bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and biochemical characterization of rice developed through conventional integration of nDart1-0 transposon gene
Authors: Jalil Sanaullah , Ali Qurban , Khan Asad Ullah , Nazir Muhammad Mudassir , Ali Sharafat , Zulfiqar Faisal , Javed Muhammad Arshad , Jin Xiaoli 
Published: May 2023

AbstractMutations, the genetic variations in genomic sequences, play an important role in molecular biology and biotechnology. During DNA replication or meiosis, one of the mutations is transposons or jumping genes. An indigenous transposonnDart1-0was successfully introduced into local indica cultivar Basmati-370 from transposon-tagged line viz., GR-7895 (japonica genotype) through conventional breeding technique, successive backcrossing. Plants from segregating populationsshowed variegated phenotypes were tagged asBM-37mutants. Blast analysis of the sequence data revealed that the GTP-binding protein, located on the BAC clone OJ1781_H11 of chromosome 5, contained an insertion of DNA transposonnDart1-0. ThenDart1-0has “A” at position 254 bp, whereasnDart1homologs have “G”, which efficiently distinguishesnDart1-0from its homologs. The histological analysis revealed that the chloroplast of mesophyll cells inBM-37was disrupted with reduction in size of starch granules and higher number of osmophillic plastoglobuli, which resulted in decreased chlorophyll contents and carotenoids, gas exchange parameters (Pn, g, E, Ci), and reduced expression level of genes associated with chlorophyll biosynthesis, photosynthesis and chloroplast development. Along with the rise of GTP protein, the salicylic acid (SA) and gibberellic acid (GA) and antioxidant contents(SOD) and MDA levels significantly enhanced, while, the cytokinins (CK), ascorbate peroxidase (APX), catalase (CAT), total flavanoid contents (TFC) and total phenolic contents (TPC) significantly reduced in BM-37 mutant plants as compared with WT plants. These results support the notion that GTP-binding proteins influence the process underlying chloroplast formation. Therefore, it is anticipated that to combat biotic or abiotic stress conditions, thenDart1-0tagged mutant (BM-37) of Basmati-370 would be beneficial.
Evaluation of rosuvastatin-induced QT prolongation risk using real-world data, in vitro cardiomyocyte studies, and mortality assessment
Authors: Koo Yeryung , Hyun Sung-Ae , Choi Byung Jin , Kim Yujeong , Kim Tae Young , Lim Hong-Seok , Seo Joung-Wook , Yoon Dukyong 
Published: May 2023

AbstractDrug-induced QT prolongation is attributed to several mechanisms, including hERG channel blockage. However, the risks, mechanisms, and the effects of rosuvastatin-induced QT prolongation remain unclear. Therefore, this study assessed the risk of rosuvastatin-induced QT prolongation using (1) real-world data with two different settings, namely case–control and retrospective cohort study designs; (2) laboratory experiments using human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM); (3) nationwide claim data for mortality risk evaluation. Real-world data showed an association between QT prolongation and the use of rosuvastatin (OR [95% CI], 1.30 [1.21–1.39]) but not for atorvastatin (OR [95% CI], 0.98 [0.89–1.07]). Rosuvastatin also affected the sodium and calcium channel activities of cardiomyocytes in vitro. However, rosuvastatin exposure was not associated with a high risk of all-cause mortality (HR [95% CI], 0.95 [0.89–1.01]). Overall, these results suggest that rosuvastatin use increased the risk of QT prolongation in real-world settings, significantly affecting the action potential of hiPSC-CMs in laboratory settings. Long-term rosuvastatin treatment was not associated with mortality. In conclusion, while our study links rosuvastatin use to potential QT prolongation and possible influence on the action potential of hiPSC-CMs, long-term use does not show increased mortality, necessitating further research for conclusive real-world applications.
The effect of decellularization protocols on characterizations of thermoresponsive and light-curable corneal extracellular matrix hydrogels
Authors: Yazdanpanah Ghasem , Jalilian Elmira , Shen Xiang , Anwar Khandaker N. , Jiang Yizhou , Jabbehdari Sayena , Rosenblatt Mark I. , Pan Yayue , Djalilian Ali R. 
Published: May 2023

AbstractTo compare the effects of two decellularization protocols on the characteristics of fabricated COrnea Matrix (COMatrix) hydrogels. Porcine corneas were decellularized with Detergent (De) or Freeze–Thaw (FT)-based protocols. DNA remnant, tissue composition and α-Gal epitope content were measured. The effect of α-galactosidase on α-Gal epitope residue was assessed. Thermoresponsive and light-curable (LC) hydrogels were fabricated from decellularized corneas and characterized with turbidimetric, light-transmission and rheological experiments. The cytocompatibility and cell-mediated contraction of the fabricated COMatrices were assessed. Both protocols reduced the DNA content to < 0.1 µg/mg (native, > 0.5 µg/mg), and preserved the collagens and glycosaminoglycans. The α-Gal epitope remnant decreased by > 50% following both decellularization methods. We observed more than 90% attenuation in α-Gal epitope after treatment with α-galactosidase. The thermogelation half-time of thermoresponsive COMatrices derived from De-Based protocol (De-COMatrix) was 18 min, similar to that of FT-COMatrix (21 min). The rheological characterizations revealed significantly higher shear moduli of thermoresponsive FT-COMatrix (300.8 ± 22.5 Pa) versus De-COMatrix 178.7 ± 31.3 Pa, p < 0.01); while, this significant difference in shear moduli was preserved after fabrication of FT-LC-COMatrix and De-LC-COMatrix (18.3 ± 1.7 vs 2.8 ± 2.6 kPa, respectively, p < 0.0001). All thermoresponsive and light-curable hydrogels have similar light-transmission to human corneas. Lastly, the obtained products from both decellularization methods showed excellent in vitro cytocompatibility. We found that FT-LC-COMatrix was the only fabricated hydrogel with no significant cell-mediated contraction while seeded with corneal mesenchymal stem cells (p < 0.0001). The significant effect of decellularization protocols on biomechanical properties of hydrogels derived from porcine corneal ECM should be considered for further applications.
Bioinformatic analysis and experimental validation of the potential gene in the airway inflammation of steroid-resistant asthma
Authors: Wei Chaochao , Wang Yang , Hu Chengping 
Published: May 2023

AbstractSteroid-resistant asthma is a troublesome clinical problem in public health. The pathogenesis of steroid-resistant asthma is complex and remains to be explored. In our work, the online Gene Expression Omnibus microarray dataset GSE7368 was used to explore differentially expressed genes (DEGs) between steroid-resistant asthma patients and steroid-sensitive asthma patients. Tissue-specific gene expression of DEGs was analyzed using BioGPS. The enrichment analyses were performed using GO, KEGG, and GSEA analysis. The protein–protein interaction network and key gene cluster were constructed using STRING, Cytoscape, MCODE, and Cytohubba. A steroid-resistant neutrophilic asthma mouse model was established using lipopolysaccharide (LPS) and ovalbumin (OVA). An LPS-stimulated J744A.1 macrophage model was prepared to validate the underlying mechanism of the interesting DEG gene using the quantitative reverse transcription-polymerase chain reaction (qRT-PCR). A total of 66 DEGs were identified, most of which were present in the hematologic/immune system. Enrichment analysis displayed that the enriched pathways were the IL-17 signaling pathway, MAPK signal pathway, Toll-like receptor signaling pathway, and so on. DUSP2, as one of the top upregulated DEGs, has not been clearly demonstrated in steroid-resistant asthma. In our study, we observed that the salubrinal administration (DUSP2 inhibitor) reversed neutrophilic airway inflammation and cytokine responses (IL-17A, TNF-α) in a steroid-resistant asthma mouse model. We also found that salubrinal treatment reduced inflammatory cytokines (CXCL10 and IL-1β) in LPS-stimulated J744A.1 macrophages. DUSP2 may be a candidate target for the therapy of steroid-resistant asthma.
YB1 modulates the DNA damage response in medulloblastoma
Authors: McSwain Leon F. , Pillsbury Claire E. , Haji-Seyed-Javadi Ramona , Rath Sandip Kumar , Chen Victor , Huang Tiffany , Shahab Shubin W. , Kunhiraman Haritha , Ross James , Price Gabrielle A. , Dey Abhinav , Hambardzumyan Dolores , MacDonald Tobey , Yu David S. , Porter Christopher C. , Kenney Anna M. 
Published: May 2023

AbstractY-box binding protein 1 (YBX1 or YB1) is a therapeutically relevant oncoprotein capable of RNA and DNA binding and mediating protein–protein interactions that drive proliferation, stemness, and resistance to platinum-based therapies. Given our previously published findings, the potential for YB1-driven cisplatin resistance in medulloblastoma (MB), and the limited studies exploring YB1-DNA repair protein interactions, we chose to investigate the role of YB1 in mediating radiation resistance in MB. MB, the most common pediatric malignant brain tumor, is treated with surgical resection, cranio-spinal radiation, and platinum-based chemotherapy, and could potentially benefit from YB1 inhibition. The role of YB1 in the response of MB to ionizing radiation (IR) has not yet been studied but remains relevant for determining potential anti-tumor synergy of YB1 inhibition with standard radiation therapy. We have previously shown that YB1 drives proliferation of cerebellar granular neural precursor cells (CGNPs) and murine Sonic Hedgehog (SHH) group MB cells. While others have demonstrated a link between YB1 and homologous recombination protein binding, functional and therapeutic implications remain unclear, particularly following IR-induced damage. Here we show that depleting YB1 in both SHH and Group 3 MB results not only in reduced proliferation but also synergizes with radiation due to differential response dynamics. YB1 silencing through shRNA followed by IR drives a predominantly NHEJ-dependent repair mechanism, leading to faster γH2AX resolution, premature cell cycle re-entry, checkpoint bypass, reduced proliferation, and increased senescence. These findings show that depleting YB1 in combination with radiation sensitizes SHH and Group 3 MB cells to radiation.
Accurate drusen segmentation in optical coherence tomography via order-constrained regression of retinal layer heights
Authors: Morelle Olivier , Wintergerst Maximilian W. M. , Finger Robert P. , Schultz Thomas 
Published: May 2023

AbstractDrusen are an important biomarker for age-related macular degeneration (AMD). Their accurate segmentation based on optical coherence tomography (OCT) is therefore relevant to the detection, staging, and treatment of disease. Since manual OCT segmentation is resource-consuming and has low reproducibility, automatic techniques are required. In this work, we introduce a novel deep learning based architecture that directly predicts the position of layers in OCT and guarantees their correct order, achieving state-of-the-art results for retinal layer segmentation. In particular, the average absolute distance between our model’s prediction and the ground truth layer segmentation in an AMD dataset is 0.63, 0.85, and 0.44 pixel for Bruch's membrane (BM), retinal pigment epithelium (RPE) and ellipsoid zone (EZ), respectively. Based on layer positions, we further quantify drusen load with excellent accuracy, achieving 0.994 and 0.988 Pearson correlation between drusen volumes estimated by our method and two human readers, and increasing the Dice score to 0.71 ± 0.16 (from 0.60 ± 0.23) and 0.62 ± 0.23 (from 0.53 ± 0.25), respectively, compared to a previous state-of-the-art method. Given its reproducible, accurate, and scalable results, our method can be used for the large-scale analysis of OCT data.
Endometriosis increases the risk of gestational diabetes: a meta-analysis stratified by mode of conception, disease localization and severity
Authors: Salmeri Noemi , Li Piani Letizia , Cavoretto Paolo Ivo , Somigliana Edgardo , Viganò Paola , Candiani Massimo 
Published: May 2023

AbstractTo review the current evidence on the risk of gestational diabetes mellitus (GDM) in women with endometriosis, taking into account relevant confounders such as the higher frequency of Assisted Reproductive Technologies (ART) conceptions. Database searches on PubMed, Medline, Embase and Scopus through June 2022, using combinations of relevant keywords. A total of 18 studies, involving N = 4,600,885 women, were included. The overall risk of GDM in endometriosis patients was significantly higher than in controls (OR, 1.23; 95% CI 1.07–1.51). This significant association persisted in natural pregnancies (OR, 1.08; 95% CI 1.04–1.12) but not in pregnancies conceived through ART (OR, 0.93;95% CI 0.70–1.24). Based on the limited number of studies that examined this association in relation to endometriosis phenotype, an increased risk was found in more severe stages (OR, 3.20; 95% CI 1.20–8.54) but independently from localization of the lesions. Endometriosis increases the risk of GDM, with a possible progressive effect in more advanced stages of the disease. Although the effect magnitude may be limited in some subgroups, this finding has a clinically relevant impact due to both the strong biological plausibility and to the relatively high incidence of both endometriosis and GDM.
Bidirectional meta-Kronecker factored optimizer and Hausdorff distance loss for few-shot medical image segmentation
Authors: Kim Yeongjoon , Kang Donggoo , Mok Yeongheon , Kwon Sunkyu , Paik Joonki 
Published: May 2023

AbstractTo increase the accuracy of medical image analysis using supervised learning-based AI technology, a large amount of accurately labeled training data is required. However, the supervised learning approach may not be applicable to real-world medical imaging due to the lack of labeled data, the privacy of patients, and the cost of specialized knowledge. To handle these issues, we utilized Kronecker-factored decomposition, which enhances both computational efficiency and stability of the learning process. We combined this approach with a model-agnostic meta-learning framework for the parameter optimization. Based on this method, we present a bidirectional meta-Kronecker factored optimizer (BM-KFO) framework to quickly optimize semantic segmentation tasks using just a few magnetic resonance imaging (MRI) images as input. This model-agnostic approach can be implemented without altering network components and is capable of learning the learning process and meta-initial points while training on previously unseen data. We also incorporated a combination of average Hausdorff distance loss (AHD-loss) and cross-entropy loss into our objective function to specifically target the morphology of organs or lesions in medical images. Through evaluation of the proposed method on the abdominal MRI dataset, we obtained an average performance of 78.07% in setting 1 and 79.85% in setting 2. Our experiments demonstrate that BM-KFO with AHD-loss is suitable for general medical image segmentation applications and achieves superior performance compared to the baseline method in few-shot learning tasks. In order to replicate the proposed method, we have shared our code on GitHub. The corresponding URL can be found:https://github.com/YeongjoonKim/BMKFO.git.
Inferential Emotion Tracking reveals impaired context-based emotion processing in individuals with high Autism Quotient scores
Authors: Ortega Jefferson , Chen Zhimin , Whitney David 
Published: May 2023

AbstractEmotion perception is essential for successful social interactions and maintaining long-term relationships with friends and family. Individuals with autism spectrum disorder (ASD) experience social communication deficits and have reported difficulties in facial expression recognition. However, emotion recognition depends on more than just processing face expression; context is critically important to correctly infer the emotions of others. Whether context-based emotion processing is impacted in those with Autism remains unclear. Here, we used a recently developed context-based emotion perception task, called Inferential Emotion Tracking (IET), and investigated whether individuals who scored high on the Autism Spectrum Quotient (AQ) had deficits in context-based emotion perception. Using 34 videos (including Hollywood movies, home videos, and documentaries), we tested 102 participants as they continuously tracked the affect (valence and arousal) of a blurred-out, invisible character. We found that individual differences in Autism Quotient scores were more strongly correlated with IET task accuracy than they are with traditional face emotion perception tasks. This correlation remained significant even when controlling for potential covarying factors, general intelligence, and performance on traditional face perception tasks. These findings suggest that individuals with ASD may have impaired perception of contextual information, it reveals the importance of developing ecologically relevant emotion perception tasks in order to better assess and treat ASD, and it provides a new direction for further research on context-based emotion perception deficits in ASD.
Anthropogenic forcing and Pacific internal variability-determined decadal increase in summer precipitation over the Asian water tower
Authors: Liu Yong , Wang Huijun , Chen Huopo , Zhang Zhongshi , Li Hua , Liu Bo 
Published: May 2023

AbstractThe increased precipitation in the Asian water tower has prompted the abrupt lake expansion and increased runoff, significantly reshaping the water resource redistribution in the Inner Tibetan Plateau (ITP). However, the dynamic attribution behind this decadal increment remains unclear. Here, analysis of observations, large ensemble simulations, and pacemaker experiments indicates that this decadal increase was mainly attributed to the synergistic effects of the external forcing (anthropogenic greenhouse and aerosol emissions) and the Pacific internal variability, while the Atlantic and the Indian Ocean play a secondary role. Observations and simulations show that thermodynamic and dynamic effects work collaboratively to this increase. Remarkably, the upper-level dynamic convergence over the ITP would be enhanced through teleconnection and atmospheric dynamic feedback when involving the Pacific internal variability, resulting in more precipitation occurrence. Further analyses show that the enhanced stationary Rossby wave propagation over Eurasia and strengthened transient eddy activity over North Pacific could contribute to the anomalous cyclone over the ITP and weakened East Asian westerly jet, which built a pathway for the external forcing and Pacific internal variability collaboratively impacting the decadal increase in precipitation in the ITP. These results can improve our understanding of ITP summer precipitation attribution and can be applied to emergent constraints on future decadal precipitation prediction.
Identification of acquired Notch3 dependency in metastatic Head and Neck Cancer
Authors: Kondratyev Maria , Pesic Aleksandra , Ketela Troy , Stickle Natalie , Beswick Christine , Shalev Zvi , Marastoni Stefano , Samadian Soroush , Dvorkin-Gheva Anna , Sayad Azin , Bashkurov Mikhail , Boasquevisque Pedro , Datti Alessandro , Pugh Trevor J. , Virtanen Carl , Moffat Jason , Grénman Reidar A. , Koritzinsky Marianne , Wouters Bradly G. 
Published: May 2023

AbstractDuring cancer development, tumor cells acquire changes that enable them to invade surrounding tissues and seed metastasis at distant sites. These changes contribute to the aggressiveness of metastatic cancer and interfere with success of therapy. Our comprehensive analysis of “matched” pairs of HNSCC lines derived from primary tumors and corresponding metastatic sites identified several components of Notch3 signaling that are differentially expressed and/or altered in metastatic lines and confer a dependency on this pathway. These components were also shown to be differentially expressed between early and late stages of tumors in a TMA constructed from over 200 HNSCC patients. Finally, we show that suppression of Notch3 improves survival in mice in both subcutaneous and orthotopic models of metastatic HNSCC. Novel treatments targeting components of this pathway may prove effective in targeting metastatic HNSCC cells alone or in combination with conventional therapies.
Developmental stage of transplanted neural progenitor cells influences anatomical and functional outcomes after spinal cord injury in mice
Authors: Aceves Miriam , Tucker Ashley , Chen Joseph , Vo Katie , Moses Joshua , Amar Kumar Prakruthi , Thomas Hannah , Miranda Diego , Dampf Gabrielle , Dietz Valerie , Chang Matthew , Lukose Aleena , Jang Julius , Nadella Sneha , Gillespie Tucker , Trevino Christian , Buxton Andrew , Pritchard Anna L. , Green Peyton , McCreedy Dylan A. , Dulin Jennifer N. 
Published: May 2023

AbstractNeural progenitor cell (NPC) transplantation is a promising therapeutic strategy for replacing lost neurons following spinal cord injury (SCI). However, how graft cellular composition influences regeneration and synaptogenesis of host axon populations, or recovery of motor and sensory functions after SCI, is poorly understood. We transplanted developmentally-restricted spinal cord NPCs, isolated from E11.5-E13.5 mouse embryos, into sites of adult mouse SCI and analyzed graft axon outgrowth, cellular composition, host axon regeneration, and behavior. Earlier-stage grafts exhibited greater axon outgrowth, enrichment for ventral spinal cord interneurons and Group-Z spinal interneurons, and enhanced host 5-HT+axon regeneration. Later-stage grafts were enriched for late-born dorsal horn interneuronal subtypes and Group-N spinal interneurons, supported more extensive host CGRP+axon ingrowth, and exacerbated thermal hypersensitivity. Locomotor function was not affected by any type of NPC graft. These findings showcase the role of spinal cord graft cellular composition in determining anatomical and functional outcomes following SCI.
Polarization behavior in a compositionally graded relaxor–ferroelectric crystal visualized by angle-resolved polarized Raman mapping
Authors: Tsukada Shinya , Fujii Yasuhiro , Kanagawa Akari , Akishige Yukikuni , Ohwada Kenji 
Published: May 2023

AbstractExplaining the properties and functions of materials in terms of their atomic arrangements and inhomogeneous structures is a fundamental challenge for the development of ferroelectric oxides. Dielectric response, a fundamental property of matter, can be explained by long-wavelength polar lattice vibrations and dipole relaxations capable of responding to electrical bias; therefore spectroscopic methods, such as Raman spectroscopy, can be used to investigate its origin. Herein, we used angle-resolved polarized Raman mapping to investigate how phase boundaries and giant dielectric responses are related in a relaxor-Pb(Mg1/3Nb2/3)O3–ferroelectric-PbTiO3 (PMN-xPT) solid-solution system using a compositionally graded crystal, with gradual changes in polarization direction visualized by Raman mapping. The variation of the width of quasielastic light scattering with position reveals the following: The huge dielectric response observed in PMN-xPT is ascribable to the slowing down of a relaxation related to mesoscopic ferroelectric domains near the phase boundary, which is characteristic of relaxor–ferroelectric solid-solution systems and differentiates them from other ferroelectrics.