bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Dual Loci Quality Assurance and Control Framework for Real-Time Evaluation of Signal Accuracy in Wastewater Surveillance of Pathogens with High Rates of Mutation
Authors: Thakali Ocean , Mercier Élisabeth , Eid Walaa , Brasset-Gorny Julia , Overton Alyssa K. , Knapp Jennifer J. , Manuel Douglas , Charles Trevor , Goodridge Lawrence , Arts Eric J. , Poon Art F.Y. , Brown R. Stephen , Graber Tyson E. , Delatolla Robert , DeGroot Christopher T. 
Published: August 2023

Abstract
Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has been achieved, in part, by monitoring two or more genomic loci of SARS-CoV-2. In Ontario, Canada, the provincial Wastewater Surveillance Initiative reports the average copies of the CDC N1 and N2 loci normalized to the fecal biomarker pepper mild mottle virus. In November 2021, the emergence of the Omicron variant of concern, harboring a C28311T mutation within the CDC N1 probe region, challenged the accuracy of the consensus between the RT-qPCR measurements of the N1 and N2 loci of SARS-CoV-2. In this study, we developed and applied a novel real-time dual loci quality assurance and control framework based on the relative difference between the loci measurements to the City of Ottawa dataset to identify a loss of sensitivity of the N1 assay in the period from July 10, 2022 to January 31, 2023. Further analysis via sequencing and allele-specific RT-qPCR revealed a high proportion of mutations C28312T and A28330G during the study period, both in the City of Ottawa and across the province. It is hypothesized that nucleotide mutations in the probe region, especially A28330G, led to inefficient annealing, resulting in reduction in sensitivity and accuracy of the N1 assay. This study highlights the importance of implementing quality assurance and control criteria to continually evaluate, in near real-time, the accuracy of the signal produced in wastewater surveillance applications that rely on detection of pathogens whose genomes undergo high rates of mutation.
Immune related gene signature derived from integrate machine learning algorithm predicts outcomes of HNSC patients
Authors: Xiao Lei , Liu Yong , Shen Zhe , Qiu Yuanzheng , Huang Donghai , Liu Chao , Zhang Xin 
Published: August 2023

Abstract
Background: Due to the highly heterogeneous of tumor, head and neck squamous cancer (HNSC) patients are in variable immunotherapeutic response and have different clinical outcomes. We since develop the immune related gene signature (IRGS) using a machine learning based integrative procedure for distinguishing the immune microenvironment subtype of diverse HNSC patients and then help improve the outcomes of HNSC.
Methods: This study integrate 10 machine learning algorithms to 111 combination for screening out the best immune related gene signature (IRGS) based on 4 multicenter cohorts. Survival analysis, multivariate Cox regression analysis, and decision curve analysis (DCA) were employed to assess the performance of IRGS. Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomesenrichment (KEGG) analyses were conducted to evaluate the potential biological functions and mechanisms of IRGS.
Results: Through the integrated machine learning algorithms, we constructed a 17-IRG signature, which demonstrated to be an excellent prognostic model in all cohorts and displayed better efficiency when compared with other 68 published prognostic signatures. IRGS exhibits a strong negative correlation with immune characteristics. The IRGS low group demonstrates increased immune infiltration and heightened sensitivity to immunotherapy, whereas the IRGS high group exhibits a higher frequency of deletion mutations in tumor suppressor genes. Besides, considering IRGS high patients insensitive to immunotherapy and their poor prognosis, we scheduled an agents screening strategy and selected dasatinib as the most potential target drug for IRGS high patients.
Conclusions: IRGS was demonstrated excellent prognostic efficiency and offer a more precise selection for assessing pre-immune efficacy, which will help improve clinical outcomes for individual HNSC patients.
The grey mould Botrytis cinerea employs multiple mechanisms to protect itself from antifungal plant metabolites
Authors: Kan Jan van , You Yaohua , Suraj HM , Valderrama Andrea Lorena Herrera , Ruigrok Paul , Shi-Kunne Xiaoqian , Pieterse Frank , Beenen Henriek , Chavarro-Carrero Edgar , Qin Si , Verstappen Francel , Kappers Iris , Matz Linda , Fleissner Andre 
Published: August 2023

Abstract
Saponins are plant secondary metabolites comprising glycosylated triterpenoids, steroids or steroidal alkaloids with a broad spectrum of toxicity to microbial pathogens and pest organisms that contribute to basal plant defence to biotic attack. Secretion of glycosyl hydrolases that enzymatically convert saponins into less toxic products was thus far the only mechanism reported to enable fungal pathogens to colonize their saponin-containing host plant(s). We studied the mechanisms that the fungus Botrytis cinerea utilizes to be tolerant to well-characterized, structurally related saponins from tomato and Digitalis purpurea. By gene expression studies, comparative genomics, enzyme assays and testing a large panel of fungal (knockout and complemented) mutants, we unraveled four distinct cellular mechanisms that participate in mitigation of the toxic activity of these saponins. The enzymatic deglycosylation is novel and unique to this fungus-saponin combination, while the genes involved in other tolerance mechanisms have orthologs that are widely distributed in the fungal kingdom. We present a spatial and temporal model on how these mechanisms jointly confer tolerance to α- tomatine and we discuss the repercussions for other fungi and different saponins.
Clinical Efficacy and Pathological Outcomes of Transanal Endoscopic Intersphincteric Resection for Low Rectal Cancer
Authors: Xu Zhiwen , Zhu Jingtao , Bai Haoyu , Hong Qingqi , You Jun 
Published: August 2023

Abstract
Purpose
Transanal endoscopic intersphincteric resection (ISR) surgery currently lacks sufficient clinical research and reporting. In this study, we present the surgical outcomes, perioperative complications, and pathological findings based on the transanal endoscopic ISR surgeries performed in our center, aiming to contribute to the clinical application and development of this technique.
Methods
This study utilized a retrospective case series study design. Clinical and pathological data of patients with low rectal cancer who underwent transanal endoscopic ISR at the First Affiliated Hospital of Xiamen University from May 2018 to May 2023 were collected. All patients underwent transanal endoscopic ISR as the surgical approach. We conducted a study to report on the perioperative recovery status, postoperative complications, and pathological specimen characteristics of this group of patients.
Results
This study included a total of 45 eligible cases, with no perioperative deaths. The overall incidence of early complications was 22.22%, with a rate of 4.44% for Clavien-Dindo ≥ III. Two patients (4.4%) developed anastomotic leakage after surgery, including one case of grade A and one case of grade B. Postoperative pathological examination confirmed negative circumferential resection margin (CRM) and distal resection margin (DRM) in all patients. The distance between the tumor lower margin and DRM was found to be 2.30 ± 0.62 cm. Transanal endoscopic ISR surgery consistently yields excellent quality pathological specimens.
Conclusions
Transanal endoscopic ISR is safe and feasible, providing a clear anatomical view. It is associated with a low incidence of postoperative complications and achieves favorable pathological outcomes, making it worthy of further research and application.
Identification of subtype recognition and prognosis model characterized by Antibody-dependent cell phagocytosis related genes in breast cancer
Authors: Wang Li , Li Menghan , Yang Hongyu , Dai Fenghuan , Xie Ning , Li Linhui , Zhu Meiying , Ding Ran 
Published: August 2023

Abstract
Background
Breast cancer (BC) is a heterogeneous tumor with a variety of etiology and clinical features. Antibody-dependent cell phagocytosis (ADCP) is the last step of immune checkpoint inhibition (ICI), and macrophages destroy tumor cells after previous recognition activation. Despite the large number, negative regulators that inhibit phagocytic activity are still a key obstacle to the full efficacy of ICI.
Patients and methods:
An ADCP -related risk score prognostic model for risk stratification as well as prognosis prediction was established in the Cancer Genome Atlas (TCGA) cohort. The predictive value of ADCP risk score in prognosis and immunotherapy was also further validated in the TCGA along with International Cancer Genome Consortium cohorts. To promote the clinical application of the risk score, a nomogram was established, with its effectiveness verified by different methods.
Results
In this study, the genes collected from previous studies were defined as ADCP-related genes. In BC patients, two ADCP-related subtypes were identified. The immune characteristics and prognostic stratification were significant different between them.
Conclusion
Based on these findings, it can be inferred that there is a significant relationship between ADCP and TME (tumor microenvironment) in BC. Risk score could be used as a good indicator for prognosis, potential in providing therapeutic advantages for chemotherapy as well as immunotherapy, thereby aiding in the clinical decision-making process for BC patients.
Study of growth-improving and sporophore-inducing endobacteria isolated from Pleurotus pulmonarius
Authors: Paul Chandana , Roy Tina , Singh Kunal , Maitra Madhumita , Das Nirmalendu 
Published: August 2023

Abstract
Several Pleurotusspecies (oyster mushrooms) are commercially cultivated in India owing to the favorable tropical agro-climatic conditions. However, there are only a few studies on the microbiome of mushrooms, especially oyster mushrooms. The aim of this study was to assess the effect of endophytic bacteria on mycelial growth, spawning, sporophore development, and proximate composition of P. pulmonarius. We isolated several bacterial strains from the sporophores of P. pulmonarius and assessed the in vitro production of indole acetic acid, ammonia, and siderophores. The selected bacteria were individually supplemented with spawn, substrate, or both for sporophore production. Three of 130 isolates were selected as mycelial growth-promoting bacteria in both solid and submerged fermentation. These bacterial isolates were identified through Gram staining, biochemical characterization, and 16S rRNA sequencing. Isolate PP showed 99.24% similarity with Priestia paraflexa, whereas isolates PJ1 and PJ2 showed 99.78% and 99.65% similarities, respectively, with Rossellomorea marisflavi. The bacterial supplementation with spawn, substrate, or both, increased the biological efficiency (BE) and nutrient content of the mushrooms. The bacterial supplementation with substrate augmented BE by 64.84%, 13.73%, and 27.13% using PJ2, PP, and PJ1, respectively; under similar conditions of spawn supplementation, BE wasincreased by 15.24%, 47.03%, 48.10%, respectively. Overall, the supplementation of endophytic bacteria to improve oyster mushroom cultivation may open a new avenue for sustainable agricultural practices in the mushroom industry.
Securing the Perceptual Layer of E-Payment-Based Internet of Things Devices Using Elliptic Curve Cryptography
Authors: Okediran T. M , Vincent O. R , Abayomi-Alli A. A , Adeniran O. J 
Published: August 2023

Abstract
The security of IoT layers has become paramount considering the various attacks facing IoT devices, especially the perceptual layer. Reported attacks in recent times include direct Denial of Service (DDoS), botnet attacks, and falsification attacks. Some security schemes, such as the symmetric polynomial concept, privacy-preserving communication protocols for IoT applications, blockchain-based secure IoT systems, and mutual authentication systems for wearable technology, cannot be directly implemented on the perceptual layer of the IoT device. This study presents a binary field elliptic curve cryptography algorithm for the security of the perceptual layer of IoT, such as mobile phones, contactless cards, and POS devices in electronic payment transactions. The IoT devices have four layers: the application, support, network, and perceptual or sensor layer. The sensors of the devices were locked against any communication between the nodes. Each device is recognised and locked against all forms of communication. Device authentication for key agreement and unlocking, communication phase for exchange of information. The evaluation of this study is based on storage capacity, computational time, and jitter. It was implemented on a contactless ATM card, POS device, and a mobile phone as an IoT device for electronic payment. The evaluation result for storage capacity showed that the mobile phone and the ATM card could run the ECC security protocol directly. The Jitter result reveals that the Jitter value did not deviate from normal for both devices. At the same time, the computational time showed that it is computationally efficient to use ECC over the binary field for the security of the perceptual layer. This scheme is efficient for the security of IoT.
Bayesian Inference on the Inverse Weibull Model Parameters Based on Kernel Prior
Authors: Maswadah M. 
Published: August 2023

Abstract
In this paper, the theory of statistical kernel density estimation has been used for deriving the kernel prior, which frees the Bayesian inference from subjectivity to a personal choice that has worried some statisticians. For measuring the performance of the informative kernel prior compared to the informative gamma prior, the mean squared error and mean percentage error have been obtained, via Monte Carlo simulations, for the inverse Weibull model parameters. The simulation results indicated that the informative kernel prior competes with and outperforms the informative gamma prior for different sample sizes. Finally, a numerical example is given to illustrate the proposed priors developed in this paper.
The wave mechanics for microwave absorption film-Part 1: A short review
Authors: Liu Yue , Liu Ying , Drew Michael 
Published: August 2023

Abstract

It has been proved from transmission line theory that the mechanism of microwave absorption in film is different from that in material. It is a simple result but has not yet been generally accepted by the research community. It is commonly argued that microwaves are trapped by the back-and-forth reflections in the film and then absorbed by material along the zigzag path and thus researchers believe the film need not be considered as a separate entity with its own unique properties. It is believed that the current theory for microwave absorption is supported by much experimental data. However, via such data, Part 1 demonstrates that the data can be interpreted differently and more accurately by invoking the crucial role of the film which will be further evaluated from a new perspective in Part 2 for the difference between film and material, and in Part 3 for multilayer film design.
YOLOv5DA: an improved YOLOv5 model for pig posture detection in a herd environment
Authors: Wang Haiyan , Liu Xiaolei , Fu Yuhua , Li Xuan , Wang Xiaopin , Shi Wenhui 
Published: August 2023

Abstract
Animal behavior is an important indicator for diagnosing diseases, and accurate posture detection is the foundation for analyzing animal behavior and emotional states, which can promote animal welfare. However, current methods for pig posture detection often suffer from problems of missed or false detection due to the aggregation, occlusion, and adhesion of pigs in a herd environment. This study proposed a new object detection model (YOLOv5DA) for pig posture detection based on YOLOv5s, which incorporates Mosaic9 data augmentation, deformable convolution, and adaptively spatial feature fusion, to effectively deal with missed or false detection in the case of mutual occlusion and bonding of pig bodies. The images of pigs were first collected and annotated, and a dataset was established. Then, by using the established dataset, an object detection model YOLOv5DA based on YOLOv5s was trained. Finally, the test results showed that YOLOv5DA could accurately identify the three postures of standing, prone lying, and side lying with an average precision (AP) of 99.4%, 99.1%, and 99.1%, respectively, and the performance is superior to that of mainstream object detection algorithms including Faster-RCNN, YOLOv4, YOLOv5, FCOS, and CenterNet. Compared with YOLOv5s, YOLOv5DA could effectively handle occlusion while increasing the mean precision (mAP) by 1.7% in complex scenarios, which reached about 86.8%. Overall, YOLOv5DA provides a highly accurate, effective, low-cost, and stress-free strategy for pig posture detection in the herd environment, which can elevate the application of intelligent technique in the pig industry.
Reproductive Toxicity of Nanoparticles: A Comprehensive Review
Authors: Ramezani Mohammad , Giesy John P. , Sahebkar Amirhossein , Mohammadi Elaheh , Behnam Behzad , Mokhtarzadeh Ahad , Rezaee Ramin , Abiri Ardavan 
Published: August 2023

Abstract:
The unique characteristics of nanoparticles (NPs) have captivated scientists in various fields of research. However, their safety profile has not been fully scrutinized. In this regard, the effects of NPs on the reproductive system of animals and humankind have been a matter of concern. In this article, we will review the potential reproductive toxicity of various types of NPs, including carbon nanomaterials, dendrimers, quantum dots, silica, gold, and magnetic nanoparticles, reported in the literature. We also mention some notable cases where NPs have elicited beneficial effects on the reproductive system. This review provides extensive insight into the effects of various NPs on sperm and ovum and the outcomes of their passage through blood-testis and placental barriers and accumulation in the reproductive organs.
In-silico Identification of Dexamethasone-similar Compounds Against
SARS-Cov-2 Spike Protein: A Drug Repurposing Approach
Authors: Pathak Yamini , Tripathi Vishwas , Camps Ihosvany , Qais Faizan Abul , Mishra Amaresh 
Published: August 2023

Abstract:
To identify potential drug candidates for the treatment of COVID-19 using a computational
method. The recent pandemic of COVID-19 is observed as not less than a natural calamity of humankind
and raised serious concerns for its immediate management. The continued spread of coronavirus
disease across the globe poses a significant threat to human health. Out of this, the application of Dexamethasone
has been correlated with reduced mortality in COVID-19 cases. This study sheds new
light on the pharmacological potential of Dexamethasone and similar compounds in mitigating SARSCoV2
infection.

:
In this study, we explored Dexamethasone-similar compounds, which can modulate the binding of
SARS-CoV-2 spike protein to the host and TH17 programming in the host using a computer-aided
drug repurposing method. The docking studies indicate that Desoximetasone can bind to the spike
proteins of SARS-CoV-2, which are crucial for viral attachment and entry into host cells. By competing
with these spike proteins, Desoximetasone may interfere with the virus's ability to attach to and
enter host cells, potentially inhibiting viral replication and spread. The results from molecular dynamic
simulation analysis further support this notion by demonstrating that Desoximetasone has a strong
interaction with the binding sites of the spike protein. Experimental validation through in vitro studies
and clinical trials is needed to evaluate its potential as a treatment option for COVID-19. Together,
these findings revealed the underlying mechanism of how Desoximetasone can influence the fate of
the virus in the host and advocated its anti-viral potential.
Computing the Energy of Certain Graphs based on Vertex Status
Authors: Khurshid Asim , Salman Muhammad 
Published: August 2023

Background:
The concept of Hückel molecular orbital theory is used to compute the graph energy numerically and graphically on the base of the status of a vertex.

Objective:
Our aim is to explore the graph energy of various graph families on the base of the status adjacency matrix and its Laplacian version.

Methods:
We opt for the technique of finding eigenvalues of adjacency and Laplacian matrices constructed on the base of the status of vertices.

Results:
We explore the exact status sum and Laplacian status sum energies of a complete graph, complete bipartite graph, star graphs, bistar graphs, barbell graphs and graphs of two thorny rings. We also compared the obtained results of energy numerically and graphically.

Conclusion:
In this article, we extended the study of graph spectrum and energy by introducing the new concept of the status sum adjacency matrix and the Laplacian status sum adjacency matrix of a graph. We investigated and visualized these newly defined spectrums and energies of well-known graphs, such as complete graphs, complete bi-graphs, star graphs, friendship graphs, bistar graphs, barbell graphs, and thorny graphs with 3 and 4 cycles.
Evaluating the Antidepressant-like Properties of Melatonin and Vitamin
D3 Combination in Mice Subjected to Restraint Stress: Investigating the
Involvement of Oxidative Stress
Authors: Mehrzadi Saeed , Hosseini Asieh , Hassani Shokoufeh , Azimirad Fahime , Hosseinzadeh Azam 
Published: August 2023

Background:
Increased levels of oxidative stress are connected with depression. Due to the
melatonin's antioxidant effects and Vitamin D3 (Vit D3)'s regulatory effect on the biosynthesis of neurotransmitters
and neurotrophic factors, the present study investigated the possible protective effect of
melatonin and Vit D3 combination on restraint stress-induced depression-like behaviors in mice.

Methods:
After being subjected to restraint stress, mice were divided into six groups using a randomization
process. These groups included non-stressed and stressed vehicle-treated groups, as well as
groups treated with Vit D3 (25 μg/kg/day), melatonin (10 mg/kg) or fluoxetine. A group also received
a combination of both melatonin and Vit D3. The Forced Swimming Test (FST), and Open Field Test
(OFT) were conducted to evaluate behavioural changes. The Malondialdehyde (MDA) level and Catalase
(CAT), Superoxide Dismutase (SOD) activity, and ADP/ATP ratio were evaluated in the hippocampus
of mice.

Results:
Restraint stress lengthened the immobility period in FST, while melatonin, Vit D3, and their
combination all significantly reversed this impact. Co-administration of melatonin and Vit D3 was
more effective than melatonin or Vit D3 administration alone at reducing immobility time. The exposure
of mice to restraint stress has been linked to an elevation in the ADP/ATP ratio and oxidative
stress in their hippocampus; however, these effects are reversed by the administration of melatonin
and Vit D3 (10 mg/kg) alone or in combination. Melatonin and Vit D3 combination increased the hippocampus
CAT activity compared with melatonin and Vit D3 alone.

Conclusion:
The current study's findings suggested that Vit D3 may enhance melatonin's potential as
an antidepressant in FST.