bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laboratory Study of the Impact of the Surface Solitary Waves Created by the Internal Solitary Waves on Optical Imaging
Authors: Zhang Meng , Wang Jing , Li Zhixin , Liang Keda , Chen Xu 
Published: February 2022

AbstractThe effects of Surface Solitary Waves (SSWs), which are created by Internal Solitary Waves (ISWs), on optical imaging were investigated in this paper. We explored the connection between SSWs and optical images using simulations and experiments with calm water surface conditions. An experimental platform was built in a controlled laboratory environment where optical images and in‐situ wave data could be gathered simultaneously. SSWs created by different ISWs were successfully observed. The optical images revealed inverse bright and dark patterns for different ISW types (depression or elevation type). Based on theories and experimental results, simulation models of the ISWs and SSWs were built in Unigraphics NX. Using the illumination simulation function of Light Tools, the reason underlying the reversed patterns was explained by the irradiance distribution. Both the experiment and simulation indicated that the SSWs created by the ISWs affected the characteristics of optical images. To further explore how SSWs affect imaging, 16 experiments were designed to investigate the effects of ISW type, amplitude, and water density ratio. It is found that the relationship among the SSW amplitude, ISW amplitude, and density ratio was consistent with earlier studies. The relationships between imaging characteristics (grayscale differences and pattern widths) and the two types of SSWs were consistent.
The Role of the Irminger Current in the Irminger Sea Northward Transport Variability
Authors: Fried Nora , de Jong M. Femke 
Published: February 2022

AbstractThe Irminger Current (IC) on the western flank of the Reykjanes Ridge is an important contributor to the northward transport in the Atlantic Meridional Overturning Circulation. Here, we combine 28 years of Copernicus Marine Environment Monitoring Service (CMEMS) ocean reanalysis data with 6 years of mooring data to investigate variability in volume transport of the IC. We found a mean volume transport for the IC of 11.6 Sv between 1993 and 2020 revealing the dominance of the IC in the total Irminger Sea northward volume transport (20.3 Sv). We found a significant decrease (−3.7 Sv) in volume transport of the IC until 2011 followed by a steeper (but shorter, leading to +2.7 Sv) increase until 2020. These changes across the Irminger Sea section are dominated by the IC, which in turn are driven by changes in the density gradient across the Irminger Sea related to convection. On decadal and interannual time scales the IC volume transport is well correlated with the decrease in the sea surface height difference over the basin. In 2019, a temporary intensification of the western IC core led to an exceptionally strong volume transport of the IC with 20 Sv. This was caused by density changes within the IC boundaries due to the presence of mesoscale eddies. Thus, IC transport variability is a superposition of basin‐wide to local processes that influence the velocity field on different time scales.
Integrated microdevice with a windmill-like hole array for the clog-free, efficient, and self-mixing enrichment of circulating tumor cells
Authors: Li Hao , Li Jinze , Zhang Zhiqi , Guo Zhen , Zhang Changsong , Wang Zixu , Guo Qiuquan , Li Chao , Li Chuanyu , Yao Jia , Zheng Anran , Xu Jingyi , Gao Qingxue , Zhang Wei , Zhou Lianqun 
Published: February 2022

AbstractCirculating tumor cells (CTCs) have tremendous potential to indicate disease progression and monitor therapeutic response using minimally invasive approaches. Considering the limitations of affinity strategies based on their cost, effectiveness, and simplicity, size-based enrichment methods that involve low-cost, label-free, and relatively simple protocols have been further promoted. Nevertheless, the key challenges of these methods are clogging issues and cell aggregation, which reduce the recovery rates and purity. Inspired by the natural phenomenon that the airflow around a windmill is disturbed, in this study, a windmill-like hole array on the SU-8 membrane was designed to perturb the fluid such that cells in a fluid would be able to self-mix and that the pressure acting on cells or the membrane would be dispersed to allow a greater velocity. In addition, based on the advantages of fluid coatings, a lipid coating was used to modify the membrane surface to prevent cell aggregation and clogging of the holes. Under the optimal conditions, recovery rates of 93% and 90% were found for A549 and HeLa cells in a clinical simulation test of our platform with a CTC concentration of 20–100 cells per milliliter of blood. The white blood cell (WBC) depletion rate was 98.7% (n = 15), and the CTC detection limit was less than 10 cells per milliliter of blood (n = 6). Moreover, compared with conventional membrane filtration, the advantages of the proposed device for the rapid (2 mL/min) and efficient enrichment of CTCs without clogging were shown both experimentally and theoretically. Due to its advantages in the efficient, rapid, uniform, and clog-free enrichment of CTCs, our platform offers great potential for metastatic detection and therapy analyses.
Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group
Authors: Priest Taylor , Heins Anneke , Harder Jens , Amann Rudolf , Fuchs Bernhard M 
Published: February 2022

Abstract
Niche concept is a core tenet of ecology that has recently been applied in marine microbial research to describe the partitioning of taxa based either on adaptations to specific conditions across environments or on adaptations to specialised substrates. In this study, we combine spatiotemporal dynamics and predicted substrate utilisation to describe species-level niche partitioning within the NS5 Marine Group. Despite NS5 representing one of the most abundant marine flavobacterial clades from across the world’s oceans, our knowledge on their phylogenetic diversity and ecological functions is limited. Using novel and database-derived 16S rRNA gene and ribosomal protein sequences, we delineate the NS5 into 35 distinct species-level clusters, contained within four novel candidate genera. One candidate species, “Arcticimaribacter forsetii AHE01FL”, includes a novel cultured isolate, for which we provide a complete genome sequence—the first of an NS5—along with morphological insights using transmission electron microscopy. Assessing species’ spatial distribution dynamics across the Tara Oceans dataset, we identify depth as a key influencing factor, with 32 species preferring surface waters, as well as distinct patterns in relation to temperature, oxygen and salinity. Each species harbours a unique substrate-degradation potential along with predicted substrates conserved at the genus-level, e.g. alginate in NS5_F. Successional dynamics were observed for three species in a time-series dataset, likely driven by specialised substrate adaptations. We propose that the ecological niche partitioning of NS5 species is mainly based on specific abiotic factors, which define the niche space, and substrate availability that drive the species-specific temporal dynamics.
Cold atmospheric plasma differentially affects cell renewal and differentiation of stem cells and APC-deficient-derived tumor cells in intestinal organoids
Authors: Hadefi Alia , Leprovots Morgane , Thulliez Max , Bastin Orianne , Lefort Anne , Libert Frédérick , Nonclercq Antoine , Delchambre Alain , Reniers François , Devière Jacques , Garcia Marie-Isabelle 
Published: February 2022

AbstractCold atmospheric plasma (CAP) treatment has been proposed as a potentially innovative therapeutic tool in the biomedical field, notably for cancer due to its proposed toxic selectivity on cancer cells versus healthy cells. In the present study, we addressed the relevance of three-dimensional organoid technology to investigate the biological effects of CAP on normal epithelial stem cells and tumor cells isolated from mouse small intestine. CAP treatment exerted dose-dependent cytotoxicity on normal organoids and induced major transcriptomic changes associated with the global response to oxidative stress, fetal-like regeneration reprogramming, and apoptosis-mediated cell death. Moreover, we explored the potential selectivity of CAP on tumor-like Apc-deficient versus normal organoids in the same genetic background. Unexpectedly, tumor organoids exhibited higher resistance to CAP treatment, correlating with higher antioxidant activity at baseline as compared to normal organoids. This pilot study suggests that the ex vivo culture system could be a relevant alternative model to further investigate translational medical applications of CAP technology.
The lncRNA TCONS_00021785/miR-21-5p/Trim33 axis regulates VMP1-mediated zymophagy, reduces the activation of trypsinogen, and promotes acinar cell recovery
Authors: Wang Qiang , Yu Jingjing , Gao Wenqi , Sun Yuanyuan , Liu Xuxu , Lv Zhenyi , Li Long , Xue Dongbo 
Published: February 2022

AbstractIn the early stage of acute pancreatitis, trypsinogen in acinar cells is activated, and the cells clear trypsin through zymophagy to avoid damage. Studies have shown that the substrate of zymophagy is ubiquitinated pancreatin, but the mechanism of pancreatin ubiquitination and the regulatory mechanism of zymophagy are not fully understood. Our results show that Trim33 can enhance cell viability, reduce cell necrosis, and reduce trypsinogen activation. Trim33 is a key E3 ligase enzyme that mediates trypsin ubiquitination. The results showed that overexpression of Trim33 can significantly increase VMP1 mRNA and protein levels. However, knocking down Trim33 produced the opposite effect, which indicates that Trim33, as a transcriptional mediator, affects zymophagy by regulating the expression of VMP1. In addition, we explored the transcriptional regulation mechanism of the Trim33 molecule. Our research shows that lncRNA TCONS_00021785 can competitively bind miR-21-5p to upregulate Trim33, thereby initiating enzyme autophagy and reducing zymogen activation.
Integrated single-cell multiomics analysis reveals novel candidate markers for prognosis in human pancreatic ductal adenocarcinoma
Authors: Fan Xiaoying , Lu Ping , Wang Hongwei , Bian Shuhui , Wu Xinglong , Zhang Yu , Liu Yang , Fu Danqi , Wen Lu , Hao Jihui , Tang Fuchou 
Published: February 2022

AbstractThe epigenomic abnormality of pancreatic ductal adenocarcinoma (PDAC) has rarely been investigated due to its strong heterogeneity. Here, we used single-cell multiomics sequencing to simultaneously analyze the DNA methylome, chromatin accessibility and transcriptome in individual tumor cells of PDAC patients. We identified normal epithelial cells in the tumor lesion, which have euploid genomes, normal patterns of DNA methylation, and chromatin accessibility. Using all these normal epithelial cells as controls, we determined that DNA demethylation in the cancer genome was strongly enriched in heterochromatin regions but depleted in euchromatin regions. There were stronger negative correlations between RNA expression and promoter DNA methylation in cancer cells compared to those in normal epithelial cells. Through in-depth integrated analyses, a set of novel candidate biomarkers were identified, including ZNF667 and ZNF667-AS1, whose expressions were linked to a better prognosis for PDAC patients by affecting the proliferation of cancer cells. Our work systematically revealed the critical epigenomic features of cancer cells in PDAC patients at the single-cell level.
Expanding the mutation and phenotype spectrum of MYH3-associated skeletal disorders
Authors: Zhao Sen , Zhang Yuanqiang , Hallgrimsdottir Sigrun , Zuo Yuzhi , Li Xiaoxin , Batkovskyte Dominyka , Liu Sen , Lindelöf Hillevi , Wang Shengru , Hammarsjö Anna , Yang Yang , Ye Yongyu , Wang Lianlei , Yan Zihui , Lin Jiachen , Yu Chenxi , Chen Zefu , Niu Yuchen , Wang Huizi , Zhao Zhi , Liu Pengfei , Qiu Guixing , Posey Jennifer E. , Wu Zhihong , Lupski James R. , Micule Ieva , Anderlid Britt-Marie , Voss Ulrika , Sulander Dennis , Kuchinskaya Ekaterina , Nordgren Ann , Nilsson Ola ,   Deciphering Disorders Involving Scoliosis and COmorbidities (DISCO) study, Zhang Terry Jianguo , Grigelioniene Giedre , Wu Nan 
Published: February 2022

AbstractPathogenic variants inMYH3cause distal arthrogryposis type 2A and type 2B3 as well as contractures, pterygia and spondylocarpotarsal fusion syndromes types 1A and 1B. These disorders are ultra-rare and their natural course and phenotypic variability are not well described. In this study, we summarize the clinical features and genetic findings of 17 patients from 10 unrelated families with vertebral malformations caused by dominant or recessive pathogenic variants inMYH3. Twelve novel pathogenic variants inMYH3(NM_002470.4) were identified: three of them werede novoor inherited in autosomal dominant way and nine were inherited in autosomal recessive way. The patients had vertebral segmentation anomalies accompanied with variable joint contractures, short stature and dysmorphic facial features. There was a significant phenotypic overlap between dominant and recessiveMYH3-associated conditions regarding the degree of short stature as well as the number of vertebral fusions. All monoallelic variants caused significantly decreased SMAD3 phosphorylation, which is consistent with the previously proposed pathogenic mechanism of impaired canonical TGF-β signaling. Most of the biallelic variants were predicted to be protein-truncating, while one missense variant c.4244T>G,p.(Leu1415Arg), which was inherited in an autosomal recessive way, was found to alter the phosphorylation level of p38, suggesting an inhibition of the non-canonical pathway of TGF-β signaling. In conclusion, the identification of 12 novel pathogenic variants and overlapping phenotypes in 17 affected individuals from 10 unrelated families expands the mutation and phenotype spectrum ofMYH3-associated skeletal disorders. We show that disturbances of canonical or non-canonical TGF-β signaling pathways are involved in pathogenesis ofMYH3-associated skeletal fusion (MASF) syndrome.
A population study of clinically actionable genetic variation affecting drug response from the Middle East
Authors: Jithesh Puthen Veettil , Abuhaliqa Mohammed , Syed Najeeb , Ahmed Ikhlak , El Anbari Mohammed , Bastaki Kholoud , Sherif Shimaa , Umlai Umm-Kulthum , Jan Zainab , Gandhi Geethanjali , Manickam Chidambaram , Selvaraj Senthil , George Chinnu , Bangarusamy Dhinoth , Abdel-latif Rania , Al-Shafai Mashael , Tatari-Calderone Zohreh , Estivill Xavier , Pirmohamed Munir ,   The Qatar Genome Program Research Consortium, Abdel-latif Rania , Saqri Tariq Abu , Zaid Tariq Abu , Afifi Nahla , Al-Ali Rashid , Al-Khodor Souhaila , Al-Muftah Wadha , Al-Sarraj Yasser , Albagha Omar , Alkhayat Eiman , Alkuwari Fatima , Almabrazi Hakeem , Alshafai Mashael , Althani Asmaa , Alvi Muhammad , Badii Ramin , Badji Radja , Chouchane Lotfi , Darwish Dima , El Khouly Ahmed , Ennaifar Maryem , Estivill Xavier , Fadl Tasnim , Fakhro Khalid , Fethnou Eleni , Hamza Mehshad , Ismail Said I. , Jithesh Puthen V. , Khatib Mohammedhusen , Liu Wei , Lorenz Stephan , Mbarek Hamdi , Mokrab Younes , Pathare Tushar , Poolat Shafeeq , Qafoud Fatima , Vempalli Fazulur Rehaman , Saad Chadi , Suhre Karsten , Syed Najeeb , Tatari Zohreh , Temanni Ramzi , Tomei Sara , Yasin Heba 
Published: February 2022

AbstractClinical implementation of pharmacogenomics will help in personalizing drug prescriptions and alleviate the personal and financial burden due to inefficacy and adverse reactions to drugs. However, such implementation is lagging in many parts of the world, including the Middle East, mainly due to the lack of data on the distribution of actionable pharmacogenomic variation in these ethnicities. We analyzed 6,045 whole genomes from the Qatari population for the distribution of allele frequencies of 2,629 variants in 1,026 genes known to affect 559 drugs or classes of drugs. We also performed a focused analysis of genotypes or diplotypes of 15 genes affecting 46 drugs, which have guidelines for clinical implementation and predicted their phenotypic impact. The allele frequencies of 1,320 variants in 703 genes affecting 299 drugs or class of drugs were significantly different between the Qatari population and other world populations. On average, Qataris carry 3.6 actionable genotypes/diplotypes, affecting 13 drugs with guidelines for clinical implementation, and 99.5% of the individuals had at least one clinically actionable genotype/diplotype. Increased risk of simvastatin-induced myopathy could be predicted in ~32% of Qataris from the diplotypes of SLCO1B1, which is higher compared to many other populations, while fewer Qataris may need tacrolimus dosage adjustments for achieving immunosuppression based on the CYP3A5 diplotypes compared to other world populations. Distinct distribution of actionable pharmacogenomic variation was also observed among the Qatari subpopulations. Our comprehensive study of the distribution of actionable genetic variation affecting drugs in a Middle Eastern population has potential implications for preemptive pharmacogenomic implementation in the region and beyond.
A perspective on spaceflight associated neuro-ocular syndrome causation secondary to elevated venous sinus pressure
Authors: Bateman Grant Alexander , Bateman Alexander Robert 
Published: February 2022

AbstractSpaceflight associated neuro-ocular syndrome (SANS) alters the vision of astronauts during long-duration spaceflights. There is controversy regarding SANS being similar to patients with idiopathic intracranial hypertension (IIH). IIH has been shown to be due to an elevation in venous sinus pressure. The literature suggests an increase in jugular vein pressure secondary to a headward shift of fluid occurs in SANS but this may not be enough to significantly alter the intracranial pressure (ICP). The literature regarding cardiac output and cerebral blood flow (CBF) in long-duration spaceflight is contradictory, however, more recent data suggests increased flow. Recent modelling has shown that an increase in CBF can significantly increase sinus pressure. The purpose of the present paper is to review the SANS vascular dynamics literature and through mathematical modelling suggest the possible underlying cause of SANS as an elevation in venous sinus pressure, secondary to the redistribution of fluids towards the head, together with a significant increase in pressure drop across the venous system related to the CBF.
Planning evaluation of a novel volume-based algorithm for personalized optimization of lung dose in VMAT for esophageal cancer
Authors: Hsu Chen-Xiong , Lin Kuan-Heng , Wang Shan-Ying , Tsai Wei-Ta , Chang Chiu-Han , Tien Hui-Ju , Shueng Pei-Wei , Wu Tung-Hsin , Mok Greta S. P. 
Published: February 2022

AbstractRadiotherapy treatment planning (RTP) is time-consuming and labor-intensive since medical physicists must devise treatment plans carefully to reduce damage to tissues and organs for patients. Previously, we proposed the volume-based algorithm (VBA) method, providing optimal partial arcs (OPA) angle to achieve the low-dose volume of lungs in dynamic arc radiotherapy. This study aimed to implement the VBA for esophageal cancer (EC) patients and compare the lung dose and delivery time between full arcs (FA) without using VBA and OPA angle using VBA in volumetric modulated arc therapy (VMAT) plans. We retrospectively included 30 patients diagnosed with EC. RTP of each patient was replanned to 4 VMAT plans, including FA plans without (FA-C) and with (FA + C) dose constraints of OARs and OPA plans without (OPA-C) and with (OPA + C) dose constraints of OARs. The prescribed dose was 45 Gy. The OARs included the lungs, heart, and spinal cord. The dose distribution, dose-volume histogram, monitor units (MUs), delivery time, and gamma passing rates were analyzed. The results showed that the lung V5 and V10 in OPA + C plans were significantly lower than in FA + C plans (p < 0.05). No significant differences were noted in planning target volume (PTV) coverage, lung V15, lung V20, mean lung dose, heart V30, heart V40, mean heart dose, and maximal spinal cord dose between FA + C and OPA + C plans. The delivery time was significantly longer in FA + C plans than in OPA + C plans (237 vs. 192 s, p < 0.05). There were no significant differences between FA + C and OPA + C plans in gamma passing rates. We successfully applied the OPA angle based on the VBA to clinical EC patients and simplified the arc angle selection in RTP. The VBA could provide a personalized OPA angle for each patient and effectively reduce lung V5, V10, and delivery time in VMAT.
BODIPY nanoparticles functionalized with lactose for cancer-targeted and fluorescence imaging-guided photodynamic therapy
Authors: Mai Duy Khuong , Kim Chanwoo , Lee Joomin , Vales Temmy Pegarro , Badon Isabel Wen , De Koushitak , Cho Sung , Yang Jaesung , Kim Ho-Joong 
Published: February 2022

AbstractA series of four lactose-modified BODIPY photosensitizers (PSs) with different substituents (-I, -H, -OCH3, and -NO2) in the para-phenyl moiety attached to the meso-position of the BODIPY core were synthesized; the photophysical properties and photodynamic anticancer activities of these sensitizers were investigated, focusing on the electronic properties of the different substituent groups. Compared to parent BODIPY H, iodine substitution (BODIPY I) enhanced the intersystem crossing (ISC) to produce singlet oxygen (1O2) due to the heavy atom effect, and maintained a high fluorescence quantum yield (ΦF) of 0.45. Substitution with the electron-donating methoxy group (BODIPY OMe) results in a significant perturbation of occupied frontier molecular orbitals and consequently achieves higher 1O2 generation capability with a high ΦF of 0.49, while substitution with the electron-withdrawing nitro group (BODIPY NO2) led a perturbation of unoccupied frontier molecular orbitals and induces a forbidden dark S1 state, which is negative for both fluorescence and 1O2 generation efficiencies. The BODIPY PSs formed water-soluble nanoparticles (NPs) functionalized with lactose as liver cancer-targeting ligands. BODIPY I and OMe NPs showed good fluorescence imaging and PDT activity against various tumor cells (HeLa and Huh-7 cells). Collectively, the BODIPY NPs demonstrated high 1O2 generation capability and ΦF may create a new opportunity to develop useful imaging-guided PDT agents for tumor cells.