bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global-temporal analysis on Phytophthora sojae resistance-gene efficacy
Authors: McCoy Austin G. , Belanger Richard R. , Bradley Carl A. , Cerritos-Garcia Daniel G. , Garnica Vinicius C. , Giesler Loren J. , Grijalba Pablo E. , Guillin Eduardo , Henriquez Maria A. , Kim Yong Min , Malvick Dean K. , Matthiesen Rashelle L. , Mideros Santiago X. , Noel Zachary A. , Robertson Alison E. , Roth Mitchell G. , Schmidt Clarice L. , Smith Damon L. , Sparks Adam H. , Telenko Darcy E. P. , Tremblay Vanessa , Wally Owen , Chilvers Martin I. 
Published: September 2023

AbstractPlant disease resistance genes are widely used in agriculture to reduce disease outbreaks and epidemics and ensure global food security. In soybean, Rps (Resistance to Phytophthora sojae) genes are used to manage Phytophthora sojae, a major oomycete pathogen that causes Phytophthora stem and root rot (PRR) worldwide. This study aims to identify temporal changes in P. sojae pathotype complexity, diversity, and Rps gene efficacy. Pathotype data was collected from 5121 isolates of P. sojae, derived from 29 surveys conducted between 1990 and 2019 across the United States, Argentina, Canada, and China. This systematic review shows a loss of efficacy of specific Rps genes utilized for disease management and a significant increase in the pathotype diversity of isolates over time. This study finds that the most widely deployed Rps genes used to manage PRR globally, Rps1a, Rps1c and Rps1k, are no longer effective for PRR management in the United States, Argentina, and Canada. This systematic review emphasizes the need to widely introduce new sources of resistance to P. sojae, such as Rps3a, Rps6, or Rps11, into commercial cultivars to effectively manage PRR going forward.
Omicron variant neutralizing antibodies following BNT162b2 BA.4/5 versus mRNA-1273 BA.1 bivalent vaccination in patients with end-stage kidney disease
Authors: Yau Kevin , Kurtesi Alexandra , Qi Freda , Delgado-Brand Melanie , Tursun Tulunay R. , Hu Queenie , Dhruve Miten , Kandel Christopher , Enilama Omosomi , Levin Adeera , Jiang Yidi , Hardy W. Rod , Yuen Darren A. , Perl Jeffrey , Chan Christopher T. , Leis Jerome A. , Oliver Matthew J. , Colwill Karen , Gingras Anne-Claude , Hladunewich Michelle A. 
Published: September 2023

AbstractNeutralization of Omicron subvariants by different bivalent vaccines has not been well evaluated. This study characterizes neutralization against Omicron subvariants in 98 individuals on dialysis or with a kidney transplant receiving the BNT162b2 (BA.4/BA.5) or mRNA-1273 (BA.1) bivalent COVID-19 vaccine. Neutralization against Omicron BA.1, BA.5, BQ.1.1, and XBB.1.5 increased by 8-fold one month following bivalent vaccination. In comparison to wild-type (D614G), neutralizing antibodies against Omicron-specific variants were 7.3-fold lower against BA.1, 8.3-fold lower against BA.5, 45.8-fold lower against BQ.1.1, and 48.2-fold lower against XBB.1.5. Viral neutralization was not significantly different by bivalent vaccine type for wild-type (D614G) (P = 0.48), BA.1 (P = 0.21), BA.5 (P = 0.07), BQ.1.1 (P = 0.10), nor XBB.1.5 (P = 0.10). Hybrid immunity conferred higher neutralizing antibodies against all Omicron subvariants. This study provides evidence that BNT162b2 (BA.4/BA.5) and mRNA-1273 (BA.1) induce similar neutralization against Omicron subvariants, even when antigenically divergent from the circulating variant.
A phylogenetically-conserved axis of thalamocortical connectivity in the human brain
Authors: Oldham Stuart , Ball Gareth 
Published: September 2023

AbstractThe thalamus enables key sensory, motor, emotive, and cognitive processes via connections to the cortex. These projection patterns are traditionally considered to originate from discrete thalamic nuclei, however recent work showing gradients of molecular and connectivity features in the thalamus suggests the organisation of thalamocortical connections occurs along a continuous dimension. By performing a joint decomposition of densely sampled gene expression and non-invasive diffusion tractography in the adult human thalamus, we define a principal axis of genetic and connectomic variation along a medial-lateral thalamic gradient. Projections along this axis correspond to an anterior-posterior cortical pattern and are aligned with electrophysiological properties of the cortex. The medial-lateral axis demonstrates phylogenetic conservation, reflects transitions in neuronal subtypes, and shows associations with neurodevelopment and common brain disorders. This study provides evidence for a supra-nuclear axis of thalamocortical organisation characterised by a graded transition in molecular properties and anatomical connectivity.
High-precision in situ 3D ultrasonic imaging of localized corrosion-induced material morphological changes
Authors: Chen Yunda , Yang Zirui , Bai Xinru , Zou Fangxin , Cegla Frederic B. 
Published: September 2023

AbstractWe present an ultrasonic research technique that can carry out in situ, direct monitoring of the 3D morphologies of corrosion substrates. The technique has a customizable lateral resolution, an ultra-high axial resolution of 100 nm, and an experimentally proven measurement accuracy. In using the technique to monitor the localized corrosion processes of carbon steel under constant DCs, it was observed that during each of the experiments conducted in alkaline environments, iron dissolution accelerated for a certain period of time and then slowed down. Based on the various features of the ultrasonic signals acquired and the XRD spectra of the corrosion products obtained, it was deduced that an increase in iron dissolution rate as such was accompanied by the depositing of solid corrosion products onto the substrate used and driven by the formation of Fe3O4, which consumed electrons. After a while, the corrosion product layer collapsed and the formation of Fe3O4 was halted.
Individual identification of endangered amphibians using deep learning and smartphone images: case study of the Japanese giant salamander (Andrias japonicus)
Authors: Takaya Kosuke , Taguchi Yuki , Ise Takeshi 
Published: September 2023

AbstractInformation obtained via individual identification is invaluable for ecology and conservation. Physical tags, such as PIT tags and GPS, have been used for individual identification; however, these methods could impact on animal behavior and survival rates, and the tags may become lost. Although non-invasive methods that do not affect the target species (such as manual photoidentification) are available, these techniques utilize stripes and spots that are unique to the individual, which requires training, and applying them to large datasets is challenging. Many studies that have applied deep learning for identification have focused on species-level identification, but few have addressed individual-level identification. In this study, we developed an image-based identification method based on deep learning that uses the head spot pattern of the Japanese giant salamander (Andrias japonicus), an endemic and endangered species in Japan. We trained and evaluated a dataset collected over two days from 11 individuals in captivity, which included 7075 images taken by a smartphone camera. Individuals were photographed three times a day at approximately 11:00 (morning), 15:00 (afternoon), and 18:00 (evening). As a result, individual identification by our method, which used the EfficientNetV2 achieved 99.86% accuracy, kappa coefficient of 0.99, and an F1 score of 0.99. Performance was lower for the evening model than for the morning and afternoon models, which were trained and evaluated using photographs taken at the corresponding time of the day. The proposed method does not require direct contact with the target species, and the effect on the animals is minimal; moreover, individual-level information can be obtained under natural conditions. In the future, smartphone images can be applied to citizen science surveys and individual-level big data collection, which is difficult using current methods.
Clinical determination of anatomical diameter in different dental groups correlating them with gender, age, tooth/canal and pulpoperiradicular diagnosis: an observational clinical study
Authors: Machado Ricardo , Pamplona Gabriel Filipe , de Souza Júnior Claudemir , Nascimento Jaqueline , Back Eduardo Donato Eing Elgelke , Comparin Daniel , Ignácio Sérgio Aparecido , Reinke Stella Maria Glaci , Kovalik Ana Cristina , da Silva Neto Ulisses Xavier 
Published: September 2023

AbstractThe aim of this observational clinical study (OCS) was to determine the clinical anatomical diameter (CAD) in several dental groups, thus correlating them with gender, age, tooth/canal and pulpoperiradicular diagnosis. Three-hundred fifty-nine teeth/584 vital or necrotic root canals from patients of both genders and different ages composed the sample. After performing the necessary previous procedures, K-Flexofiles were used to determine the CAD. Then, the gender and age of the patients, as well as the pulpoperiradicular diagnosis of the teeth were tabulated to conduct the statistical analysis (p < 0.05). Of the 359 teeth/584 root canals evaluated, 208/342 were from women (mean age 38.85 ± 13.42 years) and 151/242 were from men (mean age 45.41 ± 14.90 years). Statistically significant differences between the CAD means of root canals from women and men were not identified (p = 0.411). The analysis of the correlation between the CAD and age also showed a total independence (p = 0.271). Teeth with pulp necrosis and asymptomatic apical periodontitis diagnosed radiographically (TPNAAPDR) had a significantly larger CAD mean than teeth with pulp necrosis and no asymptomatic apical periodontitis diagnosed radiographically (TPNNAAPDR) and teeth with vital pulp and normal apical tissues (TVPNAT) (p = 0.0297); and the last two did not differ statistically (p > 0.05). The largest CAD mean was observed in single canals of maxillary central incisors. The lowest values of this variable were identified in the mesiobuccal and mesial canals of maxillary and mandibular first molars, respectively. The CAD of the root canals was influenced only by the root canal/tooth and pulpoperiradicular diagnosis.
A psychosocial network approach studying biomedical HIV prevention uptake between 2017 and 2019
Authors: Zimmermann Hanne M. L. , Davidovich Udi , van Bilsen Ward P. H. , Coyer Liza , Matser Amy , Prins Maria , van Harreveld Frenk 
Published: September 2023

AbstractBiomedical HIV-prevention strategies (BmPS) among men who have sex with men (MSM), such as pre-exposure prophylaxis (PrEP) and viral load sorting (VLS), are essential but relatively new and their uptake gradual. Using an extension of the causal attitude network approach, we investigated which beliefs are related to uptake of PrEP and VLS at each time-point. We included 632 HIV-negative MSM from the Amsterdam Cohort Studies from four data-waves between 2017 and 2019. We estimated weighted, undirected networks for each time-point, where we included pairwise interactions of PrEP and VLS uptake and related beliefs. PrEP use increased from 10 to 31% (p < 0.001), while VLS was reported by 7–10% at each time-point. Uptake of both BmPS was directly related to the perceived positive impact of the strategy on one’s quality of sex life and perceived supportive social norms. Overall network structure differed between time points, specifically in regard to PrEP. At earlier time points, perceptions of efficacy and affordability played an important role for PrEP uptake, while more recently social and health-related concerns became increasingly important.The network structure differed across data-waves, suggesting specific time changes in uptake motives. These findings may be used in communication to increase prevention uptake.
Assessing robustness of quantitative susceptibility-based MRI radiomic features in patients with multiple sclerosis
Authors: Fiscone Cristiana , Rundo Leonardo , Lugaresi Alessandra , Manners David Neil , Allinson Kieren , Baldin Elisa , Vornetti Gianfranco , Lodi Raffaele , Tonon Caterina , Testa Claudia , Castelli Mauro , Zaccagna Fulvio 
Published: September 2023

AbstractMultiple Sclerosis (MS) is an autoimmune demyelinating disease characterised by changes in iron and myelin content. These biomarkers are detectable by Quantitative Susceptibility Mapping (QSM), an advanced Magnetic Resonance Imaging technique detecting magnetic properties. When analysed with radiomic techniques that exploit its intrinsic quantitative nature, QSM may furnish biomarkers to facilitate early diagnosis of MS and timely assessment of progression. In this work, we explore the robustness of QSM radiomic features by varying the number of grey levels (GLs) and echo times (TEs), in a sample of healthy controls and patients with MS. We analysed the white matter in total and within six clinically relevant tracts, including the cortico-spinal tract and the optic radiation. After optimising the number of GLs (n = 64), at least 65% of features were robust for each Volume of Interest (VOI), with no difference (p > .05) between left and right hemispheres. Different outcomes in feature robustness among the VOIs depend on their characteristics, such as volume and variance of susceptibility values. This study validated the processing pipeline for robustness analysis and established the reliability of QSM-based radiomics features against GLs and TEs. Our results provide important insights for future radiomics studies using QSM in clinical applications.
A quantum-inspired probabilistic prime factorization based on virtually connected Boltzmann machine and probabilistic annealing
Authors: Jung Hyundo , Kim Hyunjin , Lee Woojin , Jeon Jinwoo , Choi Yohan , Park Taehyeong , Kim Chulwoo 
Published: September 2023

AbstractProbabilistic computing has been introduced to operate functional networks using a probabilistic bit (p-bit), broadening the computational abilities in non-deterministic polynomial searching operations. However, previous developments have focused on emulating the operation of quantum computers similarly, implementing every p-bit with large weight-sum matrix multiplication blocks and requiring tens of times more p-bits than semiprime bits. In addition, operations based on a conventional simulated annealing scheme required a large number of sampling operations, which deteriorated the performance of the Ising machines. Here we introduce a prime factorization machine with a virtually connected Boltzmann machine and probabilistic annealing method, which are designed to reduce the hardware complexity and number of sampling operations. From 10-bit to 64-bit prime factorizations were performed, and the machine offers up to 1.2 × 108 times improvement in the number of sampling operations compared with previous factorization machines, with a 22-fold smaller hardware resource.
Gene regulation for inflammation and inflammation resolution differs between umbilical arterial and venous endothelial cells
Authors: Michaeli Julia Caroline , Albers Sebastian , de la Torre Carolina , Schreiner Yannick , Faust Sara , Michaeli Thomas , Michaeli Daniel Tobias , Liying An , Krämer Bernhard K. , Stach Ksenija , Yard Benito A. 
Published: September 2023

AbstractSystemic inflammation affects the whole vasculature, yet whether arterial and venous endothelial cells differ in their abilities to mediate inflammation and to return to homeostasis after an inflammatory stimulus has not been addressed thoroughly. We assessed gene-expression profiles in isolated endothelial cells from human umbilical arteries (HUAEC) or veins (HUVEC) under basal conditions, after TNF-α stimulation and various time points after TNF-α removal to allow reinstatement of homeostasis. TNF-α regulates the expression of different sets of transcripts that are significantly changed only in HUAEC, only in HUVEC or changed in both. We identified three types of gene regulation, i.e. genes that were significantly regulated after 24 h of TNF-α stimulation but no longer when TNF-α was removed (homeostatic regulation), genes that maintained significantly regulated after TNF-α removal (not homeostatic regulation) and genes that were only significantly regulated when TNF-α was removed (post-regulation). HUAEC and HUVEC quantitatively differed in these types of gene regulation, with relatively more genes being post-regulated in HUAEC. In conclusion our data demonstrate that HUAEC and HUVEC respond intrinsically different to an inflammatory insult. Whether this holds true for all endothelial cells and its relevance for inflammatory insults in different organs during systemic inflammation warrants further studies.
Silymarin enhances the response to oxytetracycline treatment in Oreochromis niloticus experimentally infected with Aeromonas hydrophila
Authors: Sherif Ahmed H. , Toulan Adel E. , El-kalamwi Naglaa , Farag Enas A. H. , Mahmoud Abeer E. 
Published: September 2023

AbstractMany governments have approved the use of oxytetracycline as an antibiotic additive to food fish, with oxytetracycline now routinely used in many nations. However, oxytetracycline is known to have immunosuppression impacts. We, therefore, evaluated the immunological, antioxidative, and histopathological status of Nile tilapia fed a diet containing silymarin (100 mg/kg fish feed) for 0, 2, 4, 6, and 8 weeks. The protective effects of silymarin against Aeromonas hydrophila (A. hydrophila) infection and oxytetracycline treatment were evaluated. Blood parameters (erythrocyte count, white blood cell count, hemoglobin, and packed cell volume) improved over time in fish fed on dietary silymarin. Serum levels of alanine aminotransferase (ALT) were lower in fish fed on dietary silymarin, whereas serum levels of aspartate transferase (AST)and alkaline phosphatase (ALK) were unchanged. Dietary silymarin affected serum lipid profiles as decreases in serum triglyceride and low-density lipoprotein cholesterol levels and a trend toward lower cholesterol levels, whereas serum high-density lipoprotein cholesterol levels were increased compared to fish fed on the control diet. Dietary silymarin resulted in an increase of serum total protein levels and globulin fractions. Significant and progressive increases in catalase and glutathione peroxidase levels were observed after six weeks of feeding on a dietary silymarin before decreasing to control levels at the end of the experimental period. Fish fed on dietary silymarin, interleukin-1 and fish tumor necrosis factor-alpha were upregulated in hepatic tissues; however, interleukin-10 levels decreased to comparable levels to controls after eight weeks. Fish infected with A. hydrophila displayed septicemia (opaque eye, hemorrhagic ulcers, dentated fins, hepatomegaly, and splenomegaly). Reduced mortality was observed in Nile tilapia infected with A. hydrophila and fed a diet containing silymarin, indicating that silymarin improves fish responses to oxytetracycline with a 37% reduction in mortality.
A novel anisotropy template for an improved interpretation of elastic anisotropy data
Authors: Firdaus Gama , Prasad Manika , Behura Jyoti 
Published: September 2023

AbstractTight unconventional rocks are characterized by the presence of laminations, preferentially oriented cracks, and an interconnected network of compliant minerals. Such anisotropic features can mechanically deform due to pressure depletion during production, leading to a human-induced change of elastic and fluid transport properties. Rock physics models allow us to better predict and assess stress- and direction-dependent elastic moduli of the rock, useful for horizontal stress estimates. However, elastic anisotropy can be challenging to measure and interpret. We have developed an anisotropy template that can be used to assess stress-dependent changes in elastic moduli and investigate rock textures. We present here the template construction using an effective medium model consisting of stiff and compliant layers and crack inclusions and evaluate the origin of stress-dependent stiffness changes in acoustic data from Berea, Bakken, Three Forks, and Mancos formations.
Human–machine cooperation meta-model for clinical diagnosis by adaptation to human expert’s diagnostic characteristics
Authors: Park Hae-Jeong , Kim Sung Huhn , Choi Jae Young , Cha Dongchul 
Published: September 2023

AbstractArtificial intelligence (AI) using deep learning approaches the capabilities of human experts in medical image diagnosis. However, due to liability issues in medical decisions, AI is often relegated to an assistant role. Based on this responsibility constraint, the effective use of AI to assist human intelligence in real-world clinics remains a challenge. Given the significant inter-individual variations in clinical decisions among physicians based on their expertise, AI needs to adapt to individual experts, complementing weaknesses and enhancing strengths. For this adaptation, AI should not only acquire domain knowledge but also understand the specific human experts it assists. This study introduces a meta-model for human–machine cooperation that first evaluates each expert’s class-specific diagnostic tendencies using conditional probability, based on which the meta-model adjusts the AI’s predictions. This meta-model was applied to ear disease diagnosis using otoendoscopy, highlighting improved performance when incorporating individual diagnostic characteristics, even with limited evaluation data. The highest accuracy was achieved by combining each expert’s conditional probabilities with machine classification probability, using optimal weights specific to each individual’s overall classification accuracy. This tailored model aims to mitigate potential misjudgments due to psychological effects caused by machine suggestions and to capitalize on the unique expertise of individual clinicians.