bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arbuscular mycorrhizal fungi and Streptomyces: brothers in arms to shape the structure and function of the hyphosphere microbiome in the early stage of interaction
Authors: Jin Zexing , Jiang Feiyan , Wang Letian , Declerck Stéphane , Feng Gu , Zhang Lin 
Published: May 2024

Abstract
Background
Fungi and bacteria coexist in a wide variety of environments, and their interactions are now recognized as the norm in most agroecosystems. These microbial communities harbor keystone taxa, which facilitate connectivity between fungal and bacterial communities, influencing their composition and functions. The roots of most plants are associated with arbuscular mycorrhizal (AM) fungi, which develop dense networks of hyphae in the soil. The surface of these hyphae (called the hyphosphere) is the region where multiple interactions with microbial communities can occur, e.g., exchanging or responding to each other’s metabolites. However, the presence and importance of keystone taxa in the AM fungal hyphosphere remain largely unknown.

Results
Here, we used in vitro and pot cultivation systems of AM fungi to investigate whether certain keystone bacteria were able to shape the microbial communities growing in the hyphosphere and potentially improved the fitness of the AM fungal host. Based on various AM fungi, soil leachates, and synthetic microbial communities, we found that under organic phosphorus (P) conditions, AM fungi could selectively recruit bacteria that enhanced their P nutrition and competed with less P-mobilizing bacteria. Specifically, we observed a privileged interaction between the isolate Streptomyces sp. D1 and AM fungi of the genus Rhizophagus, where (1) the carbon compounds exuded by the fungus were acquired by the bacterium which could mineralize organic P and (2) the in vitro culturable bacterial community residing on the surface of hyphae was in part regulated by Streptomyces sp. D1, primarily by inhibiting the bacteria with weak P-mineralizing ability, thereby enhancing AM fungi to acquire P.

Conclusions
This work highlights the multi-functionality of the keystone bacteria Streptomyces sp. D1 in fungal-bacteria and bacterial-bacterial interactions at the hyphal surface of AM fungi.
Order within chaos: potential migratory strategies and individual associations in fin whales feeding off Iceland
Authors: García-Vernet Raquel , Rita Diego , Bérubé Martine , Elgueta-Serra Julia , Pascual Guasch Marina , Víkingsson Gísli , Ruiz-Sagalés Marc , Borrell Asunción , Aguilar Alex 
Published: May 2024

AbstractBackgroundThe life cycle of most baleen whales involves annual migrations from low-latitude breeding grounds to high latitude feeding grounds. In most species, these migrations are traditionally considered to be carried out according to information acquired through vertical social learning during the first months of life and made individually. However, some recent studies have suggested a more complex scenario, particularly for the species of theBalaenopteragenus.MethodsHere, we studied the variation of δ15N and δ13C values along the growth axis of the baleen plate from 24 fin whales feeding off western Iceland to delve into their pattern of movements and to identify potential associations between individuals. The segment of baleen plate analyzed informed about at least two complete migratory cycles. We performed cluster analyses through two different methodologies and, whenever possible, we genotyped 20 microsatellite loci to determine potential existence of kinship.ResultsResults of the of δ15N and δ13C values agree with a dispersion strategy in the winter breeding grounds. However, and despite the overall large variability, several pairs or groups of individuals with no kinship showed highly similar isotopic patterns for two consecutive years for both δ15N and δ13C values.ConclusionsOur results suggest that, notably, some whales without kinship share the same migratory regime and destinations. We hypothesize that this could reflect either: (i) the sharing of particularly beneficial migratory regimes, and/or (ii) long-term association between individuals.
Methods for implementing integrated step-selection functions with incomplete data
Authors: Hofmann David D. , Cozzi Gabriele , Fieberg John 
Published: May 2024

AbstractIntegrated step-selection analyses (iSSAs) are versatile and powerful frameworks for studying habitat and movement preferences of tracked animals. iSSAs utilize integrated step-selection functions (iSSFs) to model movements in discrete time, and thus, require animal location data that are regularly spaced in time. However, many real-world datasets are incomplete due to tracking devices failing to locate an individual at one or more scheduled times, leading to slight irregularities in the duration between consecutive animal locations. To address this issue, researchers typically only consider bursts of regular data (i.e., sequences of locations that are equally spaced in time), thereby reducing the number of observations used to model movement and habitat selection. We reassess this practice and explore four alternative approaches that account for temporal irregularity resulting from missing data. Using a simulation study, we compare these alternatives to a baseline approach where temporal irregularity is ignored and demonstrate the potential improvements in model performance that can be gained by leveraging these additional data. We also showcase these benefits using a case study on a spotted hyena (Crocuta crocuta).
A clinical-radiomics nomogram based on dual-layer spectral detector CT to predict cancer stage in pancreatic ductal adenocarcinoma
Authors: Wu Linxia , Cen Chunyuan , Yue Xiaofei , Chen Lei , Wu Hongying , Yang Ming , Lu Yuting , Ma Ling , Li Xin , Wu Heshui , Zheng Chuansheng , Han Ping 
Published: May 2024

Abstract
Background
This study aimed to evaluate the efficacy of radiomics signatures derived from polyenergetic images (PEIs) and virtual monoenergetic images (VMIs) obtained through dual-layer spectral detector CT (DLCT). Moreover, it sought to develop a clinical-radiomics nomogram based on DLCT for predicting cancer stage (early stage: stage I-II, advanced stage: stage III-IV) in pancreatic ductal adenocarcinoma (PDAC).

Methods
A total of 173 patients histopathologically diagnosed with PDAC and who underwent contrast-enhanced DLCT were enrolled in this study. Among them, 49 were in the early stage, and 124 were in the advanced stage. Patients were randomly categorized into training (n = 122) and test (n = 51) cohorts at a 7:3 ratio. Radiomics features were extracted from PEIs and 40-keV VMIs were reconstructed at both arterial and portal venous phases. Radiomics signatures were constructed based on both PEIs and 40-keV VMIs. A radiomics nomogram was developed by integrating the 40-keV VMI-based radiomics signature with selected clinical predictors. The performance of the nomogram was assessed using receiver operating characteristic (ROC) curves, calibration curves, and decision curves analysis (DCA).

Results
The PEI-based radiomics signature demonstrated satisfactory diagnostic efficacy, with the areas under the ROC curves (AUCs) of 0.92 in both the training and test cohorts. The optimal radiomics signature was based on 40-keV VMIs, with AUCs of 0.96 and 0.94 in the training and test cohorts. The nomogram, which integrated a 40-keV VMI-based radiomics signature with two clinical parameters (tumour diameter and normalized iodine density at the portal venous phase), demonstrated promising calibration and discrimination in both the training and test cohorts (0.97 and 0.91, respectively). DCA indicated that the clinical-radiomics nomogram provided the most significant clinical benefit.

Conclusions
The radiomics signature derived from 40-keV VMI and the clinical-radiomics nomogram based on DLCT both exhibited exceptional performance in distinguishing early from advanced stages in PDAC, aiding clinical decision-making for patients with this condition.
The significance of partial volume effect on the estimation of hypoxic tumour volume with [18F]FMISO PET/CT
Authors: Kafkaletos Athanasios , Mix Michael , Sachpazidis Ilias , Carles Montserrat , Rühle Alexander , Ruf Juri , Grosu Anca L. , Nicolay Nils H. , Baltas Dimos 
Published: May 2024

Abstract
Background
The purpose of this study was to evaluate how a retrospective correction of the partial volume effect (PVE) in [18F]fluoromisonidazole (FMISO) PET imaging, affects the hypoxia discoverability within a gross tumour volume (GTV). This method is based on recovery coefficients (RC) and is tailored for low-contrast tracers such as FMISO. The first stage was the generation of the scanner’s RC curves, using spheres with diameters from 10 to 37 mm, and the same homogeneous activity concentration, positioned in lower activity concentration background. Six sphere-to-background contrast ratios were used, from 10.0:1, down to 2.0:1, in order to investigate the dependence of RC on both the volume and the contrast ratio. The second stage was to validate the recovery-coefficient correction method in a more complex environment of non-spherical lesions of different volumes and inhomogeneous activity concentration. Finally, we applied the correction method to a clinical dataset derived from a prospective imaging trial (DRKS00003830): forty nine head and neck squamous cell carcinoma (HNSCC) cases who had undergone FMISO PET/CT scanning for the quantification of tumour hypoxia before (W0), 2 weeks (W2) and 5 weeks (W5) after the beginning of radiotherapy. Here, PVE was found to cause an underestimation of the activity in small volumes with high FMISO signal.

Results
The application of the proposed correction method resulted in a statistically significant increase of both the hypoxic subvolume (171% at W0, 691% at W2 and 4.60 × 103% at W5 with p < 0.001) and the FMISO standardised uptake value (SUV) (27% at W0, 21% at W2 and by 25% at W5 with p < 0.001) within the primary GTV.

Conclusions
The proposed PVE-correction method resulted in a statistically significant increase of the hypoxic fraction (HF) with p < 0.001 and demonstrated results in better agreement with published HF data for HNSCC. To summarise, the proposed RC-based correction method can be a useful tool for a retrospective compensation against PVE.
Pilot study with randomised control of dual site theta burst transcranial magnetic stimulation (TMS) for methamphetamine use disorder: a protocol for the TARTAN study
Authors: Yadav Tarun , Lokuge Buddhima , Jackson Melissa A. , Austin Emma K. , Fitzgerald Paul B. , Brown Amanda L. , Paton Bryan , Sequeira Marcia , Nean Martin , Mills Llewllyn , Dunlop Adrian J. 
Published: May 2024

Abstract
Background
Transcranial magnetic stimulation (TMS) (including the theta burst stimulation (TBS) form of TMS used in this study) is a non-invasive means to stimulate nerve cells in superficial areas of the brain. In recent years, there has been a growth in the application of TMS to investigate the modulation of neural networks involved in substance use disorders. This study examines the feasibility of novel TMS protocols for the treatment of methamphetamine (MA) use disorder in an ambulatory drug and alcohol treatment setting.

Methods
Thirty participants meeting the criteria for moderate to severe MA use disorder will be recruited in community drug and alcohol treatment settings and randomised to receive active TMS or sham (control) intervention. The treatment is intermittent TBS (iTBS) applied to the left dorsolateral prefrontal cortex (DLPFC), then continuous TBS (cTBS) to the left orbitofrontal cortex (OFC). Twelve sessions are administered over 4 weeks with opt-in weekly standardized cognitive behaviour therapy (CBT) counselling and a neuroimaging sub-study offered to participants. Primary outcomes are feasibility measures including recruitment, retention and acceptability of the intervention. Secondary outcomes include monitoring of safety and preliminary efficacy data including changes in substance use, cravings (cue reactivity) and cognition (response inhibition).

Discussion
This study examines shorter TBS protocols of TMS for MA use disorder in real-world drug and alcohol outpatient settings where withdrawal and abstinence from MA, or other substances, are not eligibility requirements. TMS is a relatively affordable treatment and staff of ambulatory health settings can be trained to administer TMS. It is a potentially scalable and translatable treatment for existing drug and alcohol clinical settings. TMS has the potential to provide a much-needed adjuvant treatment to existing psychosocial interventions for MA use disorder. A limitation of this protocol is that the feasibility of follow-up is only examined at the end of treatment (4 weeks).

Trial registration
Australia New Zealand Clinical Trial Registry ACTRN12622000762752. Registered on May 27, 2022, and retrospectively registered (first participant enrolled) on May 23, 2022, with protocol version 7 on February 24, 2023.
Immunoenhancing and antioxidant potentials of kimchi, an ethnic food from Korea, as a probiotic and postbiotic food
Authors: Nugroho David , Thinthasit Aphinya , Surya Ervan , Hartati  , Oh Jin-Seok , Jang Ji-Gyeol , Benchawattananon Rachadaporn , Surya Reggie 
Published: May 2024

AbstractKimchi, the traditional lactic fermented vegetables from Korea, is globally praised for its potential as a functional food owing to the presence of beneficial microorganisms known as probiotics. However, the serving of kimchi in traditional Korean dishes often involves cooking at high temperature, thus killing the probiotics. Recently, non-viable or inactivated microorganisms and their metabolites, known as postbiotics, were shown to confer health benefits when consumed, thus giving rise to a novel potential of kimchi as a postbiotic food with health functionalities. The present study aimed to explore the potential of uncooked and cooked kimchi, both as a probiotic and postbiotic food, respectively, using an animal model. Mice were fed by AIN-76 diet enriched in 10% freeze-dried uncooked or cooked kimchi for 28 days prior to kill. Several parameters related to immune system and antioxidant were evaluated. Exposure of kimchi toward heat in steaming process killed the microorganisms in kimchi, but did not alter its antioxidant activity. Interestingly, the consumption of uncooked and cooked kimchi stimulated the growth of lactic acid bacteria in the intestine indifferently, as shown in the fecal matter. In addition, kimchi supplementation, either uncooked or cooked, increased the number of splenic lymphocytes and intestinal IgA, supporting the role of kimchi in the immune system. Furthermore, kimchi supplementation reduced the level of lipid peroxidation in the fecal matter, indicating its antioxidant activity in vivo. Taken together, the findings in this study suggest the potential of kimchi both as a probiotic and postbiotic food with antioxidant and immunoenhancing properties.
Non-destructive hyperspectral imaging technology to assess the quality and safety of food: a review
Authors: Patel Dharmendrakumar , Bhise Suresh , Kapdi S. S. , Bhatt Tanmay 
Published: May 2024

AbstractThe quality and safety of food can be evaluated using a variety of conventional and scientific methods. But all of those ways are time-consuming, laborious, and harmful. There are two primary types of processes used to gauge the quality and safety of foods: 1) Destructive methods (like gas chromatography, high performance liquid chromatography, enzyme linked immuno-sorbent assay, etc.); and 2) Non-destructive methods (such imaging methods, computer vision systems, fourier transform infrared spectroscopy, and near infrared spectroscopy). Techniques for imaging are frequently employed in the food industry to assess external quality. Imaging is the process of visualizing an object, while spectroscopy is the study of how energy is transferred from light to matter. Spectroscopy and imaging are used in the hyper spectral imaging approach. A method that may offer both spectral and spatial information about a component is called hyperspectral imaging (HSI). The HSI creates a hypercube out of spectral pictures at more than ten different wavelengths. A hypercube has three dimensions: two spatial (the x and y axes) and one spectral (λ). Fruits and vegetables, dairy goods, meat products, seafood, grains, and legumes are all evaluated for quality and safety using HSI. The HSI approach is excellent for identifying both internal and exterior food problems. Anthocyanin in grapes, Penicillium digitatum in mandarins, melamine in milk powder, and the amount of fat in cheese can all be detected using HSI. In addition to recognizing the muscles in lamb meat, HSI may also be used to assess the colour, pH, and tenderness of beef, the colour, pH, and drip loss of pork, and the presence of E. coli in pork. Additionally, HSI is utilized to identify Aspergillus niger in wheat and Aflatoxin B1 in maize. Chemometric instruments are essential to HSI. Large data storage and fast processors are needed. Improved models are required for quick and simple evaluation. The HSI has limits when it comes to microbiological contaminants’ metabolites detection and quantification, model optimization, and the development of more reliable models. Validation of developed models on several storage conditions. Combining HSI with Raman microscopic imaging (RMI) and fluorescence microscopic imaging (FMI) improves the ability to analyze microbes.
Graphical Abstract
A bioinformatics approach to reveal common genes and molecular pathways shared by cutaneous melanoma and uveal melanoma
Authors: Jayaraj Perumal , Bhimwal Tanisha , Kaur Khushneet , Gupta Kritika , Taluja Shreya , Priyadarshani Anjali 
Published: May 2024

Abstract
Background
Melanomas are highly aggressive in nature known for metastasis and death. Melanocytes that gave rise to melanomas are neural crest progenitor cells. Our research was primarily concerned with uveal melanoma (UM) and cutaneous melanoma (CM), respectively. Although they both have the same melanocytic origin, the biology of their respective is different.

Aim
The aim of our study was to recognize the common differentially expressed genes (DEGs) between UM and CM.

Methodology
The gene expression profile was downloaded from the GEO and analyzed by GEO2R to recognize DEGs. By applying DAVID, GO, and KEGG, pathway enrichment analysis was performed. PPI of these DEGs was analyzed using STRING and visualized by Cytoscape and MCODE. Further, we utilized HPA and GEPIA to obtain Kaplan–Meier graph for survival analysis in order to assess the prognostic value of hub genes.

Results
We examined the UM and CM datasets and discovered three common upregulated and eight downregulated DEGs based on computational analysis. HMGCS1 and ELOVL5 were shown to be enriched in a variety of altered molecular pathways and pathways in cancer. Overexpression of HMGCS1 and ELOVL5 was linked to a poor prognosis in CM.

Conclusion
Computational evaluation found that HMGCS1 and ELOVL5 were upregulated in both melanomas. Enrichment analysis showed that these genes are involved in cancer metabolism pathway and associated with poor prognosis in CM. However, the molecular study of these genes in UM is limited. Therefore, a better understanding of the cancer metabolism pathways should be carried to pave the way for clinical benefits.
Association of leptin–melanocortin gene polymorphisms with the risk of obesity in northwest Indian population
Authors: Sharma Tanmayi , Badaruddoza Badaruddoza 
Published: May 2024

AbstractBackgroundObesity, a multifaceted endocrine issue, is adversely affecting all age groups and is posing a significant public health challenge. The genetic polymorphisms of the melanocortin 4 receptor (MC4R) and leptin (LEP) genes likely contribute to the development of obesity. The present study aimed to explore the effects ofMC4RandLEPgene polymorphisms on obesity among the northwest Indian population.MethodsThe present study was conducted among 333 obese cases and 338 non-obese controls (aged 18–50 years). All subjects underwent measurements for anthropometric, physiometric, as well as biochemical parameters. Genotyping forMC4RandLEPgene variants was performed using the polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) method. However, 10% of the samples for each variant were confirmed using the Sanger sequencing method.ResultsThe polymorphisms of leptin–melanocortin pathway genes (MC4R-LEP) were found to be significantly associated with various obesity-related parameters like waist circumference:p = 0.017, waist-to-height ratio:p = 0.009, total cholesterol:p = 0.0001 and triglycerides:p = 0.0001. Both theLEPgene variants rs2167270 and rs7799039 conferred 2.4- and 2.2-fold risk toward obesity under the recessive genetic model [OR (95% CI) 2.42 (1.44–4.07),p = 0.001; OR (95% CI) 2.26 (1.41–3.60),p = 0.0001, respectively]. All four polymorphisms of theMC4RandLEPgenes demonstrated a strong interaction of 82.1% with the lifestyle factor (p = 0.001). The haplotype combinations A–A for rs571312 and rs12970134 conferred twofold risk [OR (95% CI) 2.61 (1.10–6.20),p = 0.028]. However, the combination A–G for rs2167270 and rs7799039 predicted sixfold risk [OR (95% CI) 6.02 (3.39–10.68),p = 0.0001] toward the obesity development in this population.ConclusionOur study revealed a connection betweenMC4R(rs571312, rs12970134) andLEP(rs2167270, rs7799039) gene variants with obesity, highlighting their prominent role in assessing the risk of obesity among the northwest Indian population.
Bibliometric analysis on the structure and function of IL17
Authors: Yan Wenxia , Li Minglu , Zhang Liyun 
Published: May 2024

Abstract
Background
Interleukin17 (IL17) is an important cytokine in host defense at mucosal surfaces and also mediates many autoimmune diseases, including rheumatoid arthritis (RA). In recent years, many types of research relevant to the structure and function of IL17 have been identified. However, there is no bibliometric analysis in this research field. This study aims to explore the history, research hotspots, and emerging trends of IL17 from the perspective of the structure and function dynamics.

Methods
Articles relevant to IL17 in the last two decades were retrieved through the Web of Science Core Collection (WoSCC) database. The bibliometric analysis was performed by VOSview.

Results
A total of 882 papers in this research were analyzed from 65 countries, and the rate of published articles has increased from 2008 annually, with the USA, China, and Germany leading the research effort. Frontiers in Immunology has significantly impacted research in this field and the University of Pittsburgh was the leading institution. Gaffen, Sarah L. from the University of Pittsburgh was the most productive researcher in this field and Papp Ka from the Probity Medical Research Incorporate of Canada is the most co-cited author. The analysis of keywords showed that inflammation, expression, Th17 cells, and cytokines were the main hotspots and frontier directions of IL17. The trend of clinical application in the future is the development of new therapy drugs based on the structure of IL17 or IL17 signaling pathway molecular.

Conclusions
Our research summarized the developments and research trends of IL17 and would help researchers understand the research status of IL17 and provide a reference for future researchers as soon as possible.