bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sediment core analysis using artificial intelligence
Authors: Di Martino Andrea , Carlini Gianluca , Castellani Gastone , Remondini Daniel , Amorosi Alessandro 
Published: November 2023

AbstractSubsurface stratigraphic modeling is crucial for a variety of environmental, societal, and economic challenges. However, the need for specific sedimentological skills in sediment core analysis may constitute a limitation. Methods based on Machine Learning and Deep Learning can play a central role in automatizing this time-consuming procedure. In this work, using a robust dataset of high-resolution digital images from continuous sediment cores of Holocene age that reflect a wide spectrum of continental to shallow-marine depositional environments, we outline a novel deep-learning-based approach to perform automatic semantic segmentation directly on core images, leveraging the power of convolutional neural networks. To optimize the interpretation process and maximize scientific value, we use six sedimentary facies associations as target classes in lieu of ineffective classification methods based uniquely on lithology. We propose an automated model that can rapidly characterize sediment cores, allowing immediate guidance for stratigraphic correlation and subsurface reconstructions.
Investigation of antimicrobial susceptibility and genetic diversity among Staphylococcus pseudintermedius isolated from dogs in Rio de Janeiro
Authors: Teixeira Izabel Mello , de Moraes Assumpção Yasmim , Paletta Ana Clara Cabral , Aguiar Louise , Guimarães Luciana , da Silva Isabella Thomaz , Côrtes Marina F. , Botelho Ana Maria Nunes , Jaeger Lauren Hubert , Ferreira Renata Fernandes , de Oliveira Ferreira Eliane , Penna Bruno 
Published: November 2023

AbstractStaphylococcus pseudintermedius is an opportunistic pathogen causing a variety of infections that are difficult to treat, especially because of the development of antimicrobial resistance. It has a clonal distribution around the world. To have a better understanding of the MRSP population, we search the presence of MRSP in colonized or infected dogs. Samples from 99 dogs with infections and 35 from asymptomatic dogs were collected. Isolates were identified by mass spectrometry and Multiplex-PCR. The mecA gene was confirmed by conventional PCR. MRSP strains were analyzed by whole-genome sequencing. 75 S. pseudintermedius were identified, most from infection cases. The species were isolated from 70 out of the 135 dogs. Penicillin and Trimethoprim/Sulfamethoxazole presented higher resistance rates. Forty-seven strains were classified as multi-drug resistant (MDR), and were more isolated from dogs with infection (P < 0.05). Eighteen samples were classified as MRSP, representing 24.0% of the population. Six of 16 MRSP sequenced samples belonged to the world spread clone ST71; others belonged to unknown clones. Most samples carried the SCCmec type IIIA. Twenty-one different genetic resistance determinants were found among MRPS strains. MRSP is circulating among infected and colonized dogs in Rio de Janeiro, Brazil.
Mapping brucellosis risk in Kenya and its implications for control strategies in sub-Saharan Africa
Authors: Akoko James M. , Mwatondo Athman , Muturi Mathew , Wambua Lillian , Abkallo Hussein M. , Nyamota Richard , Bosire Caroline , Oloo Stephen , Limbaso Konongoi S. , Gakuya Francis , Nthiwa Daniel , Bartlow Andrew , Middlebrook Earl , Fair Jeanne , Ogutu Joseph O. , Gachohi John , Njenga Kariuki , Bett Bernard 
Published: November 2023

AbstractIn Sub-Saharan Africa (SSA), effective brucellosis control is limited, in part, by the lack of long-term commitments by governments to control the disease and the absence of reliable national human and livestock population-based data to inform policies. Therefore, we conducted a study to establish the national prevalence and develop a risk map for Brucella spp. in cattle to contribute to plans to eliminate the disease in Kenya by the year 2040. We randomly generated 268 geolocations and distributed them across Kenya, proportionate to the area of each of the five agroecological zones and the associated cattle population. Cattle herds closest to each selected geolocation were identified for sampling. Up to 25 cattle were sampled per geolocation and a semi-structured questionnaire was administered to their owners. We tested 6,593 cattle samples for Brucella immunoglobulin G (IgG) antibodies using an Enzyme-linked immunosorbent assay (ELISA). We assessed potential risk factors and performed spatial analyses and prevalence mapping using approximate Bayesian inference implemented via the integrated nested Laplace approximation (INLA) method. The national Brucella spp. prevalence was 6.8% (95% CI: 6.2–7.4%). Exposure levels varied significantly between agro-ecological zones, with a high of 8.5% in the very arid zone with the lowest agricultural potential relative to a low of 0.0% in the agro-alpine zone with the highest agricultural potential. Additionally, seroprevalence increased with herd size, and the odds of seropositivity were significantly higher for females and adult animals than for males or calves. Similarly, animals with a history of abortion, or with multiple reproductive syndromes had higher seropositivity than those without. At the herd level, the risk of Brucella spp. transmission was higher in larger herds, and herds with a history of reproductive problems such as abortion, giving birth to weak calves, or having swollen testes. Geographic localities with high Brucella seroprevalence occurred in northern, eastern, and southern regions of Kenya all primarily characterized by semi-arid or arid agro-ecological zones dominated by livestock pastoralism interspersed with vast areas with mixed livestock-wildlife systems. The large spatial extent of our survey provides compelling evidence for the widespread geographical distribution of brucellosis risk across Kenya in a manner easily understandable for policymakers. Our findings can provide a basis for risk-stratified pilot studies aiming to investigate the cost-effectiveness and efficacy of singular and combined preventive intervention strategies that seek to inform Kenya’s Brucellosis Control Policy.
Minimally invasive management of vital teeth requiring root canal therapy
Authors: Karatas E. , Hadis M. , Palin W. M. , Milward M. R. , Kuehne S. A. , Camilleri J. 
Published: November 2023

AbstractThe present study aimed to investigate the possible use of a non-instrumentation technique including blue light irradiation for root canal cleaning. Extracted human single rooted teeth were selected. Nine different groups included distilled water, NaOCl, intra-canal heated NaOCl, and NaOCl + EDTA irrigation after either instrumentation or non-instrumentation, and a laser application group following non-instrumentation technique. The chemical assessment of the root canal dentine was evaluated using energy dispersive spectroscopy (EDS) and Fourier transform infrared (FT-IR) spectroscopy. Surface microstructural analyses were performed by using scanning electron microscopy (SEM). The antimicrobial efficacy of different preparation techniques was evaluated using microbial tests. Light application didn’t change the calcium/phosphorus, carbonate/phosphate and amide I/phosphate ratios of the root canal dentin. The root canal dentin preserved its original chemistry and microstructure after light application. The instrumentation decreased the carbonate/phosphate and amide I/phosphate ratios of the root canal dentin regardless of the irrigation solution or technique (p < 0.05). The application of light could not provide antibacterial efficacy to match the NaOCl irrigation. The NaOCl irrigation both in the non-instrumentation and instrumentation groups significantly reduced the number of bacteria (p < 0.05). The use of minimally invasive root canal preparation techniques where the root canal is not instrumented and is disinfected by light followed by obturation with a hydraulic cement sealer reduced the microbial load and preserved the dentin thus may be an attractive treatment option for management of vital teeth needing root canal therapy.
CaV3.1 channels facilitate calcium wave generation and myogenic tone development in mouse mesenteric arteries
Authors: El-Lakany Mohammed A. , Haghbin Nadia , Arora Naman , Hashad Ahmed M. , Mironova Galina Yu. , Sancho Maria , Gros Robert , Welsh Donald G. 
Published: November 2023

AbstractThe arterial myogenic response to intraluminal pressure elicits constriction to maintain tissue perfusion. Smooth muscle [Ca2+] is a key determinant of constriction, tied to L-type (CaV1.2) Ca2+ channels. While important, other Ca2+ channels, particularly T-type could contribute to pressure regulation within defined voltage ranges. This study examined the role of one T-type Ca2+ channel (CaV3.1) using C57BL/6 wild type and CaV3.1−/− mice. Patch-clamp electrophysiology, pressure myography, blood pressure and Ca2+ imaging defined the CaV3.1−/− phenotype relative to C57BL/6. CaV3.1−/− mice had absent CaV3.1 expression and whole-cell current, coinciding with lower blood pressure and reduced mesenteric artery myogenic tone, particularly at lower pressures (20–60 mmHg) where membrane potential is hyperpolarized. This reduction coincided with diminished Ca2+ wave generation, asynchronous events of Ca2+ release from the sarcoplasmic reticulum, insensitive to L-type Ca2+ channel blockade (Nifedipine, 0.3 µM). Proximity ligation assay (PLA) confirmed IP3R1/CaV3.1 close physical association. IP3R blockade (2-APB, 50 µM or xestospongin C, 3 µM) in nifedipine-treated C57BL/6 arteries rendered a CaV3.1−/− contractile phenotype. Findings indicate that Ca2+ influx through CaV3.1 contributes to myogenic tone at hyperpolarized voltages through Ca2+-induced Ca2+ release tied to the sarcoplasmic reticulum. This study helps establish CaV3.1 as a potential therapeutic target to control blood pressure.
IGSF6 is a novel biomarker to evaluate immune infiltration in mismatch repair-proficient colorectal cancer
Authors: Rong Yu-ming , Xu Yu-cheng , Chen Xiao-chuan , Zhong Min-er , Tan Ying-xin , Liang Yu-fan , Weng Jing-rong , Liu Jun , Wang Xin-you , Luo Dan-dong , Bie Yi-ran , Chen Xi , Cai Jia-wei , Yu Zhao-liang , Zou Yi-feng 
Published: November 2023

AbstractImmunotherapy has dramatically changed the landscape of treatment for colorectal cancer (CRC), but currently lack of effective predictive biomarker, especially for tumors with mismatch repair (MMR) proficiency. The response of immunotherapy is associated with the cell–cell interactions in tumor microenvironment, encompassing processes such as cell–cell recognition, binding, and adhesion. However, the function of immunoglobulin superfamily (IGSF) genes in tumor immune microenvironment remains uncharacterized. This study quantified the immune landscape by leveraging a gene expression matrix from publicly accessible databases. The associations between IGSF6 gene expression and immune cell infiltration were assessed. The expression levels of IGSF6, CD8+ T cells, CD4+ T cells and CD68+ macrophage cells in cancer tissues from CRC patients and CRC cell lines were evaluated. IGSF6 was more highly expressed in CRC tumor tissues than adjacent normal tissues. And IGSF6 was significantly correlated with immune cell infiltration in MMR-proficient patients. Remarkably, MMR-proficient patients with high IGSF6 expression showed more sensitive to immunotherapy and chemotherapy than those with low IGSF6 expression. In summary, IGSF6 could be a novel biomarker to evaluate immune infiltration and predict therapeutic effect for MMR-proficient CRC.
Sulphides from garlic essential oil dose-dependently change the distribution of glycerophospholipids and induce N6-tuberculosinyladenosine formation in mycobacterial cells
Authors: Sawicki Rafał , Widelski Jarosław , Truszkiewicz Wiesław , Kawka Sławomir , Kai Guoyin , Sieniawska Elwira 
Published: November 2023

AbstractThe antimicrobial properties of garlic are widely known, and numerous studies confirmed its ability to inhibit the growth of Mycobacterium tuberculosis. In this work, we explored the molecular mechanism of action of sulphides present in garlic essential oil against mycobacteria. The targeted transcriptomics and untargeted LC–MS metabolomics were applied to study dose- and time-dependent metabolic changes in bacterial cells under the influence of stressing agent. Expression profiles of genes coding stress-responsive sigma factors regulatory network and metabolic observations proved that sulphides from garlic essential oil are an efficient and specific agent affecting glycerophospholipids levels and their distribution within the cell envelope. Additionally, sulphides induced the Dimroth rearrangement of 1-Tuberculosinyladenosine to N6-tuberculosinyladenosine in mycobacterial cells as a possible neutralization mechanism protecting the cell from a basic nucleophilic environment. Sulphides affected cell envelope lipids and formation of N6-tuberculosinyladenosine in M. tuberculosis.
Effect of novel botanical synergist on the effectiveness and residue behavior of prothioconazole in wheat field
Authors: Wu Yalin , Yin Yuanjian , Chen Xin , Zhou Yeping , Jiang Shan , Zhang Mingming , Cai Guangcheng , Gao Quan 
Published: November 2023

AbstractFusarium head blight (FHB) is a critical fungal disease causes serious grain yield losses and mycotoxin contaminations. Currently, utilization of chemical fungicides is the main control method which has led to serious resistance. Development of novel synergist is an important strategy to reduce the usage of chemical fungicides and postpone the development of resistance, while natural components are interesting resources. In this study, the synergistic effect of Taxodium 'zhongshansha' essential oil (TZEO) was determined and the best synergistic ratio (SR) of 3.96 in laboratory which was observed when the weight ratio of TZEO and prothioconazole was 1 : 1 with the corresponding EC50 (half maximal effective concentration) value of Fusarium graminearum was 0.280 mg L−1. Subsequently, an increase of 6.31% on the control effect to FHB index in field test was observed when compared to the treatment with prothioconazole alone, though there was no significant difference between these treatments. Furthermore, we established an effective method to detect the mycotoxin contaminations in wheat grain with the limits of quantifications (LOQs) value of 5 µg kg−1 (DON, ZEN, 3-DON, and 15-DON) and 1 µg kg−1 (OTA) and the contents were less to the maximum residue limit (MRL) values. It was also shown that the application of 20% TZEO EW led to a 20% reduction in the use of prothioconazole, which was calculated based on the control effect values of 86.41% and 90.20% between the treatments of 30% prothioconazole OD (225 g a.i ha−1, recommend dosage) and 30% prothioconazole OD (180 g a.i ha−1) + 20% TZEO EW (225 mL ha−1), significantly. The initial residue of prothioconazole and prothioconazole-desthio was increased in the treatment with TZEO, which may play an important role in the synergistic effect on FHB. Moreover, none of the treatments posed a prothioconazole residue risk in the wheat grain and the environment. In addition, the essential oil has no any negative influence on wheat growth, which was revealed by a study of the chlorophyll content. These results provide an important botanical synergist for use with prothioconazole to control Fusarium head blight, and in-depth study to the synergistic mechanism of this oil is necessary in our future research.
Habitat selection of resident and non-resident gray wolves: implications for habitat connectivity
Authors: van den Bosch M. , Kellner K. F. , Gantchoff M. G. , Patterson B. R. , Barber-Meyer S. M. , Beyer D. E. , Erb J. D. , Isaac E. J. , MacFarland D. M. , Moore S. A. , Norton D. C. , Petroelje T. R. , Price Tack J. L. , Roell B. J. , Schrage M. , Belant J. L. 
Published: November 2023

AbstractHabitat selection studies facilitate assessing and predicting species distributions and habitat connectivity, but habitat selection can vary temporally and among individuals, which is often ignored. We used GPS telemetry data from 96 Gray wolves (Canis lupus) in the western Great Lakes region of the USA to assess differences in habitat selection while wolves exhibited resident (territorial) or non-resident (dispersing or floating) movements and discuss implications for habitat connectivity. We used a step-selection function (SSF) to assess habitat selection by wolves exhibiting resident or non-resident movements, and modeled circuit connectivity throughout the western Great Lakes region. Wolves selected for natural land cover and against areas with high road densities, with no differences in selection among wolves when resident, dispersing, or floating. Similar habitat selection between resident and non-resident wolves may be due to similarity in environmental conditions, when non-resident movements occur largely within established wolf range rather than near the periphery or beyond the species range. Alternatively, non-resident wolves may travel through occupied territories because higher food availability or lower human disturbance outweighs risks posed by conspecifics. Finally, an absence of differences in habitat selection between resident and non-resident wolf movements may be due to other unknown reasons. We recommend considering context-dependency when evaluating differences in movements and habitat use between resident and non-resident individuals. Our results also provide independent validation of a previous species distribution model and connectivity analysis suggesting most potential wolf habitat in the western Great Lakes region is occupied, with limited connectivity to unoccupied habitat.
Topological magnetic structure generation using VAE-GAN hybrid model and discriminator-driven latent sampling
Authors: Park S. M. , Yoon H. G. , Lee D. B. , Choi J. W. , Kwon H. Y. , Won C. 
Published: November 2023

AbstractRecently, deep generative models using machine intelligence are widely utilized to investigate scientific systems by generating scientific data. In this study, we experiment with a hybrid model of a variational autoencoder (VAE) and a generative adversarial network (GAN) to generate a variety of plausible two-dimensional magnetic topological structure data. Due to the topological properties in the system, numerous and diverse metastable magnetic structures exist, and energy and topological barriers separate them. Thus, generating a variety of plausible spin structures avoiding those barrier states is a challenging problem. The VAE-GAN hybrid model can present an effective approach to this problem because it brings the advantages of both VAE’s diversity and GAN’s fidelity. It allows one to perform various applications including searching a desired sample from a variety of valid samples. Additionally, we perform a discriminator-driven latent sampling (DDLS) using our hybrid model to improve the quality of generated samples. We confirm that DDLS generates various plausible data with large coverage, following the topological rules of the target system.
EMT-related gene risk model establishment for prognosis and drug treatment efficiency prediction in hepatocellular carcinoma
Authors: Gao Xiaqing , Yang Chunting , Li Hailong , Shao Lihua , Wang Meng , Su Rong 
Published: November 2023

AbstractThis study was designed to evaluate the prognosis and pharmacological therapy sensitivity of epithelial mesenchymal transition-related genes (EMTRGs) that obtained from the EMTome database in hepatocellular carcinoma (HCC) using bioinformatical method. The expression status of EMTRGs were also investigated using the clinical information of HCC patients supported by TCGA database and the ICGC database to establish the TCGA cohort as the training set and the ICGC cohort as the validation set. Analyze the EMTRGs between HCC tissue and liver tissue in the TCGA cohort in the order of univariate COX regression, LASSO regression, and multivariate COX regression, and construct a risk model for EMTRGs. In addition, enrichment pathways, gene mutation status, immune infiltration, and response to drugs were also analyzed in the high-risk and low-risk groups of the TCGA cohort, and the protein expression status of EMTRGs was verified. The results showed a total of 286 differentially expressed EMTRGs in the TCGA cohort, and EZH2, S100A9, TNFRSF11B, SPINK5, and CCL21 were used for modeling. The TCGA cohort was found to have a worse outcome in the high-risk group of HCC patients, and the ICGC cohort confirmed this finding. In addition, EMTRGs risk score was shown to be an independent prognostic factor in both cohorts by univariate and multivariate COX regression. The results of GSEA analysis showed that most of the enriched pathways in the high-risk group were associated with tumor, and the pathways enriched in the low-risk group were mainly associated with metabolism. Patients in various risk groups had varying immunological conditions, and the high-risk group might benefit more from targeted treatments. To sum up, the EMTRGs risk model was developed to forecast the prognosis for HCC patients, and the model might be useful in assisting in the choice of treatment drugs for HCC patients.
Radiological artificial intelligence - predicting personalized immunotherapy outcomes in lung cancer
Authors: Roisman Laila C. , Kian Waleed , Anoze Alaa , Fuchs Vered , Spector Maria , Steiner Roee , Kassel Levi , Rechnitzer Gilad , Fried Iris , Peled Nir , Bogot Naama R. 
Published: November 2023

AbstractPersonalized medicine has revolutionized approaches to treatment in the field of lung cancer by enabling therapies to be specific to each patient. However, physicians encounter an immense number of challenges in providing the optimal treatment regimen for the individual given the sheer complexity of clinical aspects such as tumor molecular profile, tumor microenvironment, expected adverse events, acquired or inherent resistance mechanisms, the development of brain metastases, the limited availability of biomarkers and the choice of combination therapy. The integration of innovative next-generation technologies such as deep learning—a subset of machine learning—and radiomics has the potential to transform the field by supporting clinical decision making in cancer treatment and the delivery of precision therapies while integrating numerous clinical considerations. In this review, we present a brief explanation of the available technologies, the benefits of using these technologies in predicting immunotherapy response in lung cancer, and the expected future challenges in the context of precision medicine.