Miracle-dz/UniFAR-FTUs huggingface dataset:
AN ALGORITHM TO SEGMENT THE MID-BRAIN STRUCTURES USING MULTI- RESOLUTION NON-RIGID REGISTRATION

In present study, a reference based technique has been proposed to segment mid- brain structures in 3D Magnetic Resonance (MR) images using multi-resolution non-rigid registration. The proposed scheme segmented the mid-brain structures in two stages. During first stage, a target image was registered to an already segmented reference image while in second stage, segmentation information was mapped from reference to target medical image. Using this scheme, the aim was to segment nine mid-brain structures including left ventricle, right ventricle, third ventricle, anterior commissure, posterior commissure, left putamen, right putamen, left caudate nucleus and right caudate nucleus. Results of automatic segmentation achieved through reference based non-rigid registration were validated by comparing with the manual segmentation, considered as ground truth. Three metrics namely Dice Coefficient, Sensitivity and Positive Predictive Values were used for assessing the segmentation results. The proposed algorithm showed the satisfactory segmentation of mid-brain structures by achieving a mean sensitivity of 89. 85 % for five target MR images. The results indicated that the proposed scheme performed accurate segmentation of mid-brain structures.
Temporal Feature Integration for Music Organisation

In this paper music genre classification has been explored with special emphasis on the decision time horizon and ranking of tappeddelay-line short-time features. Late information fusion as e.g. majority voting is compared with techniques of early information fusion1 such as dynamic PCA (DPCA). The most frequently suggested features in the literature were employed including melfrequency cepstral coefficients (MFCC), linear prediction coefficients (LPC), zero-crossing rate (ZCR), and MPEG-7 features. To rank the importance of the short time features consensus sensitivity analysis is applied. A Gaussian classifier (GC) with full covariance structure and a linear neural network (NN) classifier are used.
Laser Micropatterning Promotes Rete Ridge Formation and Enhanced Engineered Skin Strength without Increased Inflammation

Rete ridges play multiple important roles in native skin tissue function, including enhancing skin strength, but they are largely absent from engineered tissue models and skin substitutes. Laser micropatterning of fibroblast-containing dermal templates prior to seeding of keratinocytes was shown to facilitate rete ridge development in engineered skin (ES) both in vitro and in vivo. However, it is unknown whether rete ridge development results exclusively from the microarchitectural features formed by ablative processing or whether laser treatment causes an inflammatory response that contributes to rete ridge formation. In this study, laser-micropatterned and non-laser- treated ES grafts were developed and assessed during culture and for four weeks post grafting onto full-thickness wounds in immunodeficient mice. Decreases in inflammatory cytokine secretion were initially observed in vitro in laser-treated grafts compared to non-treated controls, although cytokine levels were similar in both groups five days after laser treatment. Post grafting, rete ridge-containing ES showed a significant increase in vascularization at week 2, and in collagen deposition and biomechanics at weeks 2 and 4, compared with controls. No differences in inflammatory cytokine expression after grafting were observed between groups. The results suggest that laser micropatterning of ES to create rete ridges improves the mechanical properties of healed skin grafts without increasing inflammation.
Experimental Study on the Effects of Vibrational Frequency on the Permeability of Gas-Containing Coal Rocks

Low-frequency mechanical vibrations can trigger disasters such as coal-gas outbursts. An in-house “vibration-triaxial stress-seepage” experimental apparatus was used to measure the gas flow rate of rock specimens with varying vibrational frequency, gas pressure, and confining pressure. The results of these tests were then used to derive expressions that describe how the permeability of gas-containing coal rocks is related to these aforementioned factors. in addition, sensitivity coefficients were defined to characterise the magnitude of the permeability response to each permeability-affecting factor (i.e., vibrational frequency and gas pressure). The following insights were gained, regarding the effects of vibrational frequency on the permeability of gas-containing coal rocks: (1) if gas pressure and confining pressure are fixed, the permeability of gas-containing coal rocks rapidly increases, before gradually decreasing, with increasing vibrational frequency. Thus, the permeability of the gas-containing coal rock is always larger with vibrations than without. (2) if vibrational pressure and confining pressure are fixed, the relationship between the permeability of gas-containing coal rocks and gas pressure is consistent with the “Klinkenberg effect,” i.e., the permeability initially decreases, and then increases, with increasing gas pressure. (3) The change in permeability induced by each unit change in gas pressure is proportional to the gas pressure sensitivity coefficient. (4) The change in permeability induced by each unit change in vibrational frequency is proportional to the vibrational frequency sensitivity coefficient.
Integrated approaches for increasing plant yield under salt stress

Salt stress affects large cultivated areas worldwide, thus causing remarkable reductions in plant growth and yield. To reduce the negative effects of salt stress on plant growth and yield, plant hormones, nutrient absorption, and utilization, as well as developing salt-tolerant varieties and enhancing their morpho-physiological activities, are some integrative approaches to coping with the increasing incidence of salt stress. Numerous studies have been conducted to investigate the critical impacts of these integrative approaches on plant growth and yield. However, a comprehensive review of these integrative approaches, that regulate plant growth and yield under salt stress, is still in its early stages. The review focused on the major issues of nutrient absorption and utilization by plants, as well as the development of salt tolerance varieties under salt stress. In addition, we explained the effects of these integrative approaches on the crop’s growth and yield, illustrated the roles that phytohormones play in improving morpho-physiological activities, and identified some relevant genes involve in these integrative approaches when the plant is subjected to salt stress. The current review demonstrated that HA with K enhance plant morpho-physiological activities and soil properties. In addition, NRT and NPF genes family enhance nutrients uptake, NHX1, SOS1, TaNHX, AtNHX1, KDML, RD6, and SKC1, maintain ion homeostasis and membrane integrity to cope with the adverse effects of salt stress, and sd1/Rht1, AtNHX1, BnaMAX1s, ipal-1D, and sft improve the plant growth and yield in different plants. The primary purpose of this investigation is to provide a comprehensive review of the performance of various strategies under salt stress, which might assist in further interpreting the mechanisms that plants use to regulate plant growth and yield under salt stress.
SAppKG: Mobile App Recommendation Using Knowledge Graph and Side Information-A Secure Framework

Due to the rapid development of technology and the widespread usage of smartphones, the number of mobile applications is exponentially growing. Finding a suitable collection of apps that aligns with users’ needs and preferences can be challenging. However, mobile app recommender systems have emerged as a helpful tool in simplifying this process. But there is a drawback to employing app recommender systems. These systems need access to user data, which is a serious security violation. While users seek accurate opinions, they do not want to compromise their privacy in the process. We address this issue by developing SAppKG, an end-to- end user privacy-preserving knowledge graph architecture for mobile app recommendation based on knowledge graph models such as SAppKG-S and SAppKG-D, that utilized the interaction data and side information of app attributes. We tested the proposed model on real-world data from the Google Play app store, using precision, recall, mean absolute precision, and mean reciprocal rank. We found that the proposed model improved results on all four metrics. We also compared the proposed model to baseline models and found that it outperformed them on all four metrics.
Improving Link Prediction in Network Representation Learning with Feature Fusion and Local Outlier Factor

Complex networks are a diverse set of networks found in various fields, such as social, technological, and biological networks. One important task in complex network analysis is link prediction, which involves detecting missing links or predicting future link formation. Many methods based on network structure analysis have been developed for link prediction, including network representation learning (NRL) models that represent nodes in a low-dimensional space. Fusion-based attributed NRL methods are particularly effective, as they capture both content and structure information. However, NRL models for link prediction are binary classification models, which face challenges in identifying negative links and prioritizing predicted links. To address these challenges, we propose a novel approach that treats link prediction as a novelty detection problem. Our approach uses the Local Outlier Factor (LOF) algorithm to quantify the novelty of non-existent links based on the representations of existing links. Our experimental results show that our proposed approach outperforms existing methods, particularly when used with fusion-based attributed NRL models
Updated analytical expressions for critical bandwidth and critical-band rate.

The concept of critical bands as introduced based on studies of Fletcher and Munson (1937) by Zwicker et al. (1957) describes frequency bands of frequency dependent spectral width with no fixed position on the frequency scale, as they appear in various psychoacoustic experiments (cf. Fastl and Zwicker 2007, pp. 150–158). Among those are studies on loudness summation (Zwicker et al. 1957), absolute thresholds (Gassler 1954), and masking patterns of narrow-band noises (Fastl and Schorer 1986). All these experiments show a change of results if the spectral width of one of the stimuli involved is increased beyond the critical bandwidth (CBW) ∆fG (f) centered at the respective frequency f . Based on the critical bands, a critical-band rate (CBR) function z (f) has been proposed (Zwicker 1961), relating frequency to CBR so that all critical bands are equally wide on the CBR scale. Different formulae to calculate CBR, its inverse f (z), and CBW were proposed (Zwicker and Terhardt 1980, Traunmuller 1990). A similar concept based on equivalent-rectangular bandwidths (ERBs) ∆fE (f) (Patterson 1976) was introduced by Moore and Glasberg (1983, 1987).
Hybrid plasmonic waveguide-assisted Metal–Insulator–Metal ring resonator for refractive index sensing

Abstract A highly sensitive refractive index sensor based on an integrated hybrid plasmonic waveguide (HPWG) and a Metal–Insulator–Metal (M–I–M) micro-ring resonator is presented. In our design, there are two slot-waveguide-based micro-rings that encircle a gold disc. The outer slot WG is formed by the combination of Silicon–Air–Gold ring and the inner slot-waveguide is formed by Gold ring–Air–Gold disc. The slot-waveguide rings provide an interaction length sufficient to accumulate a detectable wavelength shift. The transmission spectrum and electric field distribution of this sensor structure are simulated using Finite Element Method (FEM). The sensitivity of this micro-ring resonator is achieved at 800 nm/RIU which is about six times higher than that of the conventional Si ring with the same geometry. Our proposed sensor design has a potential to find further applications in biomedical science and nano-photonic circuits.
Nonlinear frequency doubling characteristics of asymmetric vortices of tunable, broad orbital angular momentum spectrum

We report on a simple experimental scheme to generate and control the orbital angular momentum (OAM) spectrum of the asymmetric vortex beams in a nonlinear frequency conversion process. Using a spiral phase plate (SPP) and adjusting the transverse shift of the SPP with respect to the incident Gaussian beam axis, we have transformed the symmetric (intensity distribution) optical vortex of order l into an asymmetric vortex beam of measured broad spectrum of OAM modes of orders l, l − 1, l − 2, …, 0 (Gaussian mode). While the position of the SPP determines the distribution of the OAM modes, we have also observed that the modal distribution of the vortex beam changes with the shift of the SPP of all orders and finally results in a Gaussian beam (l = 0). Using single-pass frequency doubling of the asymmetric vortices, we have transferred the pump OAM spectra, l, l − 1, l − 2, …, 0, into the broad spectra of higher order OAM modes, 2l, 2l − 1, 2l − 2, …, 0 at green wavelength, owing to OAM conservation in nonli.
Pharmacological and Genetic Suppression of VDAC1 Alleviates the Development of Mitochondrial Dysfunction in Endothelial and Fibroblast Cell Cultures upon Hyperglycemic Conditions

Prolonged hyperglycemia related to diabetes and its complications leads to multiple cellular disorders, the central one being the dysfunction of mitochondria. Voltage-dependent anion channels (VDAC) of the outer mitochondrial membrane control the metabolic, ionic, and energy cross-talk between mitochondria and the rest of the cell and serve as the master regulators of mitochondrial functions. Here, we have investigated the effect of pharmacological suppression of VDAC1 by the newly developed inhibitor of its oligomerization, VBIT-4, in the primary culture of mouse lung endotheliocytes and downregulated expression of VDAC1 in human skin fibroblasts on the progression of mitochondrial dysfunction upon hyperglycemic stress. The cells were grown in high-glucose media (30 mM) for 36 h. In response to hyperglycemia, the mRNA level of VDAC1 increased in endotheliocytes and decreased in human skin fibroblasts. Hyperglycemia induced overproduction of mitochondrial ROS, an increase in the susceptibility of the organelles to mitochondrial permeability transition (MPT) pore opening and a drop in mitochondrial membrane potential, which was accompanied by a decrease in cell viability in both cultures. Treatment of endotheliocytes with 5 µM VBIT-4 abolished the hyperglycemia-induced increase in susceptibility to spontaneous opening of the MPT pore and ROS generation in mitochondria. Silencing of VDAC1 expression in human skin fibroblasts exposed to high glucose led to a less pronounced manifestation of all the signs of damage to mitochondria. Our data identify a mitochondria-related response to pharmacological and genetic suppression of VDAC activity in vascular cells in hyperglycemia and suggest the potential therapeutic value of targeting these channels for the treatment of diabetic vasculopathies.
Art of the Kill: Designing and Testing Viral Inactivation Procedures for Highly Pathogenic Negative Sense RNA Viruses

The study of highly pathogenic viruses handled under BSL-4 conditions and classified as Select Agents frequently involves the transfer of inactivated materials to lower containment levels for downstream analyses. Adhering to Select Agent and BSL-4 safety regulations requires validation or verification of the inactivation procedures, which comes with an array of challenges for each method. This includes the use of cytotoxic reagents for chemical inactivation and defining the precise inactivation parameters for physical inactivation. Here, we provide a workflow for various inactivation methods using Ebola, Nipah, and Lassa viruses as our examples. We choose three distinct inactivation methods (TRIzol/TRIzol LS, aldehyde fixation using different fixatives, and heat) to highlight the challenges of each method and provide possible solutions. We show that, whereas published chemical inactivation methods are highly reliable, the parameters for heat inactivation must be clearly defined to ensure complete inactivation. In addition to the inactivation data, we also provide examples and templates for the documentation required for approval and use of inactivation SOPs, including an inactivation report, the procedure sections of developed SOPs, and an electronic inactivation certificate that accompanies inactivated samples. The provided information can be used as a roadmap for similar studies at high and maximum containment laboratories.
Protein Structure Predictions, Atomic Model Building, and Validation Using a Cryo-EM Density Map from Hepatitis B Virus Spherical Subviral Particle

Hepatitis B virus (HBV) infection is a global public health concern. During chronic infection, the HBV small-surface antigen is expressed in large excess as non-infectious spherical subviral particles (SVPs), which possess strong immunogenicity. To date, attempts at understanding the structure of HBV spherical SVP have been restricted to 12–30 Å with contradictory conclusions regarding its architecture. We have used cryo-electron microscopy (cryo-EM) and 3D image reconstruction to solve the HBV spherical SVP to 6.3 Å. Here, we present an extended protocol on combining AlphaFold2 prediction with a moderate-resolution cryo-EM density map to build a reliable 3D model. This protocol utilizes multiple software packages that are routinely used in the cryo-EM community. The workflow includes 3D model prediction, model evaluation, rigid-body fitting, flexible fitting, real-space refinement, model validation, and model adjustment. Finally, the described protocol can also be applied to high-resolution cryo-EM datasets (2–4 Å).
Application of parallel algorithms for numerical simulation of quasi-one dimensional blood flow

The main goal of modern hemodynamic simulation is the prediction of blood pressure in the arteries, as well as the study of the various factors complex effect on the cardiovascular system characteristics. Quasi-one dimensional models of blood flow through blood vessels are the most popular. They allow to model the blood flow in the entire vascular system. Since full-scale simulation of the cardiovascular system requires large computational costs, the problem of parallelizing computation is actual. In this paper, the efficiency study was carried out for parallel algorithms in the numerical simulation of blood flow in the quasi-one-dimensional approximation. For simplicity, we consider the problem of the blood flow simulation in a separate blood vessel. When constructing a parallel algorithm, the domain decomposition method was applied. In each subdomain, the problem at each time step splits into a hyperbolic and parabolic subproblems. To solve the hyperbolic subtask, an integro-interpolation method based on the MUSCL scheme is used. To integrate over time, the second order Runge-Kutta and Adams-Bashfort methods are applied. The Crank-Nicholson method is used to solve the parabolic subproblem. At the subdomains conjunctions, the interface conditions are non-linear systems with three unknowns. These systems are solved using the Newton method. The time-cost structure was obtained for solving the test problem in a serial mode using the AMD CodeAnalyst profiler. Computations were carried out at the cluster of the BMSTU "Applied Mathematics" FN-2 department. The computational results showed that the time gain achieved by using the MPI library does not exceed a few percent in comparison with the OpenMP technology usage. Taking into account the simplicity of parallelizing algorithms through OpenMP, we can choose this technology, but MPI usage allows to make the software package universal (it can work both on shared memory systems and on distributed memory systems).
Inverse kinematics solution for humanoid robot minimizing gravity-related joint torques

A method of solving the inverse kinematics problem for a humanoid robot modeled as a tree-shaped manipulator is presented. Robot trajectory consists of a set of trajectories of the characteristic points (the robot’s center of mass, origins of feet and hands frames) in the discrete time domain. The description of motion in the frame associated with the supporting foot allows one to represent the robot as a composite of several serial open-loop redundant manipulators. Stability during the motion is provided by the trajectory of the robot’s center of mass which ensures that the zero moment point criterion is fulﬁlled. Inverse kinematics solution is performed oﬄine using the redundancy resolution at the velocity level. The proposed method utilizes robot’s redundancy to fulﬁll joint position limits and to reduce gravity-related joint torques. The method have been tested in simulations and experiments on a humanoid robot Melson, and results are presented.
Patient and caregiver return to work after a primary brain tumor

Abstract Background Studies focusing on the return to work (RTW) experiences of patients with a brain tumor (BT) are scarce. We aimed to explore, in-depth, the occupational expectations, experiences, and satisfaction of patients who RTW after a BT diagnosis and treatment, those not able to, and their family caregivers. Methods This multicenter, cross-sectional study utilized semi-structured interviews and reflexive thematic analysis. Interviews were conducted with adults diagnosed with primary BT, in employment/self-employed before diagnosis, currently in follow-up care, and also with their caregivers. Results In total, 23 interviews (17 patients/6 caregivers) took place. Five themes were developed: (1) Early (adjustments and) expectations: “Thought I would be back at work the following Monday”; pre-treatment patients wanted to be better informed about potential recovery time and side-effects. (2) Drivers to RTW: “Getting my life back on track”; RTW was seen as a symbol of normality and also dictated by financial pressures. (3) Experiences returning to work: “It’s had its ups and downs”: patients who had successfully returned were supported by employers financially, emotionally, and practically. (4) Required support: “He had surgery and that was it”: suggested support included a back-to-work scheme and comprehensive financial support. (5) Caring and paid work: The “juggling act”: carer’s work was significantly impacted; often reducing/increasing their working hours while managing increasing caring demands. Conclusions Future research focusing on RTW in neuro-oncology populations is needed. Interventions should be developed to improve employer/employee communication, and increase knowledge about BT care and possibilities for RTW, to support patients and caregivers towards sustained employment.