced drug efficiency index (DEI) to the PTSD gene expression datasets. Generally, omics-based personalized medicine evaluates individual drug action using two classes of data: (1) gene expression, mutation, and Big Data profiles, and (2) molecular pathway graphs that reflect the protein–protein interaction. In the particular case of the DEI metric, we evaluate the drug action according to the drug’s ability to restore healthy (control) activation levels of molecular pathways. We have curated five PTSD and one TRD (treatment-resistant depression) cohorts of next-generation sequencing (NGS) and microarray hybridization (MH) gene expression profiles, which, in total, comprise 791 samples, including 379 cases and 413 controls. To check the applicability of our DEI metrics, we have performed three differential studies with gene expression and pathway activation data: (1) case samples vs. control samples, (2) case samples after treatment or/and observation vs. before treatment, and (3) samples from patients positively responding to the treatment vs. those responding negatively or non-responding patients. We found that the DEI values that use the signaling pathway impact activation (SPIA) metric were better than those that used the Oncobox pathway activation level (Oncobox PAL) approach. However, SPIA, Oncobox PAL, and DEI evaluations were reliable only if there were differential genes between case and control, or treated and untreated, samples.
Electronic structure and optical properties of Nb-doped anatase TiO2

The electronic structure and optical properties of pure and Nb-doped TiO2 with anatase structure were calculated using local-density approximation based on the density-functional theory. For the undoped TiO2, the Fermi level locates in the band gap between the conduction band and valence band, while it moves into the conduction band and shows metal-like characteristic after Nb atom was introduced into the TiO2 supercell. The optical absorption coefficients for both compounds are very small in the visible light range. Our calculations provide electronic structure evidence that the Nb-doped anatase TiO2 is a new type transparent conducing metal.
Predictive Control of a Human–in–the–Loop Network System Considering Operator Comfort Requirements

We propose a model-predictive control (MPC)-based approach to solve a human-in-the-loop control problem for a network system lacking sensors and actuators to allow for a fully automatic operation. The humans in the loop are, therefore, essential; they travel between the network nodes to provide the remote controller with measurements and to actuate the system according to the controller’s commands. Time instant optimization MPC is utilized to compute when the measurement and actuation actions are to take place to coordinate them with the network dynamics. The time instants also minimize the burden of human operators by tracking their energy levels and scheduling the necessary breaks. Fuel consumption related to the operators’ travel is also minimized. The results in a digital twin of the Dez Main Canal illustrate that the new algorithm outperforms previous methods in terms of meeting operational objectives and taking care of human well-being, but at the cost of higher computational requirements.
Immune profiling of experimental murine mastitis reveals conserved response to mammary pathogenic Escherichia coli, Mycoplasma bovis, and Streptococcus uberis

Mastitis is one of the most prevalent and economically important diseases of dairy animals. The disease is caused by ascending bacterial infection through the teat canal. Among the most common mastitis-causing bacteria are Gram-negative coliforms, Gram-positive streptococci and staphylococci, and mycoplasma. The most prominent cellular hallmark of acute mammary infection is a massive recruitment of blood neutrophils into the tubular and alveolar milk spaces. The complex biological processes of leukocyte recruitment, activation, adhesion, and migration in the mammary gland remain largely elusive to date. While field research of mastitis in dairy animals contributed a lot to the development of mitigation, control, and even eradication programs, little progress was made toward understanding the molecular mechanisms underlying the pathogenesis of the disease. We report here experimental mastitis model systems in lactating mice challenged with field strains of common udder pathogens in dairy cows. We used these model systems to apply recently developed multiplex gene expression technology (Nanostring nCounter), which enabled us to study the expression of over 700 immune genes. Our analysis revealed a core of 100 genes that are similarly regulated and functionally or physically interacting in E. coli, M. bovis, and Strep uberis murine mastitis. Common significantly enriched gene sets include TNFɑ signaling via NFkB, Interferon gamma and alpha response, and IL6-JAK-STAT3 signaling. In addition, we show a significantly enriched expression of genes associated with neutrophil extracellular traps (NET) in glands challenged by the three pathogens. Ligand-receptor analysis revealed interactions shared by the three pathogens, including the interaction of the cytokines IL1β, IL1ɑ, and TNFɑ with their receptors, and proteins involved in immune cell recruitment such as complement C3 and ICAM1 (with CD11b), chemokines CCL3 and CCL4 (with CCR1), and CSF3 (with CSF3R). Taken together, our results show that mammary infection with E. coli, M. bovis, and Strep uberis culminated in the activation of a conserved core of immune genes and pathways including NET formation.
A hybrid features based image matching algorithm

In this paper, we present a novel image matching method to find the correspondences between two sets of image interest points. The proposed method is based on a revised third-order tensor graph matching method, and introduces an energy function that takes four kinds of energy term into account. The third-order tensor method can hardly deal with the situation that the number of interest points is huge. To deal with this problem, we use a potential matching set and a vote mechanism to decompose the matching task into several sub-tasks. Moreover, the third-order tensor method sometimes could only find a local optimum solution. Thus we use a cluster method to divide the feature points into some groups and only sample feature triangles between different groups, which could make the algorithm to find the global optimum solution much easier. Experiments on different image databases could prove that our new method would obtain correct matching results with relatively high efficiency.
Active Learning Integrated Portable Skin Lesion Detection System Based on Multimodel Fusion

In skin lesion detection systems, a large number of labeled images are usually required to achieve high segmentation accuracy (ACC), which hinders the effectiveness and timeliness of disease diagnosis. To this end, a high-precision skin lesion detection system is proposed in this article. The hardware part of the system adopts a modular design, fully considering ergonomics, portability, and miniaturization. In the software part, an active learning ensemble with a multimodel fusion method (ALEM) is proposed to achieve efficient and accurate skin lesion region segmentation. The core idea of ALEM is to use multiple uncertainty strategies of active learning to obtain the most uncertain pixels to be marked in the skin lesion image when marking image pixels. The experiment shows that the average Dice coefficient (DIC) and average Jaccard index (JAI) of ALEM on International Skin Imaging Collaboration (ISIC)-2016 are 82.81% and 92.4%, respectively, and that on ISIC-2017 are 87.51% and 79.26%, respectively. It is worth noting that ALEM still outperforms in tests with only 80% of the training data and no more than 15% pixel annotation per image on average. Our system achieves an average AUC of 91.01% on the ISIC2017 and is tested for effectiveness on real skin. The skin lesion detection system developed in this article is expected to bring convenience to doctors and patients and speed up the diagnosis of diseases.
A cloud-base quasi-balance constraint for parameterized convection : Application to the kain-fritsch cumulus scheme

Abstract A quasi balance with respect to parcel buoyancy at cloud base between destabilizing processes and convection is imposed as a constraint on convective cloud-base mass flux in a modified version of the Kain–Fritsch cumulus parameterization. Supporting evidence is presented for this treatment, showing a cloud-base quasi balance (CBQ) on a time scale of approximately 1–3 h in explicit simulations of deep convection over the U.S. Great Plains and over the tropical Pacific Ocean with the Naval Research Laboratory’s Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS). 1 With the exception of the smaller of two convective events in the Great Plains simulation, a CBQ is still observed upon restriction of the data analysis to instances where the available buoyant energy (ABE) exceeds a threshold value of 1000 J kg−1. This observation is consistent with the view that feedbacks between convection and cloud-base parcel buoyancy can control the rate of convection on shorter time scales than those asso.