bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRIM28 down-regulation on methylation imprints in bovine preimplantation embryos
Authors: Ma Xin , Zhang Sheng , Zhang Meiling , Zhu Yiran , Ma Panpan , Yang Shubao , Su Liyan , Li Ziyi , Lv Wenfa , Luan Weimin 
Published: January 2019

SummaryTRIM28/KAP1/TIF1β was identified as a universal transcriptional co-repressor and is critical for regulating post-fertilization methylation reprogramming in preimplantation embryos. In this study, three siRNAs (si647, si742, and si1153) were designed to target the TRIM28 mRNA sequence. After transfection of the mixture of the three siRNA (siMix) into bovine fibroblast cells, the most effective one for TRIM28 knockdown was selected. By injecting RNAi directed against TRIM28 mRNA, we found that TRIM28 knockdown in oocytes had the most effect on the H19 gene, in which differentially methylated region (DMR) methylation was almost completely absent at the 2-cell stage (1.4%), while control embryos showed 74% methylation. In addition, global H3K9me3 levels at the 2-cell stage were significantly higher in the in vitro fertilization (IVF) group than in the TRIM28 knockdown group (P<0.05). We further show that TRIM28 is highly expressed during oocyte maturation and reaches peak levels at the 2-cell stage. In contrast, at this stage, TRIM28 expression in somatic cell nuclear transfer (SCNT) embryos decreased significantly (P<0.05), suggesting that Trim28 transcripts are lost during SCNT. TRIM28 is required for the maintenance of methylation imprints in bovine preimplantation embryos, and the loss of TRIM28 during SCNT may contribute to the unfaithful maintenance of imprints in cloned embryos.
Real-time high-resolution mid-infrared optical coherence tomography
Authors: Israelsen Niels M. , Petersen Christian R. , Barh Ajanta , Jain Deepak , Jensen Mikkel , Hannesschläger Günther , Tidemand-Lichtenberg Peter , Pedersen Christian , Podoleanu Adrian , Bang Ole 
Published: January 2019

AbstractThe potential for improving the penetration depth of optical coherence tomography systems by using light sources with longer wavelengths has been known since the inception of the technique in the early 1990s. Nevertheless, the development of mid-infrared optical coherence tomography has long been challenged by the maturity and fidelity of optical components in this spectral region, resulting in slow acquisition, low sensitivity, and poor axial resolution. In this work, a mid-infrared spectral-domain optical coherence tomography system operating at a central wavelength of 4 µm and an axial resolution of 8.6 µm is demonstrated. The system produces two-dimensional cross-sectional images in real time enabled by a high-brightness 0.9- to 4.7-µm mid-infrared supercontinuum source with a pulse repetition rate of 1 MHz for illumination and broadband upconversion of more than 1-µm bandwidth from 3.58–4.63 µm to 820–865 nm, where a standard 800-nm spectrometer can be used for fast detection. The images produced by the mid-infrared system are compared with those delivered by a state-of-the-art ultra-high-resolution near-infrared optical coherence tomography system operating at 1.3 μm, and the potential applications and samples suited for this technology are discussed. In doing so, the first practical mid-infrared optical coherence tomography system is demonstrated, with immediate applications in real-time non-destructive testing for the inspection of defects and thickness measurements in samples that exhibit strong scattering at shorter wavelengths.
Large optical nonlinearity enabled by coupled metallic quantum wells
Authors: Qian Haoliang , Li Shilong , Chen Ching-Fu , Hsu Su-Wen , Bopp Steven Edward , Ma Qian , Tao Andrea R. , Liu Zhaowei 
Published: January 2019

AbstractNew materials that exhibit strong second-order optical nonlinearities at a desired operational frequency are of paramount importance for nonlinear optics. Giant second-order susceptibility χ(2) has been obtained in semiconductor quantum wells (QWs). Unfortunately, the limited confining potential in semiconductor QWs causes formidable challenges in scaling such a scheme to the visible/near-infrared (NIR) frequencies for more vital nonlinear-optic applications. Here, we introduce a metal/dielectric heterostructured platform, i.e., TiN/Al2O3 epitaxial multilayers, to overcome that limitation. This platform has an extremely high χ(2) of approximately 1500 pm/V at NIR frequencies. By combining the aforementioned heterostructure with the large electric field enhancement afforded by a nanostructured metasurface, the power efficiency of second harmonic generation (SHG) achieved 10−4 at an incident pulse intensity of 10 GW/cm2, which is an improvement of several orders of magnitude compared to that of previous demonstrations from nonlinear surfaces at similar frequencies. The proposed quantum-engineered heterostructures enable efficient wave mixing at visible/NIR frequencies into ultracompact nonlinear optical devices.
Preclinical study using circular RNA 17 and micro RNA 181c-5p to suppress the enzalutamide-resistant prostate cancer progression
Authors: Wu Gang , Sun Yin , Xiang Zhendong , Wang Keliang , Liu Bo , Xiao Guangqian , Niu Yuanjie , Wu Denglong , Chang Chawnshang 
Published: January 2019

AbstractAndrogen-deprivation therapy (ADT) with newly developed antiandrogen enzalutamide (Enz) may increase the castration-resistant prostate cancer (CRPC) patients survival an extra 4.8 months. Yet eventually most patients may fail with development of Enz resistance. While recent clinical studies indicated that the increased expression of the androgen receptor (AR) splicing variant ARv7 might have key roles for the development of Enz resistance in CRPC, its detailed mechanism, especially its linkage to the circular RNAs (circRNAs), a form of non-coding RNA, however, remains unclear. Here we found from human clinical sample survey that circRNA17 (hsa_circ_0001427) has a lower expression in higher Gleason score PCa, and results from in vitro cell lines studies also revealed the lower expression in CRPC C4–2 Enz-resistant (EnzR-C4–2) cells compared to their parental Enz-sensitive (EnzS-C4–2) cells. Mechanism dissection indicated that suppressing circRNA17 in EnzS-C4–2 cells increased ARv7 expression that might then lead to increase the Enz resistance and cell invasion. Mechanism dissection demonstrated that Enz could suppress the circRNA17 expression at the transcriptional level via suppressing transcription of its host gene PDLIM5, and circRNA17 could regulate ARv7 expression via altering the expression of miR-181c-5p that involved the direct binding of miR-181c-5p to the 3′UTR of ARv7. Preclinical study using in vivo mouse model with xenografted EnzR-CWR22Rv1 cells revealed that adding circRNA17 or miRNA-181c-5p could suppress the EnzR-CWR22Rv1 cells growth. Together, results from these preclinical studies suggest that circRNA17 may function as suppressor to alter the Enz sensitivity and cell invasion in CRPC cells via altering the miR-181c-5p/ARv7 signaling and targeting this newly identified signaling may help in the development of a better therapy to further suppress the EnzR cell growth.
PPARα and PPARγ activation attenuates total free fatty acid and triglyceride accumulation in macrophages via the inhibition of Fatp1 expression
Authors: Ye Guozhu , Gao Han , Wang Zhichao , Lin Yi , Liao Xu , Zhang Han , Chi Yulang , Zhu Huimin , Dong Sijun 
Published: January 2019

AbstractLipid accumulation in macrophages interacts with microenvironment signals and accelerates diabetic atherosclerosis. However, the molecular mechanisms by which macrophage metabolism interacts with microenvironment signals during lipid accumulation are not clearly understood. Accordingly, an untargeted metabolomics approach was employed to characterize the metabolic reprogramming, and to identify potential regulatory targets related to lipid accumulation in macrophages treated with oleate, an important nutrient. The metabolomics approach revealed that multiple metabolic pathways were significantly disturbed in oleate-treated macrophages. We discovered that amino acids, nucleosides, lactate, monoacylglycerols, total free fatty acids (FFAs), and triglycerides (TGs) accumulated in oleate-treated macrophages, but these effects were effectively attenuated or even abolished by resveratrol. Notably, 1-monooleoylglycerol and 2-monooleoylglycerol showed the largest fold changes in the levels among the differential metabolites. Subsequently, we found that oleate triggered total FFA and TG accumulation in macrophages by accelerating FFA influx through the activation of Fatp1 expression, but this effect was attenuated by resveratrol via the activation of PPARα and PPARγ signaling. We verified that the activation of PPARα and PPARγ by WY14643 and pioglitazone, respectively, attenuated oleate triggered total FFA and TG accumulation in macrophages by repressing FFA import via the suppression of Fatp1 expression. Furthermore, the inhibition of Fatp1 by tumor necrosis factor α alleviated oleate-induced total FFA and TG accumulation in macrophages. This study provided the first demonstration that accumulation of amino acids, nucleosides, lactate, monoacylglycerols, total FFAs, and TGs in oleate-treated macrophages is effectively attenuated or even abolished by resveratrol, and that the activation of PPARα and PPARγ attenuates oleate-induced total FFA and TG accumulation via suppression of Fatp1 expression in macrophages. Therapeutic strategies aim to activate PPAR signaling, and to repress FFA import and triglyceride synthesis are promising approaches to reduce the risk of obesity, diabetes and atherosclerosis.
Increased expression of lncRNA CASC9 promotes tumor progression by suppressing autophagy-mediated cell apoptosis via the AKT/mTOR pathway in oral squamous cell carcinoma
Authors: Yang Yixin , Chen Dan , Liu Huan , Yang Kai 
Published: January 2019

AbstractRecent studies showed that lncRNA CASC9 was upregulated and acted as an oncogene in a variety of tumors. However, the expression and biological functions of CASC9 in oral squamous cell carcinoma (OSCC) remain unknown. In this study, we found for the first time that CASC9 was remarkably upregulated in OSCC tissues and cell lines compared with paired noncancerous tissues and normal oral epithelial cells. Highly expressed CASC9 is strongly associated with tumor size, clinical stage, regional lymph node metastasis and overall survival time in OSCC patients. In vitro, CASC9 knockdown in OSCC cells SCC15 and CAL27 significantly promotes autophagy and apoptosis, while inhibiting proliferation. Moreover, the expression levels of p-AKT, p-mTOR, P62 and BCL-2 were significantly decreased, while the expression levels of BAX and the LC3BII/LC3BI ratio were increased in CASC9-knockdown SCC15 and CAL27 cells. After the addition of the AKT activator SC79 in CASC9-knockdown SCC15 and CAL27 cells, we found that the increased autophagy and apoptosis were remarkably rescued. Furthermore, the increased apoptosis was remarkably rescued in CASC9-knockdown OSCC cells treated with the autophagy inhibitor Autophinib. In addition, CASC9 depletion suppressed tumor growth in vivo. In conclusion, our findings demonstrate that lncRNA CASC9 promotes OSCC progression through enhancing cell proliferation and suppressing autophagy-mediated cell apoptosis via the AKT/mTOR pathway. CASC9 could potentially be used as a valuable biomarker for OSCC diagnosis and prognosis.
Glutaminase 1 expression in colorectal cancer cells is induced by hypoxia and required for tumor growth, invasion, and metastatic colonization
Authors: Xiang Lisha , Mou Jun , Shao Bin , Wei Yuquan , Liang Houjie , Takano Naoharu , Semenza Gregg L. , Xie Ganfeng 
Published: January 2019

AbstractCancer cells re-program their metabolic machinery to meet the requirements of malignant transformation and progression. Glutaminase 1 (GLS1) was traditionally known as a mitochondrial enzyme that hydrolyzes glutamine into glutamate and fuels rapid proliferation of cancer cells. However, emerging evidence has now revealed that GLS1 might be a novel oncogene involved in tumorigenesis and progression of human cancers. In this study, we sought to determine whether GLS1 implicated in invasion and metastasis of colorectal carcinoma, and its underlying molecular mechanism. By analyzing a large set of clinical data from online datasets, we found that GLS1 is overexpressed in cancers compared with adjacent normal tissues, and associated with increased patient mortality. Immunohistochemical analysis of GLS1 staining showed that high GLS1 expression is significantly correlated with lymph node metastasis and advanced clinical stage in colorectal cancer patients. To investigate the underlying mechanism, we analyzed the Cancer Genome Atlas database and found that GLS1 mRNA expression is associated with a hypoxia signature, which is correlated with an increased risk of metastasis and mortality. Furthermore, reduced oxygen availability increases GLS1 mRNA and protein expression, due to transcriptional activation by hypoxia-inducible factor 1. GLS1 expression in colorectal cancer cells is required for hypoxia-induced migration and invasion in vitro and for tumor growth and metastatic colonization in vivo.
Next-generation ferroelectric domain-wall memories: principle and architecture
Authors: Jiang An Quan , Zhang Yan 
Published: January 2019

AbstractThe downscaling of commercial one-transistor–one capacitor ferroelectric memory cells is limited by the available signal window for the use of a charge integration readout technique. However, the erasable conducting charged walls that occur in insulating ferroelectrics can be used to read the bipolar domain states. Both out-of-plane and in-plane cell configurations are compared for the next sub-10-nm integration of ferroelectric domain wall memories with high reliability. It is highlighted that a nonvolatile read strategy of domain information within mesa-like cells under the application of a strong in-plane read field can enable a massive crossbar connection to reduce mobile charge accumulation at the walls and crosstalk currents from neighboring cells. The memory has extended application in analog data processing and neural networks.
Functionalized magnetic biopolymeric graphene oxide with outstanding performance in water purification
Authors: Sarkar Amit Kumar , Bediako John Kwame , Choi Jong-Won , Yun Yeoung-Sang 
Published: January 2019

AbstractGraphene oxide (GO) is an attractive material for water treatment, although its high surface energy restricts its practical application. To overcome this challenge, we have developed a well-dispersed and interconnected, functionalized biopolymeric GO with magnetic activity, namely, cl–CS–p(MA)/Fe3O4NPs. This three-dimensional, sponge-like nanostructured material is composed of graphene oxide nanosheets dispersed in functionalized chitosan/poly(methacrylic acid) and is cross-linked with in situ-developed Fe3O4 nanoparticles. Methacrylic acid (MA)-functionalized chitosan (CS) cross-linked with N,N-methylenebis(acrylamide) (MBA), designated as cl–CS–p(MA), facilitates the stable dispersion of GO nanosheets, providing a proper solid matrix for the generation of well-dispersed in situ Fe3O4NPs. The methodology allows for the generation of numerous binding sites with an interconnected morphology, facilitating the rapid uptake of a cationic dye in significant quantity, e.g., methylene blue (MB), which is used as a model water pollutant. In this work, the structural architecture of cl–CS–p(MA)/Fe3O4NPs was characterized with multiple approaches, and the adsorption mechanism was revealed to be an electrostatic interaction. The synthesized nanocomposite showed significant recyclability and structural stability. Adsorption equilibrium was achieved within 20 min, and the maximum adsorption capacity was 2478 mg/g for MB, surpassing the values reported for any other adsorbents to date.
Photoinduced semiconductor-metal transition in ultrathin troilite FeS nanosheets to trigger efficient hydrogen evolution
Authors: Zhou Gang , Shan Yun , Wang Longlu , Hu Youyou , Guo Junhong , Hu Fangren , Shen Jiancang , Gu Yu , Cui Jingteng , Liu Lizhe , Wu Xinglong 
Published: January 2019

AbstractThe exploitation of the stable and earth-abundant electrocatalyst with high catalytic activity remains a significant challenge for hydrogen evolution reaction. Being different from complex nanostructuring, this work focuses on a simple and feasible way to improve hydrogen evolution reaction performance via manipulation of intrinsic physical properties of the material. Herein, we present an interesting semiconductor-metal transition in ultrathin troilite FeS nanosheets triggered by near infrared radiation at near room temperature for the first time. The photogenerated metal-phase FeS nanosheets demonstrate intrinsically high catalytic activity and fast carrier transfer for hydrogen evolution reaction, leading to an overpotential of 142 mV at 10 mA cm−2 and a lower Tafel slope of 36.9 mV per decade. Our findings provide new inspirations for the steering of electron transfer and designing new-type catalysts.
Multiscale core-periphery structure in a global liner shipping network
Authors: Kojaku Sadamori , Xu Mengqiao , Xia Haoxiang , Masuda Naoki 
Published: January 2019

AbstractMaritime transport accounts for a majority of trades in volume, of which 70% in value is carried by container ships that transit regular routes on fixed schedules in the ocean. In the present paper, we analyse a data set of global liner shipping as a network of ports. In particular, we construct the network of the ports as the one-mode projection of a bipartite network composed of ports and ship routes. Like other transportation networks, global liner shipping networks may have core-periphery structure, where a core and a periphery are groups of densely and sparsely interconnected nodes, respectively. Core-periphery structure may have practical implications for understanding the robustness, efficiency and uneven development of international transportation systems. We develop an algorithm to detect core-periphery pairs in a network, which allows one to find core and peripheral nodes on different scales and uses a configuration model that accounts for the fact that the network is obtained by the one-mode projection of a bipartite network. We also found that most ports are core (as opposed to peripheral) ports and that ports in some countries in Europe, America and Asia belong to a global core-periphery pair across different scales, whereas ports in other countries do not.
Independent validation of induced overexpression efficiency across 242 experiments shows a success rate of 39%
Authors: Munkácsy Gyöngyi , Herman Péter , Győrffy Balázs 
Published: January 2019

AbstractAlthough numerous studies containing induced gene expression have already been published, independent authentication of their results has not yet been performed. Here, we utilized available transcriptomic data to validate the achieved efficiency in overexpression studies. Microarray data of experiments containing cell lines with induced overexpression in one or more genes were analyzed. All together 342 studies were processed, these include 242 different genes overexpressed in 184 cell lines. The final database includes 4,755 treatment-control sample pairs. Successful gene induction (fold change induction over 1.44) was validated in 39.3% of all genes at p < 0.05. Number of repetitions within a study (p < 0.0001) and type of used vector (p = 0.023) had significant impact on successful overexpression efficacy. In summary, over 60% of studies failed to deliver a reproducible overexpression. To achieve higher efficiency, robust and strict study design with multi-level quality control will be necessary.
Specific refolding pathway of viscumin A chain in membrane-like medium reveals a possible mechanism of toxin entry into cell
Authors: Volynsky Pavel E. , Nolde Dmitry E. , Zakharova Galina S. , Palmer Rex A. , Tonevitsky Alexander G. , Efremov Roman G. 
Published: January 2019

AbstractHow is a water-soluble globular protein able to spontaneously cross a cellular membrane? It is commonly accepted that it undergoes significant structural rearrangements on the lipid-water interface, thus acquiring membrane binding and penetration ability. In this study molecular dynamics (MD) simulations have been used to explore large-scale conformational changes of the globular viscumin A chain in a complex environment – comprising urea and chloroform/methanol (CHCl3/MeOH) mixture. Being well-packed in aqueous solution, viscumin A undergoes global structural rearrangements in both organic media. In urea, the protein is “swelling” and gradually loses its long-distance contacts, thus resembling the “molten globule” state. In CHCl3/MeOH, viscumin A is in effect turned “inside out”. This is accompanied with strengthening of the secondary structure and surface exposure of hydrophobic epitopes originally buried inside the globule. Resulting solvent-adapted models were further subjected to Monte Carlo simulations with an implicit hydrophobic slab membrane. In contrast to only a few point surface contacts in water and two short regions with weak protein-lipid interactions in urea, MD-derived structures in CHCl3/MeOH reveal multiple determinants of membrane interaction. Consequently it is now possible to propose a specific pathway for the structural adaptation of viscumin A with respect to the cell membrane – a probable first step of its translocation into cytoplasmic targets.
Genome-wide transcriptome analysis to further understand neutrophil activation and lncRNA transcript profiles in Kawasaki disease
Authors: Ko Tai-Ming , Chang Jeng-Sheng , Chen Shih-Ping , Liu Yi-Min , Chang Chia-Jung , Tsai Fuu-Jen , Lee Yi-Ching , Chen Chien-Hsiun , Chen Yuan-Tsong , Wu Jer-Yuarn 
Published: January 2019

AbstractKawasaki disease (KD) is the most common cause of acquired cardiac disease in children in developed countries. However, little is known regarding the role of transcriptomic targets of KD in the disease progression and development of complications, especially coronary artery aneurysms (CAA). The aim of our study was to identify transcripts affected by KD and their potential role in the disease. We enrolled 37 KD patients and collected blood samples along a comprehensive time-course. mRNA profiling demonstrated an abundance of CD177 transcript in acute KD, and in the intravenous immunoglobulin (IVIG)-resistant group compared to in the IVIG-sensitive group. lncRNA profiling identified XLOC_006277 as the most highly expressed molecule. XLOC_006277 expression in patients at acute stage was 3.3-fold higher relative to patients with convalescent KD. Moreover, XLOC_006277 abundance increased significantly in patients with CAA. XLOC_006277 knockdown suppressed MMP-8 and MMP-9 expression, both associated with heart lesions. Our result suggested that the increase of CD177pos neutrophils was associated with KD. Moreover, this study provided global long non-coding RNA transcripts in the blood of patients with KD, IVIG-resistant KD, or CAA. Notably, XLOC_006277 abundance was associated with CAA, which might contribute to further understanding of CAA pathogenesis in KD.