bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Buoyant Sediment Overlying Subducting Plates on Trench Geometry: 3D Viscoelastic Free Subduction Modeling
Authors: Keum Jae‐Yoon , So Byung‐Dal 
Published: April 2021

AbstractBuoyant trench sediment generates an isostatic restoring force that opposes the slab pull of subducting plates; however, the influence of this force on subduction dynamics is poorly understood. Here, we performed three‐dimensional free subduction simulations adopting a variety of sediment distributions along a trench to investigate the correlation between trench motions and heterogeneous buoyant forces. Two endmembers, sediment‐rich and sediment‐starved centers, induced convex and concave trenches, respectively. The trench curvatures obtained from the natural subduction zones are well constrained by our models over wide magnitudes (1–9 km) and wavelengths (100–400 km) of deficient and excess sediments. Conversely, a uniform sediment distribution leads to an extremely narrow range of trench curvatures. These results imply that trench sediment contributes significantly to deviated curvatures along trench strikes. Finally, we observed stress localization at shallow slab hinges that lie beneath abundant sediments, clarifying the relationship between sediment thickness and subduction earthquakes.
High Pressure‐Temperature Single‐Crystal Elasticity of Grossular: Implications for the Low‐Velocity Layer in the Bottom Transition Zone
Authors: Wei Wei , Mao Zhu , Sun Ningyu , Sun Daoyuan , Tkachev Sergey N. 
Published: April 2021

AbstractWe determined the single‐crystal elasticity of Fe3+‐bearing grossular using Brillouin scattering up to 22 GPa and 1,000 K. Using the obtained results, we modeled mantle velocity profiles to investigate the origin of low‐velocity zones (LVZs) in the bottom 100 km of the mantle transition zone. Our modeling revealed that although a water‐saturated transition zone could be seismically detected as the LVZs, it would also cause a negative velocity jump across the 520‐km discontinuity, which has not been seismically detected. However, mid‐ocean ridge basalts (MORB) with an FeO content of 10–17 wt.% in garnet will have VS 2.0(5)%–3.0(5)% lower than that in the pyrolitic mantle. Oxidizing (FeO = 17 wt.%, Fe3+/(Fe2+ + Fe3+) = 0.3–0.8) or lowering the Ca content of garnet to 1.4 wt.% can further decrease the VS of MORB. Such Fe‐enriched, oxidized MORB or Ca‐depleted, oxidized MORB, with a 3.5(5)%–7.6(5)% lower VS and distinct dln ρ/dln VS ratio, have a seismic signature consistent with the observed LVZs in the region.
Respiratory muscle function in the newborn: a narrative review
Authors: Dassios Theodore , Vervenioti Aggeliki , Dimitriou Gabriel 
Published: April 2021

Abstract
Our aim was to summarise the current evidence and methods used to assess respiratory muscle function in the newborn, focusing on current and future potential clinical applications. The respiratory muscles undertake the work of breathing and consist mainly of the diaphragm, which in the newborn is prone to dysfunction due to lower muscle mass, flattened shape and decreased content of fatigue-resistant muscle fibres. Premature infants are prone to diaphragmatic dysfunction due to limited reserves and limited capacity to generate force and avoid fatigue. Methods to assess the respiratory muscles in the newborn include electromyography, maximal respiratory pressures, assessment for thoraco-abdominal asynchrony and composite indices, such as the pressure–time product and the tension time index. Recently, there has been significant interest and a growing body of research in assessing respiratory muscle function using bedside ultrasonography. Neurally adjusted ventilator assist is a novel ventilation mode, where the level of the respiratory support is determined by the diaphragmatic electrical activity. Prolonged mechanical ventilation, hypercapnia and hypoxia, congenital anomalies and systemic or respiratory infection can negatively impact respiratory muscle function in the newborn, while caffeine and synchronised or volume-targeted ventilation have a positive effect on respiratory muscle function compared to conventional, non-triggered or pressure-limited ventilation, respectively.

Impact

Respiratory muscle function is impaired in prematurely born neonates and infants with congenital anomalies, such as congenital diaphragmatic hernia.

Respiratory muscle function is negatively affected by prolonged ventilation and infection and positively affected by caffeine and synchronised compared to non-synchronised ventilation modes.

Point-of-care diaphragmatic ultrasound and neurally adjusted ventilator assist are recent diagnostic and therapeutic technological developments with significant clinical applicability.
Transplant-associated thrombotic microangiopathy: theoretical considerations and a practical approach to an unrefined diagnosis
Authors: Young Joanna A. , Pallas Christopher R. , Knovich Mary Ann 
Published: April 2021

AbstractTransplant-associated thrombotic microangiopathy (TA-TMA) is an increasingly recognized complication of hematopoietic stem cell transplant (HSCT) with high morbidity and mortality. The triad of endothelial cell activation, complement dysregulation, and microvascular hemolytic anemia has the potential to cause end organ dysfunction, multiple organ dysfunction syndrome and death, but clinical features mimic other disorders following HSCT, delaying diagnosis. Recent advances have implicated complement as a major contributor and the therapeutic potential of complement inhibition has been explored. Eculizumab has emerged as an effective therapy and narsoplimab (OMS721) has been granted priority review by the FDA. Large studies performed mostly in pediatric patients suggest that earlier recognition and treatment may lead to improved outcomes. Here we present a clinically focused summary of recently published literature and propose a diagnostic and treatment algorithm.
Mirtronic miR-4646-5p promotes gastric cancer metastasis by regulating ABHD16A and metabolite lysophosphatidylserines
Authors: Yang Liping , Hou Yixuan , Du Yan-e , Li Qiao , Zhou Fanlin , Li Yu , Zeng Huan , Jin Ting , Wan Xueying , Guan Shengdong , Wang Rui , Liu Manran 
Published: April 2021

AbstractThe aberrant classical miRNAs are considered to play significant roles in tumor progression. However, it remains unclear for nonclassical miRNAs, a set of Drosha-independent miRNAs in the process of various biology. Here, we reveal that a nonclassical miR-4646-5p plays a pivotal role in gastric cancer (GC) metastasis. MiR-4646-5p, one of Drosha-independent mirtronic miRNA, is aberrant up-regulated in Drosha-low expressed GC and Drosha-knockdown gastric cancer cells. Mirtronic miR-4646-5p is a specific transcription splicing product of intron 3 of the host gene Abhd16a with the aid of SRSF2. The enhanced miR-4646-5p can stabilize HIF1A by targeting PHD3 to positive feedback regulate Abhd16a and miR-4646-5p itself expressions. ABHD16A, as an emerging phosphatidylserine-specific lipase, involves in lipid metabolism leading to lysophosphatidylserines (lyso-PSs) accumulation, which stimulates RhoA and downstream LIMK/cofilin cascade activity through GPR34/Gi subunit, thus causes metastasis of gastric cancer. In addition, miR-4646-5p/PHD3/HIF1A signaling can also up-regulate RhoA expression and synergistically promote gastric cancer cell invasion and metastasis. Our study provides new insights of nonclassical mirtronic miRNA on tumor progress and may serve as a new diagnostic biomarker for gastric cancer. MiR-4646-5p and its host gene Abhd16a mediated abnormal lipid metabolism may be a new target for clinical treatment of gastric cancer.
Overexpression of circRNA SNRK targets miR-103-3p to reduce apoptosis and promote cardiac repair through GSK3β/β-catenin pathway in rats with myocardial infarction
Authors: Zhu Yeqian , Zhao Pengcheng , Sun Ling , Lu Yao , Zhu Wenwu , Zhang Jian , Xiang Chengyu , Mao Yangming , Chen Qiushi , Zhang Fengxiang 
Published: April 2021

AbstractIschemic cardiomyopathy seriously endangers human health leading to a poor prognosis. Acute myocardial infarction (AMI) is the primary etiology, and the pathophysiological process concludes with the death of cardiomyocytes caused by acute and persistent ischemia and hypoxia in the coronary arteries. We identified a circRNA (circSNRK) which was downregulated in rats with myocardial infarction (MI), however, the role it plays in the MI environment is still unclear. This study contained experiments to investigate the role of circSNRK in the regulation of cardiac survival and explore the mechanisms underlying circSNRK functions. Quantitative real-time PCR (qRT-PCR) was performed to determine the circSNRK expression patterns in hearts. Gain-of-function assays were also conducted in vitro and in vivo to determine the role of circSNRK in cardiac repair. qRT-PCR, western blot, and luciferase reporter assays were used to study circRNA interactions with micro RNAs (miRNAs). Overexpression of circSNRK in cardiomyocytes reduced apoptosis and increased proliferation. Adeno associated virus 9 (AAV9) mediated myocardium overexpression of circSNRK in post MI hearts reduced cardiomyocyte apoptosis, promoted cardiomyocyte proliferation, enhanced angiogenesis, and improved cardiac functions. Overall, upregulation of circSNRK promotes cardiac survival and functional recovery after MI. Mechanistically, circSNRK regulates cardiomyocyte apoptosis and proliferation by acting as a miR-103-3p sponge and inducing increased expression of SNRK which can bind GSK3β to regulate its phosphorylated activity. And thus circSNRK may be a promising therapeutic target for improving clinical prognosis after MI.
Germline variants in UNC13D and AP3B1 are enriched in COVID-19 patients experiencing severe cytokine storms
Authors: Luo Hui , Liu Dan , Liu Wenbing , Wang Gaoxiang , Chen Liting , Cao Yang , Wei Jia , Xiao Min , Liu Xin , Huang Gang , Wang Wei , Zhou Jianfeng , Wang Qian-fei 
Published: April 2021

AbstractCritically ill coronavirus disease 2019 (COVID-19) is characterized by severe cytokine storms, a hyperinflammatory condition intimately related to the development of fatal outcomes. Why some individuals seem particularly vulnerable to severe cytokine storms is still unknown. Primary immunodeficiency (PID)-related genes are inherited factors that dysregulate host inflammatory responses to infection, especially hemophagocytic lymphohistiocytosis (HLH)-related genes, established as contributors to the development of excessive cytokine storms. We analyzed the association between PID gene variants with severe cytokine storms in COVID-19. We conducted whole-exome sequencing in 233 hospitalized COVID-19 patients and identified four PID gene (UNC13D, AP3B1, RNF168, DHX58) variants were significantly enriched in COVID-19 patients experiencing severe cytokine storms. The total percentage of COVID-19 patients with variants in UNC13D or AP3B1, two typical HLH genes, was dramatically higher in high-level cytokine group than in low-level group (33.3 vs. 5.7%, P < 0.001). Germline variants in UNC13D and AP3B1 were associated with the development of severe cytokine storms, fatal outcomes in COVID-19. These findings advance the understanding of individual susceptibility to severe cytokine storms and help optimize the current management of COVID-19.
On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae)
Authors: Bachmann Jörg A. , Tedder Andrew , Fracassetti Marco , Steige Kim A. , Lafon-Placette Clément , Köhler Claudia , Slotte Tanja 
Published: April 2021

AbstractPolyploidy, or whole-genome duplication, is a common speciation mechanism in plants. An important barrier to polyploid establishment is a lack of compatible mates. Because self-compatibility alleviates this problem, it has long been hypothesized that there should be an association between polyploidy and self-compatibility (SC), but empirical support for this prediction is mixed. Here, we investigate whether the molecular makeup of the Brassicaceae self-incompatibility (SI) system, and specifically dominance relationships among S-haplotypes mediated by small RNAs, could facilitate loss of SI in allopolyploid crucifers. We focus on the allotetraploid species Capsella bursa-pastoris, which formed ~300 kya by hybridization and whole-genome duplication involving progenitors from the lineages of Capsella orientalis and Capsella grandiflora. We conduct targeted long-read sequencing to assemble and analyze eight full-length S-locus haplotypes, representing both homeologous subgenomes of C. bursa-pastoris. We further analyze small RNA (sRNA) sequencing data from flower buds to identify candidate dominance modifiers. We find that C. orientalis-derived S-haplotypes of C. bursa-pastoris harbor truncated versions of the male SI specificity gene SCR and express a conserved sRNA-based candidate dominance modifier with a target in the C. grandiflora-derived S-haplotype. These results suggest that pollen-level dominance may have facilitated loss of SI in C. bursa-pastoris. Finally, we demonstrate that spontaneous somatic tetraploidization after a wide cross between C. orientalis and C. grandiflora can result in production of self-compatible tetraploid offspring. We discuss the implications of this finding on the mode of formation of this widespread weed.
Large-scale sequencing of flatfish genomes provides insights into the polyphyletic origin of their specialized body plan
Authors: Lü Zhenming , Gong Li , Ren Yandong , Chen Yongjiu , Wang Zhongkai , Liu Liqin , Li Haorong , Chen Xianqing , Li Zhenzhu , Luo Hairong , Jiang Hui , Zeng Yan , Wang Yifan , Wang Kun , Zhang Chen , Jiang Haifeng , Wan Wenting , Qin Yanli , Zhang Jianshe , Zhu Liang , Shi Wei , He Shunping , Mao Bingyu , Wang Wen , Kong Xiaoyu , Li Yongxin 
Published: April 2021

AbstractThe evolutionary and genetic origins of the specialized body plan of flatfish are largely unclear. We analyzed the genomes of 11 flatfish species representing 9 of the 14 Pleuronectiforme families and conclude that Pleuronectoidei and Psettodoidei do not form a monophyletic group, suggesting independent origins from different percoid ancestors. Genomic and transcriptomic data indicate that genes related to WNT and retinoic acid pathways, hampered musculature and reduced lipids might have functioned in the evolution of the specialized body plan of Pleuronectoidei. Evolution of Psettodoidei involved similar but not identical genes. Our work provides valuable resources and insights for understanding the genetic origins of the unusual body plan of flatfishes.
PathoNet introduced as a deep neural network backend for evaluation of Ki-67 and tumor-infiltrating lymphocytes in breast cancer
Authors: Negahbani Farzin , Sabzi Rasool , Pakniyat Jahromi Bita , Firouzabadi Dena , Movahedi Fateme , Kohandel Shirazi Mahsa , Majidi Shayan , Dehghanian Amirreza 
Published: April 2021

AbstractThe nuclear protein Ki-67 and Tumor infiltrating lymphocytes (TILs) have been introduced as prognostic factors in predicting both tumor progression and probable response to chemotherapy. The value of Ki-67 index and TILs in approach to heterogeneous tumors such as Breast cancer (BC) that is the most common cancer in women worldwide, has been highlighted in literature. Considering that estimation of both factors are dependent on professional pathologists’ observation and inter-individual variations may also exist, automated methods using machine learning, specifically approaches based on deep learning, have attracted attention. Yet, deep learning methods need considerable annotated data. In the absence of publicly available benchmarks for BC Ki-67 cell detection and further annotated classification of cells, In this study we propose SHIDC-BC-Ki-67 as a dataset for the aforementioned purpose. We also introduce a novel pipeline and backend, for estimation of Ki-67 expression and simultaneous determination of intratumoral TILs score in breast cancer cells. Further, we show that despite the challenges that our proposed model has encountered, our proposed backend, PathoNet, outperforms the state of the art methods proposed to date with regard to harmonic mean measure acquired. Dataset is publicly available inhttp://shiraz-hidc.comand all experiment codes are published inhttps://github.com/SHIDCenter/PathoNet.
Changes in complement activation products after anti-VEGF injection for choroidal neovascularization in age-related macular degeneration and pachychoroid disease
Authors: Tanaka Keiichiro , Oguchi Yasuharu , Omori Tomoko , Ishida Yumi , Shintake Hiroaki , Tomita Ryutaro , Kasai Akihito , Ogasawara Masashi , Sugano Yukinori , Itagaki Kanako , Ojima Akira , Machida Takeshi , Sekine Hideharu , Sekiryu Tetsuju 
Published: April 2021

AbstractWe evaluated changes in the complement system resulting from anti-vascular endothelial growth factor (VEGF) in eyes with age-related choroidal neovascularization (CNV) including neovascular age-related macular degeneration, pachychoroid neovasculopathy, and polypoidal choroidal neovasculopathy. We measured the concentrations of the complement activation products (C3a, C4a), VEGF, and monocyte chemotactic protein-1 in the aqueous humor during intravitreal anti-VEGF injections for CNV. The VEGF level decreased significantly (P < 0.001), while the C3a and C4a levels increased significantly (P < 0.001 for both comparisons) 1 month after two monthly anti-VEGF injections. The VEGF level was correlated with the C3a (R = 0.328, P = 0.007) and C4a (R = − 0.237, P = 0.055) levels at baseline, but the correlation between the VEGF and C3a levels (R = − 0.148, P = 0.242) changed significantly (P = 0.028 by analysis of covariance) after anti-VEGF treatment. The C3a increase after anti-VEGF therapy did not change the visual outcomes in eyes with CNV for 1 year. Dysregulation of the complement system can be induced after anti-VEGF therapy.
A deep learning model to detect pancreatic ductal adenocarcinoma on endoscopic ultrasound-guided fine-needle biopsy
Authors: Naito Yoshiki , Tsuneki Masayuki , Fukushima Noriyoshi , Koga Yutaka , Higashi Michiyo , Notohara Kenji , Aishima Shinichi , Ohike Nobuyuki , Tajiri Takuma , Yamaguchi Hiroshi , Fukumura Yuki , Kojima Motohiro , Hirabayashi Kenichi , Hamada Yoshihiro , Norose Tomoko , Kai Keita , Omori Yuko , Sukeda Aoi , Noguchi Hirotsugu , Uchino Kaori , Itakura Junya , Okabe Yoshinobu , Yamada Yuichi , Akiba Jun , Kanavati Fahdi , Oda Yoshinao , Furukawa Toru , Yano Hirohisa 
Published: April 2021

AbstractHistopathological diagnosis of pancreatic ductal adenocarcinoma (PDAC) on endoscopic ultrasonography-guided fine-needle biopsy (EUS-FNB) specimens has become the mainstay of preoperative pathological diagnosis. However, on EUS-FNB specimens, accurate histopathological evaluation is difficult due to low specimen volume with isolated cancer cells and high contamination of blood, inflammatory and digestive tract cells. In this study, we performed annotations for training sets by expert pancreatic pathologists and trained a deep learning model to assess PDAC on EUS-FNB of the pancreas in histopathological whole-slide images. We obtained a high receiver operator curve area under the curve of 0.984, accuracy of 0.9417, sensitivity of 0.9302 and specificity of 0.9706. Our model was able to accurately detect difficult cases of isolated and low volume cancer cells. If adopted as a supportive system in routine diagnosis of pancreatic EUS-FNB specimens, our model has the potential to aid pathologists diagnose difficult cases.
Features of sacral alar fatigue fractures in adolescent athletes with overuse
Authors: Tatsumura Masaki , Eto Fumihiko , Nagashima Katsuya , Okuwaki Shun , Gamada Hisanori , Iwabuchi Sho , Ogawa Takeshi , Mammoto Takeo , Hirano Atsushi , Yamazaki Masashi 
Published: April 2021

AbstractThree types of sacral alar fatigue fractures are elderly, postnatal, and sport-related. They are most prevalent in athletes during adulthood; there are few reports of sacral alar fatigue fractures in young athletes. The purpose of this study was to analyze sacral alar fatigue fractures in adolescent athletes. Of the 920 patients hospitalized with low back pain, 13 were diagnosed with sacral alar fatigue fractures with magnetic resonance imaging (MRI) abnormalities. We investigated age, sex, sports discipline, span from symptom onset to consultation, laterality, complication with spondylolysis, computed tomography (CT) findings, and treatment span. The average age was 14.5 years old (8-men and 5-women). The most frequent discipline was basketball. The span to consultation was 13.2 days. The number of right-side cases was 9. Seven cases were complicated by bilateral spondylolysis. MRI abnormalities were observed in all the cases. Only two patients showed abnormal findings on CT. Averagely 67 days after treatment, participants returned to their sports. Sacral alar fatigue fractures suggest that the span from onset to consultation is short. Fracture lines are often unclear on CT, and MRI is useful for diagnosis. More than half of the cases in this study were complicated by lumbar spondylolysis.
Gene expression rearrangements denoting changes in the biological state
Authors: Gonzalez Augusto , Nieves Joan , Leon Dario A. , Bringas Vega Maria Luisa , Sosa Pedro Valdes 
Published: April 2021

AbstractIn many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may be the result of a selective pressure, as in the Long Term Evolution Experiment with E. Coli populations, or the progression to Alzheimer disease in aged brains, or the progression from a normal tissue to the cancer state. The first two cases seem to belong to a class of transitions, where the initial and final states are relatively close to each other, and the distribution function for the differential expressions is short ranged, with a tail of only a few dozens of strongly varying genes. In the latter case, cancer, the initial and final states are far apart and separated by a low-fitness barrier. The distribution function shows a very heavy tail, with thousands of silenced and over-expressed genes. We characterize the biological states by means of their principal component representations, and the expression distribution functions by their maximal and minimal differential expression values and the exponents of the Pareto laws describing the tails.
Investigation of antioxidant and anticancer activities of unsaturated oligo-galacturonic acids produced by pectinase of Streptomyces hydrogenans YAM1
Authors: Hosseini Abari Afrouzossadat , Amini Rourani Hamed , Ghasemi Seyed Mahdi , Kim Hyun , Kim Yun-Gon 
Published: April 2021

AbstractPectin, a diverse carbohydrate polymer in plants consists of a core of α-1,4-linked D-galacturonic acid units, includes a vast portion of fruit and agricultural wastes. Using the wastes to produce beneficial compounds is a new approach to control the negative environmental impacts of the accumulated wastes. In the present study, we report a pectinase producing bacterium Streptomyces hydrogenans YAM1 and evaluate antioxidative and anticancer effects of the oligosaccharides obtained from pectin degradation. The production of oligosaccharides due to pectinase activity was detected by thin layer chromatography (TLC) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Our results revealed that S. hydrogenans YAM1 can degrade pectin to unsaturated pectic oligo-galacturonic acids (POS) with approximately 93% radical scavenging activity in 20 mg/mL which it is more than 50% of the same concentration of pectin. Flow cytometric analysis revealed that MCF-7 cells viability decreased more than 32 and 92% following treatment with 6 and 20 mg/mL POS after 24 h, respectively. It is suggested that pectin degradation by S. hydrogenans YAM1 is not only a new approach to produce highly active compounds from fruit wastes, but also is an effective method to remove fibrous pollutants from different environments.