bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting schizophrenia with 3D structural brain MRI using deep learning
Authors: Zhang Junhao , Rao Vishwanatha M. , Tian Ye , Yang Yanting , Acosta Nicolas , Wan Zihan , Lee Pin-Yu , Zhang Chloe , Kegeles Lawrence S. , Small Scott A. , Guo Jia 
Published: September 2023

AbstractSchizophrenia is a chronic neuropsychiatric disorder that causes distinct structural alterations within the brain. We hypothesize that deep learning applied to a structural neuroimaging dataset could detect disease-related alteration and improve classification and diagnostic accuracy. We tested this hypothesis using a single, widely available, and conventional T1-weighted MRI scan, from which we extracted the 3D whole-brain structure using standard post-processing methods. A deep learning model was then developed, optimized, and evaluated on three open datasets with T1-weighted MRI scans of patients with schizophrenia. Our proposed model outperformed the benchmark model, which was also trained with structural MR images using a 3D CNN architecture. Our model is capable of almost perfectly (area under the ROC curve = 0.987) distinguishing schizophrenia patients from healthy controls on unseen structural MRI scans. Regional analysis localized subcortical regions and ventricles as the most predictive brain regions. Subcortical structures serve a pivotal role in cognitive, affective, and social functions in humans, and structural abnormalities of these regions have been associated with schizophrenia. Our finding corroborates that schizophrenia is associated with widespread alterations in subcortical brain structure and the subcortical structural information provides prominent features in diagnostic classification. Together, these results further demonstrate the potential of deep learning to improve schizophrenia diagnosis and identify its structural neuroimaging signatures from a single, standard T1-weighted brain MRI.
Substituted salicylic acid analogs offer improved potency against multidrug-resistant Neisseria gonorrhoeae and good selectivity against commensal vaginal bacteria
Authors: Almolhim Hanan , Elhassanny Ahmed E. M. , Abutaleb Nader S. , Abdelsattar Abdallah S. , Seleem Mohamed N. , Carlier Paul R. 
Published: September 2023

AbstractDrug-resistant Neisseria gonorrhoeae represents a major threat to public health; without new effective antibiotics, untreatable gonococcal infections loom as a real possibility. In a previous drug-repurposing study, we reported that salicylic acid had good potency against azithromycin-resistant N. gonorrhoeae. We now report that the anti-gonococcal activity in this scaffold is easily lost by inopportune substitution, but that select substituted naphthyl analogs (3b, 3o and 3p) have superior activity to salicylic acid itself. Furthermore, these compounds retained potency against multiple ceftriaxone- and azithromycin-resistant strains, exhibited rapid bactericidal activity against N. gonorrhoeae, and showed high tolerability to mammalian cells (CC50 > 128 µg/mL). Promisingly, these compounds also show very weak growth inhibition of commensal vaginal bacteria.
Sensitivity of standardised radiomics algorithms to mask generation across different software platforms
Authors: Whybra Philip , Spezi Emiliano 
Published: September 2023

AbstractThe field of radiomics continues to converge on a standardised approach to image processing and feature extraction. Conventional radiomics requires a segmentation. Certain features can be sensitive to small contour variations. The industry standard for medical image communication stores contours as coordinate points that must be converted to a binary mask before image processing can take place. This study investigates the impact that the process of converting contours to mask can have on radiomic features calculation. To this end we used a popular open dataset for radiomics standardisation and we compared the impact of masks generated by importing the dataset into 4 medical imaging software. We interfaced our previously standardised radiomics platform with these software using their published application programming interface to access image volume, masks and other data needed to calculate features. Additionally, we used super-sampling strategies to systematically evaluate the impact of contour data pre processing methods on radiomic features calculation. Finally, we evaluated the effect that using different mask generation approaches could have on patient clustering in a multi-center radiomics study. The study shows that even when working on the same dataset, mask and feature discrepancy occurs depending on the contour to mask conversion technique implemented in various medical imaging software. We show that this also affects patient clustering and potentially radiomic-based modelling in multi-centre studies where a mix of mask generation software is used. We provide recommendations to negate this issue and facilitate reproducible and reliable radiomics.
Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly
Authors: Glunčić Matko , Vlahović Ines , Rosandić Marija , Paar Vladimir 
Published: September 2023

AbstractIt is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.
Deciphering migraine pain mechanisms through electrophysiological insights of trigeminal ganglion neurons
Authors: Vongseenin S. , Ha-ji-a-sa N. , Thanprasertsuk S. , Bongsebandhu-phubhakdi S. 
Published: September 2023

AbstractMigraine is a complex neurological disorder that affects millions of people worldwide. Despite extensive research, the underlying mechanisms that drive migraine pain and related abnormal sensation symptoms, such as hyperalgesia, allodynia, hyperesthesia, and paresthesia, remain poorly understood. One of the proposed mechanisms is cortical spreading depression (CSD), which is believed to be involved in the regulation of trigeminovascular pathways by sensitizing the pain pathway. Another mechanism is serotonin depletion, which is implicated in many neurological disorders and has been shown to exacerbate CSD-evoked pain at the cortical level. However, the effects of CSD and serotonin depletion on trigeminal ganglion neurons, which play a critical role in pain signal transmission, have not been thoroughly studied. In this study, we aimed to investigate the association between CSD and serotonin depletion with peripheral sensitization processes in nociceptive small-to-medium (SM) and large (L) -sized trigeminal ganglion neurons at the electrophysiological level using rat models. We divided the rats into four groups: the control group, the CSD group, the serotonin depletion group, and the CSD/serotonin depletion group. We induced CSD by placing KCl on a burr hole and serotonin depletion by intraperitoneal injection of PCPA (para-chlorophenoxyacetic acid). We then isolated trigeminal ganglion neurons from all groups and classified them according to size. Using patch-clamp recording, we recorded the excitability parameters and action potential (AP) properties of the collected neurons. Our results showed that in SM-sized trigeminal ganglion neurons, the CSD-SM and CSD/serotonin depletion groups had a higher positive resting membrane potential (RMP) than the control-SM group (p = 0.001 and p = 0.002, respectively, post-hoc Tukey’s test). In addition, the gap between RMP and threshold in the CSD-SM group was significantly narrower than in the control-SM group (p = 0.043, post-hoc Tukey’s test). For L-sized neurons, we observed prolongation of the AP rising time, AP falling time, and AP duration in neurons affected by CSD (p < 0.05, pairwise comparison test). In conclusion, our study provides new insights into the underlying mechanisms of migraine pain and abnormal somatosensation. CSD and serotonin depletion promote the transmission of pain signals through the peripheral sensitization process of nociceptive small-to-medium-sized trigeminal ganglion neurons, as well as nociceptive and non-nociceptive large-sized trigeminal ganglion neurons.
Design, synthesis, computational study and cytotoxic evaluation of some new quinazoline derivatives containing pyrimidine moiety
Authors: Zare Somayeh , Emami Leila , Faghih Zahra , Zargari Farshid , Faghih Zeinab , Khabnadideh Soghra 
Published: September 2023

AbstractQuinazoline derivatives, as an important category of heterocyclic compounds, have received much attention for the design and development of new drugs due to their various pharmacological properties. Besides, there is a great deal of evidence showing pyrimidine analogs as anticancer agents. Thus, in the present study, for the design of new target compounds with cytotoxic activity, we focused on various quinazolinone and pyrimidine hybrids. A new series of quinazoline-pyrimidine hybrid derivatives (6a-6n) have been designed and synthesized as novel antiproliferative agents. All the synthesized compounds characterized based on their IR, NMR and Mass spectroscopic data. Antiproliferative activities of the new compounds were evaluated against three human cancer cell lines (MCF-7, A549, SW-480). The compounds were found to have appropriate potential with IC50 values ranging from 2.3 ± 5.91 to 176.5 ± 0.7 μM against the tested cell lines. Compound 6n exerted the highest antiproliferative activity with IC50 values of 5.9 ± 1.69 μM, 2.3 ± 5.91 μM and 5.65 ± 2.33 μM against A549, SW-480 and MCF-7 respectively. The results indicated that 6n could induce apoptosis in A549 cell line in a dose dependent manner and arrest in the S phase of cell cycle. Docking studies were also done to investigate the detailed binding pattern of the synthesized compounds against EGFR. Furthermore, molecular dynamic simulation and binding free energy calculation have been done to rescore initial docking pose of the synthesized compounds using ensemble-based MMGB/PBSA free energy method. According to the results, free energy calculation confirmed biological activity of compounds and also, Arg 817 and Lys 721 residues had the pivotal role in the high potency of 6n. Finally, the drug likeness and in silico ADME study were also predicted.
Lifestyle patterns influence the composition of the gut microbiome in a healthy Chinese population
Authors: Ren Yi , Wu Jiawei , Wang Yilin , Zhang Lanying , Ren Jing , Zhang Zhiming , Chen Binghan , Zhang Kejian , Zhu Baoli , Liu Wei , Li Sabrina , Li Xu 
Published: September 2023

AbstractHigh-throughput sequencing allows for the comprehensive analysis of the human intestinal microbiota. However, extensive association analyses between the microbiome and lifestyle differences in the Chinese population are limited. Here, we carried out an independent cohort study—the Chinese Healthy Gut Project (n = 483)—where correlations between the gut microbiota and dietary and lifestyle variables in a healthy Chinese population are defined. We collected both questionnaire data, including basic information and lifestyle and dietary variables, and fecal stools from the enrolled volunteers. We then performed 16S rRNA sequencing on the microbial DNA isolated from the stools to assess the composition of the intestinal microbiota. We found that Prevotella and Bacteroides were the most abundant genera in the healthy Chinese gut microbiome. Additionally, 9 out of 29 clinical and questionnaire-based phenotype covariates were found to be associated with the variation in the composition of the gut microbiota. Among these lifestyle phenotypes, sleep procrastination, negative mood, and drinking habits had the largest effect size. Additionally, an appreciable effect of urbanization was observed, resulting in decreased intra-individual diversity, increased inter-individual diversity, and an increased abundance of the Bacteroides enterotype. The results of this study provide a foundation for assessing the healthy Chinese gut microbiota community structure at baseline in a healthy Chinese population. Furthermore, this study also provides insights into understanding how distinctive living habits influence the relationships between the Chinese gut microbiome and systemic health state.
Azithromycin promotes proliferation, and inhibits inflammation in nasal epithelial cells in primary ciliary dyskinesia
Authors: Varenyiova Zofia , Rojas-Hernandez Laura S. , Spano Jacquelyn , Capek Vaclav , Rosenberg-Hasson Yael , Holmes Tyson , Milla Carlos 
Published: September 2023

AbstractPrimary ciliary dyskinesia (PCD) is a genetic disorder associated with recurrent and chronic respiratory infections due to functional defects of motile cilia. In this study, we aimed to elucidate inflammatory and proliferative responses in PCD respiratory epithelium and evaluate the effect of Azithromycin (AZT) on these responses. Airway basal cells (BCs) were isolated from nasal samples of Wild-type (WT) epitope of healthy donors and PCD donors with bi-allelic mutations in DNAH5, DNAH11 and CCDC39. Cells were expanded in vitro and stimulated with either Lipopolysaccharide (LPS) or vehicle control. Post stimulation, cells were treated with either Azithromycin (AZT) or vehicle control. Cell proliferation was imaged in real-time. Separately, BCs from the same donors were expanded and grown at an air–liquid interface (ALI) to generate a multi-ciliated epithelium (MCE). Once fully mature, cells were stimulated with LPS, AZT, LPS + AZT or vehicle control. Inflammatory profiling was performed on collected media by cytokine Luminex assay. At baseline, there was a significantly higher mean production of pro-inflammatory cytokines by CCDC39 BCs and MCEs when compared to WT, DNAH11 and DNAH5 cells. AZT inhibited production of cytokines induced by LPS in PCD cells. Differences in cell proliferation were noted in PCD and this was also corrected with AZT treatment.
Increased impact of the El Niño–Southern Oscillation on global vegetation under future warming environment
Authors: Le Thanh 
Published: September 2023

AbstractThere are broad effects of vegetation changes on regional climate, carbon budget, the water cycle, and ecosystems’ productivity. Therefore, further knowledge of the drivers of future vegetation changes is critical to mitigate the influences of global warming. The El Niño–Southern Oscillation (ENSO) is a major mode of interannual climate variability and is likely to affect vegetation on the global scale. Nonetheless, little is known about the causal impacts of ENSO on future vegetation cover with changes in land use and a warming environment. Here, we examined the connections between ENSO and vegetation using leaf area index (LAI) data over the period 2015–2100 from Coupled Modeling Intercomparison Project Phase 6. Our findings indicate that, compared with the historical period 1915–2000, the vegetated areas influenced by ENSO are projected to rise by approximately 55.2% and 20.7% during the twenty-first century of the scenarios SSP2-4.5 and SSP5-8.5, respectively. Though uncertainty for the causal link between ENSO and vegetation changes remains in several regions (i.e., parts of North America, southern Australia, and western Asia), ENSO signature on LAI variations is robust over northern Australia, Amazonia, and parts of Southeast Asia. These results indicate that the influences of ENSO on global vegetation may strengthen in the future.
Numerical study of ice loads on different interfaces based on cohesive element formulation
Authors: Xing Wenqiang , Cong Shengyi , Ling Xianzhang , Li Xinyu , Cheng Zhihe , Tang Liang 
Published: September 2023

AbstractWith the increase of marine activities in the Arctic area, the demand for reliable design of marine structures is growing. Numerous publications can be found regarding simulations of ice action on structures using cohesive element models of the ice. However, previous studies have rarely discussed the influence of structural form, that is, the form of ice-structure interaction interface, on the ice load. Thus, a more comprehensive understanding of the ice load on structures with different interface geometries needs to be explored. In the present paper, three-dimensional finite element models with the cohesive element method are developed to investigate the ice load on different structures. The numerical results are validated based on in-situ testing data and the results of the previous numerical model. Parametric studies considering structure widths, inclination angles, ice velocity as well as structure roughness are conducted to explore the horizontal force and failure process of the ice sheet. The process of ice-structure interaction and ice loads on different structural forms were discussed and simplified diagrams of ice load distribution on the interface were developed.
The complete mitochondrial genome of Wellcomia compar (Spirurina: Oxyuridae) and its genome characterization and phylogenetic analysis
Authors: Huo Chunmao , Bao Fengyun , Long Hong , Qin Tingyang , Zhang Shibin 
Published: September 2023

AbstractWellcomia compar (Spirurina: Oxyuridae) is a pinworm that infects wild and captive porcupines. Despite clear records of its morphological structure, its genetics, systematics, and biology are poorly understood. This study aimed to determine the complete mitochondrial (mt) genome of W. compar and reconstruct its phylogenetic relationship with other nematodes. We sequenced the complete mt genome of W. comparand conducted phylogenetic analyses using concatenated coding sequences of 12 protein-coding genes (PCGs) by maximum likelihood and Bayesian inference. The complete mt genome is 14,373 bp in size and comprises 36 genes, including 12 protein-coding, two rRNA and 22 tRNA genes. Apart from 28 intergenic regions, one non-coding region and one overlapping region also occur. A comparison of the gene arrangements of Oxyuridomorpha revealed relatively similar features in W. compar and Wellcomia siamensis. Phylogenetic analysis also showed that W. compar and W. siamensis formed a sister group. In Oxyuridomorpha the genetic distance between W. compar and W. siamensis was 0.0805. This study reports, for the first time, the complete W. compar mt genome sequence obtained from Chinese porcupines. It provides genetic markers for investigating the taxonomy, population genetics, and phylogenetics of pinworms from different hosts and has implications for the diagnosis, prevention, and control of parasitic diseases in porcupines and other animals.
Atmosphere injection of sea salts during large explosive submarine volcanic eruptions
Authors: Colombier M. , Ukstins I. A. , Tegtmeier S. , Scheu B. , Cronin S. J. , Thivet S. , Paredes-Mariño J. , Cimarelli C. , Hess K.-U. , Kula Taaniela , Latu’ila Folauhola H. , Dingwell D. B. 
Published: September 2023

AbstractThe 15 January 2022 submarine eruption at Hunga volcano was the most explosive volcanic eruption in 140 years. It involved exceptional magma and seawater interaction throughout the entire submarine caldera collapse. The submarine volcanic jet breached the sea surface and formed a subaerial eruptive plume that transported volcanic ash, gas, sea salts and seawater up to ~ 57 km, reaching into the mesosphere. We document high concentrations of sea salts in tephra (volcanic ash) collected shortly after deposition. We also discuss the potential climatic consequences of large-scale injection of salts into the upper atmosphere during submarine eruptions. Sodium chloride in these volcanic plumes can reach extreme concentrations, and dehalogenation of chlorides and bromides poses the risk of long-term atmospheric and weather impact. Salt content in rapidly collected tephra samples may also be used as a proxy to estimate the water:magma ratio during eruption, with implications for quantification of fragmentation efficiency in submarine breaching events. The balance between salt loading into the atmosphere versus deposition in ash aggregates is a key factor in understanding the atmospheric and climatic consequences of submarine eruptions.
Meaningful objects avoid attribute amnesia due to incidental long-term memories
Authors: Sasin Edyta , Markov Yuri , Fougnie Daryl 
Published: September 2023

AbstractAttribute amnesia describes the failure to unexpectedly report the attribute of an attended stimulus, likely reflecting a lack of working memory consolidation. Previous studies have shown that unique meaningful objects are immune to attribute amnesia. However, these studies used highly dissimilar foils to test memory, raising the possibility that good performance at the surprise test was based on an imprecise (gist-like) form of long-term memory. In Experiment 1, we explored whether a more sensitive memory test would reveal attribute amnesia in meaningful objects. We used a four-alternative-forced-choice test with foils having mis-matched exemplar (e.g., apple pie/pumpkin pie) and/or state (e.g., cut/full) information. Errors indicated intact exemplar, but not state information. Thus, meaningful objects are vulnerable to attribute amnesia under the right conditions. In Experiments 2A-2D, we manipulated the familiarity signals of test items by introducing a critical object as a pre-surprise target. In the surprise trial, this critical item matched one of the foil choices. Participants selected the critical object more often than other items. By demonstrating that familiarity influences responses in this paradigm, we suggest that meaningful objects are not immune to attribute amnesia but instead side-step the effects of attribute amnesia.