bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wideband Low-RCS and Gain-Enhanced Antenna Using Frequency Selective Absorber Based on Patterned Graphene
Authors: Wang Fuwei , Wang Yi , Zhang Xiaoyu , Liu Lu , Li Ke , Ren Yuhui 
Published: January 2024

Abstract

In this paper, a double-layer patterned graphene-based frequency-selective absorber (DGFSA) is proposed as a means of reducing an antenna's radar cross-section (RCS) while simultaneously increasing its gain. The antenna consists of a patch antenna with MGFSA mounted on top. The DGFSA consists of double-layer patterned graphene and a band-pass frequency selective surface (FSS). Two patterned graphene lossy layers with different square resistances are used, which broaden the electromagnetic (EM) wave absorption bandwidth of the DGFSA, thus greatly reducing the out-band monostatic RCSs of the patch antenna. Meanwhile, due to the quasi-Fabry-Perot (F-P) effect, the gain of the proposed antenna is enhanced by 2.4 dB. Additionally, the low-RCS antenna reduces the monostatic RCS from 1.32 to 17 GHz under y-polarization and from 1.4 to 16.8 GHz under x-polarization, respectively. Furthermore, a decrease in the bistatic RCS is accomplished. Results from simulations and measurements match up nicely, which means the antenna we proposed has a good application on the stealth platform.
Binding affinity optimization and structural evaluation of designed antibodies against PD-1 and PD-L1 as critical immune checkpoints involved in cancer treatment
Authors: Abdolmaleki Sarah , hakemi Mazdak Ganjalikhani , Ganjalikhany Mohamad Reza 
Published: January 2024

Abstract
Cancer control and treatment remain a significant challenge in cancer therapy and recently immune checkpoints has considered as a novel treatment strategy to develop anti-cancer drugs. Many cancer types use the immune checkpoints and its ligand, PD-1/PD-L1 pathway, to evade detection and destruction by the immune system, which is associated with altered effector function of PD-1 and PD-L1 overexpression on cancer cells to deactivate T cells. In recent years, mAbs have been employed to block immune checkpoints, therefore normalization of the anti-tumor response has enabled the scientists to develop novel biopharmaceuticals. In vivo antibody affinity maturation in targeted therapy has sometimes been failed and highlight the importance of in silico design methods in this area. Here, we used the in silico methods to design improved mAbs with high affinity for PD-1 and PD-L1. At first, using the RosettaDesign protocol, thousands of antibodies have been generated for 11 different regions on PD-1 and PD-L1 and then the designs with higher stability, affinity, and shape complementarity were selected. We obtained high affinity antibodies with success rates of 33.2% and 30.6% for PD-1 and PD-L1. Then, MD simulation and MM-PBSA techniques were used to understand the dynamic, structural features of the complexes, measure the stability and binding affinity of the final designs. This study provides comprehensive information regarding the potential binding epitopes on PD-1 which could be considered as hotspots for designing potential biopharmaceuticals. We also showed that mutations in the CDRs regions will rearrange the interaction pattern between the designed antibodies and targets (PD-1 and PD-L1) with improved affinity to effectively inhibit protein-protein interaction and block the immune checkpoint.
Climate Oscillations influence on GoM Circulation
Authors: Souza Alejandro , Gallegos-DiezBarroso Gabriel 
Published: January 2024

Abstract
Atmosphere - Ocean processes share large amount of energy through sea surface. This energy interactions has a signi cant contribution on climate and ocean dynamic variability. EOF principal components from Gulf of Mexico (GoM) circulation, wind  eld velocity and the indexes of NAO and ENSO were cross spectra analysed to depict mode by mode which are the frequencies and how much energy are shared in each one. GoM circulation behavior is an important step at the AMOC heat transfer from lower to higher latitudes, this energy transfer should enhance or weaken ocean-atmosphere processes . Atmospheric NAO-ENSO tele connections seems to have strong forcing implications in GoM circulation. Loop current (LC) length variability and Loop Current Eddies (LCE's) shedding frequencies, which governs GoM circulation dynamics, have several shared frequencies with climate oscillations that can enhance or weaken AMOC intensity
[1]. Several frequency/phase synchronization were observed from the cross spectra analysis which is a very common phenomena in complex oscillations such as
NAO, ENSO and AMOC can be conceived.
Efficient Implementation of the Lattice Boltzmann Method on a GPU for Predicting Near-Field and Far-field Jet Noise
Authors: Noah Khalid , Abdelrahim Suleiman , Mosa Mohamed , Adam Saad 
Published: January 2024

Abstract
The lattice Boltzmann method (LBM) is a powerful technique for the computational modelling of a wide variety of single and multiphase flows in complex geometries. It is a discrete computational approach based on solving the Boltzmann equation numerically. LBM has recently become one of the new and promising CFD methods to solve many computational fluid mechanics problems. LBM works particularly well when solving incompressible flow problems, but limitations arise when solving compressible flow, especially at high Mach numbers. Compressible LBM was applied for the simulation jet flow in order to demonstrate the ability of the fifth-order equilibrium distribution function to simulate compressible flows efficiently. The near-field flow physics and noise simulations were performed using the compressible LBM. The results from the LBM simulation were then employed in Kirchhoff’s surface integral approach to predict far-field jet noise. Because of the ability of the lattice Boltzmann technique to be used in parallel computing and to improve LBM computational efficiency with respect to the numerical simulations of turbulent flows in predicting far-field noise, the final step in this research was to use the compute unified device architecture (CUDA) for implementing the LBM in a graphics processing unit (GPU), thus creating a hybrid code, LBM-MRT-LES, through the utilization of the Kirchhoff integral method, a powerful tool for simulating aeroacoustics problems.
VR-GNN: Variational Relation Vector Graph Neural Network for Modeling Homophily and Heterophily
Authors: Shi Fengzhao , Li Ren , Cao Yanan , Lin Xixun , Shang Yanmin , Zhou Chuan , Wu Jia , Pan Shirui 
Published: January 2024

Abstract

Graph Neural Networks (GNNs) have achieved remarkable success in diverse real-world applications. Traditional GNNs are designed based on homophily, which leads to poor performance under heterophily scenarios. Most current solutions deal with heterophily mainly by modeling the heterophily edges as data noises or high-frequency signals, treating all heterophilic edges as being of the same semantic. Consequently, they ignore the rich semantic information of these edges in heterophily graphs. To overcome this critic problem, we propose a novel GNN model based on relation vector translation named as Variational Relation Vector Graph Neural Network (VR-GNN). VR-GNN models relation generation and graph aggregation into an end-to-end model based on a variational inference framework. To be specific, the encoder utilizes the structure, feature and label to generate a fine-grained relation vector for each edge, which aims to infer its implicit semantic information. The decoder incorporates the generated relation vectors into the message-passing framework for deriving better node representations. We conduct extensive experiments on eight real-world datasets with different homophily-heterophily properties to verify model effectiveness. Extensive experimental results show that VR-GNN gains consistent and significant improvements against existing strong GNN methods under heterophily and competitive performance under homophily.
Peripheral Nerve Decompression for Pain Relief in the Setting of Previous Obstetrical Brachial Plexus Injury: A Retrospective Case Series
Authors: Gormley Jessica , Isak Pavlo , Gjertsen Deborah , Bain James R 
Published: January 2024

Abstract
Purpose
In children with previous obstetrical brachial plexus injury (OBPI) upper extremity pain is present in 45 to 66% of patients. Recent literature reports this as musculoskeletal or neuropathic in nature. The purpose of the study is to demonstrate that peripheral nerve decompression and neurolysis may be an effective treatment for patients with upper extremity pain in the context of previous OBPI.
Methods
A retrospective chart review was performed on patients undergoing peripheral nerve decompression and neurolysis after OBPI by senior author. The primary outcome assessed was pain and secondary outcome measure was range of motion of the wrist and elbow. Outcome measures were assessed preoperatively as well as at their subsequent follow-up.
Results
Six patients were included, with a mean age of 14 years old at time of decompression. Three patients underwent median nerve, two patients underwent ulnar nerve and one patient underwent posterior interosseous nerve decompression. There was a substantial improvement in pain post-operatively, demonstrated by reduction or resolution of subjective pain in all patients and resolution of Tinel’s sign. There was a modest improvement in range of motion.
Conclusion
This study demonstrates an improvement in subjective pain and range of motion after decompression and neurolysis in OBPI patients with peripheral neuropathy. Appropriate identification of this pathology through routine follow-up with a multidisciplinary clinic allows for early recognition and symptom relief. Future research should focus on assessment and treatment of pain in this population on a larger scale.
Monitoring Thoracic Surgery Patients: A Heart Rate Variability Perspective on Postoperative Recovery and Therapeutic Interventions
Authors: Miri Seyedsadra , Lähteenmäki Sabina , Mahrberg Heidi , Vehkaoja Antti , Laurikka Jari , Viik Jari 
Published: January 2024

Abstract
Purpose
In this study we aim to adopt heart rate variability (HRV) as a non-invasive monitoring technique to assess the recovery process of pulmonary surgery patients. In order to advance the recovery process, two different physiotherapy interventions; positive expiratory pressure (PEP) and inspiratory muscle training (IMT) were utilized to see how effectively they can enhance the recovery process.
Methods
Electrocardiogram (ECG) measurements were performed for 72 minor pulmonary (PM) and pulmonary resection (PR) surgery patients pre-operatively and on two first post-operative days and the recovery process was promoted using PEP and IMT therapeutic interventions by dividing the patients into two groups, one for each intervention. Time and frequency domain HRV parameters were calculated during different days and statistical analysis was performed between the days and the intervention groups.
Results
A reduction in all investigated HRV parameters was observed post-operatively. Low frequency components of HRV (LF power) faced the most significant reduction for PEP intervention of PM surgery group (from 290.02 ms2 to 229.04 ms2). There was no sign of recovery and returning to the baseline level within the two-day timeframe. Also, no statistically significant difference was found between intervention groups (\(\alpha\) \(\ge\) 0.05); however, IMT technique seemed to have a slightly improved effects for PM surgery group.
Conclusion
Based on the results, the investigated HRV parameters are able to assess the status of pulmonary surgery patients, the recovery process and inspecting the difference between therapeutic interventions; however, larger studies with extended monitoring timeframe and more subjects can possibly improve the results.
The transcription factor STE12 influences growth on several carbon sources and production of dehydroacetic acid (DHAA) in Trichoderma reesei
Authors: Schalamun Miriam , Hinterdobler Wolfgang , Schinnerl Johann , Brecker Lothar , Schmoll Monika 
Published: January 2024

Abstract

The filamentous ascomycete Trichoderma reesei, known for its prolific cellulolytic enzyme production, recently also gained attention for its secondary metabolite synthesis. Both processes are intricately influenced by environmental factors like carbon source availability and light exposure. Here, we explore the role of the transcription factor STE12 in regulating metabolic pathways in T. reesei in terms of gene regulation, carbon source utilization and biosynthesis of secondary metabolites. We show that STE12 is involved in regulating cellulase gene expression and growth on carbon sources associated with iron homeostasis. STE12 impacts gene regulation in a light dependent manner on cellulose with modulation of several CAZyme encoding genes as well as genes involved in secondary metabolism. STE12 selectively influences the biosynthesis of the sorbicillinoid trichodimerol, while not affecting the biosynthesis of bisorbibutenolide, which was recently shown to be regulated by the MAPkinase pathway upstream of STE12 in the signaling cascade. We further report on the biosynthesis of dehydroacetic acid (DHAA) in T. reesei, a compound known for its antimicrobial properties, which is subject to regulation by STE12. We conclude, that STE12 exerts functions beyond development and hence contributes to balance the energy distribution between substrate consumption, reproduction and defense.
Next Generation Sequence-Based Targeted Somatic Mutation Analysis in Thyroid Nodules with Pathologically Diagnosed as Indeterminate Cytology
Authors: Kök Gizem , Nart Deniz , Ertan Yeşim , Özbek Suha Sureyya , Mizrak Ali , Makay Özer , Erdoğan Mehmet , Özışık Hatice , Akın Haluk , Durmaz Burak , Özgür Su , Özdemir Murat , Karaca Emin 
Published: January 2024

Abstract
Purpose: The management of indeterminate thyroid nodules remains a topic of ongoing debate, particularly regarding the differentiation of malignancy. Somatic mutation analysis offers crucial insights into tumor characteristics. This study aimed to assist the clinical management of indeterminate nodules with somatic mutation analysis.
Methods: Aspiration samples from 20 indeterminate thyroid nodules were included in the study. A next-generation sequencing panel containing 67 genes was used for molecular profiling. The results were compared with pathology data from surgical material, which is considered the gold standard. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated.
Results: Variants in six genes (NRAS, BRAF, TP53, TERT, PTEN, PIK3CA) were detected in 10 out of 20 samples. We identified nine Tier 1 or 2 variants in 10 (67%) out of 15 malignant nodules (NRAS, BRAF, TP53, TERT, PTEN, PIK3CA) and one Tier 2 (PIK3CA) variant in one out of five benign nodules. The study demonstrated an NPV of 40%, a PPV of 90%, a specificity of 60%, and a sensitivity of 80%.
Conclusion: Based on the detected molecular markers, at least nine patients (45%) could be managed correctly without needing a repeat FNAB attempt. This study underscores the clinical practicality of molecular tests in managing nodules with indeterminate cytology. Additionally, this study emphasizes the importance of considering the patient's age when determining the DNA- or RNA-based genetic testing method. Finally, we discussed the significance of the somatic mutation profile and its impact on the current pathological classification.
Draft genome from facultatively parthenogenetic Opiliones indicates frequent mitonuclear sequence transfer and novel full-length insertions
Authors: Stellwagen Sarah , Burns Mercedes 
Published: January 2024

Abstract

Background: Facultative parthenogenesis and intra-population mixed ploidy are rare in animals. These unique characteristics allow opportunities to investigate the relationship between sexual modality and ploidy. We have completed a draft genome of the Japanese harvester ("daddy-longlegs") Leiobunum manubriatum, a species which reproduces sexually and asexually, and with mixed diploid and tetraploid populations in some areas.
Results: We combined Oxford Nanopore’s MinION long-read sequencing platform with Dovetail Hi-C scaffolding to assemble the haploid genome for the diploid race, which is approximately 336 MBp after collapsing heterozygous sequence. The assembly’s completeness was measured using BUSCOs from Eukaryota (complete: 92.6%), Arthropoda (complete: 96.9%), and Arachnida (complete: 95.3%). We searched raw sequence reads and the draft genome for nuclear mitochondrial DNA (numt) sequences. While only one complete mitochondrial genomic transfer was found in the draft genome, there are at least 12 complete numts across 9 reads within the raw sequencing data that were lost during the assembly process.
Conclusions: The genome of the L. manubriatum diploid race is an invaluable resource not only for opilionid research, but also for facilitating studies investigating the evolution of their unique reproductive mode and mixed ploidy. To our knowledge, this is the first published genome of a wild-derived facultative parthenogen. Future work will leverage this resource in comparative genomics and transcriptomics of L. manubriatum to understand the connection between ploidy and sexual strategy.
Mendelian Randomization Suggests Major Depression Increases Risk of Allergic Rhinitis
Authors: Shao Dianran , Kang Xiaoming 
Published: January 2024

Abstract
Background: Observational studies have suggested a potential correlation between major depression (MD) and a higher occurrence of allergic rhinitis (AR).
Methods: By employing two-sample Mendelian randomization (MR), this study explored the genetic causality between MD and AR. The summary-level data on MD were derived from the GWAS Catelog. The summary-level GWAS data on AR were extracted from the FinnGen Consortium. The MR analysis was carried out using the inverse-variance weighted (IVW), MR Egger, weighted median, and weighted mode methods. To further identify heterogeneity in the MR results, we applied the Cochrane's Q test. The sensitivity of this association was investigated by using leave-one-out analysis. We used the MR-Egger intercept method and the MR pleiotropy residual sum and outliers (MR-PRESSO) method to assess and address horizontal pleiotropy.
Limitation: Stratified analyses for other nations, races, or age ranges could not be performed due to the fact that our MR analysis relied on GWAS data of European ancestry.
Results: The Mendelian randomization analysis indicated that major depression is a significant risk factor for allergic rhinitis (P = 0.007, OR = 1.23, 95% confidence interval [CI] = [1.057-1.428]). No indication of genetic variation heterogeneity was discovered (P > 0.05), and horizontal pleiotropy seemed unlikely to influence causality. Last but not least, the leave-one-out test revealed that this link was strong and consistent.
Conclusion: This study genetically predicted major depression increased the risk of Allergic Rhinitis.
Pharmacokinetics and drug-likeness of anticancer phytoconstituents: ADMET, Molecular docking, and Simulation studies
Authors: Singh Nootan , Yadav Piyush Kumar , Israr Juveriya , Vaish Swati , Basantani Mahesh Kumar , Singh Ajay Kumar , Gupta Divya , Gupta Garima 
Published: January 2024

Abstract
Breast cancer (BC) is the most commonly diagnosed cancer in women around the world. Several genetic mutations tend to induce the risk of BC progression. SPDEF (Sam pointed domain containing ETS transcription factor) is a prostate-derived ETS factor that maintains homeostasis, differentiation of epithelial tissues, and heritable alterations in cancer. Plant secondary metabolites like flavonoids, terpenoids, and alkaloids have shown anticarcinogenic effect in several literatures. Therefore, in this study the SPDEF protein was used as potential breast cancer therapeutic target. Pharmacokinetic properties (ADMET), drug-likeness, and molecular docking of the fifteen phytoconstituents were assessed against SPDEF protein by various in silico approaches. The results showed that genistein, 2-hydroxychalcone, ajoene, and allicin had no toxicity. As per toxicological endpoints prediction study, the median lethal dosage (LD50) values vary from 159 to 3919 mg/Kg. All of the phytoconstituents derivatives taken into account in this investigation, are projected to be good candidates for P-glycoprotein (p-gp). Using in silico methods, the fifteen phytoconstituents identified from the different plants were predicted for their inhibitory actions against SPDEF protein, suggesting their breast cancer therapeutic potential. Silibinin, codonolactone and genistein have showed the lowest binding energy (-7.7, -6.1 and -6.1 kcal/mol) respectively and predicted to have the best inhibitory effect against SPDEF protein. We selected these three phytoconstituents for molecular dynamic simulation at 200 ns. In a comparison analysis, the Silibinin-receptor complex structure qualifies for the maximum parameters.
The predictions about the pharmacokinetic properties of these phytoconstituents would form the basis for future in vivo, and in vitro experiments to identify the most appropriate therapeutic compound.
Security Enhancement of Playfair Cipher Using Modified Blum Blum Shub Algorithm and Keystream Values
Authors: Muhammed Alemu Jorgi , Woldiegiworgies Tefera Alagaw , Tsegaye Getaneh Geto 
Published: January 2024

Abstract
The Playfair cipher operates as a symmetric en-cryption method, simultanously encrypting pairs of letters. This research aims to enhance the Playfair cipher’s security by incorporating a modified Blum Blum Shub algorithm and utilizing Keystream values. The Blum Blum Shub algorithm undergoes modification through the introduction of four Blum prime numbers, complicating prime factorization. These primes are employed to generate random numbers, subsequently forming a key by mapping the equivalent characters of the generated sequences. In this investigation, we ensure secure key swapping, eliminating the necessity for filler characters when combining related characters in to bigrams.
Additionally, we obscure the relationship between plaintext and ciphertext bigrams by altering the Playfair cipher’s encryption mechanism. Notably, the recipient does not directly receive the key; instead , it independently generates the same key as the sender, resolving the key exchange challenge. The proposed algorithm undergoes evaluation on an HP computer using Matlab software, assessing its performance in terms of the avalanche effect, frequency analysis, key generation, key exchange, and resistance against brute force attack.
The simulation results demonstrate that the proposed algorithm yields a high avalanche effect ratio. It generates a complex key, challenging to predict , and requires a substantial amount of time for cryptanalysis attacks to crack. A slight modification in a single plaintext character results in an average avalanche effect of 80%. Consequently, the proposed approach is more secure than the extended algorithm.