bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustained antigen delivery improves germinal center reaction and increases antibody responses in neonatal mice
Authors: Lotspeich-Cole Leda , Parvathaneni Swetha , Sakai Jiro , Liu Lunhua , Takeda Kazuyo , Lee Robert C. , Akkoyunlu Mustafa 
Published: May 2024

AbstractNeonates and young infants are known to have limited responses to pediatric vaccines due to reduced germinal center formation. Extended vaccine antigen dosing was previously shown to expand germinal center formation and improve humoral responses in adult mice. We report that sustained antigen delivery through sequential dosing overcomes neonatal limitations to form germinal center reactions and improves humoral immunity. Thus, vaccine strategies that extend the release of vaccine antigens may reduce the number of doses, and time needed, to achieve protective immunity in neonates and young infants.
Long-term kidney outcomes of semaglutide in obesity and cardiovascular disease in the SELECT trial
Authors: Colhoun Helen M. , Lingvay Ildiko , Brown Paul M. , Deanfield John , Brown-Frandsen Kirstine , Kahn Steven E. , Plutzky Jorge , Node Koichi , Parkhomenko Alexander , Rydén Lars , Wilding John P. H. , Mann Johannes F. E. , Tuttle Katherine R. , Idorn Thomas , Rathor Naveen , Lincoff A. Michael 
Published: May 2024

AbstractThe SELECT trial previously reported a 20% reduction in major adverse cardiovascular events with semaglutide (n = 8,803) versus placebo (n = 8,801) in patients with overweight/obesity and established cardiovascular disease, without diabetes. In the present study, we examined the effect of once-weekly semaglutide 2.4 mg on kidney outcomes in the SELECT trial. The incidence of the pre-specified main composite kidney endpoint (death from kidney disease, initiation of chronic kidney replacement therapy, onset of persistent estimated glomerular filtration rate (eGFR) < 15 ml min−1 1.73 m−2, persistent ≥50% reduction in eGFR or onset of persistent macroalbuminuria) was lower with semaglutide (1.8%) versus placebo (2.2%): hazard ratio (HR) = 0.78; 95% confidence interval (CI) 0.63, 0.96; P = 0.02. The treatment benefit at 104 weeks for eGFR was 0.75 ml min−1 1.73 m−2 (95% CI 0.43, 1.06; P < 0.001) overall and 2.19 ml min−1 1.73 m−2 (95% CI 1.00, 3.38; P < 0.001) in patients with baseline eGFR <60 ml min−1 1.73 m−2. These results suggest a benefit of semaglutide on kidney outcomes in individuals with overweight/obesity, without diabetes.ClinicalTrials.gov identifier: NCT03574597.
The reference genome of Macropodus opercularis (the paradise fish)
Authors: Fodor Erika , Okendo Javan , Szabó Nóra , Szabó Kata , Czimer Dávid , Tarján-Rácz Anita , Szeverényi Ildikó , Low Bi Wei , Liew Jia Huan , Koren Sergey , Rhie Arang , Orbán László , Miklósi Ádám , Varga Máté , Burgess Shawn M. 
Published: May 2024

AbstractAmongst fishes, zebrafish (Danio rerio) has gained popularity as a model system over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (Macropodus opercularis), an “air-breather” species has a highly complex behavioral repertoire and has been the subject of many ethological investigations but lacks genomic resources. Here we report the reference genome assembly of M. opercularis using long-read sequences at 150-fold coverage. The final assembly consisted of 483,077,705 base pairs (~483 Mb) on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ~90% of them to orthogroups.
REAL-Colon: A dataset for developing real-world AI applications in colonoscopy
Authors: Biffi Carlo , Antonelli Giulio , Bernhofer Sebastian , Hassan Cesare , Hirata Daizen , Iwatate Mineo , Maieron Andreas , Salvagnini Pietro , Cherubini Andrea 
Published: May 2024

AbstractDetection and diagnosis of colon polyps are key to preventing colorectal cancer. Recent evidence suggests that AI-based computer-aided detection (CADe) and computer-aided diagnosis (CADx) systems can enhance endoscopists' performance and boost colonoscopy effectiveness. However, most available public datasets primarily consist of still images or video clips, often at a down-sampled resolution, and do not accurately represent real-world colonoscopy procedures. We introduce the REAL-Colon (Real-world multi-center Endoscopy Annotated video Library) dataset: a compilation of 2.7 M native video frames from sixty full-resolution, real-world colonoscopy recordings across multiple centers. The dataset contains 350k bounding-box annotations, each created under the supervision of expert gastroenterologists. Comprehensive patient clinical data, colonoscopy acquisition information, and polyp histopathological information are also included in each video. With its unprecedented size, quality, and heterogeneity, the REAL-Colon dataset is a unique resource for researchers and developers aiming to advance AI research in colonoscopy. Its openness and transparency facilitate rigorous and reproducible research, fostering the development and benchmarking of more accurate and reliable colonoscopy-related algorithms and models.
Head model dataset for mixed reality navigation in neurosurgical interventions for intracranial lesions
Authors: Qi Ziyu , Jin Haitao , Xu Xinghua , Wang Qun , Gan Zhichao , Xiong Ruochu , Zhang Shiyu , Liu Minghang , Wang Jingyue , Ding Xinyu , Chen Xiaolei , Zhang Jiashu , Nimsky Christopher , Bopp Miriam H. A. 
Published: May 2024

AbstractMixed reality navigation (MRN) technology is emerging as an increasingly significant and interesting topic in neurosurgery. MRN enables neurosurgeons to “see through” the head with an interactive, hybrid visualization environment that merges virtual- and physical-world elements. Offering immersive, intuitive, and reliable guidance for preoperative and intraoperative intervention of intracranial lesions, MRN showcases its potential as an economically efficient and user-friendly alternative to standard neuronavigation systems. However, the clinical research and development of MRN systems present challenges: recruiting a sufficient number of patients within a limited timeframe is difficult, and acquiring low-cost, commercially available, medically significant head phantoms is equally challenging. To accelerate the development of novel MRN systems and surmount these obstacles, the study presents a dataset designed for MRN system development and testing in neurosurgery. It includes CT and MRI data from 19 patients with intracranial lesions and derived 3D models of anatomical structures and validation references. The models are available in Wavefront object (OBJ) and Stereolithography (STL) formats, supporting the creation and assessment of neurosurgical MRN applications.
Exploring the “gene–metabolite” network of ischemic stroke with blood stasis and toxin syndrome by integrated transcriptomics and metabolomics strategy
Authors: Liu Yue , Cui Wenqiang , Liu Hongxi , Yao Mingjiang , Shen Wei , Miao Lina , Wei Jingjing , Liang Xiao , Zhang Yunling 
Published: May 2024

AbstractA research model combining a disease and syndrome can provide new ideas for the treatment of ischemic stroke. In the field of traditional Chinese medicine, blood stasis and toxin (BST) syndrome is considered an important syndrome seen in patients with ischemic stroke (IS). However, the biological basis of IS-BST syndrome is currently not well understood. Therefore, this study aimed to explore the biological mechanism of IS-BST syndrome. This study is divided into two parts: (1) establishment of an animal model of ischemic stroke disease and an animal model of BST syndrome in ischemic stroke; (2) use of omics methods to identify differentially expressed genes and metabolites in the models. We used middle cerebral artery occlusion (MCAO) surgery to establish the disease model, and utilized carrageenan combined with active dry yeast and MCAO surgery to construct the IS-BST syndrome model. Next, we used transcriptomics and metabolomics methods to explore the differential genes and metabolites in the disease model and IS-BST syndrome model. It is found that the IS-BST syndrome model exhibited more prominent characteristics of IS disease and syndrome features. Both the disease model and the IS-BST syndrome model share some common biological processes, such as thrombus formation, inflammatory response, purine metabolism, sphingolipid metabolism, and so on. Results of the “gene–metabolite” network revealed that the IS-BST syndrome model exhibited more pronounced features of complement-coagulation cascade reactions and amino acid metabolism disorders. Additionally, the “F2 (thrombin)–NMDAR/glutamate” pathway was coupled with the formation process of the blood stasis and toxin syndrome. This study reveals the intricate mechanism of IS-BST syndrome, offering a successful model for investigating the combination of disease and syndrome.
Bioinformatics approach for structure modeling, vaccine design, and molecular docking of Brucella candidate proteins BvrR, OMP25, and OMP31
Authors: Elrashedy Alyaa , Nayel Mohamed , Salama Akram , Salama Mohammed M. , Hasan Mohamed E. 
Published: May 2024

AbstractBrucellosis is a zoonotic disease with significant economic and healthcare costs. Despite the eradication efforts, the disease persists. Vaccines prevent disease in animals while antibiotics cure humans with limitations. This study aims to design vaccines and drugs for brucellosis in animals and humans, using protein modeling, epitope prediction, and molecular docking of the target proteins (BvrR, OMP25, and OMP31). Tertiary structure models of three target proteins were constructed and assessed using RMSD, TM-score, C-score, Z-score, and ERRAT. The best models selected from AlphaFold and I-TASSER due to their superior performance according to CASP 12 – CASP 15 were chosen for further analysis. The motif analysis of best models using MotifFinder revealed two, five, and five protein binding motifs, however, the Motif Scan identified seven, six, and eight Post-Translational Modification sites (PTMs) in the BvrR, OMP25, and OMP31 proteins, respectively. Dominant B cell epitopes were predicted at (44–63, 85–93, 126–137, 193–205, and 208–237), (26–46, 52–71, 98–114, 142–155, and 183–200), and (29–45, 58–82, 119–142, 177–198, and 222–251) for the three target proteins. Additionally, cytotoxic T lymphocyte epitopes were detected at (173–181, 189–197, and 202–210), (61–69, 91–99, 159–167, and 181–189), and (3–11, 24–32, 167–175, and 216–224), while T helper lymphocyte epitopes were displayed at (39–53, 57–65, 150–158, 163–171), (79–87, 95–108, 115–123, 128–142, and 189–197), and (39–47, 109–123, 216–224, and 245–253), for the respective target protein. Furthermore, structure-based virtual screening of the ZINC and DrugBank databases using the docking MOE program was followed by ADMET analysis. The best five compounds of the ZINC database revealed docking scores ranged from (− 16.8744 to − 15.1922), (− 16.0424 to − 14.1645), and (− 14.7566 to − 13.3222) for the BvrR, OMP25, and OMP31, respectively. These compounds had good ADMET parameters and no cytotoxicity, while DrugBank compounds didn't meet Lipinski's rule criteria. Therefore, the five selected compounds from the ZINC20 databases may fulfill the pharmacokinetics and could be considered lead molecules for potentially inhibiting Brucella’s proteins.
Diversity of Wolbachia infections in Sri Lankan mosquitoes with a new record of Wolbachia Supergroup B infecting Aedes aegypti vector populations
Authors: Wijegunawardana N. D. A. D. , Gunawardene Y. I. N. Silva , Abeyewickreme W. , Chandrasena T. G. A. N. , Thayanukul P. , Kittayapong P. 
Published: May 2024

AbstractWolbachiabacteria are common endosymbionts of insects and have recently been applied for controlling arboviral vectors, especiallyAedes aegyptimosquito populations. However, several medically important mosquito species in Sri Lanka were present with limited information for theWolbachiainfection status. Therefore, the screening ofWolbachiain indigenous mosquitoes is required prior to a successful application ofWolbachia-based vector control strategy. In this study, screening of 78 mosquito species collected from various parts of the country revealed that 13 species were positive forWolbachiainfection, giving ~ 17% infection frequency ofWolbachiaamong the Sri Lankan mosquitoes. TwelveWolbachia-positive mosquito species were selected for downstreamWolbachiastrain genotyping using Multi Locus Sequencing Type (MLST),wspgene, and16S rRNAgene-based approaches. Results showed that theseWolbachiastrains clustered together with the presentWolbachiaphylogeny of world mosquito populations with some variations. Almost 90% of the mosquito populations were infected with supergroup B while the remaining were infected with supergroup A. A new record ofWolbachiasupergroup B infection inAe. aegypti, the main vectors of dengue, was highlighted. This finding was further confirmed by real-time qPCR, revealingWolbachiadensity variations betweenAe. aegyptiandAe. albopictus(p = 0.001), and between males and females (p < 0.05). The evidence of natural Wolbachia infections in Ae. aegypti populations in Sri Lanka is an extremely rare incident that has the potential to be used for arboviral vector control.
Systematic review and meta-analysis: proton pump inhibitors slightly decrease the severity of chronic cough
Authors: Floria Diana-Elena , Obeidat Mahmoud , Kávási Sarolta Beáta , Teutsch Brigitta , Veres Dániel Sándor , Hagymási Krisztina , Hegyi Péter , Drug Vasile-Liviu , Erőss Bálint 
Published: May 2024

AbstractThe Montreal consensus recognizes chronic cough as an extra-esophageal manifestation of gastroesophageal reflux disease. We performed a meta-analysis to assess the effects of acid-suppressive medications in adults with non-specific chronic cough. The protocol was registered on PROSPERO (CRD42022368769). Placebo-controlled randomized trials evaluating the impact of acid-suppressive medications on persistent cough were included. The systematic search was performed on the 1st of November 2022 in three databases. A random-effects model was used for the calculations. The effect size was the standardized mean difference (SMD) with 95% confidence interval (CI). A total number of 11 double-blinded placebo-controlled randomized trials were included in the meta-analysis. Data showed that compared to placebo, PPIs decreased the severity of cough (SMD 0.33; CI 0.05; 0.61). Therapeutic response was not different in patients with non-specific chronic cough only, compared to those with laryngopharyngeal reflux. Prolonged treatment durations did not result in greater symptomatic improvement, with SMD 0.33 (CI − 0.22; 0.88), 0.31 (CI − 1.74; 2.35), 0.32 (CI − 0.29; 0.93) and 0.34 (CI − 0.16; 0.85), following 4, 6, 8 and 12 weeks of treatment, respectively. The pooled analysis of the improvement in quality of life with PPIs found an SMD of 0.39 (CI − 0.51; 1.29). PPIs mildly decrease the severity of non-specific chronic cough, irrespective of treatment duration.
Analysis of Soret and Dufour effects on radiative heat transfer in hybrid bioconvective flow of carbon nanotubes
Authors: Hussain Azad , Raiz Saira , Hassan Ali , Hassan Ahmed M. , Karamti Hanen , Bognár Gabriella 
Published: May 2024

AbstractNumerous heat transfer applications, such as heat exchangers, solar trough collectors, and fields including food processing, material research, and aerospace engineering, utilize hybrid nanofluids. Compared to conventional fluids, hybrid nanofluids exhibit significantly enhanced thermal conductivity. The aim of this work is to explore flow and heat transmission features under of magneto-hydrodynamic bioconvective flow of carbon nanotubes over the stretched surface with Dufour and Soret effects. Additionally, comparative dynamics of the carbon nanotubes (SWCMT − MWCNT/C2H6O2 with SWCMT − MWCNT/C2H6O2 − H2O) flow using the Prandtl fluid model in the presence of thermal radiation and motile microorganisms has been investigated. Novel feature Additionally, the focus is also to examine the presence of microorganisms in mixture base hybrid nanofluid. To examine heat transfer features of Prandtl hybrid nanofluid over the stretched surface convective heating is taken into consideration while modeling the boundary conditions. Suitable similarity transform has been employed to convert dimensional flow governing equations into dimensionless equations and solution of the problem has been obtained using effective, accurate and time saving bvp-4c technique in MATLAB. Velocity, temperature, concentration and microorganisms profiles have been demonstrated graphically under varying impact of various dimensionless parameters such as inclined magnetization, mixed convection, Dufour effect, Soret effect, thermal radiation effect, and bioconvection lewis number. It has been observed that raising values of magnetization (0.5 ≤ M ≤ 4), mixed convection (0.01 ≤ λ ≤ 0.05) and inclination angle (0° ≤ α ≤ 180°) enhance fluid motion rapidly in Ethylene glycol based Prandtl hybrid nanofluid (SWCMT − MWCNT/C2H6O2) when compared with mixture base working fluid of carbon nanotubes SWCMT − MWCNT/C2H6O2 − H2O). Raising thermal radiation (0.1 ≤ Rd ≤ 1.7) and Dufour number (0.1 ≤ Du ≤ 0.19) values improves temperature profile. Moreover, a good agreement has been found between the current outcome and existing literature for skin friction outcomes.
Prognostic value of neutrophil-to-lymphocyte ratio change in patients with locally advanced non-small cell lung cancer treated with thoracic radiotherapy
Authors: Yin Xiaoming , Chen Haijun , Sun Yunchuan , Xiao Li , Lu Hongling , Guo Wei , Yang Hongjuan , Zhou Jianxi , Fan Kui , Liang Wei 
Published: May 2024

AbstractIn prior investigations, a correlation was established between patient outcomes in locally advanced non-small cell lung cancer (LA-NSCLC) following thoracic irradiation and parameters, such as pre/post-treatment neutrophil-to-lymphocyte ratio (NLR) and NLR change (ΔNLR). However, these parameters could potentially be influenced by radiation-related variables, such as gross tumor volume (GTV). The primary aim of this study was to elucidate the factors impacting post-treatment NLR and ΔNLR and to further assess their prognostic relevance. In this retrospective study, a cohort of 188 LA-NSCLC patients who underwent thoracic radiation between 2012 and 2017 was assessed. The calculation of pre/post-treatment NLR involved the use of absolute neutrophil and lymphocyte counts. ΔNLR was defined as the difference between post- and pre-treatment NLR values. To assess the relationships between various variables and overall survival (OS), local progression-free survival (LPFS), and distant metastasis-free survival (DMFS), the Kaplan–Meier technique and Cox proportional hazards regression were employed. Additionally, Spearman’s rank correlation analysis was carried out to investigate correlations between the variables. The analysis revealed that both post-treatment NLR (r = 0.315, P < 0.001) and ΔNLR (r = 0.156, P = 0.032) were associated with GTV. However, OS, LPFS, and DMFS were not independently correlated with pre/post-treatment NLR. ΔNLR, on the other hand, exhibited independent associations with OS and DMFS (HR = 1.054, P = 0.020, and P = 0.046, respectively). Elevated ΔNLR values were linked to poorer OS (P = 0.023) and DMFS (P = 0.018) in the Kaplan–Meier analysis. Furthermore, when stratifying by GTV, a higher ΔNLR remained to be associated with worse OS and DMFS (P = 0.047 and P = 0.035, respectively) in the GTV ≤ 67.41 cm3 group, and in the GTV > 67.41 cm3 group (P = 0.028 and P = 0.042, respectively), highlighting ΔNLR as the sole independent predictive factor for survival and metastasis, irrespective of GTV.
Assessment of the dynamics of inpatient health care delivery in Poland before and throughout the COVID-19 pandemic
Authors: Śliwczyński Andrzej , Jewczak Maciej , Furlepa Kamila , Gołębiak Izabela , Rzeźnicki Adam , Marczak Michał , Ptak-Chmielewska Aneta , Olszewski Paweł , Orlewska Katarzyna , Wierzba Waldemar , Nojszewska Ewelina , Orlewska Ewa 
Published: May 2024

AbstractA situation of emergency involving the whole population introduces changes in the dynamics of the health services that are provided. The magnitude of these shifts should be also linked to the medical speciality within which the health benefits are delivered. The aim of the paper was to identify changes in tendencies in inpatient medical service delivery during the COVID-19 pandemic by medical specialties. On the basis of a database extracted for in-patient treatment received from the public payer, a retrospective analysis was carried out. Comparing the values of the dynamics of the services provided in each medical speciality, the period before the COVID-19 pandemic was collated to the years of the pandemic (2020–2021). In the period before COVID-19, positive patient dynamics were observed in more than half of the specialities. Between 2020 and 2021, virtually all specialties reversed the trend and negative dynamics were recorded. The dynamics in 2021 indicate a process of return to the values from 2015 to 2019. Emergency situation has affected the dynamics of healthcare provision in different specialities to various extent. The most resistant to the negative impulses of the state of emergency were the areas that are strictly organisationally and financially defined (e.g. the group of “therapeutic and drug programmes”).
Extremely compact sources (ECS): a new potential field filtering method
Authors: Maiolino Marco , Florio Giovanni , Fedi Maurizio 
Published: May 2024

AbstractWe present a new filtering method for potential fields, based on modelling the fields in terms of very compact solutions, i.e., the sources are expected to occupy the smallest allowable volume in the source domain. The selected solutions, which we call “Extremely Compact Sources” (ECS) form a sort of atomized model, which still satisfies the non-unique inverse problem of gravity and magnetic fields. The ECS model is not only characterized by sparsity, but also by large values of the physical property (density or magnetic susceptibility). The sparse nature of the model allows for the definition of a highly localized filter, which can be obtained by simply specifying the atoms to be selected in a given area. This feature allows managing tasks normally impossible with traditional filters, such as the separation of interfering anomalies having a similar wavenumber content. In addition, the procedure can perform a very effective regional/residual separation. We demonstrate the method on synthetic cases and apply it in the real case of gravity data of Campi Flegrei volcanic area (Italy), where we use the ECS filtering to isolate the gravity effect of the Mount Olibano dome.