bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrochemical DNA Biosensor for detection of Avian Infectious Bronchitis virus (IBV) using Gold Modified Electrode with Glutaraldehyde as cross linker
Authors: Bhuiyan Md. Safiul Alam 
Published: September 2023

Abstract
Infectious bronchitis virus (IBV) belongs to the Gamma coronavirus family of avian species, which is characterized by respiratory infections, nephropathy, and permanent damage to the oviduct, resulting in high mortality in both layer and broiler chickens. IBV has caused significant financial losses and a lack of on-farm diagnostic tools, posing a significant challenge for disease prevention and control. The development of DNA biosensors has increased the importance of rapid and accurate detection of the viral disease in poultry. In this study, an electrochemical DNA biosensor was developed based on a gold electrode fabricated with a nanocomposite of chitosan (CS), multi-walled carbon nanotubes (MWNTs), and highly reactive glutaraldehyde (GLU). The biosensor utilized the target-specific Orf gene of IBV. Under optimal parameters, immobilization and hybridization efficiencies were evaluated using cyclic voltammetry (CV) and differential pulse voltammetry (DPV), with methylene blue used as the redox indicator. The proposed DNA biosensor successfully detected the target DNA in a range of 2.0 x 10–12 to 2.0 x 10− 5 molL-1, with a limit of detection (LOD) and limit of quantitation (LOQ) of 2.6 nM and 0.79 nM, respectively. Cross-reactivity studies were performed against non-IBV viruses, consistently validating its sensitivity for detection. The hybridization event was analyzed in real samples by applying the selected probe to the modified gold electrode, using crude cDNA and PCR products. The recovery rate ranged from 95.41–104.55%. These results demonstrate that the proposed DNA biosensor has the potential to accurately detect various strains of IBV in real samples. Additionally, it offers a rapid, sensitive, and alternative technique for diagnosing IBV disease, addressing the current challenges in disease prevention and control.
Pathogenicity of the root lesion nematode Pratylenchus neglectus depends on pre-culture conditions
Authors: Fatemi Ehsan , Jung Christian 
Published: September 2023

Abstract
The ability of a plant parasitic nematode to infect and reproduce within a host plant depends on its genotype and the environmental conditions before and during infection. We studied the culturing conditions of the root lesion nematode Pratylenchus neglectus to produce inoculum for plant infection tests. Nematodes were either cultivated on carrot calli for different periods or directly isolated from the roots of the host plants. After infection of wheat and barley plants in the greenhouse, nematodes were quantified by RT-qPCR and by visual counting of the nematodes. We observed drastically reduced infection rates after long-term (> 96 weeks) cultivation on carrot callus. In contrast, fresh isolates from cereal roots displayed much higher pathogenicity. We recommend using root lesion nematodes cultivated on carrot calli no longer than 48 weeks to guarantee uniform infection rates.
Natural deep eutectic solvents characteristics determine their extracting and protective power on chlorogenic acids from sunflower meal
Authors: Bezerra Fernanda de Sousa , Ramos Gabriela Soares Macello , Carvalho Matheus Grilo de Oliveira , Koblitz Maria Gabriela Bello 
Published: September 2023

Abstract
Sunflower meal is a residue of the edible oil extraction and a promising source for the extraction of phenolic compounds, especially the chlorogenic acid family. Their clean extraction and later conservation may be improved by the use of natural deep eutectic solvents (NaDES). This study evaluated the extraction and stability of phenolic compounds from sunflower meal using different combinations of NaDES and ethanol, as control. The principal aim was finding a clean extraction method for this rich bioactive compound by-product. The results showed that all solvents extracted similar phenolic compounds, but the most acidic NADES showed higher efficiency. In terms of stability, this acidic NaDES showed better protection against heat treatment and storage, while ethanol exhibited better stability under light exposure. The findings suggest that the NaDES composition, pH and other characteristics may influence both, extraction efficiency and stability, enabling the clean use and valorization of this residue from the agroindustry.
Cytogenomic investigation in 151 Brazilian infertile male patients: Experience of 14 years in a public genetic service
Authors: Adriano Márcia Regina Gimenes , Bortolai Adriana , Madia Fabricia Andreia Rosa , Carvalho Gleyson Francisco da Silva , Nascimento Amom Mendes , Zanardo Evelin Aline , Wolff Beatriz Martins , Waisberg Jaques , Bos-Mikich Adriana , Kulikowski Leslie Domenici , Dias Alexandre Torchio 
Published: September 2023

Abstract
Objectives
Male infertility accounts for approximately 30% of cases of reproductive failure. The characterization of genetic variants using cytogenomic techniques is essential for the adequate clinical management of these patients. We aimed to conduct a cytogenetic investigation of numerical and structural rearrangements and a genomic study of Y chromosome microdeletions/microduplications in infertile men derived from a single centre with over 14 years of experience.
Results
We evaluated 151 infertile men in a transversal study using peripheral blood karyotypes and 15 patients with normal karyotypes through genomic investigation by multiplex ligation-dependent probe amplification (MLPA) or polymerase chain reaction of sequence-tagged sites (PCR-STS) techniques. Out of the 151 patients evaluated by karyotype, 13 presented chromosomal abnormalities: 2 had numerical alterations, and 11 had structural chromosomal rearrangements. PCR-STS detected a BPY2 gene region and RBMY2DP pseudogene region microdeletion in one patient. MLPA analysis allowed the identification of one patient with CDY2B_1 and CDY2B_2 probe duplications (CDY2B gene) and one patient with BPY2_1, BPY2_2, and BPY2_4 probe duplications (BPY2 gene).
Virseqimprover: An Integrated Pipeline for Viral Contig Error Correction, Extension, and Annotation
Authors: Song Haoqiu , Tithi Saima , Aylward Frank , Jensen Roderick , Zhang Liqing 
Published: September 2023

Abstract
Background: Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference.
Methods: We have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality. Virseqimprover first examines whether there is any chimeric sequence based on read coverage, breaks the sequence into segments if there is, then extends the longest segment with uniform coverage, and repeats these procedures until the sequence cannot be extended. Finally, Virseqimprover annotates the gene content of the resulting sequence.
Conclusion: Virseqimprover has good performance on correcting and extending viral contigs to their full lengths, hence can be a useful tool to improve the completeness and minimize the assembly errors of viral contigs. Both a web server and a conda package for Virseqimprover are provided to the research community free of charge.
Reactive oxygen species profiles reveal the tumor immune micro-environment and clinical outcomes of skin cutaneous melanoma
Authors: Yue Chao , Lian Wenqin , Duan Mengying , Xia Die , Cao Xianbin , Peng Jianzhong 
Published: September 2023

Abstract
Skin cutaneous melanoma (SKCM) is a cancer formed by the malignant transformation of melanocytes in the basal layer of the skin. Reactive oxygen species (ROS) are thought to be a significant factor influencing tumor development, yet the link between SKCM and ROS is still unclear. Four datasets (TCGA-SKCM and GEO-GSE19234, GSE54467, and GSE65904) were adapted to perform multi-omics analysis. A total of 28 prognostic ROS-related genes (ROSRGs) were identified, and consensus clustering analysis was conducted to elucidate the prognostic value of ROSRGs in SKCM. ssGSEA and GSVA analyses were used to explore the potential biological and immunological implications of ROS clusters in SKCM patients. In addition, we built and validated a risk prognostic model for the ROSRGs signature in SKCM. The results indicated significantly shorter survival times for high-risk patients. The applicability of the established ROSRG signature to different patient populations was also demonstrated in the study. Go, KEGG, and mutation analysis were employed to explore the functions of the 446 DEGs. We used various algorithms to examine immune cell infiltration to discover insights into the immune microenvironment of SKCM. The high-risk group was also found to exhibit lower TIDE scores, suggesting the possibility of higher responsiveness to immunotherapy. Besides, we explored the possibility of personalized therapy regimens based on patient subgroups. Finally, we gain further insight into the immune microenvironment of SKCM at the single-cell level. Signature expression levels were higher in monocytes, macrophages, and B cells. In Conclusion, we explored the relationship between SKCM and ROS through multi-omics approaches and further investigated potential immune checkpoints in SKCM and genes affecting tumor heterogeneity in SKCM. Our findings provided novel ideas for personalized clinical treatment of SKCM patients and new evidence for improving the prognosis and preventing metastasis in SKCM patients.
Ontology Supported Semantic Based Image Retrieval
Authors: Gasi Akif , Dagtekin Mustafa , Ensari Tolga 
Published: September 2023

Abstract
Semantic-Based Image Retrieval (SBIR) is the process of searching for images in a database that have similar relationships between the objects detected in an image and the defined objects. The relationships in the subject-predicate-object structure are transformed into a structure that computers can make sense out of with Ontologies and are used to search for semantically similar images. In this study, a two-stage approach for developing a Semantic Based Image Retrieval system supported by Ontology is proposed. In the first stage, objects are detected with the Object Detection process from the image and a predicate describing the relationship between the two objects is determined with the developed Bi-directional Recurrent Neural Network (Bi-RNN) model. In the second stage, relations defined as are converted into Ontologies and used to search for semantically similar images. The Visual Genome dataset is used in the training of the developed Bi-RNN model and generation of the ontologies. In the performance measurement of the developed model, 91\% accuracy was obtained according to the Recall@100 (Top-5 accuracy) result. The proposed approach has the characteristics of a new method used in this field and gives more effective results compared to other similar methods that are used in Semantic Based Image Retrieval by using Ontologies.
C-terminal agrin fragment as a novel biomarker of kidney function in obese children and adolescents.
Authors: Medyńska Anna , Chrzanowska Joanna , Zubkiewicz-Kucharska Agnieszka , Zwolińska Danuta 
Published: September 2023

Abstract
Background: Obesity is a global health problem which has a negative impact on many organs, including kidneys. Studies, conducted mainly in obese adults have confirmed that obesity is associated with increased risk of chronic kidney disease (CKD) development. So, the detection of early kidney lesions is crucial for the patients.
The aim of the study was to determine the usefulness of serum C-terminal fragment of agrin (t-CAF) and cystatin C levels along with hyperfiltration as indicators of kidney function damage in obese children and their relationship with the severity of obesity.
Material and methods: 125 children and adolescents with simple obesity and 33 healthy peers with normal body mass were enrolled. Patients were divided into two groups, depending on SDS BMI values (below and over 4). The serum concentration of t-CAF and cyststic C were assessed by ELISA, eGFR was calculated using Schwartz formula
Results: t-CAF and cystatin C as well as eGFR were significantly higher in obese children compared to healthy peers (p< 0.000). However, there were no differences in t-CAF, cystatin C and eGFR between the obese groups. Albumin excretion did not distinguish obese groups from the controls.
Conclusions:
In obese children without overt signs of kidney damage, hyperfiltration promotes early kidney dysfunction. This is supported by elevated serum cystatin C and t-CAF levels. t-CAF seems to be a better biomarker than cystatin C due to its potential role in adipogenesis. The degree of obesity in children without significant metabolic disorders does not affect kidney function but further studies are needed to confirm it.
On a Simple Connection Between ∆-modular ILP and LP, and a New Bound on the Number of Integer Vertices
Authors: Gribanov Dmitry , Malyshev Dmitry , Shumilov Ivan 
Published: September 2023

Abstract
In our note we present a very simple and short proof of a new interesting fact about the faces of an integer hull of a given rational polyhedron. This fact has a complete analog in Linear Programming theory and can be useful to establish new constructive upper bounds on the number of vertices in integer hulls of $\Delta$-modular polyhedra, which can theoretically be useful for integer linear maximization problems with a convex or quasiconvex objective function. Additionally, we introduce the notion of \emph{deep bases} of a linear program. The problem to estimate their number by a non-trivial way seems to be quite challenging.
Alterations in the Tear Film and Ocular Surface in Pediatric Migraine Patients
Authors: Aşık Abdulvahit , Aydemir Gözde Aksoy , Aydemir Emre , Bilen Abdurrahman , İpek Rojan , Ballı Haci , Bayat Alper Halil , Türk Bilge Aydın 
Published: September 2023

Abstract
Purpose:To evaluate the ocular surface (OS) parameters in the pediatric migraine patients (PMPs).
Methods: This prospective case-control designed study consisted of 51 PMPs (PMP Group) and 55 healthy pediatric patients (HPP Group). In all participants were evaluated of tear function by subjective (Ocular Surface Disease Index (OSDI) questionnaire), objective (Schirmer tear test (STT) and tear film break-up time (TBUT)), clinical and laboratory investigations (conjunctival impression cytology (CIC)). The PMP Group was divided into 2 according to their aura.
Results: The mean age and gender distribution of the study groups were almost the same (for both of them: P > 0.05). In the PMP Group, both the STT value and the TBUT value were significantly lower than those determined in the HPP Group (P = 0.021, P = 0.018, respectively). In the PMP Group the OSDI scores of were higher than those in the HPP Group (P = 0.032). In the PMP Group, the goblet cell density (GCD) values were lower than those in the HPP Group (P = 0.01). In regard to the aura, the TBUT and STT values were non-significantly lower in the PMP aura-positive group than in the PMP aura-negative group (for both of them: P > 0.05). The OSDI assessment was similar in both of the groups. In regard to the goblet cell count, it was observed to be less in the PMP aura-positive group than in the PMP aura-negative group (P = 0.01).
Conclusion: Influence of the OS in children with migraine was also demonstrated with samples taken from the conjunctiva. These changes were also demonstrated by objective tests such as STT and TBUT. Both clinical objective evaluations and pathological changes were more prominent in the migraine with aura group.
Use of choline alfoscerate for newly diagnosed patients with Alzheimer’s disease in Korea
Authors: Kim Yeon Hee , Jeon Nakyung , Je Nam Kyung 
Published: September 2023

Abstract
Purpose: Choline alfoscerate, a cholinergic precursor in the brain, improves dementia-related symptoms. Although it is widely available as a dietary supplement in several countries, including the U.S., the Korean healthcare system has incorporated it into its insurance coverage. Therefore, in this study, we aimed to investigate the utilization status of choline alfoscerate and factors influencing it in patients newly diagnosed with Alzheimer’s disease (AD) using real-world data.Methods: We analyzed the Health Insurance Review and Assessment Service research dataset to identify patients ≥ 60 years old who were newly diagnosed with AD. We determined whether the study population was prescribed choline alfoscerate in addition to AD medications (donepezil, rivastigmine, galantamine, and memantine) within 60 d of the initial diagnosis. Moreover, the Cochran–Armitage test was used to confirm the statistical differences in the annual drug utilization trends.Results: Among the 330,326 study participants, 99,845 (33.08%) were consuming choline alfoscerate. Its use increased from 15.96% in 2012 to 47.65% in 2019. Factors that positively influenced the use of choline alfoscerate included male sex, MedAid insurance, and osteoarthritis. However, its use tended to decrease in the presence of certain comorbidities (hypertension, congestive heart failure, stroke/transient ischemic attack, chronic kidney disease, and depression).Conclusion: Utilization of choline alfoscerate has gradually increased in Korea, in part due to the absence of a disease-modifying therapy for AD and its inclusion in the country’s insurance coverage system. However, its use should be monitored due to the unclear efficacy and risk profile of this drug.
Ultrasonic Bone Curette‐Assisted Unilateral approach for bilateral decompression with MISTLIF for Severe lumbar spinal stenosis
Authors: Shao Minglei , Ren Yuebing , Nian Ying , Sun Tongxin 
Published: September 2023

Abstract
Purpose
We aim to evaluate the clinical efficacy of bilateral decompression with minimally invasive transforaminal lumbar interbody fusion (MISTLIF) assisted by ultrasonic bone Curette (UBC) in treating severe degenerative lumbar spinal stenosis (DLSS) and traditional tool laminectomy decompression MISTLIF in treating severe DLSS.
Methods
The clinical data of 128 patients with single-segment severe DLSS admitted between January 2017 and December 2021 were retrospectively analyzed. Among them, 67 patients were treated with unilateral fenestration and bilateral decompression MIS-TLIF using ultrasonic bone Curette (UBC group), whereas 61 patients were treated with unilateral fenestration and bilateral decompression MIS-TLIF using traditional tools (traditional group, control). A visual analog scale (VAS) was used to evaluate the low back pain before the operation, one week, and 1, 3, 6, 12, and 24 months after the operation. Oswestry disability index (ODI) and Zurich claudication score (ZCQ) were used to evaluate the improvement of low back function. At the last follow-up, the Bridwell bone graft fusion standard was used to evaluate the bone graft fusion.
Results
The decompression time of laminectomy was significantly shorter in the UBC group than in the traditional group (control group), and the intraoperative blood loss and postoperative drainage volume were significantly less than those in the control group (P < 0.05). The VAS, ODI, and ZCQ scores of the two groups after the operation were significantly improved compared to those before the operation (P < 0.05). The UBC group had better VAS and ODI scores than the control group one week after operation (P < 0.05). The incidence of perioperative complications, hospitalization time, dural sac cross-sectional area (CSA), and dural sac CSA improvement rate did not differ significantly between the two groups (P > 0.05). VAS and ODI scores did not differ significantly between the two groups before, six months, one year, and two years after operation (P > 0.05). ZCQ score did not differ significantly between the two groups before the operation, one week, six months, one year, and two years after the operation (P > 0.05). According to the Bridwell bone graft fusion standard, bone graft fusion did not occur significantly between the two groups (P > 0.05) at the last follow-up.
Conclusions
UBC unilateral fenestration bilateral decompression MIS-TLIF in treating severe DLSS can obtain similar clinical efficacy as traditional tools unilateral fenestration bilateral decompression MIS-TLIF and can reduce intraoperative blood loss and postoperative drainage. It can also shorten the operation time, effectively reduce the work intensity of the operator, and reduce the degree of low back pain during short-term follow-up. It is a safe and effective surgical method.
Few−shot learning of frame structure damage detection based on Meta−Learning and DCCMN model
Authors: Cai Chaozhi , Guo Xiaoyu , Fu Wenmei , Ren Jianhua 
Published: September 2023

Abstract
In response to the poor detection performance of frame structure under limited data conditions, this paper proposes a novel approach. This approach is based on the concepts of dynamic convolution and models such as ResNet and ShuffleNet. It introduces a Cross − Mix module and builds upon it to formulate the DCCMN (Dynamic Convolution Cross − Mix Network) model. Meta − Learning and the DCCMN model are applied to detect frame structure damage under few − shot scenarios (Meta + DCCMN). Experiments are conducted on the floor frame structure of Columbia University to validate the effectiveness of this approach. The proposed approach is subjected to N − way K − shot experiments and compared under the same conditions with SVM, ResNet − 18, DCCMN, and Meta + ResNet − 18 models. Experimental results demonstrate that, in the case of few − shot learning, the accuracy of this approach can reach 100% in 2 − way 5 − shot and 9 − way 10 − shot scenarios. Furthermore, the proposed damage detection approach outperforms other models, effectively addressing frame structure detection challenges under limited data conditions.
Biogenic synthesis of silver nanoparticles from marine fungi Aspergillus flavus OQ651270: Their characterization and biological studies
Authors: Hamed Moaz , Kelany Mahmoud S 
Published: September 2023

Abstract
Background
Silver nanoparticles (Ag-NPs) have an astounding range of modern applications, which has led to extensive and cutting-edge research and development. Studies on the antibacterial properties of silver nanoparticles (Ag-NPs) were the focus of this work, along with their manufacture, characterization and some biological studies.
Results
Our extracellular biosynthetic approach to creating Ag-NPs was eco-friendly. Extracts of the marine fungus Aspergillus flavus MK4 were utilized as reducing agents to create the nanoparticles. UV-Visible spectroscopy was used to observe the production of colloidal Ag-NPs. The Plasmon absorbance of the Ag-NPs was observed as a peak in the UV-Visible spectrum at 450 nm. Transmission Electron Microscopy (TEM) techniques were used to characterize the Ag-NPs in terms of size and shape, and the results showed a size range of 15 nm with a spherical shape. Both Gram-negative and Gram-positive bacteria were used to examine Ag-NPs' potential antibacterial effects. All the bacterial strains are demonstrating good antibacterial activity. The cytotoxic activity was tested against the HepG-2 cell line using the MTT assay, while the antioxidant property was analyzed using the radical scavenging (DPPH) assay. Silver nanoparticles synthesized in this way have properties that make them promising for antibacterial, anticancer, and wound-healing uses.
Conclusion
Aspergillus flavus MK4 has a strong ability to synthesize Ag-NPs, which has been well characterized and has been shown to have good antibacterial, antioxidant, anticancer and wound healing ability.